Spring 2009 term post-mortem of CHEM 241 orgo course

Another term at Drexel is over. Following my previous post-mortem analysis for the winter 09 term here are some thoughts about how things went teaching CHEM241:

1) My Second Life extra credit assignment was very different this term. Instead of having students create exhibits with 3D molecules I focused on the networking opportunities in chemistry. Students had to interview 3 people on Second Life and 3 more on FriendFeed and find out why they are participating in social software and how it relates to their interest in chemistry. They also were asked to take snapshots of chemistry related objects in Second Life. Even though only 4 students did the project what results is a wiki page that could be useful for briefing people about what exists for chemistry on social software platforms and why people bother to participate. Think about what helpful resources could be generated if a few teachers from various academic fields gave out similar assignments for just one term.

2) ChemTiles game: Leveraging the code that he used for the Spectral Game, Andrew Lang created a web version of the quizzes that I have used in Second Life and Unreal Tournament. Having browser access made it much easier for students to participate and the use of high scores allowed me to run contests over a week instead of just one class session. I ran three contests and gave out a textbook as a prize. I added a lot more content to cover chirality, nucleophilic reactions and eliminations. In addition to the contests, sometimes we just played the game in small groups at the workshops. Just like with the Spectral Game, when run in groups I used the images that appeared as opportunities to discuss in depth some of the related course material.

Some students were motivated to beat the high score and the game was a useful addition to the resources available to teach the course materials. There isn't a single tool that will appeal to all students. A recurrent finding in my teaching is that the more channels are offered to students the more choice they have and that can make learning more pleasant and interesting. But all methods of instruction require active participation on the student's part.

Even though I will not be teaching organic chemistry again till January (I am teaching Chemical Information Retrieval in the fall) the ChemTiles and Spectral Games will be freely available to other teachers and students.

Second Life and Lucid Dreaming

I have been fortunate throughout my life to have had lucid dreams on a fairly regular basis. This is an extremely interesting experience on many levels.

Since you know you are dreaming, in principle none of the rules of reality are necessarily applicable. For example walking through walls and flying around are usually possible. But other powers are curiously not on the menu.

I have not been able to make objects materialize or directly control the actions of people. However, telekinesis is often possible.

I find it interesting that the ways of invoking these actions is almost identical to the technologies that I have become accustomed to using, especially Second Life. Telekinesis is achieved by holding out my arm in the direction of the object and executing a kind of mental "right mouse click" then moving the object freely in 3D.

Flying can usually be initiated by lifting my arms, exactly the way it appears in Second Life. Last night I was following somebody flying around and his arms were in the classic Second Life flying position. He was going so fast that I was wishing I could pull up a mini-map view and chase him as a green dot, as is done in Second Life.


My interpretation of this is that the way our subconscious solves problems is governed by following rules that it has learned from experience. And the technology we spend time using sets the parameter space of what is allowed or possible. If this is true it suggests that spending time in diverse complex environments could make us more creative.

I think this has implications for how researchers think about and plan their experiments and how they collaborate and teach others.

I would bet that getting used to telekinesis in an environment like Second Life makes you more susceptible to thinking about remotely controlling experiments or using robotics. Similarly using a tool like the Amazon Mechanical Turk extensively in research must change the way you automatically conceptualize the role of people in projects.

It is fascinating how simulated people behave in lucid dreams. I think my subconscious does a good job of replicating the social mores to which I am accustomed, whether in person or via social software. Basically the people in lucid dreams display a range of personalities. To get them to interact, first you have to find the friendly ones then approach them politely. I wonder if the simulated people in the lucid dreams of those in the military obey direct orders without any problem. Because they certainly don't take kindly to it when I try.

Another surprising property of the subconscious in a lucid dream is that it behaves like a separate individual. You can speak to it and it understands, sometimes responding with a sense of humor. As I mentioned before, I have never been able to make an object materialize in front of me just by willing it. But what I can do is say out loud "You know it would be very nice for you to make me a nice juicy steak - and don't forget to activate my sense of taste." Nothing will happen for a few seconds but as I turn a corner there will be a meal waiting.

So in a very real sense, if the subconscious plays the role of God in lucid dreams, "prayers" do get answered sometimes!

Chemistry in Second Life April 09 Talks

Update: the recording is now available here

Andrew Lang and I just did two presentation on applications of chemistry in Second Life.

The first was on April 24, 2009 at the "Virtual Worlds: Libraries, Education and Museums" (VW LEM) conference on Infotainment Island. The second was on April 29, 2009 at "Education Days" on Orange Island.

This was basically an updated version of the talk we gave at the ACS last summer. We showed how the ChemTiles and Spectral Games evolved from Second Life. That is interesting because usually Second Life applications are adaptations of projects initially conceived elsewhere.

As I mentioned previously, giving talks on Second Life or using some other form of tele-presence certainly has its advantages. It does not replace face to face interaction but I think people get a good idea of what we do and they can follow up later for more discussion or possibly even collaborations.

I enjoy presenting with Andy - we go back and forth depending on the content on the slide and when it is relevant Andy does a demo of how to rez a molecule right on stage. So far we have not had any technical problems with that and I think it drives home the message of how easy it is to use the orac rezzer.

The talk on Orange Island was recorded and I'll update a link to it here when available.

Chemistry on Second Life April 09

View more presentations from Jean-claude Bradley.

FriendFeed and Second Life chemistry networking assignment

This term I am teaching introductory organic chemistry (CHEM 241). As an extra credit assignment, students had to use FriendFeed and Second Life to find 3 people on each platform doing something related to chemistry. They also were asked to take 4 pictures of chemistry content in Second Life.

The first of 2 deadlines related to this assignment has just passed and 4 students completed the assignment. I think they did a great job - take a look.

I think the networking aspects of these platforms is immense in educational fields. But it requires overcoming a bit of a barrier to entry, which was the purpose of this assignment. Students did need a bit of guidance at our workshops to get going but they caught on very quickly.

Thanks to everyone who agreed to be interviewed!

Winter 09 term post-mortem: SpectralGame implementation

Our winter term at Drexel just ended. Following up on my previous post-mortem analysis, here are some observations from having taught Organic Chemistry II (CHEM242) this term:

1) The big news of the term is that I had a chance to try out the SpectralGame in my class for the first time (mainly to teach NMR). Andrew Lang first created the game in Second Life and it worked fine but there were only a few students willing to go to the trouble of setting up an account there. By creating a web version the game became much easier for anyone to access. Antony Williams then assisted us with providing spectra from ChemSpider and Robert Lancashire made some modifications of JSpecView to increase security.

Andy also happened to create a top score list, which turned out to be a key to the success of the game and removed the necessity to set aside time during the workshops to run races. Now I could just specify a date and give out a prize to the student from our class who scored highest. That worked well and I gave out 3 prizes this term (molecular model kits and a textbook). We're submitting this for publication soon - see draft.

2) I usually provide a small (2%) extra credit assignment for students who want to go beyond what we learned in class. During the past few terms I have asked them to do projects in Second Life to learn how to create 3D molecules and posters. Since we didn't do any races in Second Life this term I asked them to focus on NMR analysis and upload their reports on the class wiki. They had to find an NMR spectrum on ChemSpider and explain the peaks. Normally I get maybe hald a dozen submissions but this term there were 35! (out of 135 students). Next term, I will have to re-evaluate Second Life to see how to leverage what is best done there.

Web based Spectra Game

Yesterday I used the NMR game in Second Life during our 2-hour Friday workshop in CHEM242. (We used a new location on Drexel island SLURL) The students who attended had looked at little or no material prior to the workshop. By the end I ended up explaining chemical shifts, complex coupling patterns and diastereotopic hydrogens differentiated by the presence of a chiral center. The only concept we didn't cover is integration, although we used peak size to take a guess about groups with lots of hydrogens (like trimethyl).

I think it was a very efficient way to teach NMR and the students can now go off and continue to practice till our next workshop Monday. Second Life has some advantages - such as the ability to mediate group study sessions where students from remote location can come together to play and discuss spectral assignments using either voice or chat. It is also nice to see the molecules in 3D, especially for bridged cyclic systems.

However, there is a bit of a learning curve to get into Second Life and not all computers have a suitable video card. So it is nice to now have the ability to play the game on a web browser. Andy set up the game play so that the score reflects the number of correct answers obtained in a row. There are also only 3 molecules to choose from instead of 5 in Second Life.

We're using JSpecView to render the spectra so expanding peaks simply requires dragging the mouse across the area of interest. It is also possible to integrate and view the metadata by right clicking.

Currently we mainly have H NMR spectra but we'll be adding lots more C NMR, IR, UV, MS, etc. It all depends on how many Open Data contributions we can find. If anyone has spectra to donate please upload them to ChemSpider and don't forget to check the box for Open Data.

This has been a wonderful example of rapid collaboration by Andrew Lang, Rajarshi Guha, Antony Williams, Robert Lancashire and myself.

Give the web Spectra Game a spin and see if you can beat the high score....

NMR game on Second Life

Andrew Lang and I have been discussing publishing our work on chemistry and Second Life. We're working on the draft here. When going over the game section, it became clear that we'll probably need to make two manuscripts out of this. This is an opportunity to wrap up my previous work on the EduFrag project - using Unreal Tournament to teach organic chemistry. I had submitted that article but as it was going through the peer-review process the approach was essentially made obsolete when we adapted the quizzes to Second Life.

So Andy and I brainstormed some new chemistry games that we could introduce to Second Life to leverage our recent tools. One of the applications is the NMR game. By combining the orac molecule rezzer, the SL spectral viewing tool and ChemSpider Open Data spectra I think we have a pretty good game.

The idea simple: click on the molecule that is represented by the spectrum. If it is correct you get 2 points and get another spectrum. You lose a point by clicking on an incorrect molecule. After going through all the spectra your score gets posted on the web to a top10 list. For equal scores the best time takes it.

From an educational perspective this is useful I think on several levels.

First the ability to look at the molecule in 3D makes it easier in many cases to demonstrate the relationship between Hs, which is critical in NMR.

Second we are using real spectra - not simulations. That is a great opportunity to teach students about how to deal with impurities, solvent peaks or quirks in the peaks. The viewer allows for easy zooming by typing commands like "zoom 1.5-2.5" in the chat box.

Third this spectrum viewer uses Open Source JCAMP-DX files so it can (and will) be adapted to all kinds of spectra - like IR, UV, MS, C NMR, etc. I'm teaching (CHEM 242) all of those techniques this term so I'll have an opportunity to see how well it works.

There is currently a copy of the game on ACS island (SLURL) - give it a try and give us some feedback.

Here is picture of the game area (Viv is sitting on the molecule and I'm on the spectrum):

Opening Up Education Review in Nature

My review of the new book "Opening Up Education" has appeared in Nature today [Bradley, J.-C. Nature 457, 151-152 (8 January 2009) ]. The entire book is freely available online by MIT press. In addition, Nature has agreed to make my review freely available. Given the topic, this is very satisfying.

Education is changing. The ethos of openness that increasingly pervades activities from journalism to software to finance is being adopted by the educational community. The series of essays in Opening Up Education offers examples, opportunities and thoughts on the use of shared and freely available resources in education. The book is arranged in three sections: software, content and pedagogy.

more...

Can the success of Scientific Blogging be measured?

Timo Hannay recently gave a talk "Scientific Researchers and Web 2.0: Social Not Working?", which is reproduced in this Nascent blog post.

This is a sobering review of the state of social software in science and he lists several roadblocks to its widespread adoption. It is important to counterbalance the almost unavoidable hype that emerges from the enthusiasm of those energized by a movement.

However, it can be a tricky endeavor to attempt to define success or failure, especially within systems that are evolving rapidly.

Are you a failure if you only get 10% of your proposals funded? What about a telemarketer who has a 95% failure rate of making a sale from dialing the phone? Are you a failure if you send a paper to Nature and get turned down 90% of the time?

The way I see it, Web2.0 technologies are just communication vehicles and should be measured using similar metrics to the telephone, email, lunch meetings, conferences, talking to somebody during a flight, etc.

You don't decide to use a telephone based on an analysis of the number of people on the other side of the line - you use it when you need to communicate. And sometimes that communication may be intended primarily for your future self. I absolutely agree with Ben Good that you should blog even if there is a chance that nobody will read it:

Well, as one graduate student that continues to blog even though only 2 or 3 people read most of my posts (namely my Dad and occasionally, if she is bored, my wife), I feel compelled to say that yes, some people and even some scientists will continue to blog even if no one ends up listening at all.

For me, keeping a blog is a very convenient way to write-up my annual reports and keep track of my progress. But, as a bonus, if others read it and give me feedback or collaborate, all the better. And this is where the sweetest part of the icing is found. As Rich Apodaca mentions, it comes down to jobs, funding and collaborations.

I have personally experienced very good examples of that. My recent trip to the UK (generously funded by Cameron Neylon) would have never happened without my active participation with Web2.0 tools. The same goes for the last paper (submitted to JoVE - Precedings version here) and proposal that I submitted.

The best reason for blogging is self-interest.

Future of Education Room in FriendFeed

I have created the FriendFeed room Future-of-Education as a means of gathering and sharing information about the future of education to assist a task force at Drexel seeking to create an environment to nurture new educational initiatives.

At the first meeting last week I shared my thoughts about the growing importance of openness in both education and research. I invite other members of our task force and any others from around the world to share relevant information and thoughts.

Hopefully I'll be able to liveblog one of our upcoming meetings on FriendFeed. This has worked very well at recent conferences - see for example the Southampton Open Science Workshop. More info on this after I discuss it with the committee.

Chemistry Search at Drexel

The Department of Chemistry at Drexel University is seeking an outstanding candidate for a tenure-track position at the assistant professor level in any area of chemistry. Candidates must hold a Ph.D. degree in chemistry or closely related field, have a strong commitment to teaching, and are expected to establish a vigorous, externally funded research program. Postdoctoral experience is preferred. Teaching responsibilities may include general chemistry as well as undergraduate and graduate courses in your area of specialization. A C.V., publication list, statement of present and future research interests (5-10 pages), statement of teaching philosophy (1-2 pages), and at least three letters of reference should be sent to Dr. Kevin Owens, Search Committee Chair, Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104. The review process will start on October 1, 2008 and continue until the position is filled. The successful candidate must be qualified to work in the United States. Drexel University is an affirmative action/equal opportunity employer and encourages applications from qualified women, members of minority groups, disabled individuals and veterans.

Happy Accidents: A Must-Read for Open Scientists

I usually limit my book reviews to Goodreads or Shelfari but this one deserves much more attention.

In Happy Accidents: Serendipity in Modern Medical Breakthroughs; When Scientists Find What They're NOT Looking for, Morton Meyers reviews examples of the unpredictability of scientific progress.

This could just be a collection of interesting anecdotes - and some of the stories are truly fascinating. My favorite is probably the discovery of platinum compounds for the treatment of cancer. It came about from the accidental electro-dissolution of a platinum electrode during an experiment studying the effect of electricity on cell cultures!

But Meyers goes further and uses these examples to make larger observations about the way science operates today in both academia and industry. A quote from the preface foreshadows the tone of the book:

The dominant convention of all scientific writing is to present discoveries as rationally driven and to let the facts speak for themselves. This humble ideal has succeeded in making scientists look as if they never make errors, that they straightforwardly answer every question they investigate. It banishes any hint of blunders and surprises along the way. Consequently, not only the general public but the scientific community itself is unaware of the vast role of serendipity in medical research. Typically, a discoverer may finally admit this only towards the end of his or her career, after the awards have been received.

And starting on page 304:

An applicant for a research grant is expected to have a clearly defined program for a period of three to five years. Implicit is the assumption that nothing unforeseen will be discovered during that time and, even if something were, it would not cause distraction from the approved line of research. Yet the reality is that many medical discoveries were made by researchers working on the basis of a fallacious hypothesis that led them down an unexpected fortuitous path.
....
The peer review system forces investigators to work on problems others think are important and to describe the work in a way that convinces the reviewers that results will be obtained. This is precisely what prevents funded work from being highly preliminary, speculative or radical. How can a venture into the unknown offer predictability of results?(my emphasis)
....
Indeed the basic process of peer review demands conformity of thinking and disdains a maverick's approach.
....
What it comes down to is this: Who on a review committee is the peer of a maverick? (my emphasis)

The fact that some of us in the Open Science community are discussing this does not mean that we are advocating for the abolition of peer review or the NIH. We are not that naive. We still submit proposals and manuscripts for publication in peer-reviewed journals (although given a choice we probably would pick an Open Access journal over one running on a paid subscription model).

The point is what we do in addition to all those traditional processes.

We can share our failed experiments. We can share our research plans. We can discuss science freely admitting what we don't know. We can record our talks at closed meetings and make them public. We can initiate and participate in serious scientific conversations going on in the blogosphere without worrying about everyone's title and rank.

Basically, we can collaborate in ways that are most conducive to serendipitous discoveries. The free social software, databases and other infrastructure now available make this information exchange easier than ever.

The key question for a researcher today: to hoard or not to hoard?

To me, it seems likely that data hoarders will find it more and more difficult to claim priority for a contribution when competing against loose associations of open collaborators motivated by insatiable curiosity.

Some of the folks from the funding side are getting it. Take a look at SubMeta.

Einstein Rejected Peer Review

According to Silvan Schweber (page 9 of Einstein & Oppenheimer):

By 1930, every European scientific journal would automatically accept and publish any paper that Einstein had submitted.

When the Physical Review dared to submit his paper for peer review, Einstein responded:

We (Mr. Rosen and I) had sent you our manuscript for publication and had not authorized you to show it to specialists before it is printed. I see no reason to address the - in any case erroneous - comments of your anonymous expert. On the basis of this incident I prefer to publish the paper elsewhere.

There are many ways to look at this, depending on one's agenda.

On the positive side, it looks like Einstein was able to contribute to science, despite using the publication system much like we would now use Nature Precedings or a blog. But did the readers know his papers were not peer reviewed? At least with our current Science2.0 tools the assumptions are more explicit. And it is much easier for the community to comment.

Demographics of Organic Chemistry on YouTube

I was just looking at the YouTube Insight feature showing demographic and access info on my uploaded videos. Since I use my YouTube account mainly to provide solutions to organic chemistry problems in my undergrad classes it was surprising to see that the most active group of viewers were 45-55 year old men.


And the most popular video is the NMR of an ester, where I explain the effect of a chiral center on the splitting pattern of methylene groups.

Spring 2008 post-mortem on organic chemistry courses

It has been 2 terms since I posted a post-mortem analysis of my teaching experience. In the Winter08 quarter I taught intermediate organic chemistry CHEM242 and in Spring08 I taught the introductory organic course CHEM241.

I have two major points to make:

1) I still struggled to find a good way to proctor my online tests for up to 150 students without the advantage of a dedicated testing facility. My experience with having students sign up for test sessions of their choice during a previous term was so negative that I actually considered going back to paper and running Scantron. But after working out how much trouble it would be to prepare and track different paper test versions and report back to students their grades in a confidential and timely manner I decided to avoid that route.

I still ended up using WebCT/Blackboard to deliver the tests but I only set up two back to back testing periods. By reserving all the computer rooms on Sundays I assigned students with last names starting A-L the first session and M-Z the second. That way there was no problem with students not signing up in time or repeatedly changing sessions.

For students who could demonstrate a genuine conflict I let them schedule a time with the proctor, as long as it was BEFORE the Sunday test date. Most students who reschedule want to take the test as late as possible so there were few students who requested this.

Also, instead of creating several tests in WebCT/Blackboard for different sessions, the proctor just used one version and kept changing the password. That made it convenient for everyone.

I do miss the ability to provide students the convenience of a walk-in testing policy over the course of several days. I think that a testing facility where live human beings simply check student IDs and make sure nobody is talking or using notes during certain hours would be vastly more useful than any high tech browser lock-down or screen capture tools and cameras. These could be the same rooms that are used for teaching or general student use during other times. Students from any course using a course management system could reserve a certain time or simply try their luck during one of the scheduled general proctoring times.

It is my impression that the absence of such facilities in most universities is a major obstacle for the widespread adoption of online courses, or at minimum online testing. I think the problem is that it doesn't obviously fall under the responsibilities of any single academic unit.

2) I continued to use Second Life on an optional basis both for running races, giving out molecular model kits to the winners. I also continued to accept extra credit assignments involving building 3D molecules with a poster explaining a concept related to class content.

In the image shown below, Netty showed an example of an SN1 reaction involving a ring expansion via a 1,2-alkyl shift. This is a really difficult concept to grasp on paper - I remember struggling with it as an undergrad. I think it is helpful for the student to construct both the 2D and 3D representations in Second Life. There are a few more examples on ACS island - on my skylab in the SouthEast corner.


Andrew Lang has continued to make small improvements to the orac molecule rezzer to make it even easier to use. There is nothing like having students who have never seen or even heard of Second Life use a tool like this to determine user-friendliness and make necessary improvements.

New Communication Channels for Biology Workshop

I'll be attending the "New Communication Channels for Biology" Workshop at UCSD on Wednesday. It looks like it will be very intense and I hope to see a few people from the Open Science movement there!

The workshop will focus on the range of emerging approaches within e-science, community engagement in dialogue knowledge input/review or assessment, science blogs, and authenticated wiki-like research discussions and analysis, as well as the potential to formalize such community level contributions. These new approaches to communication are becoming important for biology as biological scientists attempt to address the inherent complexity of life, manage both high information content and high throughput data streams, and employ the opportunities emerging from advances in e-communication/networking and information technology. In part, this meeting has been stimulated by the success of the PSI KB Annotation Workshop, and by the general need within research both in metagenomics and structural genomics to understand the changing means of scientific communication and how we can best reach out to the community and have our work be enhanced in timely impact. The general case of getting input to genomic data from the entire community, third party annotation and not from only the original provider, is another driver for the need to extend communication beyond traditional publications, but the transformations in scientific dialogue / communication are much broader than just that within the genome community.

SciFoo 2008

Just got my invite for SciFoo 08 (August 8-10) - I look forward to another intense meeting and catching up with friends and collaborators!
Last year was truly enlightening.

My Interview on Rod's Pulse Podcast

Rodney B. Murray interviewed me last week for his educational podcast:

Interview with Jean-Claude Bradley, Associate Professor of Chemistry and E-Learning Coordinator, College of Arts and Sciences, Drexel University

• Drexel CoAS E-Learning Blog
• Drexel CoAS E-Learning Podcast
• Drexel Island on Second Life

• Open Notebook Science using Blogs and Wikis
• Teaching Chemistry with Second Life
• Other topics and tools mentioned:
• Audacity - free audio editing tool
• Blogger - free blog service
• Camtasia Studio - screen recorder
• Creative Commons - licenses for authors, artists, and educators
• Feedburner - manage RSS feeds and track subscribers
• Second Life - a 3D virtual world
• SMILES - for describing chemical molecules
• WikiSpaces - free Wiki service

X2 Project

I was asked by the Institute for the Future to highlight a dozen "Signals" that may point to new trends in science as part of the X2 Project:

Today, science is entering another period of accelerated change, thanks to the growth of the Internet and dawn of pervasive computing; the explosive growth of new sciences like genetic engineering, nanotechnology, biotechnology, and simulation; the rise of new scientific powers in the developing world, the revival of amateur scientists, and the growth of citizen science movements in the United States and Europe; the growth of new institutions supporting scientific research and innovation, and changes in the structure and funding of universities, government, and corporate R&D labs. Science in 2025 and 2050 is going to look very different than it does today.

To map and make sense of all these changes, the Institute for the Future (IFTF) launched the X2 Project in late 2007. The purpose of X2 is to identify future disruptions, opportunities, and competitive landscapes related to the content and dynamics of global science and technology innovation; to develop a new platform for understanding global innovation trends; and to present this information to policy- and decision-makers, as well as the general public, in a useful form. The project conducts its research online, through an innovative experiment in open forecasting; in workshops with young scientists and engineers around the world; and in online games.

Here are the 12 that I came up with:

1. Open Collaborative Research Proposals
2. Communicating Science with Blogs
3. Spontaneous Publication of Raw Research Data
4. Routine Virtual Meetings in Second Life
5. Empirical Investigation of Virtual World Properties
6. Uploading of Spectra on ChemSpider
7. Open Source Drug Discovery
8. Automation of Crystallization by an Academic Group
9. Robot Scientist Creates and Evaluates Microbiology Hypotheses
10. Data Vizualization Group in Second Life
11. InChIKey Web Services Facilitates Indexing of Molecules
12. The X2 Project!

Chemical Heritage Foundation Talk

Earlier this week, I attended the LISE08 conference at the Chemical Heritage Foundation in Philadelphia. The theme this year was New Media and Technology in Science Education and I talked about using Second Life in the chemistry classroom.

David Shaffer gave a very entertaining and thoughtful presentation on epistemic games. These are games simulating complex systems like urban planning.

Tom Tritton reviewed the conference for CHF.

Scholar2Scholar Conference Tomorrow

The Scholar2Scholar conference is upon us. Jay Bhatt and Anita Chiodo did an amazing job with organizing this from the start. I'll be giving the introductory talk on "Enhancing Scientific Communication through Open Notebook Science". Here are the slides - I'm starting with an introduction to Web2.0 using FriendFeed as an example.

| View | Upload your own

date: April 16, 2008 8:30-1:30
location: Drexel University Bossone Lobby

Join us to discuss how Web2.0 is changing scholarship. Dr. Jean-Claude Bradley will give a presentation, followed by a panel discussion featuring: Andre Brown, Nicole Engard, James Mitchell, Banu Onaral, Beth Ritter-Guth, and Scott Warnock. Small round-table discussions will follow. An optional Dutch-treat lunch concludes the day.

NFAIS 2008 Sunday afternoon

Yesterday afternoon I attended the NFAIS conference in downtown Philadelphia. The talks were actually very engaging.

First up was David Weinburger, who co-wrote the "Cluetrain Manifesto", an enjoyable book that I caught on audio book a few years back. His talk was mainly about his new book "Everything is Miscellaneous", which looks interesting based on his talk. His main point was that hierarchical classification systems are not as useful for many systems compared with spontaneous tagging by online communities. He also indicated that information overload was not as big of a problem as many people suggest, something that I definitely think is the case in science.

Lee Rainie's presentation was also well done. He presented the results of the Pew Internet & American Life project. I thought the most interesting portion was at the end, where he described the 10 different types of people, classified according to their attitude towards technology. Hopefully his report will be available shortly along with the rest. (In the meantime, Bryan Alexander took some good notes on this session.)

I presented at the next session on "The Emerging Culture of the New Information Order" on Open Notebook Science, which was a good fit, giving a laboratory researcher's perspective of Web 2.0.

My co-panelists included Chris Willis from Footnote.com and Bryan Alexander from NITLE. Chris gave many good examples of the power of community tagging, including a new project bringing relatives of Vietnam veterans together on a massive digital "wall". Bryan also gave a stimulating talk but he was so addicted to his social software that he was recording video blog posts as we were waiting to speak :)

Scholar 2 Scholar Meeting at Drexel

I am co-organizing the Scholar 2 Scholar conference with Jay Bhatt and Anita Chiodo on the morning of April 16, 2008 at Drexel University in Philadelphia. Anyone wishing to attend add your name to the participant list on the wiki.

Drexel University Libraries’ Scholarly Communication Symposium
Scholar 2 Scholar: How Web 2.0 is Changing Scholarly Communication as We Know It
Web 2.0 technologies are more than just web-based games and social networks; these virtual environments are building communities of thought and practice which have very real implications for education and research in academia. How do educators, administrators, and librarians use or repurpose these tools to their advantage? What are the implications for teaching and research? Is the return on our investment of time and energy worth the engagement? How well do students learn through these collaborative avenues? What are the true benefits for scientific research? What are the potential conflicts or roadblocks? We will explore these questions and many more.

Open Medicine Editorial

The Journal "Open Medicine" has published a very thoughtful editorial on "Open science, open access and open source software at Open Medicine" by Sally Murray, Stephen Choi, John Hoey, Claire Kendall, James Maskalyk and Anita Palepu.

Not only are they writing about it but they want to get their hands dirty as well:

Open Medicine is an open access journal because we believe that free and timely access to research results allows scientific knowledge to be used by all those who need it, not just those who can afford expensive journal subscriptions or user fees for individual articles. But is access to the final polished version of research enough? Could we do more to en­courage the collaborative reuse and reanalysis of existing data, or the verification of analyses? Could we move from open access to open science?

Virtual Poster Session on ACS Island

The American Chemical Society will be offering a virtual poster session in Second Life from selected posters at the Sci-Mix session taking place April 6, 2008 at the next national meeting in New Orleans.

I'm helping out with that effort and I'm pleased to say that we have our first submission from Jodye Selco, Mary Bruno and Sue Chan: "Safe and economical chemistry inquiry for the K-12 classroom".


ACS island has the same shape as its logo of a phoenix, thanks to the skilled hand of Eloise Pasteur who carved out the Drexel island's dragon shape. The posters will be placed on the right wing, next to a "chemistry museum" area, also under development.


ACS island is currently open to everyone - feel free to stop by and explore as we develop the area (Andrew Lang, Hiro Sheridan in SL is also on the project). Gus Rosania has been a very active "resident scientist" - you can see his activities on drug transport near the middle.

Kate Sellar (Finola Graves in SL), who spearheaded this initiative at ACS, has just started a blog where she will chronicle activities on the island.

The easiest way to find the island is to type ACS in the Map search box in Second Life.

Chemical Heritage Foundation Podcast

Drexel Island and my teaching of chemistry on Second Life is covered in a recent Chemical Heritage Foundation podcast "Distillations". Cyrus Farivar interviews me and my student Charles Sineri.

Campus Technology Articles about Teaching in Virtual Worlds

Linda Briggs wrote a nice article in Campus Technology about using Second Life to teach and highlighted the chemistry application that I used last term:

Creating Life-Size Molecules in Second Life

A Conversation with Drexel University's Jean-Claude Bradley

1/9/2008

By Linda L Briggs

CT: Conversely, what are some things that work really well in Second Life?

JCB: One thing new that I've done this term is have students do a project in Second Life.

CT: Yes, you recently wrote in your blog that one of your students created a life-size model of a molecule as part of that. That sounded really cool.

JCB: Right. To be able to stand next to a molecule that is as tall as you are, and to have your teacher be able to walk around it with you and comment,... that's pretty useful.

[....]

CT: Do you have advice for instructors who want to integrate Second Life into their course?

JCB: You should have a really good reason to do it. The best advice is to find another teacher who is actually using it, and try to experience what the student is experiencing. You'll get some ideas and advice from that. I was just talking to another teacher an hour ago who might be doing some things in Second Life. She's also an organic chemistry teacher. I told her, just send your students to Drexel Island; have them interact with my students, click around on the quizzes, and if you think it might make sense, you can spawn off from that.

A lot of people have bad experiences in Second Life because they don't have a good reason for going there. It's like having people go to the Internet without a Web address. You want to be guided. That's the best possible scenario.

It's just another tool. I wouldn't teach exclusively on Second Life. We have WebCT Blackboard; I have my wiki; I have my blogs; and those things all have their strengths. You've got to leverage them all.

Drexel Island also got a mention in Matt Villano's article in Campus Technology: 13 Tips for Virtual World Teaching

Fall 2007 Post Mortem - the Closed Book Problem

Another quarter done at Drexel and it is time for a brief post-mortem analysis of my teaching this term.

I taught CHEM 241, introductory organic chemistry.

In order to standardize testing conditions with other instructors of the course, my tests were run under closed book rules. Many years ago I opted for an open book policy after comparing performance under open and closed conditions. There was no significant difference, which I would expect for subject matter that has more to do with understanding rather than memorization. Open book tests are much easier to monitor and I was able to run a walk-in testing policy lasting several days using only video surveillance.

Moving to closed book conditions required a proctor. This would not be a big problem for a small class. But my class had 175 students and our computer rooms only have about 25 machines and are usually in demand. Based on previous student behavior with a walk-in policy in effect, not more than half the class typically showed up before the last day. So I booked a room with more time (at least 6 hours) on the last day and shorter sessions on previous days.

This worked fine for the 90 minute tests but we ran into a crunch on the last day of the final exam with a 3 hour duration. Luckily, I had an extremely competent and flexible proctor who handled the situation by finding additional rooms and extending the time. In fact the proctor was there for a total of 13 hours on the last day.

In terms of security, I made use of the "proctor password" tool in Blackboard/WebCT and changed it at least once per day. Although there is some IP filtering possible with BB/WebCT, the restriction is not specific enough to isolate specific classrooms.

Next term, we can solve a lot of these problems by allocating specific students to designated classrooms and using a printed class list where the students will show ID to the proctor and check off their name immediately before taking the test.

Unfortunately, this removes the convenience of multi-day walk-in testing, which many students appreciated.

There are probably many instructors out there with large online classes and I would like to get some feedback on how they handle testing under closed book conditions.

From what I gather most online programs rely on the honor system.

The other major news this term is that one of my students executed his extra credit assignment building molecules in Second Life.

Virtual Biomed Workshop on Second Life

On Friday November 30, 2007 I was part of a panel for a Virtual Biomed Workshop at Drexel. I gave a little tour of Drexel Island. My account froze for a few minutes. Luckily Sean Brown took the reins and showcased the Biomed Floor that he built in the main building. The projection screen was huge and the video recorder did a great job of capturing the tour.

Watch my presentation here.

Chemistry Assignments in Second Life

This term, the students in my organic chemistry class were presented with an opportunity to do an extra credit assignment using Second Life to represent concepts they learned in the course.

When I was an undergraduate, finding molecules in articles was mainly done using the Chemical Abstracts books. A convenient way to find a specific molecule would be to look up the molecular formula and find the corresponding IUPAC name. Theoretically, one could figure out the IUPAC name from scratch but this can be very tricky for complex molecules and prone to error. With the correct name, I could look for analogues of a molecule of interest in alphabetical catalogues by understanding how the chemical name works.

But when computer databases started to be used in chemistry, using the name of a compound became far less important. Searching for molecules now comes down to drawing them on computer screens and using computer generated text representations like SMILES and InChI. Knowing how to use these tools on free software and services is key to being fluent and flexible on the chemical web. And I think that is the most important benefit that students get from doing these assignments.

As an example, take a look at the project created by my student Charles Sineri (Chaz Balbozar in SL). In the image below he is standing between two molecules of camphor that are mirror images of each other, demonstrating the concept of chirality that we covered in class. This is a particularly difficult example to demonstrate on paper.

Using molecular models that are bigger than my body is not something that I have ever done in real life and it provides an interesting perspective to what the molecule really looks like. Another advantage is that you can fly the molecule like an airplane by wearing it. Here is Chaz flying up to a buckyball on his camphor ship:


In order to get his project done Chaz had to learn about and use SMILES, InChIs, ChemSpider and ChemSketch. These are free tools that he will use again in future chemistry applications.

The main challenge in getting this implemented in Second Life is providing tools that are easy to use. We used Andy Lang's (Hiro Sheridan in SL) molecule rezzer to do this because it now has the capability of understanding InChIs and SMILES. Hiro was kind enough to make some further modifications to make it even easier to use. It was gratifying to see that it understood chiral SMILES code.

Visit Chaz's project on Second Nature island - see SLURL.

Nature's Role in e-Science Talks

Berci Mesko will be moderating a session on Nature's Role in e-Science on SciFoo Lives On (in Second Life) tomorrow Monday December 10, 2007 at 12:00 ET/17:00 GMT.

There will be 4 talks:

Matt Brown: Nature Network
Ian Mulvany: Connotea
Hillary Spencer: Nature Precedings
Helen King: Dissect Medicine

Run for Malaria in Philly

For anyone in the Philadelphia area who cares about malaria:

Drexel University Crossings Stair Run

Beta Beta Beta and the Office of Residential Living will sponsor a stair run Saturday, December 8, 2007, from 9 a.m. to noon in University Crossings (101 N. 32nd Street).

Registration is $3 per person, $5 if two people sign up together. Sign-up in the lobby of University Crossings.

All the proceeds generated from the event will purchase mosquito netting to be placed over beds for an African village. Each net costs $10, and can potentially save three people, as children in the villages typically share beds.

More information about this initiative is available at http://malarianomore.org/.

Cameron's Drexel Talk on ONS

Cameron Neylon gave a very thoughtful talk at Drexel on Friday about using blogs to capture the science going on in his group then deciding to open his laboratory notebooks to the world.

He was refreshingly honest about his progress and motivations. For example, at one point he noted that a gel image was missing on one of the posts. Instead of glossing over it, he pointed out how this just makes transparent how difficult it is to properly maintain a laboratory notebook. As long as you don't have to show it to anyone, it is tempting to claim that your lab notebook is better maintained than it really is.

And this is a positive thing - science is messy and even through the human failings of ideal record keeping, science gets done. Now if we finally admit to that and are willing to work transparently, we have an opportunity and an incentive to set a higher standard.

That is one of the tangible benefits of Open Notebook Science.

Cameron's talk was recorded and is available here.

Cameron Neylon ONS Talk at Drexel

I am very pleased to announce a talk by Cameron Neylon at Drexel next month:

A Beginner’s Guide to Open Science
(not for beginners but by beginners)

2:00 Friday November 2, 2007
Disque 109, Drexel University
32nd and Chestnut streets, Philadelphia, PA

Cameron Neylon, STFC Rutherford Appleton Laboratory and School of Chemistry, University of Southampton

The modern biochemistry or molecular biology laboratory generates large quantities of data that are generally stored across multiple computers attached to multiple instruments. Much of this data is never published and the majority languishes on old computers and is ultimately lost. At a local level this is a frustration for investigators who will often struggle to obtain specific pieces of data produced in their own laboratory. On a larger scale this is becoming a much more serious issue with the obligation of researchers to funding bodies to both preserve research data and make it available to other users increasingly becoming a formal a condition of publicly funded grants. Systems are required that can capture and preserve data along with sufficient information and metadata to make it possible for others to use this data.

In parallel with this a movement is growing within the research community that advocates greater openness in providing both the raw data from published studies as well as making available the large quantities of data that are never published. The logical extreme of this approach is Open Notebook Science [1], pioneered at Drexel University [2], where the researcher’s laboratory notebook is made available on the internet as it is recorded. Achieving the aims of Open Notebook Science also requires systems which can capture data and provide it in a useful format. In addition these systems must make the data visible to relevant online searches.

We are developing and using an electronic laboratory notebook based on a Blog format to capture experimental data in a biochemistry laboratory [3,4]. Within the system each sample is recorded in a single post. Analysis and manipulations of the sample are recorded in separate posts with links back to the input sample and forward to any products. All the information is made immediately available on the Web as it is recorded. The Blog engine has been specially built in house and has a number of features designed to enable and encourage the effective capture of data and metadata in the environment of a biochemistry laboratory. I will describe the Blog system and our evolving approach to capturing metadata as well as the process of integrating this with other web services to provide an open environment for recording work in the laboratory, laboratory materials, and validated procedures. The challenges and problems encountered in reconciling the twin aims of capturing data and making it available and readable will also be discussed along with the similarities and differences emerging between different approaches to Open Notebook Science [2,5,6].

[1] http://drexel-coas-elearning.blogspot.com/2006/09/open-notebook-science.html
[2] http://usefulchem.wikispaces.com/
[3] http://chemtools.chem.soton.ac.uk/projects/blog/blogs.php/blog_id/10
[4] http://chemtools.chem.soton.ac.uk/projects/blog/blogs.php/blog_id/13
[5] http://www.jeremiahfaith.com/open_notebook_science/
[6] http://www.michaelbarton.me.uk/

Periodic Table in Second Life

Further adding to the set of chemistry tools in Second Life, Hiro Sheridan has created a 3D periodic table with rotating atoms. Although not directly proportional, the relative sizes of the spheres are in the correct order. Clicking on them provides basic information about the corresponding element.

The 3D periodic table is available on the Chemistry Corner on Drexel Island (SLURL).

The Value of Dark Data

Tom Goetz wrote a thoughtful article "It's Time to Free the Dark Data of Failed Scientific Experiments" in Wired this week.

So what happens to all the research that doesn't yield a dramatic outcome —or, worse, the opposite of what researchers had hoped? It ends up stuffed in some lab drawer. The result is a vast body of squandered knowledge that represents a waste of resources and a drag on scientific progress. This information — call it dark data — must be set free.

...

There are some islands of innovation. Since 2002, the Journal of Negative Results in Biomedicine has offered a peer-reviewed home to results that go negative or against the grain. Earlier this year, the journal Nature started Nature Precedings, a Web-based forum for prepublication research and unpublished manuscripts in biomedicine, chemistry, and the earth sciences. At Drexel University, chemist Jean-Claude Bradley practices "open notebook" science — chronicling his lab's work and sharing data via blog and wiki. And PLoS is planning an open repository for research and data that is other wise abandoned.

The main focus of the article is on results that don't make it to an article because they are not interesting enough. "Failed Experiments" in this sense are those that do not uncover a hoped for correlation or, in synthetic organic chemistry, those where the desired product is not obtained.

However, there are many more shades of Dark Data. One large category often downplayed consists of experiments aborted because of mistakes and accidents. For example in EXP096, the product was spilled and lost. But all of the spectra and data collected up to that point are still perfectly usable for someone wanting to repeat this or a similar experiment. That is the reason researchers don't tear out pages from their lab notebooks when accidents happen. The same logic applies to Open Notebook Science, where the audience extends to the whole world.

Thanks to Attila for posting an early report.

Open Notebook Science Case Studies SFLO Session

Just a reminder that the ONS case studies session on SciFoo Lives On is tomorrow Sept 24, 2007 at 9:00 PT/12:00 ET/16:00 GMT.

The idea here is to get our hands dirty and look at the guts of our operations. What is working/what is not -what technologies are we using and where you can get them.

Cameron Neylon and I will be presenting but we hope there will be lots of discussion.

ChemBioFoo Area First Poster

Ding dong - one of my bells emailed me today.


Someone was at the gate of the BioChemFoo area on Nature Island in Second Life and wanted assistance with setting up a poster.

When I logged on I found Lali Ewry (a researcher) and Bronwen Pizzicato (from Nature Precedings) still waiting there. Since there were no posters yet in the ChemBioFoo area I took them over to the adjacent SciFoo Lives On section to show them examples of what posters can look like in Second Life.

Lali had some slides available so I gave her one of Hiro's boards and showed her how to upload, re-size and move the poster. (By the way Hiro's boards have the nice feature that, as a presenter, you can go backwards in your presentation and the boards reset to the starting slides after a few minutes of inactivity)

We took her board to the ChemBioFoo area and Lali positioned it at poster #1. She also put a bell so others could summon her to discuss her work on "Transcription of Inflammatory Genes in Crohn's Disease". There are wonderful images in that presentation about the mechanics of the disease and Lali is still adding more. She had some animations that have to be converted to still images before posting.

Lali's real name is Laura Ferrero-Miliani and she is at Herlev Hospital, Medical-Gastroenterology Lab 54O3 in Denmark.

This is a perfect example of what I had in mind for ChemBioFoo. In keeping with the SciFoo un-conference, the SciFoo Lives On area has some great posters to promote and discuss Open Science and new Science Communication Technologies. However, I think there needs to be a place to host domain-specific scientific discussion as perpetual poster sessions in Second Life.

This is actually very much in keeping with the format of the Nature journal itself. The articles are typically high level and are collected from various scientific fields. I am starting with Chemistry and Biology because I feel that these areas have a strong potential for improving human lives directly (in terms of affecting disease processes for example). Also these areas are most closely related to my domain specific research of organic synthesis and drug design. (And we only have 36 booths in this area for now). Of course I would be happy to assist anyone in creating a poster area with another scientific focus.

I often tell people that they should only enter Second Life if they have a good reason for doing so. By putting posters that are similar in format and content to those that the typical researcher is likely to find at the physical conferences that they attend is probably a pretty good way to attract traditional scientists to media platforms like Second Life. If they see a poster that is interesting they can ring the bell, talk with the presenter then decide how that experience compares with a physical meeting.

So I am asking for anyone interested in contributing to let me know (or Lali - she is trained now to help the next presenters after all).

My presentation is coming up - I have a few more slides to put together. Tony Williams from ChemSpider also sent me a presentation that I'll put up shortly.

PodCamp Philly at Drexel

For anyone in the Philadelphia area, PodCamp Philly starts this weekend Sept 7-9, 2007. Topics include anything related to podcasting and social software.

I'll be doing a session on Drexel Island and Second Life.

The event is free but you must register.

Ring for SciFoo Service

If you wander around the SciFoo Lives On area, you will notice that some of the poster booths have bells.

If the text above them is green, it indicates that the presenter is somewhere in Second Life. The visitor can then just click on the bell to summon the presenter with a quick message.

If the text is red, the presenter is not in world. However, a message can still be sent and it will show up the next time they log in.

Now this can be problematic for users who created a Second Life account exclusively for the purpose of presenting or attending a SciFoo Lives On session since they are unlikely to login again and retrieve IM messages. There is a trick around that: in SL hit control-P and turn on the setting to forward IM to email.

This effectively transforms the SciFoo Lives On area into a perpetual session with the cumulative content of all prior sessions, which now include "Tools for Open Science" and "Medicine and Web 2.0". We are now getting ready for the "Definitions in Open Science" session on Tuesday Sept 4, 2007 at 16:00 GMT and there are still slots available to present.

The bells can be purchased for 150L (about 60 cents) on PixelTrix Island (SLURL) - thanks to Ron Comer for help in locating these!

The location and list of all upcoming SciFoo Lives On sessions can be found on the SFLO wiki.

SciFoo Lives On Upgrade and Wiki

There have been a few additions to the SciFoo Lives On area on Nature Island in Second Life.

The area has been divided into 36 numbered plots and most posters from the first two sessions have been moved to fill the first 10 spots. Posters for future sessions will be added sequentially as they are created. (Thanks to Eloise and Beth for help with this!)

This makes the area much more appealing and permits regular poster sessions where people can meet at any time to present and discuss. I have been a huge fan of the effectiveness of poster sessions in Second Life after my first experience. We will still do talks at the scheduled sessions but afterwards groups can break out to posters from any previous SciFoo Lives On session.

I have also created a wiki to keep track of dates and topics of past and future sessions. Presenters are welcome to record their names (Second Life and Real Life), affiliations and presentation titles next to their poster number.

First SciFoo Lives On Session on Tools for Open Science

We had our first SciFoo Lives On session today on Nature Island (Second Nature) in Second Life. We had about a dozen people participate.

The topic was "Tools for Open Science". I wanted to explore more fully the actual technology that people are starting to use towards doing more open science. I started off by showing screenshots of UsefulChem wiki and blogs from my poster. The other posters there (and still there) included MyExperiment, Nature Precedings, Bill Hooker's Thoughts, Knowble and Connotea.

Overall it went very well I think. Initially I was disappointed that most people did not have voice working but it turned out to be a good thing because I was able to capture the entire chat transcript (see below).

Based on Berci's suggestion, we'll do "Medicine and Web 2.0" next week on Monday Aug 27, 2007 ET noon. So bring your posters and join us!

Here is the transcript:
[9:00] You: I think many of you were at scifoo
[9:00] You: one of the problems is ther was not enough time to cover everything
[9:01] You: this is a continuation on that
[9:01] You: on Tools for Open Science
[9:01] You: this really should be a discussion
[9:01] You: so we'll just take a few minutes each to explain
[9:01] You: I'll start on the Open Notebook Science poster
[9:02] You: then we'll go to the right and around the corner
[9:02] You: please stop me if you have a comment or question
[9:02] You: I was hoping to do this by voice but not enough people have it
[9:03] Max Chatnoir: good to have the chat record.
[9:03] Berci Dryke: sure
[9:03] You: what I would like for my 5 mins is to show screenshots of our Open Notebook Science
[9:03] You: so we have one component that is a blog
[9:04] You: the idea is to record everything from ongoing research in my lab
[9:04] You: I'm skipping over stuff because I don't want to take 1 hour :)
[9:04] You: we started tracking molecules in my lab using a blog like this
[9:05] You: but now we are moving this to Chemspider
[9:05] Stew Alito: Um.... can Phoenix move to the side a bit? It's the wings... can't see!
[9:05] Berci Dryke: lol
[9:05] You: we started tracking experimnents using a blog
[9:05] You: but there were too many edits
[9:05] Troy McLuhan: To adjust your camera position, hold down ALT and then click-drag with your mouse
[9:05] You: so we moved to a wiki
[9:06] You: the wiki has all the lab notebook pages and organization pages
[9:06] You: the wiki tracks nicely the contribution of everybody over time
[9:06] You: and we can prove who-knew-what-when
[9:06] You: with each version
[9:07] You: we use Wikispaces because it is free and offers thridparty time stamps
[9:07] Max Chatnoir: These are suggestions for the synthesis?
[9:07] You: which one max?
[9:07] You: there were comments from others yes
[9:08] You: but it turns out our collaborators prefer to use our mailing list to share
[9:08] You: so the wiki is mainly my students in the lab
[9:08] You: I will leave the rest here - tha's it for me
[9:08] You: any comments/questions?
[9:08] Berci Dryke: What about competition?
[9:09] You: you mean fear of being scooped berci?
[9:09] Berci Dryke: yes
[9:09] You: I think that this is safer than many other things scientists do
[9:09] You: like proposals
[9:09] You: because all this is indexed quickly in google
[9:10] You: it would be very embarrasing to get caught stealing text
[9:10] Max Chatnoir: So this is a sort of ongoing multicontributor proposal presentation?
[9:10] Max Chatnoir: But very publicly documented!
[9:10] Stew Alito: Have you ever been scooped, to your knowledge?
[9:10] You: max this simply our standard lab notebook on a public wiki
[9:10] You: no I don't know of anyone having "stolen" anything
[9:11] Max Chatnoir: So the contributors are mostly your own students?
[9:11] You: max - yes the wiki is mainly my students
[9:11] Berci Dryke: your wiki can be edited by anyone (or just those who have access to it?)
[9:11] You: on the mailing list we have great collaborators like
[9:11] Max Chatnoir: Do you get external contributions as well?
[9:11] You: Rajarshi Guha that does docking for us
[9:11] You: max - you have to register
[9:12] Troy McLuhan: Which mailing list service/software do you use?
[9:12] You: simply because otherwise my students forget to login!
[9:12] Max Chatnoir: But the registration is open?
[9:12] You: we use Google groups
[9:12] suhky Rezillo: now I am here
[9:12] You: we are ALL google - blog, wiki, lists
[9:12] Berci Dryke: why is better than creating an own wiki (I mean used in an internal network)
[9:12] Max Chatnoir: Like WebCT?
[9:12] You: Google has been a huge gift to open science
[9:12] You: what is like webct maX?
[9:13] Max Chatnoir: Internal network.
[9:13] Stew Alito: Do you share references with Zotero or Connotea etc.?
[9:13] Max Chatnoir: I was adding to Berci's question.
[9:13] You: I have used Connotea with my class students
[9:13] You: but not systematically
[9:13] Rakerman Yellowjacket: I wonder about the amount of information - do you think there's any difference between someone getting a protocol from your notebook, or a "refined" version from myExperiment or Nature Protocols?
[9:14] You: good point raker
[9:14] Corwin Carillon is Offline
[9:14] You: Nature protocols is great for established protocols
[9:14] You: but it takes time to get the info in there
[9:14] You: UsefulChem is real time so by necessity messy
[9:14] You: BUT - the question is can scientist use the info
[9:15] You: and based on the types of searches we observe - I say yes
[9:15] You: we can always collect and publish these as full papers later
[9:15] Rakerman Yellowjacket: I am wondering - if everyone published their lab notebooks online, what would google search results look like - how would be be able to find the most relevant results? Would online notebooks s scale?
[9:15] You: well we have to add metadata
[9:15] Adastar Galsworthy: how do people feel about citing online resources?
[9:15] Max Chatnoir: So this is one way to get "tried this, didn't work" into a publicly accessib le space.
[9:16] You: for example in chemistry we tag with inchis
[9:16] Adastar Galsworthy: particularly informal resources
[9:16] You: each field will have to add metadata
[9:16] You: do we have our myexperiment guy here?
[9:17] You: ok, someone want to say a few words about Precedings?
[9:17] You: we can move to that poster
[9:17] Max Chatnoir: Can people not in your class register for the wiki?
[9:17] You: max - yes they can
[9:18] You: suhky?
[9:18] suhky Rezillo: yes?
[9:18] Max Chatnoir: So, Berci, that would be why it is in a public forum rather than an internet network like WebCT or Blackboard.
[9:18] You: would you like to say a few words about precedings
[9:18] Berci Dryke: understood, Max :)
[9:19] Joanna Wombat: Hilary's just coming now
[9:19] You: I've use precedings myself
[9:19] Joanna Wombat: I think she can say something about precedings
[9:19] suhky Rezillo: one moment Hilary will talk about Nature Precedings as she co-developed the site...
[9:19] You: and I think it is a fantastic addition to tools for open science
[9:19] You: oh good
[9:19] Max Chatnoir: Indeed!
[9:19] Hilary Serevi: hi everyone
[9:19] Troy McLuhan: Would it make sense to publish the transcript of this discussion on Nature Preceedings?
[9:19] Joanna Wombat: Hi Hilary
[9:19] You: hilary you have the floor
[9:19] suhky Rezillo: Everyone, let me well you to Hilary Serevi
[9:20] Berci Dryke: nice to meet you!
[9:20] Hilary Serevi: thanks--I haven't spent too much time in second life
[9:20] Hilary Serevi: but hopefully I can answer some questions about Precedings
[9:21] You: hilary what was your role in precedings
[9:21] You have offered friendship to Krystine Qinan
[9:21] Hilary Serevi: I'm the Product Development Manager
[9:21] Krystine Qinan is Online
[9:21] You: did you make this poster?
[9:22] suhky Rezillo: Yes she did, with Timo Hannay
[9:22] Hilary Serevi: yes
[9:22] You: anyone else here use precedigns?
[9:22] Troy McLuhan: Can you summarize what it is?
[9:22] You: basically you can publish in any format
[9:22] You: the submissions are editorially reviewed
[9:22] You: but not peer reviewed
[9:23] Hilary Serevi: that's correct, Horace
[9:23] You: but it does not have to be an article format
[9:23] You: I have published blog posts there
[9:23] You: well the poster will stay there after this session
[9:23] Berci Dryke: can I have a personal question about it?
[9:23] yucca Gemini is Online
[9:23] You: yes berci
[9:23] Berci Dryke: I'm a medical student and have a presentation about web 2.0 and medicine (Medicine 2.0). Why would it be good for me to publish it on Precedings? And could I publish it?
[9:24] You: they do have a lot of presentations
[9:24] You: I published my ppt as well that we were loking at
[9:24] You: let's move on
[9:24] You: Bill could not make it
[9:24] You: so I'll say a few things
[9:25] Stew Alito is Offline
[9:25] You: Bill Hooker has been reporting on Open Science for a long time
[9:25] Hilary Serevi: since we've moved on, perhaps I can answer your question later, berci
[9:25] You: and he asked me to ask you about what you thought about the def o open science
[9:25] Berci Dryke: ok, Hilary
[9:25] You: sorry hilary
[9:26] You: please answer
[9:26] You: does anyone have thoughts about the definitions?
[9:27] You: the term open science has been used so much we don't know what it means somtimes
[9:27] Samara Barzane is Online
[9:27] Rakerman Yellowjacket: it's more like "publically shared pre-publication science"
[9:28] Adastar Galsworthy: i have a thought about the reasons for the need for open science
[9:28] Troy McLuhan: PLoS is open though, and is for publication
[9:28] Adastar Galsworthy: I think it was in the middle of the 18th century that the last man to have read everythin lived,
[9:28] Emile Pintens: Rakerman, I do not know if that it has to be pre-published. I think the ultimate goal would be for pre-published, and published works to be open.
[9:29] You: so you don't consider precedings to be "published"
[9:29] You: according to patent law that is certainly a publication
[9:29] Hilary Serevi: so precedings doesn't "publish" documents--they'i think that the term "open access" tends to be applied to peer-reviewed publication
[9:29] You: it is not peer-reviewed
[9:29] Troy McLuhan: Sorry, that's what I mean
[9:30] Hilary Serevi: i think the definition of a "publication" is changing with the development of the internet
[9:30] You: so when people say pre-publication they mean pre-peer-reviewed
[9:30] Emile Pintens: Isn't Precedings screened? It isn't peer-reviewed, but it is reviewed
[9:30] Rakerman Yellowjacket: pre-peer-reviewed is maybe a better term
[9:30] Troy McLuhan: I guess what I really mean is, does the tenure review committee consider it "published"?
[9:30] You: definition confusion was big at scifoo i think
[9:30] Hilary Serevi: It's screened, but the screening process is mainly to prevent the posting of obviously commercial documents (e.g. spam)
[9:31] Hilary Serevi: or pseudoscience
[9:31] Hilary Serevi: although pseudoscience is also another term that is difficult to devine
[9:31] Hilary Serevi: define--sorry
[9:31] You: but without defining "peers", it is hard to define peer review
[9:31] Emile Pintens: Ok thank you for the clarification. Is there a time lag between an item being submitted and the time it makes it on the site?
[9:31] Adastar Galsworthy: in peer reviewed journals there is plenty of pseudo-science. that was my experience as an editor for a few smaller physics journals for a while
[9:32] Hilary Serevi: yes--the mean time between submission and posting is less than a day
[9:32] DrDoug Pennell is Offline
[9:32] You: yes precedings made me change my abstract to they did read it!
[9:32] Adastar Galsworthy: I'd like to jump the discussion back a few rungs
[9:32] Max Chatnoir: That's a really fast turnaround.
[9:33] suhky Rezillo: Horace - what or how much do you submit to precedings?
[9:33] Adastar Galsworthy: less about the specifics of what the mechanics of open science are, and discuss the issue of accreditation
[9:33] You: suhky - I only submitted 3 times
[9:33] Troy McLuhan: Preceedings is quite new I think
[9:33] Hilary Serevi: it's because we don't send the submissions out to scientists currently working in the field
[9:33] Emile Pintens: Change the abstract? Thats the first time I've heard of that happening in Preceedings
[9:33] You: Emile - well they had some good points
[9:34] Emile Pintens: Ah gotcha
[9:34] Troy McLuhan: Adastar - What do you mean by accreditation?
[9:34] You: told me to be more explicit
[9:34] Max Chatnoir: The fact that there is some editorial review should carry some weight with things like tenure committees.
[9:34] You: absolutely max
[9:34] Adastar Galsworthy: the point someone raised earlier about the leve of acceptance by tenure committees and so forth.
[9:34] You: we have to explain it to the tenure committees
[9:35] Hilary Serevi: Adastar--is your question about whether accredation is a prerequisite for participation in open science?
[9:35] Emile Pintens: The question is how long with the tenure committees take in accepting Web 2.0 tools like the ones we are talking about
[9:35] Emile Pintens: How long will*
[9:36] You: it is certainly an issue (accreditation) and that is why it is important that we continue to talk
[9:36] You: we will need each other to support what we are doing
[9:36] Max Chatnoir: I would think that this kind of publication would at least have the status that a presentation at a meeting would have.
[9:36] You: to explain, to validate
[9:37] You: max that is true presentations count and are not peer reviewed
[9:37] Adastar Galsworthy: I'm working for Nature, and there is certainly belief within this comapny that such metrics will emerge.
[9:37] Max Chatnoir: Also, you're putting your work out in a very public venue, so there is a very wide potential peer pool for comments.
[9:37] Troy McLuhan: I don't think it's a matter of accepting tools. Scientists are always bringing new tools into use. It's a matter of determining "what counts". For example, the recent proof of the Poincare Conjecture was never published in a Peer Reviewed journal as far as I know, but certainly "counts"
[9:37] You: adastar - we are looking for Nature to take some lead in that
[9:38] Emile Pintens: Adastar, metrics from where?
[9:38] Hilary Serevi: there's an interesting paper by the PLoS medicine editors about how impact factor will change in response to web 2.0 tools
[9:38] Berci Dryke: Hilary: could you please give a link to that?
[9:38] Hilary Serevi: troy's reference is to Perelman's use of ArXiv rather than a math journal to distribute his work
[9:38] You: hilary - yes Heather Piwooar
[9:38] You: piwowar
[9:38] Hilary Serevi: doi: 10.1371/journal.pmed.0030291
[9:39] Berci Dryke: thank you
[9:39] Hilary Serevi: the chronicle of higher education also had an article about that
[9:39] Hilary Serevi: i don't have the link available
[9:39] Rakerman Yellowjacket: I think scientists need to push back against impact factor and move to a concept of "science portfolio" - what work have you done - there are going to be all different types of contributions
[9:39] Adastar Galsworthy: at the moment we are building social tools, but they are mostly in their first generation
[9:40] You: racker very good point - metrics are limited compared to portfolios
[9:40] Adastar Galsworthy: the obvious things to start looking for are the spoead of influence of ideas through social networks
[9:40] Adastar Galsworthy: but there is a bit of a way to go before anything solid is around to this robustly
[9:40] You: but we can still play with metrics - let just not give everything else up
[9:41] Adastar Galsworthy: however, I want to stress that I feel the reason that we need to do this is so that we can support open science, which I happen to think is vital in the presence of too much information to sift through
[9:41] Adastar Galsworthy: open science goes hand in hand with social networking, and this provides a platform for collaborative filtering
[9:42] You: Ada - do you wnat to talk about Connotea/Emile about Knowble
[9:42] suhky Rezillo: Doesn't Connotea acknowledge users' contribution to the site?
[9:42] Rakerman Yellowjacket: ISI algorithms shouldn't be the end-all of evaluating a scientist for tenure and promotion - we already have a system to evaluate grants - tenure committees should recognize the full work of the scientist - SOME of which must pass both the review of peers and hopefully be tested through being reproduced
[9:42] Emile Pintens: I can talk about Knowble anytime
[9:42] Emile Pintens: Am I next?
[9:42] You: sure
[9:43] Emile Pintens: Knowble is a knowledge community for researchers to connect, communicate, and collaborate.
[9:43] You: hold on
[9:43] Emile Pintens: ok
[9:44] You: sorry emile not for you - go on
[9:44] You: brb
[9:44] Emile Pintens: O ok, sorry.
[9:45] Emile Pintens: I came up with the idea while I was an undergrad at UNC, and we received funding from the School of Medicine as a part of UNC's CTSA proposal.
[9:45] Emile Pintens: Right now we are in Beta, but the idea is to provide a common community where researchers, professors, and scientists may connect based upon common research areas or methodologies.
[9:45] Max Chatnoir: Brilliant, Emile.
[9:45] You: I've tried Knoble recently
[9:45] Troy McLuhan: Wow this is a great idea
[9:45] Berci Dryke: is it similar to Tiromed.com?
[9:46] You: to specify our need for a docking expert
[9:46] Hilary Serevi: Over here!
[9:46] Emile Pintens: We are taking an approach similar to Facebook where we must accept your institution before a person may be able to register.
[9:46] Emile Pintens: I have not seen Tiromed.com
[9:46] Emile Pintens: Hilary, you have a question?
[9:46] Max Chatnoir: I just discovered that, Emile!
[9:46] Berci Dryke: that is a medical community site with the same goals
[9:46] Hilary Serevi: sorry - no
[9:47] suhky Rezillo is Offline
[9:48] You have offered friendship to Troy McLuhan
[9:48] Troy McLuhan is Online
[9:48] Emile Pintens: Ah ok. While the School of Medicine provided the initial funding, we are moving to allow researchers from really any discipline to join. Our tools are not at the level of any discipline, but we are working on it. An example, we are linked to PubMed, which some professors at UNC feel it does not include all of their works.
[9:48] Rakerman Yellowjacket: how does knowble compare to pronetos and other scholar community sites?
[9:48] You have offered friendship to Rakerman Yellowjacket
[9:48] Rakerman Yellowjacket is Online
[9:48] You have offered friendship to Xantha Oe
[9:49] You have offered friendship to Joanna Wombat
[9:49] You have offered friendship to Hilary Serevi
[9:49] Emile Pintens: From what we know about Pronetos, they are focused on Publishing. We are focused on connecting people.
[9:49] Hilary Serevi is Online
[9:49] Emile Pintens: But since Pronetos isn't online yet, I do not know for sure, but we wish them luck!
[9:50] Troy McLuhan: I gather that Knowble is mainly for scientists and academics, as opposed to the general public with an interest in science?
[9:51] Joanna Wombat is Online
[9:51] Xantha Oe is Online
[9:51] Emile Pintens: Right now yes. We are trying to ensure a fairly tight user base. In time, I would not count us out in opening up to the general public.
[9:52] Emile Pintens: We are in beta, so user feedback is being gathered and we will be making further changes in the coming weeks.
[9:52] Emile Pintens: Are there any further questions?
[9:52] You: Ada do you want to say something about Connotea
[9:52] Adastar Galsworthy: sure
[9:52] Troy McLuhan: What is the underlying development tools for Knowble? A CMS? A web language?
[9:53] Emile Pintens: Troy, we use LAMP
[9:53] Adastar Galsworthy: first, sorry about the mess
[9:53] Visitor Counter 1.8: Welcome Xantha Oe. You have been counted.
[9:53] Adastar Galsworthy: I just threw these together 1/2 an hour ago.
[9:53] Visitor Counter 1.8: Welcome Berci Dryke. You have been counted.
[9:53] Adastar Galsworthy: am giving a talk on friday and will post the full presentation here in a nice format next week,.
[9:54] You: thanks ada
[9:54] Adastar Galsworthy: as many of you know there are a bunch of tools for bookmarking on hte internet
[9:54] Adastar Galsworthy: the great grand daddy is delicious.
[9:54] Adastar Galsworthy: Nature, and me spcifically, work on a tool for scientists called connotea
[9:55] Adastar Galsworthy: there are about three other specific tools out there for scientists.
[9:55] Adastar Galsworthy: I'd say take em for a test drive and pick the one you like best (as long as it's conotea ;)
[9:56] Adastar Galsworthy: as I was alluding to earlier, one of the things we are trying to do with connotea is make it into a rccomendation engine for scientsits
[9:56] Adastar Galsworthy: to help filter the huge number ot papers out there
[9:56] Adastar Galsworthy: but it is early days yet
[9:56] Adastar Galsworthy: There is an api and some people have bulit some cool apps using conontea as an engine
[9:56] You: what is an example ada
[9:57] Adastar Galsworthy: most of the exentions are greasmonkey extensions.
[9:57] Hilary Serevi: can you use greasemonkey to connect to the api?
[9:57] Adastar Galsworthy: one called Stack it, creates digg like buttons next to doi's on any poge and lets you see if the paper has been bookmarked
[9:58] Adastar Galsworthy: another called the entity describor (which was just provisionally released last week, so give it another week or so)
[9:58] Adastar Galsworthy: connects tags in conntea to a structured ontology, such as the MeSH ontology
[9:59] Adastar Galsworthy: There is another that uses conntoea as a backbone for connecting XML stlysheets for scehmas representing systems biology7
[9:59] Adastar Galsworthy: you can see them at http://www.connotea.org/wiki/ConnoteaTools [9:59] You: Ada - do you think you would be able to take Nature Predecings posts in connotea
[9:59] Adastar Galsworthy: yes, we are working on that
[10:00] Adastar Galsworthy: rather than waiting for everything to be perfect our philosophy is torelease and improve
[10:00] You: that would really help push the more open side
[10:00] You: thanks adastar!
[10:00] Adastar Galsworthy: no probs.
[10:00] You: before we go -
[10:00] You: any suggestions for the theme of the next session?
[10:00] Berci Dryke: medicine and web 2.0 :)
[10:01] You: nice berci
[10:01] Max Chatnoir: Horace, it it always in this time block?
[10:01] Hilary Serevi: i'm very intested in the ethical issues associated with putting medical
(theraputic/clinical) infomation on the web
[10:01] You: max I think same time next week
[10:01] Adastar Galsworthy: I gotta go now, thank's guy's
[10:01] Berci Dryke: Hilary: this is a crucial question...
[10:01] Adastar Galsworthy is Offline
[10:01] Hilary Serevi: thanks for organizing horace
[10:01] You: I'll post the transcript also on usefulchem.blogpspot.com
[10:01] You: sure my pleasure
[10:02] Berci Dryke: thank you, Horace!
[10:02] Max Chatnoir: Sigh.... I'll have a class then, but will look for the TS!
[10:02] You: thank you all!
[10:02] Berci Dryke: I'll also post about it with many images
[10:02] Max Chatnoir: Excellent, Berci.
[10:02] You: yes please send me you images it you want
[10:02] You: we'll leave these posters up
[10:02] Max Chatnoir: Got a RL faculty meeting. Thanks, Horace!
[10:02] Emile Pintens: I have already made a post in the Knowble blog! http://www.knowble.net/blog/
[10:03] Berci Dryke: next week, same time?
[10:03] You: so Berci lets do that then
[10:03] You: yes same time
[10:03] Emile Pintens: Same time next week sounds good
[10:03] You: thanks to joanna too for the space!
[10:03] Hilary Serevi: nice meeting everyone
[10:03] Hilary Serevi: thanks again!
[10:03] Joanna Wombat: thanks!
[10:03] You: bye everyone
[10:04] Berci Dryke: Bye!
[10:04] Emile Pintens: thanks Jean-Claude this was great! Talk to you soon
[10:04] Max Chatnoir is Offline
[10:04] Joanna Wombat is Offline
[10:05] Troy McLuhan: If you're interested in science-related events in SL, feel free to join the Science Center group
[10:05] Emile Pintens: Troy how do we do that?
[10:05] Rakerman Yellowjacket: thanks Jean-Claude

SciFoo Lives On Second Life

After complaining that there was not enough time to cover everything at the Science Foo Camp, and after getting some very positive feedback from our chemical reaction mechanism representation in Second Life, it occurred to me that it would make sense to attempt to continue the conversation in a virtual medium.

I have previously presented a poster in Second Life and I was thoroughly impressed with how well it worked. People would walk around, look at my poster, ask me for more information and share their experience. And just like in real life, when there was a lull in the traffic, I would chat with my poster neighbor. One big difference was that I didn't have a draining and expensive trip to deal with.

Yes, I know that there is no replacement for face to face interactions during lunch and breaks. But it is surprising just how much one can get out of the experience, given the minimal effort it takes.

So I have set up an area on one of Nature's islands called SciFoo Lives On. I have put up my poster on Open Notebook Science. Clicking on the images flips to the next one in the presentation. Clicking on a side panel opens a browser to a screencast recording of my presentation. I have also included a headshot of myself - clicking on that takes you to my UsefulChem research wiki.

But Second Life allows not only images but also 3D objects. As examples, I included a molecule and an obelisk that generates an organic chemistry quiz upon clicking. Later on I'll copy the reaction mechanism that is currently on display on Drexel Island.

I invite any other SciFoo participants to put up a poster. If you have a Powerpoint presentation it is fairly easy to put it up. Just let me know if you need help. Powerpoint style panels are available for free at the Drexel Island store but you will need to be invited to Nature's island by either by a member like me or the owner Joanna Wombat (Joanna Scott in real life) to build there.

Although we can create a nice place to visit and view posters anytime, it would be very interesting to see how un-conference sessions would work. Keep in mind that Second Life now has voice in addition to chat.

I propose to moderate a session on "Tools for Open Science" at noon EDT (9:00 PDT, 16:00 GMT) on August 20, 2007 for the convenience of our European and US West coast participants. In the spirit of SciFoo, this will be a discussion, not be a presentation, although we should feel free to use pages from our posters to facilitate communication.

I will also set up a thread on the Second Life section of Nature Networks for people to propose sessions.

SciFoo Lives On slurl.

SciFoo07 Ends

The past few days have been quite stimulating.

The SciFoo conference started right after I got off the plane in San Francisco on Friday evening around 18:00 and lasted till midnight. With the jetlag from the east coast I was exhausted but the energy of the meeting definitely kept my interest.

Friday night was the only part of the conference deliberately set up with the traditional format of speakers. The most impressive talk was on the big picture of planetary energy input and consumption. It was refreshing because the speakers seemed genuinely concerned with reporting on the actual state of things, instead of building up evidence to support their pet eco-solution. Lets just say things look grim for maintaining current energy consumption with existing renewable and non-renewable energy sources. (However, since we haven't been good at predicting scientific discoveries in the past my guess is this model will become irrelevant in 100 years). If the slides are released I'll link to them in an update.

On Friday night people suggested sessions for Saturday and Sunday and I tried to attend as many of them related to Open Science and scientific publication. The idea of this "un-conference" was to create brainstorming and discussion sessions. A few sessions really were like that but most ended up with significant presentation portions, some taking up the whole slot.

There was just enough time during the hour long sessions for people to state their opinions but not enough to innovate and make progress. That will have to wait for discussions and collaborations following the meeting. Anyone following the discussions in the blogosphere on Open Science and scientific publication will be familiar with the debates: peer review, academic credit, fear of getting scooped, etc.

The discussion was much like the blogosphere, except that the more introverted individuals probably did not contribute as much as they would have liked. I'll find out what they were thinking when they get to update their blogs and post comments.

Sometimes it felt like the Googleplex was the tower of Babel. It is apparent that there are enormous differences in the way science is done in various fields. Terms like raw data, peer review, experiment, reproducibility, citation, publication, workflow, etc. can have very different meanings.

This was probably the source of some heated discussions at times. As an organic chemist, if I find a report of a synthesis on the web with full characterization of the product, I can inspect the raw data from the spectra fairly quickly and determine if it makes any sense. I can then use that information to make that product or similar compounds with confidence. In that case, the presence or absence of peer review does nothing to affect my ability to use the information. For a cosmologist, analyzing raw data is so time consuming that the analogous situation does not apply. The only way to remove these misunderstandings is to continue to have conversations. This may be one of the most important functions of science blogs.

I met several scientists who expressed their intent to move at least part of their research to a more open format, beyond the framework of the traditional journal article. I also discussed collaboration on our drug-discovery efforts with a few people. As these materialize, I will be sure to blog about them.

Drexel Island in the Bulletin

Adam Paul wrote an article on Drexel Island on August 2, 2007 in the Philadelphia Evening Bulletin : Drexel Students Get a "Second Life".

USA Today Second Life Article

Beth Sussman's August 2, 2007 article on Second Life in Education has appeared.

Drexel Island got a mention:

Jean-Claude Bradley, chemistry professor and e-learning coordinator for the College of Arts and Sciences at Drexel University, says he uses it as an optional study tool but wouldn't be comfortable teaching a class exclusively in Second Life.

Bradley says only about 10 of his 200 organic chemistry students used Second Life more than once last spring. But those who did found it an effective way to study.

"This is a new way to interact with me and each other," he says. "I can show them molecules in three dimensions. We can walk around the molecule and discuss it."

"Kids who used Second Life put more time into the class," says chemistry major Tim Bohinski.

Bradley is trying to get more departments to use the "land" the university bought in Second Life; Drexel Island is shaped like a dragon, the school's mascot.

Universities and other academic institutions pay a reduced rate to buy land to build structures and develop the environment. The first-time cost for a 16-acre private university island is $980, and monthly land fees are $150.

Drexel also pays for developers to build up the island, Bradley says. Students can sign up for free basic membership and use Second Life at no cost, just as anyone can.

Beth's work was also featured:

On a Tuesday night, Beth Ritter-Guth joins her eight literature students for class. Next to a grave.
Well, not a real grave. She teaches her contemporary literature course online, in Second Life.

The class met on Willow Springs-Mama Day Island, designed around the novel that the class was reading, Mama Day by Gloria Naylor. The students visited the grave of a character, then wrote obituaries.

"I build environments where students can really explore the literature," says Ritter-Guth, of DeSales University in Center Valley, Pa., and Lehigh Carbon Community College in Schnecksville, Pa. "It's the novel in 3-D."

Teaching Chemistry Mechansims in Second Life

I have previously commented on how organic chemistry can be incorporated into Second Life.

Andrew Lang has created a script to generate 3D structures of molecules and shown how to represent the docking of a molecule in the receptor site of a protein (this is important for demonstrating how drugs can interfere with infectious agents like the parasite that causes malaria).

I have also described how these molecules can be indexed by common search engines, like Google, so that people can discover locations in Second Life where chemistry is displayed.

Now, with the help of Andrew and my students Jessica and Khalid, we can demonstrate a chemical reaction. Andrew came up with an elegant solution for controlling animation in Second Life. Simply by saying "back" or "next" in regular chat next to the molecules, the reaction will proceed to the next step. (see video below)

Jessica minimized the conformation of each intermediate in ChemSketch so that its 3D structure is probably fairly close to what it actually looks like. This should provide an additional perspective to use in the teaching of organic chemistry reaction mechanisms. Walking around a giant molecule with a student is certainly a contrast to looking at a 2D representation in a textbook, especially with the control of animation.

This is actually just the first step in the Ugi reaction that Jessica and Khalid are performing in my lab for the synthesis of anti-malarial compounds. This example starts with the reaction of benzaldehyde with 5-methylfurfurylamine to form an imine. (Note: we generally form the imine without adding an acid catalyst and so the mechanism under basic conditions is displayed).

For the full Ugi reaction keep climbing the staircase on Drexel Island that starts with imine formation here: slurl.

(These reactions are also going to be indexed on the SL molecule wiki)

Drexel Triangle Second Life Article

The Drexel Triangle published an article about Drexel Island on July 27, 2007.

I think it is great that the library is installing Second Life on its desktop computers:

Drexel opens Second Life campus
By: Nancy Lan

The next time you log in to Second Life, the 3-D virtual world run by its residents, you might run in to a Drexel professor teaching a course.

The University bought land on Second Life, May 9. The property has been named Drexel Island and cost about $900 to purchase plus an additional $150 per month for maintenance, according to Jean-Claude Bradley, E-Learning Coordinator for the College of Arts and Sciences.

Bradley said Second Life can help faculty members take their classroom materials to a new level.

"It's a more engaging kind of environment than, say, a message board or instant messaging … it's a lot more intuitive, I think, than blind chat," Bradley said.

...

Second Life will also be available soon on all desktop computers in the library. Siftar said that this implementation will provide "Heightened fun … all on your own computers collocated in virtual space, flying with one another, going and teleporting to different sites. That's a very teambuilding experience."

Philadelphia Inquirer Second Life Article

The Philadelphia Inquirer published an article on Drexel Island Sunday July 29, 2007.

Here is a sample:

Adventurous avatars
Drexel opens a new educational frontier in cyberspace.

By Katie Stuhldreher
Inquirer Staff Writer

Drexel University professor Jean-Claude Bradley can log in from his lab or home and teleport to his organic chemistry classroom, fly around his three-dimensional molecular models, and teach wearing a cat suit.

Bradley, 38, uses the virtual world of Drexel Island - an e-campus shaped like a dragon, Drexel's mascot.

My Upcoming Second Life Talk at Drexel

New Guest Lecture Series: Jean Claude Bradley on "Second Life"

New technologies and tools emerge every day in the marketplace to enrich and expand our computing experiences. Social networking, virtual worlds, digital object repositories, all are intriguing and promising. Students dive right in to use these resources for recreational and social purposes. Faculty members wonder if they have merit and relevance in the academic experience.

IRT is starting a “guest lecturer” series to highlight some of these innovations, explain what they are and give examples of their applicability. Technologies featured will include both those that are part of the Drexel supported repertory and those that are currently outside it.

We begin the series with a review of "Second Life" by Jean Claude Bradley. He will demonstrate what it is and discuss how he is using it in his courses and what impact it has. Please join us in Korman 116 at noon on Tuesday, July 24, 2007, to find out about "Second Life" and what it has to offer.

Bring your lunch - IRT will provide drinks and dessert. If you are interested in attending, let us know at olt@drexel.edu so we can save a cookie for you!

Bora and PLoS ONE Need Your Help

Bora Zivkovik recently sent out this request after starting his position as Online Community Coordinator at PLoS ONE. The fact that he actually got this job from recommendations on comments in his blog should be a wake-up call to people who still think social software is about teenage diaries.

See if you can help him out:

So, my #1 goal is to dramatically increase the number of comments and
annotations on the PLoS ONE papers, without compromising their quality.
I have many ideas how to go about it, but I am always interested in hearing others.

Scientists are generally shy about posting stuff online, but a growing number of science bloggers shows that it is possible for them to change their habits! Please help me in that difficult task ;-)

While my CV and the cover letter were fine, what really got me the job were my
blog commenters! They demonstrated my ability to build an online community
better than any Resume can reveal.

- take a look at the visual/psychological effect of the changes I made to the site and give me feedback about it
- test a new application I introduced on the site and let me know how it works and how it can be improved
- post a comment or annotation yourself
- ask the readers of your blog/website/newsgroup/mailing-list to do
some of the above.

In order for you to be able to do this, i.e., to be able to compare the before' and 'after', I'd like you (and your readers and friends/colleagues) to go over the next few days and familiarize yourself with PLoS ONE, its look and feel:

http://www.plosone.org/home.action

Also, you may want to get more familiar with PLoS as a whole:

http://www.plos.org/index.php

...with all of its journals:

http://www.plos.org/journals/index.html

...and with the principle of Open Access:

http://www.plos.org/oa/index.html

It will also be helpful if you register for the site, subscribe to RSS
feeds of journals, and to e-mail notifications of new articles:

http://www.plos.org/connect.html

You can also help me if you use
some of these ready-made PR materials:

http://www.plos.org/downloads/index.html

...and here are some
other ideas of the ways you can help:

http://www.plos.org/support/index.html

You can join the PLoS group and PLoS cause on Facebook and invite all
your 'friends' to join:

http://facebook.com/group.php?gid=2401713690

http://apps.facebook.com/causes/view_cause/5612?recruiter_id=990

One of the first things I am going to do is try to breathe new life into the PLoS Blog and make it a pretty central (and frequently updated) spot on the site. This may also require some re-design:

http://www.plos.org/cms/blog

So it is not a bad idea for you to subscribe to its feed and to check in regularly and post comments. Linking to its posts or placing them on services like digg, delicious and redditt will also be appreciated.

Oh, almost forgot - think about publishing your papers in PLoS-ONE. As long as it is good science and well written, it is acceptable. It does not need to be Earth-shaking, revolutionary stuff that goes to Science or Nature (though that is certainly acceptable!). It does not need to be of 'general interest' either - a very specialized paper is fine.

The pre-publication peer-review is fast and simple - the papers are evaluated on 'correctness' of methodology and writing. Once a paper is accepted and all the editing and modifications (if suggested by reviewers) is done, the average time between the date of acceptance and the date of publication is 19 days. No other journal can beat that!

Then, and this is where I hope you will help me, the post-publication peer-review kicks in. The community at large, over a span of time, decides if the paper is 'Earth-shaking' or not. Thus, unlike on a blog where only the latest posts are commented on, on PLoS ONE papers, comments may appear, with validity, months and years later as new information on a topic comes to life.

Finally, a study by PNAS last year showed that papers published in Open Access are substantially more likely to get cited, than similar papers hidden behind the pay-walls of subscription-only journals.

Also, while currently most of the papers in PLoS ONE are in the biology/genetics/medicine areas, the journal takes anything from math and astronomy to archaeology and anthropology, so please help us become more diverse!

Finding Molecules in Second Life

As I've recently commented, there has been media interest in the use of the virtual online world Second Life for chemistry. We also recently demonstrated on Drexel Island that it was possible to visualize molecular docking using the molecular rezzer developed by Andrew Lang.

Nature Island also hosts several common molecules, including buckyballs. As more people start to experiment with representing chemicals and chemistry research in Second Life it would be nice if such examples were discovered by a simple Google search.

All that really needs to be done to accomplish this is to co-locate molecular descriptors with corresponding SLURLs (Second Life URLs) on the same web page. When clicked, the SLURL will automatically start Second Life and teleport the user to the location where the molecule can be found. If the user does not have Second Life, a page pops up explaining how to set up a free account and download the software. This could be a good way to introduce the mainstream chemical community to new modalities of communicating science.

As for descriptors, I am suggesting that we use InChIs and common names at the very least. Google does a fairly good job of finding molecules by InChI.

I created a wiki,
http://secondlifemolecules.wikispaces.com/
and seeded it with a molecule from our malaria research that I've used in several places and with caffeine, which is displayed on Nature Island. I invite anyone to contribute to the wiki and add information that could be useful. (The indexing on Google can take a few days for a new wiki)

There are several other ways of creating this index and I think the more redundancy the better. For example, we could make Second Life a "supplier" on ChemSpider. It might also be possible for Andrew's molecule rezzer to note the location of a molecule when it gets created in Second Life and automatically send off an email to a Blogger account to create a post.

Drexel Island Mailing List

I created a mailing list to discuss Drexel's Island on Second Life.

Although I'll still use this blog to post about major events relating to our island, the mailing list will make it easier for users to ask questions and respond.

Trash Can Be Fun

We just had our third Drexel-wide Second Life workshop last Thursday. Most people brought their laptops and we were able to do more hands-on work than previous workshops.

We currently have 10 floors assigned in the main building and Neo has added as many floors as possible (15 total). In fact the top floors are literally in the clouds :)



Beth (Desideria) has also added some more goodies in the School Store. Check out the trash can - just right click it and select harvest - you'll get a free random gift!

Spring 07 Post-Mortem

With the term now over, it is time to reflect on my CHEM241 Organic Chemistry I class.

Following up on the last post-mortem, I continued to use a content page and Google co-op when appropriate during workshops with students. Again, like last term, this did not cause the majority of students to change work habits but it certainly did help some.

Also, with the recent Blogger podcasting problems, I ended up just creating a few large zip files with all the mp3s and all the m4vs. That turns out to be a much simpler way to distribute the archived lectures. Students don't even need iTunes, just Quicktime. The lesson is: for archival materials with no new updates, stick to old school delivery. (Although it is still really handy to have links to individual files in different formats (Flash, m4v, pdf, mp3) on the blog or wiki)

But, of course, the big change this term was using Second Life from the start of the term, instead of Unreal Tournament. About half a dozen students out of 100 participated. I continued to make use of the blue obelisk quiz objects on Drexel Island in the form of races and giving out books and molecular model kits to the winner.

I found that Second Life vastly surpassed Unreal Tournament on several levels. Students did come for the races but they also looked around and interacted with the environment, each other and visitors. In addition to accessing Second Life off campus, some students brought their laptops to the workshops. Wireless access was fine in most cases.

Chat was fine in most cases to interact but next time I would like to use whiteboards so that we can draw molecules as well. I would also like to encourage them to do their extra credit assignments on Second Life. That should prove to be an engaging and collaborative experience for everybody.

Chemistry in Second Life Article

Sarah Everts from Chemical and Engineering News has just published an article about chemistry activities in Second Life. Drexel Island got a mention:

My avatar was then deposited at a place in Second Life called Orientation Island. As I walked my avatar into a geodesic information dome, I happened to notice the "Fly" button. Intrigued, I wasted no time pressing it—and I shot up into the air, hitting the ceiling of the information dome like a clumsy goth-bird. It was around this time that Horace Moody, the avatar of a real-life chemist at Drexel University named Jean-Claude Bradley, came to the rescue and offered to teleport me to Drexel Island. Horace has been experimenting with Second Life as a way to teach undergraduate organic chemistry, a topic he says can definitely benefit from 3-D visualization. Several of his students have met on Drexel Island to challenge each other's organic know-how by touching an obelisk, which then flashes a sequence of quiz questions on Newman projections and Lewis dot structures.

I think that there are some terrific opportunities in Second Life for people with an interest in chemistry at all levels to explore and contribute. (see here for a recent example on molecular docking)

It is certainly a good way to meet curious and smart people.

Nature Precedings Rocks

Following up on my initial comments, my first two posts in Nature Precedings have appeared.

Most people have been posting Powerpoint presentations so I started there with a recent presentation at the American Chemical Society about Open Notebook Science.

Open Notebook Science Using Blogs and Wikis (doi:10.1038/npre.2007.39.1)

Next, I posted an update on the CombiUgi project by basically combining two blog posts (one and two).




It took a lot longer to do this than I expected, experimenting with the format and trying to make it fairly self-contained. I ended up using Powerpoint, which I like for its modular nature and flexibility with image-rich materials. For example, it is easy to spin off as a SlideShare document (which I just noticed supports hyperlinks while embedded - nice!).



There are a few reasons I think Precedings will be one of the key breakthrough apps for Open Science.

1) Nature Publishing Group brings a serious amount of credibility to the table. That is going to make it much easier to convince people in mainstream scientific circles to contribute and read.

2) Flexibility of format: although files must currently be submitted as Powerpoint, Word or PDF file types, the organization of the information within these files is fairly open. The "article" format is not currently required. Although there is no peer review requirement, there is definitely editorial control (which I experienced as I was asked to rewrite my first abstract). They want to make sure that submissions are genuine scientific communications.

3) Referenceability: each accepted submission gets a DOI and clear citation instructions.

4) A convenient system for acknowledging collaborators as co-authors, including affiliation info.

5) Web 2.0 bells and whistles: tags, comments, RSS feeds, etc.

6) The price is right - free read/write.

7) Creative Commons License - Non-Commercial Use with Attribution.

What they do not yet accept are large data files but it looks like that is coming down the road.

Molecule Docking in Second Life

A while back, I posted about how we have been experimenting with representing our research work on UsefulChem in Second Life. With the help of Andrew Lang (Hiro Sheridan on SL), we put up one of the molecules that we had been trying to make as an anti-malarial compound.

Hiro has now taken this to the next level and has the molecule actually moving into the binding pocket of the targeted enzyme (enoyl reductase) upon clicking on it. There are 4 hydrogen-bonding interactions between the molecules and the atoms involved are tagged in green.

I'm grateful that Hiro took the time to show the self-docking animation because it is really hard to manually connect these two 3D puzzle pieces in Second Life (give it a try! - slurl).

In order to get to this point required a considerable amount of collaboration and I would like to thank everyone involved: Goeff Hutchison, Keith Davies, Sean Gardner, Tsu-Soo Tan and Eloise Pasteur.

First Full Drexel Second Life Workshop

Last Friday (June 15, 2007), I ran the first Second Life workshop at Drexel after the general announcement to the entire university.

About 25 people from all areas showed up and a few listed their interests on our DrexelIsland wiki. I'm using that page to enable people to sign up for future workshops as well. The next one will be on Friday June 22, 2007 at noon.

It was basically a Q & A session and this is probably a useful way to see how one moves around in Second Life and what types of activities are possible for teaching and informing.

That morning, Eloise helped me create some more free user-friendly basic tools, like a board that links to the web simply by placing the URL in the description. See the school store for the full list.

Since the workshop, most of the activity has been from our Colleges of Medicine and Nursing.

Drexel Island Wiki

I have created a wiki to help people get onto Drexel Island on Second Life:
http://drexelisland.wikispaces.com/

It has basic instructions for people with no Second Life experience, a map of the island and a presentation showcasing what we have done so far.

There are also pages for individuals (like faculty) and groups (like CoAS, Libraries, DEL, iSchool, etc). This can be handy for looking up avatar names of people you know. Also you can include a slurl (Second Life URL) that will link directly to your part of the island.

If you are involved with Drexel Island, feel free to contribute a summary of what you have done or include your plans.

City of Pods

This has been a productive week with setting up Drexel Island on Second Life. We have settled on a pod tree structure to house departments and faculty in the College of Arts and Sciences. Eloise helped with the pods and Beth and I selected most of the content. The chemistry pod has a list of recent student awards, some images of our equipment and a 3D Bunsen burner and molecule.



The faculty pods are arranged like leaves hovering above the departmental base pods. There are plenty of spaces that we'll populate as we get more faculty involved. For my pod, I have my picture, a link to my organic chemistry class wiki, my research wiki and an example of a quiz obelisk. Other pods have desks. I think that this would be a nice arrangement for virtual open houses where prospective students could visit a few professors from each department in their pods.

The library is now also set up with this pod city framework, organized by guides to literature and databases. There are teleports connecting the chemistry department pod (slurl) to the chemistry resource pod (slurl) in the library section. I think that this type of navigation is important to leverage our resources and make the island as useful as possible to students and faculty.

I ran a Second Life workshop on Friday for CoAS and assisted more faculty from English and Math to set up their avatars. Already we have had participation from Enrollment Management, Drexel E-Learning and the iSchool in the main building. It looks like Nursing is next...

Here is a presentation that I used this week with some representative screenshots:

Second Life Best Practices Poster

Well my poster is up (#12) at the Second Life Best Practices in Education Conference 2007. I'm displaying some pics about showing research results and teaching organic chemistry using Second Life on Drexel and Second Nature islands.

Beth, Eloise and Neo have been working like crazy to get this done and there are now 1000 registrants!

I'll be coming in and out over the day tomorrow at my poster. I'm right next to Max Chatnoir's Gene Pool poster. I'll see you there!

Depression on Drexel Island

Yesterday Beth, Eloise and I helped James Herbert put some course material on Drexel Island. James decided to start with his PowerPoint and a video on depression. It looks like we can play mpg files as easily as mov or m4v in Second Life.

Now we a representative from the department of Psychology in CoAS!

So if you want to see a little segment on bunny suicide come take a look: slurl.

Orgo Lectures on Drexel Island

We met with the librarians today and Beth gave them movie screens that play on Second Life. I also got to put a few of my lectures from CHEM241, introductory organic chemistry in the chemistry area.

Since I already have a blog used for vodcasting with files in m4v format, all I had to do is put links to those files in Second Life. The screen is placed between the quiz obelisks on the left and the UsefulChem project on the right. Although it is more convenient to view lectures from the vodcast or blog because they can be paused or rewinded there, one of the objectives here is to show prospective students what Drexel is all about. For organic chemistry, they can now sample testing, lectures and research on Drexel Island.

Visit here: slurl.

Also Beth gave me a helicopter and I found that the rabbits make good chairs :)

Drexel has a Blimp!

Beth, Eloise and Neo have been busy over the weekend fleshing out Drexel Island on Second Life. There is now a building on the dragon's back (in the minimap) to be shared between the libraries and the College of Arts and Sciences.

This week we'll be filling in content for the CoAS side to the East and the libraries to the West. My class and research are already there in the head region and Beth has some class content on women's studies with videos and a beautiful conference room near the front feet of the dragon. Other early adopters will be populating the island soon.

There are also lots of fun vehicles, like helicopters, canoes, cars, dragons and blimps!

Come check it out here: slurl.

Chemistry Dept Up on Drexel Island

Based on a suggestion by Beth and a rapid implementation by Eloise, the terrain of Drexel Island on Second Life is now shaped like the Drexel dragon mascot. That makes it pretty convenient to specify where things are located.

I started with the dragon's head to create a little section for the chemistry department, showing a picture of our building and adding some info as a note attached to the image. Clicking on the image opens a browser window to the department website.

This is also where I put the obelisks that my students in my organic chemistry class CHEM241 can use for quizzing.

Because the shape of the island requires a lot of water surrounding the dragon shape, we are making full use of 3D space to position the content. Some of the obelisks are floating in air above the water. It is easy to fly up and down in Second Life using the PgUp and PgDn keys.

I think this open design is much better so we removed the existing building on the island.

Come take a look! (slurl)

Drexel Island is Live on Second Life!

The Drexel Island on Second Life is now live and open to the public (slurl).

There is not much on there right now except for a building with signs for the College of Arts and Sciences and the Drexel Libraries. Jane Bryan from the libraries was brave enough to jump in and contribute half the cost with CoAS.

Beth and Eloise were kind enough to help put this together along with some whiteboards where we'll be adding info. There are also obelisks where we can run quizzes on any topic.

And there are dragons! One of my students stopped by and took a ride with one of them. In case you don't know, Mario the dragon is Drexel's mascot. Beth helped me paint him gold.

If anyone wants to help us add content let me know and I'll send along an invite to the Drexel group. My in-world name is Horace Moody. If you have already met me there, note that I may be looking somewhat more feline than before.

Of course, I'll be reporting on who gets involved and what kind of projects are explored. Now to recruit some faculty....

Open Science in Education and the Library

This past month I've had the chance to present Open Notebook Science to groups of educators and librarians. The more I talk with people from different perspectives, the more I realize just how extensive are the ramifications of this general trend towards openness.

Going to Science Foo Camp

I just got an invitation to attend Science Foo Camp in August 07, a unique meeting organized by Nature, O'Reilly and Google. Based on what I heard from last year's attendees this will be an amazing opportunity to bounce ideas around.

I'd like to hear more from others who are going or who attended last year.

As before, we will be inviting around 200 people who are doing particularly interesting work in a wide range of scientific disciplines, as well as in areas of technology and culture that influence, and are influenced by, science. The aim is to encourage cross-fertilization of ideas, creating a unique opportunity to explore topics that transcend traditional boundaries. Of course, senior colleagues from Nature, O'Reilly, and Google will also be present.

Five Blogs That Make Me Think

Hari Jayaram just listed my blog as one that makes him think. Keeping the meme going, I'll list 5 that have had an impact on me.

1. Beth's Second Life Beth Ritter-Guth has been a huge inspiration for me and she is the main reason I pulled the trigger on getting involved with Second Life for my teaching and research. We have collaborated on many other projects involving social software and new approaches to education - Google her name for many more goodies.

2. Chem-bla-ics Egon Willighagen has been instrumental to the cheminformatics community. From the description on his blog: "chemblaics only uses open source software, making experimental results reproducable and validatable". What I like about his blog is that he posts or links to real usable code (like chemistry enhancing GreaseMonkey scripts) or implements simple but powerful tools that can be used immediately (like making Chemical Blogspace more semantically aware).

3. Peter Murray-Rust's blog - Peter is a pioneer of cheminformatics, including the creation of Chemical Markup Language (CML) with Henry Rzepa. For anyone working in any area of cheminformatics and Open Chemistry, his blog is indispensable.

4. Open Reading Frame Bill Hooker is one of the strongest champions of Open Science that I know and has written probably the most comprehensive series of articles on the topic that I have seen.

5. business/bytes/genes/molecules Deepak Singh tends to write about stuff that interests me. Although there are many bioinformatics blogs out there, most of them don't have a high enough signal to noise ratio to make it to my most frequently checked list.

I didn't include several other blogs that I also follow closely - I'll add these to my blogroll shortly (which I have been meaning to do for a while).

Instructions for the next group, copied from Hari's post:

(1) If, and only if, you get tagged, write a post with links to 5 blogs that make you think; (2) Link to this post so that people can easily find the exact origin of the meme; and (3) Optional: Proudly display the ‘Thinking Blogger Award’ with a link to the post that you wrote.

Assignment Zero

Fans of Open Source Science (or just the open source concept in general) should take a look at Assignment Zero. Jay Rosen writes on the About page:

Inspired by the open-source movement, this is an attempt to bring journalists together with people in the public who can help cover a story. It's a collaboration among NewAssignment.Net, Wired, and those who choose to participate.

The investigation takes place in the open, not behind newsroom walls. Participation is voluntary; contributors are welcome from across the Web. The people getting, telling and vetting the story are a mix of professional journalists and members of the public -- also known as citizen journalists. This is a model I describe as "pro-am."

The "ams" are simply people getting together on their own time to contribute to a project in journalism that for their own reasons they support. The "pros" are journalists guiding and editing the story, setting standards, overseeing fact-checking, and publishing a final version.

There is a page for crowdsourcing science, where I added some info about Open Source Chemistry. The existing info on that page is pretty sparse - maybe Bill Hooker can pick out a few gems from his comprehensive reports on Open Science in 3QuarksDaily.

The site functions like a wiki in that information from anyone is sought but it looks like only an editor can include the contributions in the main content pages. There is no edit button - in order to submit you have to find an existing open item and respond to it, just like in a forum.

The final article will be published in Wired magazine.

More info about crowdsourcing from Jeff Howe

C&E News Article on Social Software in Chemistry

The April 23, 2007 Chemistry and Engineering News article on the Social Software in Education symposium at the American Chemical Society spring meeting in Chicago has come out. I gave a talk there on using blogs and wikis to teach organic chemistry.

The article is a pretty comprehensive report on the session and does a good job of summarizing the key technologies currently being tried without much hype. Podcasting, vodcasting, tagging and wikis were discussed from teachers and librarians using them in different ways. Of course the controversial issue of attendance was highlighted.

Although the session was primarily about education, UsefulChem got a nice plug.

Bradley posts his lectures and all other information for his class on a wiki with open access. He also has an open-access wiki for his research group (usefulchem.wikispaces.com), where the students' lab notebooks are freely available to anyone in the world who wants to read them. His group will write and edit manuscripts using the wiki itself and invite any interested person to edit them.

Edison Predicted Educational Podcasting?

I often find that books on the history of science and technology are fun to read because they give me an opportunity to try to forget what I know about how things turned out and piece together an older worldview.

For example, I am currently reading the new book by Tom McNichol "AC/DC - The Savage Tale of the First Standards War". On p. 38 is reprinted part of Edison's article in North American Review, written in 1878, shortly after his invention of the phonograph:

Among the many uses to which the phonograph will be applied are the following:
...
2. Phonographic books, which will speak to blind people without effort on their part.
...
9. Educational purposes; such as preserving the explanations made by a teacher, so that the pupil can refer to them at any moment, and spelling and other lessons placed upon the phonograph for convenience in committing to memory.

and on p. 39:

Edison predicted that the motion picture camera would one day be a great tool for education, with film eventually supplanting books in schools and universities.

Here we are 130 years later and we are still talking about this like it is a bold new concept. In the short term, it turned out that the killer app for the phonograph was music. Edison didn't anticipate the strong demand in that direction.

With the wide adoption of phonographs and the existing infrastructure of the postal system, there is really no good technical reason for the delay in the evolution of mainstream education towards multi-media dominance.

It seems that, most often, progress happens by combining existing technologies in new ways instead of waiting for radically new inventions. But these combinations must wait for the right conditions to facilitate the process.

Podcasting is a really good example of that. The technology itself, the delivery of files via RSS subscription, is really very simple by the standards of the late 90s, when it was developed. But I think it took the marketing genius of Apple with their iPod campaign to make all things pod desirable, even (or perhaps especially) to people who didn't really know what it was.

Ironically, the reality is that, at least in my current classes, most students use their laptops and not their ipods to access podcasts. But it doesn't matter - the social impact has been to make podcasting generally desirable and the pressure is being felt now in educational institutions to provide it.

I also think that the recent availability of high quality free and hosted services, exemplified on a mass scale by Google, is also key to the current transformation.

Going forward we have to remember that we can't predict the timing of technological change, even if it is inevitable.

UsefulChem and Skateboarding

I just came across Karl Bailey's blog, a chemistry teacher at Clark College who happens to teach virtually the same 3 organic chemistry classes that I do, in the same sequence following the Wade book. Clark has a quarter system like Drexel.

But what really caught my attention was his mention of UsefulChem and the image of skateboarders he used on the post. What a great representation of Open Source Science, at least the way that many of my friends and I conceive of it. I also get the same vibe from many of the young people that see me after I speak on the topic.

I suppose it represents a form of rebellion from the status quo, but not without standards for competence and dedication. Without that rebellion is just cynicism.

Second Race in Second Life

We just ran a quiz race in Second Life for the second time this morning in my organic chemistry class. Two of the students were physically with me in the classroom and two were coming in remotely.

Initially, Beth was still the owner of the obelisks and we learned the hard way that all but one stop working when the owner is not on the island. We worked it out this morning by transferring the ownership to me and as long as I was next to my students all of them could do the quizzes.

Beth is always talking about the community spirit in Second Life and I got a taste of it first hand when Beth invited many of her friends, including Eloise who built the quiz, to come help. This is such a different experience from using Unreal Tournament to construct the races. When I would run into a problem, I was basically completely alone and had to read the manual or try to make contact on a forum.

We got started about 10 minutes late and there was confusion but now that we understand the problem next week should go smoothly. There is still a problem that not all the obelisks will work when I am not there but Beth and Eloise assure me that can be fixed also.

We also had a few random visitors taking a peek at what we were up to and, if I had a bit of time between helping students, I chatted with them. Some also talked with my students. Since we are on Nature Island, the type of people who tend to visit generally have a great interest in science and are eager to share.

Here is a pic of this morning's race.

Post-mortem of Winter 07 term

Another term done and and it is time to evaluate what I had planned to do in January and what I learned.

1) One of the key new implementations was to offer an alternative to the lecture format by detailing every concept covered in the course on a wiki content page and linking to free online study materials, mainly online textbooks. This turned out to be fairly time-consuming but I'm glad that I have this resource available now to use at workshops in combination with the Google co-op search on organic chemistry. And because the content is fully open, anyone is free to use it.

2) The content page did not induce a vast shift away from the recorded lectures as the primary information source for the class. There is still an expectation from most students that "lectures are the way to take a class", whether in person or recorded. I am not sure that they prefer that but that's what they are used to. Thinking back to my own experience as an undergrad, I always felt that the lecture format is a terribly inefficient and painful way to learn because it is intrinsically linear. For me, the random access feature of books, web pages and discussion is vastly superior, as long as it is with the right text and teacher. But I realize that not all students are like that so I'll keep the lectures around.

3) I didn't have time to organize any Unreal Tournament races last term. This term, I'm using Second Life and it will be interesting to see how it compares.

Fatal Flaw in new Blogger Atom Feed for Education

I started the Spring term with a nasty surprise: over half of my podcast files were missing from my organic chemistry CHEM241 class.

After some digging around I found the problem to be that the Blogger Atom feed post limit was reduced from 100 to 25. What that means is that it is no longer possible to use the Blogger/Feedburner system to create podcasts with more than 25 files at any one time.

Courses at Drexel generally run three times a week for 10 weeks. So generating 3 file types per class (mp3, m4v and pdf) runs close to the previous limit of 100 posts for the Atom feed. And as soon as a file drops out of the Atom feed, it drops off of Feedburner and then iTunes. So both of my classes on iTunes are broken now.

Students can still access all of the class files directly off of the blog (stressing once again the importance of redundancy).

iTunes was supposed to be a convenient vehicle to deliver the class content. Now I think I am just going to zip up all the files for simplicity, although I do want to fix the feed at some point since people do happen upon my courses via iTunes.


image of Nasty Surprise taken with permission from Cake That!

MarketPlace Open Science Interview

The NPR interview on Open Science I discussed two weeks ago has aired and is now available.

I think it was very well balanced. The positive aspects of not losing failed experiments was weighed against the difficulties in publishing in some journals and of deriving profit.

Chemistry Wide Open Column

I now have a column on ScientificBlogging.com called Chemistry Wide Open.

As you may guess from the title, I'll be discussing issues related to chemistry and Open Science. The challenge here is to post for a more general audience but I'll likely repost or restructure selected content from my blogs, mainly from this one and UsefulChem.

But who knows? Maybe there are some hard core organic chemists on there that might appreciate some NMR problems. We'll see from the comments what makes sense.

Chemists Without Borders Conference Calls on Open Access

Chemists Without Borders is running a special series of conference calls in the next few months with speakers on Open Access and Open Science. While online virtual conferences are nice, it is sometimes difficult to get all participants on board with the technology. What can be more convenient and simple than picking up the phone to join a conference call?

I'll be speaking on Open Source Science in September.

Thursday, April 5 9:00 a.m. Pacific Time / Noon Eastern Time
Heather Joseph: Federal Research Public Access Act

Heather Joseph, Executive Director, Scholarly Publishing and Academic Resources Coalition (SPARC), will talk about the Federal Research Public Access Act (FRPAA). FRPAA is anticipated to be re-introduced this spring. The purpose of this bill is to require all U.S. Federal research granting agencies with portfolios of over $100 million (11 agencies altogether) to develop policies requiring open access to the results of the research they fund. FRPAA has been endorsed by many higher education leaders and the Alliance for Taxpayer Access. Chemists Without Borders is a member of the Alliance for Taxpayer Access; should we support FRPAA?
More information about FRPAA can be found on the SPARC website.

As the Executive Director of SPARC, Heather Joseph is very involved in advocacy for FRPAA. Before joining SPARC, Heather worked for many years in the publishing industry, and was formerly Executive Director of the BioOne publishing cooperative.

Thursday, June 7, 9:00 a.m. Pacific Time / Noon Eastern Time
Peter Suber: Open Access Questions & Answers
Peter Suber, Open Access Project Director, Public Knowledge Project, author of Open Access News
Peter Suber, one of the world's leading academics in the area of open access, will join Chemists Without Borders for a question and answer session on any aspect of open access.

Thursday, September 6 9:00 a.m. Pacific Time / Noon Eastern Time
Jean-Claude Bradley: Open Source Chemistry
Chemists Without Borders' own Jean-Claude Bradley, Coordinator for E-Learning at the College of Arts and Sciences at Drexel University, will talk about the Useful Chemistry approach to open source chemistry, founded by Bradley.

Chemical Heritage Foundation Talk on Open Science

I'll be giving a talk and participating in a panel about Open Source/Open Notebook Science on April 17, 2007 at the Chemical Heritage Foundation in Philadelphia.

See Registration info here

The 7th Annual Leadership Initiative in Science Education (LISE 7)
21st Century Science Education: Preparing
Teachers and Students for the Future

Monday, 16 April 2007

3:30–4:00 p.m. Workshop Registration

4:00–5:30 Workshop – 21st century skills in the science classroom
Susan Van Gundy

5:30–6:00 Dinner Registration and Reception

6:00–7:15 Dinner

7:15–8:00 Keynote Address : Chemistry is About the Future, not just the Past. Let’s Keep it that Way Ron Breslow

Thursday, 17 April 2006

7:30–8:15 a.m. Conference Registration and Breakfast

8:15–8:30 Welcome

8:30–9:15 Kickoff Address: Preparing Teachers for the Future I Bruce Fuchs

9:15–10:15 Panel – Today’s Discoveries in Tomorrow’s Classrooms
Mary Kirchhoff (Green Chemistry), Kathy Frame (Biotechnology)

10:15–10:30 Break

10:30–11:20 Panel - New Technologies for Teaching and Research: Perspectives
Susan Van Gundy (National Science Digital Library), Jean-Claude Bradley (Open Source Science)

11:20-12:15 Panel – New Practices in Teaching and Research: Incorporating New Ideas
John Penick (Teacher Preparation in Global Context), Diane Jass Ketelhut (Using Games and Simulations in Teaching)

12:15 -1:30 p.m. Lunch

1:30–2:15 Address – Preparing Teachers for the Future II
Jeanne Narum

2:15-3:15 Address – Using New Technologies Today: Web-based Teaching Tools
Dennis Liu (Howard Hughes Medical Institute), Robert De Groot (Southern California Earthquake Center)

3:15–3:45 Roundtable - Teaching in the Science Classroom of the Future Today
Representatives of Philadelphia High Schools, TBA


3:45–4:15 Wrap-up

Feb 2007 PAETC done

I just finished processing all of the files for the podcast and screencast of the Philadelphia Area Educational Technology Conference held on Feb 22 and 23 at Drexel this year. I've gone back to a standard audio podcast with the screencast in streaming Flash format. The quality is so much better than the much larger (vodcast) m4v files generated by Camtasia 4, especially for slides with lots of small text.

We had some good discussions during my workshop on the afternoon of Feb 22 on the use of blogs and wikis in education. Here is the wiki I used as an outline and to add notes.

More comments from my co-organizer Laura on day1 and day2.

Where is technology most effective: inside or outside of the classroom?
Dan King, Drexel University

iTunes U Implementation
Brian Gall and Russ Pritchard, Philadelphia University

Don't Make Me Think - I'm Here to Learn
Mike Zarro, Drexel University

Leveraging Wikis and Blogs for Teaching and Research in Chemistry
Jean-Claude Bradley, Drexel University

Interactivism: Blogging in Freshman Writing
Laura Blankenship, Bryn Mawr College

Towards Preparing Educators for Multiliteracy
Tim McGee, Philadelphia University

PAETC this week

There are still a few more seats available - register here.

Philadelphia Area Educational Technology Conference (PAETC)
"Multiliteracies"
February 22-23, 2007
Drexel University
Philadelphia, PA

Program Schedule

Thursday, February 22

Workshops from 1-5

Registration Open beginning 12:30

Using Moodle

Marcie Hull, Science Leadership Academy
1-3, Korman 110

Using Blogs and Wikis

Jean-Claude Bradley, Drexel University
1-3, Location, Korman 111

Learn how to incorporate blogs and wikis into your classes. Learn how to set up a blog and a wiki and how to use them effectively in your courses.

Powerpoint: It's not just for lectures anymore!

Michelle Sims, Gwynedd-Mercy College
3-5, Korman 116

Podcasting

Brian Gall and Russ Pritchard, Philadelphia University
3-5, 110 Korman

Friday, February 23

All Sessions will be taking place in 2019 MacAlister

8:30 Registration open

9:00-10:00 Opening Keynote, Chris Lehmann

10:00-10:15 Break

10:15-11:15 What does it all mean?: Exploring Issues in Multiliteracy

Towards Preparing Educators for Multiliteracy
Tim McGee, Philadelphia University

What are the digital natives doing before they get to college?
Jean Bennett, Ursinus College

11:15-12:00 Blogging, a new way of looking at text literacy

Interactivism: Blogging in Freshman Writing
Laura Blankenship, Bryn Mawr College

Leveraging Wikis and Blogs for Teaching and Research in Chemistry
Jean-Claude Bradley

12:00-1:00 Lunch

1:00-2:30 Assessment: What are students learning and how do they learn it

Where is technology most effective: inside or outside of the classroom?
Daniel King, Drexel University

Don't Make Me Think! I Just Want to Learn
Mike Zarro, Drexel University

Assessing Aesthetic Responses
Christine Boyland, Bryn Mawr College

2:30-2:45 Break

2:45-3:45 BOF gatherings and Planning meeting

3:45-4:00 Break

4:00-5:00 Podcasting: Using Audio in Education

Podcasting and Web 2.0: Implications for Education
Rodney Murray, Thomas Jefferson University

iTunes U Implementation
Brian Gall and Russ Pritchard, Philadelphia University

Australian Visitor in April

Update: Thangaes just told me that he is canceling this visit

Thangaes Waran, a secondary school teacher in Adelaide, will be visiting Drexel on April 2, 2007 as part of an amazing month long world-wide journey starting in Australia and bridging India, Europe and North America.

From his blog, here is the ambitious plan:

This is my blog of my study tour to USA, UK and India in 2007. The purpose of my tour is to study how technology is used in schools in other parts of the world. In particular, I would like to find out how schools are using web 2.0 technologies such as blogs, wikis and podcasts in their teaching and learning. I was awarded the Westfield Premiers Scholarship, to undertake this study.

I invite anyone at Drexel or in the Philadelphia area with an interest in educational technology to contact me for details about meeting times.

My Talks at Spring 07 ACS

The schedule for the American Chemical Society meeting in Chicago is finalized. There are some really great sessions on Web2.0 tools and chemistry.

Here are my talks - I hope to see some of you there!

PAPER TITLE; "Teaching organic chemistry with blogs and wikis" (final paper number: 25)
DIVISION: Division of Chemical Education
SESSION: Using Social Networking Tools to Teach Chemistry
DAY & TIME OF PRESENTATION: Sunday, 25 March 2007 from 11:15 AM to 11:35 AM
LOCATION: McCormick Place North, Room: Room N230B, Level 2

PAPER TITLE; "Open notebook chemistry using blogs and wikis" (final paper number: 1607)
DIVISION: Division of Chemical Education
SESSION: Communicating Chemistry
DAY & TIME OF PRESENTATION: Tuesday, 27 March 2007 from 9:45 AM to 10:05 AM
LOCATION: McCormick Place North, Room: Room N227B, Level 2

Open Science going Mainstream?

It is encouraging to see more and more articles in the mainstream press on Open Science and the changes in scientific publication. For example USA Today has "Is this the end of scholarly journal?" Here are the examples cited:

Two new scientific publications, both available only online, may signal what's ahead. The PLoS ONE (plosone.org), a journal begun by the Public Library of Science (PLoS) last month, aims to put as many new scientific articles as possible on the Internet to be read by anyone, free of charge. The Journal of Visualized Experiments, or JoVE (myjove.com), is a kind of YouTube for researchers. It operates on the theory that a short video showing how an experiment is done is better than thousands of words that attempt to describe it.

[...]

Since its launch Dec. 20, PLoS ONE has published well over 100 papers and expects to publish 15 to 20 more per week. Readers access the articles for free. PLoS ONE pays its way by charging authors $1,250 to publish an article. While that might seem a barrier to publication, Surridge says most research is financed by grants or large institutions, meaning individual scientists rarely have to pay themselves. But just in case, PLoS ONE is waiving the fee for any authors who request it.

I had not really considered PLoS ONE to be a vehicle for our work because of the hefty author charges but I might consider it now if they really are serious about waiving the fee simply by request. From my conversations with people at the NC science blogging conference, such fees are not that much of a barrier for molecular biologists who are used to paying page charges. But things are different in chemistry.

I also have reported on JoVE and I think that it is a great idea, especially since there are no fees for authors or readers. But don't discount YouTube for science - I think it is perfectly suited to communicate experimental details.

Thanks to Deepak for the link.

Google co-op Workshop

Update: the recording is here.

I am running a workshop on the use Google co-op to create customized search engines for teaching on Monday Jan 29, 2007 at 11:00 in 4020 MacAlister at Drexel. The session is filling quickly - please RSVP if you would like to attend.

The event will be recorded and posted on the CoAS E-Learning Podcast.

Back from Science Blogging Conference

The North Carolina Science Blogging Conference turned out to be a much needed opportunity for physically meeting a lot of the people that have only interacted online. Most notably, I finally got to meet Bill Hooker, author of Open Reading Frame and a strong supporter of the open science movement. We discussed concrete ways of collaborating and I look forward to continuing the discussion online.

Based on the discussion during my Open Source/Open Notebook Science session, there appeared to be significant interest in ways of doing science more openly and of understanding the consequences of doing so. The typical issues came up: intellectual property, recognition, archiving and getting scooped. I had planned on updating a wiki page with ideas generated from the session in a way that Dave Warlick had done at PodcasterCon last year. However, I found that there was not enough time to do that and engage in the discussion. Next time I'll try asking someone to take notes, like Dave did.

My presentation was recorded and is available here.

Technorati tag: scienceblogginconference

Science Blogging Conference in 3 Days

There are still a few more seats available for the Science Blogging Conference in Chapel Hill, NC this Saturday Jan 20, 2007.

Here is a rough agenda for my breakout session on Open Notebook/Open Source Science:

This session will cover the dissemination of primary scientific information via blogs, wikis and other non-traditional vehicles.

Types of information.

* raw experimental data (Open Notebook Science)
* analyzed data
* hypotheses
* “failed” experiments
* generalized protocols
* traditional article format

Issues.

* Intellectual Property
* Referencing and claims to priority
* Academic Validation
* Peer Review – mandatory and elective

Opportunities.

* Increasing productivity in terms of universally usable knowledge units
* Making explicit the nature and quantity of work in collaborations
* Using semantically rich formats and automation at zero publication cost – is this the way to the technological singularity?

2007 Winter term starts

I had the first session of my Organic Chemistry II class this morning. I took some time over the break to take this course to what I see as the next level. Although students are still able to take in the content via archived screencast lectures in multiple formats (mp3 podcast, m4v vodcast, streaming Real or downloadable AVIs), this content is password protected due to copyright issues.

Instead of simply re-recording the lectures using unencumbered reference material, I decided to make full use of multimedia resources that would not be as intuitively available from a screencast. In the place of lectures is a detailed summary of the content to be covered with links to high quality resources. This is still a work in progress and I will add, remove and clarify as I come to appreciate what works and what doesn't during our workshops.

This ties in nicely with the assortment of sources that I pulled together in a Google co-op search for high level organic chemistry. Although I was not planning to include it, Wikipedia has turned out to be so useful that I have added it to my Google co-op collection. There is probably not enough in there to make a university level organic chemistry course entirely out of it but it does fill in some useful gaps between textbooks. If it stops being useful for any reason, Google co-op gives me the flexibility to block out certain pages or just remove it entirely. We'll see how it goes.

The main free online textbook I have been using so far is Reusch but there are several others to choose from. The Poon organic pre-lectures on iTunes also look like they could have a place when we get to the latter part of the course.

I will still be recording some brief screencasts to fill a need that is still largely open for this material: the screencast explanations of problem solutions. For example, under the practice problems section for alkynes, I have included a pic of a problem. Clicking on the image will open up my explanation of the solution in YouTube. This is an extension of something I started to do at the end of last term and I think that this is a place where screencasts shine. These will complement the links to interactive tutorials that I have also listed in the problem sections.

The first workshop is Wednesday - it should be interesting.

Communicating Chemistry at ACS

I just got the schedule for the symposium on Communicating Chemistry at the Spring 2007 American Chemical Society meeting in Chicago. It is being run by the Chemical Education (CHED) and Chemical Information (CINF) divisions. My talk on Open Notebook Chemistry using Blogs and Wikis is at 9:45 on March 27. It looks like there will be lots of interesting presenters and talks. Here is the schedule:

Communicating Chemistry — Part I — Tuesday, March 27

Cosponsored with CINF

L. Fine, Organizer

J. C. Kotz, Organizer, Presiding

8:30 — Introductory Remarks.

8:35 —1604. Pod casting and general chemistry: what is my chemistry professor doing in my iPod? H. D. Bapat

8:55 —1605. Hybrid learning as the bridge between technology and pedagogy in the first and second year chemistry curriculum. T. Poon, T. Morkin

9:15 —1606. Chemistry breaks the Top 100: Podcasting quantum mechanics. M. M. Francl

9:35 — Intermission.

9:45 —1607. Open notebook chemistry using blogs and wikis. J -C. Bradley, K. Mirza, J. Giammarco, A. Holsey, D. Strumfels, S. Gardner, L. Chen

10:05 —1608. What role do grades play in communicating chemistry? W. J. Vining

10:25 —1609. Improving the communication and efficiency in grading of laboratory reports. M. Hadley, J. R. Pribyl, J. A. Kaliski

10:45 — Intermission.

10:55 —1610. Enhancing communication in chemistry courses using DyKnowTM. B. L. Gourley

11:15 —1611. Taking ownership of learning:Can adding technology to the traditional classroom increase the opportunity for students to be more responsible for their own learning? C. M. Turner

11:35 —1612. E-learning chemistry. J. Reeves, J. Tyrell

Communicating Chemistry — Part II — Tuesday, March 27

Cosponsored with CINF

J. C. Kotz, Organizer

L. Fine, Organizer, Presiding

1:30 — Introductory Remarks.

1:35 —1651. Visualizing acid/base chemistry: Using electostatic potential surfaces to teach acid/base strengths. R. W. Morrison, R. Hubbard IV, K. Soncha

1:55 —1652. Open access peer reviewed portal for communicating chemistry: Analytical Sciences Digital Library. H. A. Bullen

2:15 —1653. Comparison of student discourse in online and face-to-face environments. G. C. Weaver, K. F. Green

2:35 — Intermission.

2:45 —1654. Chemical Eye on ears tuned to public radio. P. J. MacDougall

3:05 —1655. Science Outreach in the City of Chicago. M. C. Lach, M. Davis

3:25 —1656. "Smart Cities": Summer science in the mean streets of France. G. P. Niccolai

3:45 — Intermission.

3:55 —1657. Collaborative efforts by Illinois local American Chemical Society sections to promote chemistry at the Illinois state fair. H. D. Bapat

4:15 —1658. Analysis of how scientists explain their research and parallels to how science teachers explain science. H. Sevian, L. Gonsalves

4:35 —1659. Service-learning with a general chemistry lab: Communicating chemistry through application. M. J. Harvey

Communicating Chemistry — Part III — Wednesday, March 28

Cosponsored with CINF

L. Fine, Organizer

J. C. Kotz, Organizer, Presiding

8:30 — Introductory Remarks.

8:35 —1698. Teaching chemical information: Tips and techniques from the Division of Chemical Information Education Committee. S. Cardinal, S. Yu

8:55 —1699. Communicating the chemistry behind issues. B. Venkataraman

9:15 —1700. Teaching chemistry majors to write like chemists. M. S. Robinson, F. L. Stoller

9:35 — Intermission.

9:45 —1701. Investigational writing exercises to complement undergraduate biochemistry experiments. P. J. Higgins

10:05 —1702. Readability levels of college chemistry textbooks from introductory chemistry to physical chemistry. E. A. Drommerhausen, J. R. Pribyl

10:25 —1703. Student opinions of writing assignments in organic chemistry courses for majors. D. P. Cartrette

10:45 — Intermission.

10:55 —1704. How to think logically about organic chemistry. E. T. Papish

11:15 —1705. Communicating the concepts of resonance and conjugation. J. J. Mullins

11:35 —1706. Use of humor and illustrations in organic chemistry lectures. V. Dragojlovic

Fall 2006 Post-Mortem

Another quarter at Drexel is done. I taught the introductory organic chemistry course CHEM241 to about 170 students and special online only sections of CHEM242 and CHEM243 for about 20 students with demonstrable conflicts in their schedule. All lectures were assigned as pre-recorded screencasts and the class time was used as a workshop in the case of CHEM241.

This is what I did and learned.

1) Instead of a blog assignment on any topic for extra credit, I required that they relate some aspect of reactions from the lab notebook of my research group with something learned in class. Here are some selected reports. There were 2 deadlines, each worth 1%. This was tricky for the first deadline because of the limited amount of material covered but the students who were serious in doing this worked with me well before the deadline to come up with a question that they could answer. I used a wiki this term instead of a blog and it worked much better because the evolution of each assignment can be tracked, including my feedback. This was time-consuming but I think that it was beneficial to the students to stretch their understanding of chemistry in a way that relates to the real world.

2) YouTube is a good way to answer student questions that are not directly answered in the lecture archive. The resolution is not as high as a Flash screencast but copying molecules drawn with the default settings of ChemSketch and pasting in a 256 x 256 pixel window in Paint works well. Paint is perfect for drawing curly arrows. Not bad for 100% free software. All of these images are then also standard format for an EduFrag map or a WebCT quiz. I used Camtasia 4 to record and produce an m4v file (for eventual publication as a vodcast), which I uploaded directly into YouTube. This part is not free but I'll bet uploading the avi file generated by the free CamStudio into YouTube would work. However, you can't edit the video in CamStudio.

3) I started to use my collection of high quality sources on Google Co-op to help students in the workshops. For me, this is clearly the way forward in open courseware. More on this next term.

4) All of my Flash files created by Camtasia 2 stopped working on Firefox on PCs and Macs. This is a known issue and we found a solution for this that we are still in the process of implementing. The files were also available as a vodcast on iTunes so the Mac people were fine. With all of the things that can go wrong with technology, redundancy is imperative.

5) The feedback from the evaluations was overall very positive. A few students suggested that I provide a more detailed timeline for watching lectures and doing problems. I gave them a guideline of about 4 hours/week and an inventory of what would be on each test but I can appreciate how something more definite would be comforting for some. I can implement that easily. The freedom to set their own schedule was empowering for many. Others commented on their struggle with procrastination. I don't think there is much difference between an online class the way that I run it compared to face to face lectures. Organic chemistry is about doing problems. In a F2F class, students who procrastinate have the problem of getting good notes from their friends for the classes they skipped in addition to doing problems at the last minute. I learned early on, way before doing anything online, that a good wake-up call for procrastinators is to have a test, a review session then an automatic make-up with more questions in the same amount of time. Failing on the first test is usually motivating.

6) Drexel migrated to a +/- grading system this term and I learned that Excel cannot support more than 7 nested functions in a formula. I use nested IF functions to convert numbers to letter grades.

7) Students who could not make it to the workshops or wanted quicker feedback emailed me their work. Chemistry is very visual. We interacted via text, chemistry program generated structures and scanned paper. But when both student and teacher have TabletPCs, it is probably the most effective way to communicate. Here is an example by Justin, who made really good use of that technology over the term:

YouTube Peer Review

As I mentioned last week, I have started to use YouTube to post brief solutions to organic chemistry problems. This is convenient on many levels, including a nice built in mechanism to accept comments.

This morning someone commented on my Wittig synthesis post, pointing out that the name should be pronounced as a "V" instead of the "W" I was using. That is an interesting point and I'll poll my fellow chemistry colleagues to see how they learned it. Chemistry is usually tested in written format and I know from my interaction with students in workshops that chemistry terms and names are mangled in every way possible. With all the German and Russian names in organic chemistry I will probably be corrected again as I put up more problem solutions.

Another nice feature of YouTube is the ability to easily post video responses. This should prove to be particularly useful for discussing chemistry.

Scientific Reflections

It is not always clear what we learn from each stage of life until they are done.

It is only after completing my undergraduate degree that I realized the most important thing I learned was tolerating pain. I still remember what is was like to sit in an interminable lecture and that is one reason I am happy to provide alternative modes of learning for my students.

It is only after my Ph. D. that I understood it was really about learning how to solve problems. The chemistry skills are certainly useful, but completely impotent without that key understanding.

It is only after my postdocs that I realized the most useful thing I learned was how to network effectively and sell myself.

The students working in my lab are also learning and reflecting on what they have learned. The difference is some of them are choosing to make their thoughts public via our UsefulChem wiki. James had this to say last night:

Yes, chemistry is an art. I received the December 4, 2006 issue of C&ENews in the mail and while I can't seem to link to it, there is a very good article on reproducibility by William G Schulz. Here, Schulz has a good quote from a chemistry Professor from Harvard, George M. Whitesides, who says "Sometimes part of the art of chemistry doesn't get included in published papers". I will admit that the first paper we used to make DOPAL we did not follow to the "T" for safety reasons as perchloric acid was a component used at high temperatures, however, it can be frustrating to attempt something again and again and have it seem like no visible improvement has been made. This is in fact not the case. For every 100 experiments done, there are 100 small things learned and they are 100 experiments closer to that 1 in a 1000 that works. Luckily, it did not take 1000 trials to get DOPAL, and in Exp016, success was had! This also brings back into context the Open source nature of the project. All of the "failed" experiments would never be reported in a published paper.

I came across a similar sentiment this morning in a John Eccles quote from the book "In Search of Memory":

In fact I learned from him [Popper] even to rejoice in the refutation of a cherished hypothesis, because that, too, is a scientific achievement and because much has been learned by the refutation.

Orgo Quiz Questions on YouTube

YouTube automatically selects a frame in the middle of an uploaded video to use as the thumbnail image. People have been exploiting this recently by inserting "alluring" but irrelevant images in the middle of their clips to attract more views.

It occurred to me that one could use this feature to deliver quiz questions. I could record a screencast of the solution to a true/false problem then upload it on YouTube. I would just have to make sure that the intended problem appears exactly as I want in the middle of the clip. One could get the answer by watching and listening to my explanation or could fast forward to the end to see the answer.

The nice thing about this is that I can leverage the same 256 x 256 pixel bitmap images that I use in the EduFrag project and in the WebCT quizzes and tests for my organic chemistry classes.
I created an organic chemistry example on the E-2 elimination reaction (also see embedded below). I used Camtasia 4 to do this recording and uploaded to YouTube as an m4v file, which should play quite nicely on a video ipod.

Subscribe to the orgoquiz channel for more.

Google Co-op for Organic Chemistry

Recently I posted about using Google Co-op to consolidate the searching of blogs, wikis and other webpages related to the UsefulChem project. I have been very impressed with the convenience and I wanted to do something similar for my organic chemistry classes.

I included my class blogs, wikis, transcripts in addition to other online textbooks and resources that I consider to be of the highest quality:

http://www.chem.usyd.edu.au/~todd_m/Teaching.htm
http://www.uni-regensburg.de/Fakultaeten/nat_Fak_IV/Organische_Chemie/...htm
http://www.colby.edu/chemistry/OChem/
http://www.cem.msu.edu/%7Eparrill/
http://www.chemgapedia.de/vsengine/
http://www.chem.ox.ac.uk/vrchemistry/
http://www.chem.ucalgary.ca/courses/351/Carey5th/
http://www.ochem4free.com/
http://chem241transcripts.blogspot.com/
http://chem241.wikispaces.com/
http://chem242.wikispaces.com/
http://chem243.wikispaces.com/
http://chem241.blogspot.com/
http://chem242.blogspot.com/
http://chem243.blogspot.com/
http://jcbclasses.blogspot.com
http://www.cem.msu.edu/%7Ereusch/VirtualText/

I put the search box at the top of the class wiki for CHEM 241, for example. Try searching for concepts like "ketone" and see almost nothing but good stuff in the results. I started using it to access content during this morning's workshop and I am convinced that this is one of the most powerful things to come along for bottom-up open courseware.

Instead of relying on third parties to validate content or generate all purpose federated searches, as teacher I can make the decision of what I want to recommend for my students to use. At any point, for any reason, I can prune or add to the search space. My students can also make their own search engines, for just the class transcript and wiki, for example.

A lot of the search results consist of or link to interactive tutorials or quizzes. I tried to create a separate search engine specifically for assessments but it turns out to be easier just to add the keywords "exercise" or "problem set" in the general orgo search.

When choosing open content, it becomes evident that not all open sources are equally "open". Sites, like the 1200 page Daley and Daley textbook, with free access but requiring registration are completely inaccessible to this type of searching. From the user's perspective this is not really a problem since there is already a healthy redundancy in most of the basic undergraduate organic chemistry materials that are freely available and indexable.

Some would predict the death of the textbook but tradition and habits die hard. Advertisement driven television has survived Tivo and I think textbooks will survive open courseware no matter how good it gets. At least for a while.

Camtasia 2.0 Flash Problems with Firefox and Macs

Something strange has been happening this term with students trying to access my recorded lectures in Flash format (e.g. CHEM241). At first it was Mac users, which was surprising because I know that there was not a problem for at least a year before that. Then I noticed that I could no longer access Flash recordings using Firefox.

Since I also offer my lectures in m4v format viewable in iTunes or with a Quicktime player, Mac users could still get access to the video content. Also the Firefox problem does not show up on Internet Explorer. Once again, here is an example where taking the time to build in a redundancy really pays off. But it is still annoying for everybody.

I asked Tim Jones, the webmaster for our CoAS server, to look into the issue and he found that the problem could be fixed by making a file location explicit. For example, for this lecture,

flashvars ="FA06CHEM241intro_config.xml"

is changed to

flashvars ="csConfigFile=FA06CHEM241intro_media/FA06CHEM241intro_config.xml"

Tim will have to write a script to fix all the affected files this weekend. Given Camtasia's popularity, I imagine a lot of people will be impacted by this. The problem seems to be limited to Camtasia 2. According to Kevin Owens, the Flash files produced by Camtasia 3 (and presumably 4) work fine on Macs. I think the Firefox on PC issue only popped up recently so I assume it is related to the Firefox 2 upgrade.

Communicating Science through Video

Pedro Beltrao just posted about the Journal of Visualized Experiments, publishing videos of biological experiments. Submissions are supposed to be reviewed within 2 weeks and it is Open Access.

It really is true that we can save an awful lot of words with a quick video or image when reporting experiments. Even for ostensibly simple procedures like distillation it is amazing how everyone in our group had different assumptions about a "standard setup". In these cases the pics were invaluable to fill in for everything not said in the log. Videos are usually even more useful because the dynamics of a reaction can be ascertained. We have found that YouTube is a good place to post these because it is a public hosted site and the delay in showing up after uploading is just a few minutes usually. Google video can host much longer videos but it can take days to be accessible.

I can hear some cringing because this does not immediately move us towards the use of the semantic web to do science and facilitate automation. But lets not forget that the first priority for a scientist has to be effective and efficient communication of what they have done and it is hard to top the message richness delivered through video.

Even explaining the analysis of an experiment is really convenient using an audio/video interface (a screencast to be precise).

More Constructivist Chemistry

We're about midway through our Fall term at Drexel and the students have just completed their first extra credit project in my organic chemistry class.

In the Spring term, I had given my students a few options, including doing a blog assignment relating a research article to some concept that they were learning in class. In order to maintain a reasonable quality on the blog and help the students learn, I would give feedback using comments on the blog right up to the deadline when no more changes were accepted. Although this worked pretty effectively in terms of the final product, when a lot of changes were required, it was impossible to follow the evolution of the process.

This term I made a few changes to the extra credit assignment. First, I moved it to a wiki so that it would be clear who contributed what and how the post evolved. Second, the only option I gave was correlating what was learned in class with real lab research conducted on the synthesis of new anti-malarial compounds. This is a luxury that I now have because the lab notebook of my research group is posted directly in real time to a wiki.

Here is the result. Six out of 170 students participated. I purposefully make the extra credit very low (1% of final grade) because this is fairly time-consuming for an instructor and I mainly want students who are already intrinsically motivated in this side of chemistry to participate. Remember that we are talking about undergraduates taking introductory organic chemistry trying to make sense of graduate level research work in progress.

Contrary to many of my colleagues, I strongly encourage students to use Wikipedia as a reference. It turns out that for data like boiling points for simple compounds, it is pretty reliable. It is not the only source but it is a good place to start. One of my students was doing a post on the chirality of adrenaline, which is one of the compounds we use in our research. Surprisingly, the chirality of naturally occurring adrenaline was not posted on Wikipedia. After digging around and finding 2 separate sources confirming that the chirality was R, my student updated the Wikipedia entry for adrenaline. (If you don't know what chirality is follow the link in that post to the recorded lecture and learn some chemistry :) - it has to do with the mirror images of molecules)

There is a lot of leverage in this system:

• Imagine if teachers from around the world included updating Wikipedia as part of the process of evaluating student projects.
• Imagine if students from around the world made constructive comments about our lab work as it is being posted.
• Imagine if more research labs made their work in progress available for open evaluation.

Semantic Searching using MEDIE

From Nodalpoint :

MEDIE is an "“intelligent" semantic search engine that retrieves biomedical correlations from over 14 million articles in MEDLINE. You can find abstracts and sentences in MEDLINE by specifying the semantics of correlations; for example, What activates tumour suppressor protein p53?

What is does is identify the subject, verb and object of concepts in the articles. For example, using "inhibits" as verb and "enoyl reductase" as object pulls up valid entries such as:

Triclosan acts by blocking enoyl acyl carrier protein reductase , an enzyme essential for fatty acid biosynthesis.

In this case, blocking is semantically equivalent to inhibits. It even color codes the subject, verb and object in the results!

I wish this were available for chemical information, although QueryChem does something similar for molecule searches.

Stewart Mader Wiki Talk at Drexel

Drexel CoAS E-Learning Lecture Series
Time: 11:00 Thursday October 26, 2006
Location: Disque 109

See recording here.

Four Letter Words: How wiki and edit are making the Internet a better learning tool

Stewart Mader, Senior Instructional Technologist, Life Sciences and Brown Medical School, Brown University

A Wiki can be thought of as a combination of a Web site and a Word document. At its simplest, it can be read just like any other web site, but its real power lies in the fact that groups can collaboratively work on the content of the site using nothing but a standard web browser. The Wiki is gaining traction in education, as an ideal tool for the increasing amount of collaborative work done by both students and teachers. Students might use a wiki to collaborate on a group report, compile data or share the results of their research, while faculty might use the wiki to collaboratively author the structure and curriculum of a course, and the wiki can then serve as part of each person's course materials. I'll show how using the wiki has improved collaboration and data collection in several courses, and transformed a well-known science education website by allowing the teachers who use it to collaboratively author and edit its content. Participants will also learn about the range of wiki tools available, from free, web-based tools to enterprise solutions that can serve an entire digital campus. I'll also discuss my recently released wiki-based book, Using Wiki in Education, which is a compilation of case studies showing how teachers are using the wiki in a variety of environments.

Doing Science in the Nude

Dave Weinberger from Joho the Blog has an interesting commentary on a talk by Timo Hannay, director of web publishing for Nature magazine, on What the Web Means for Science. (There are also some other talks on the Berkman Luncheon Series dealing with Open Source Science.)

Open WetWare and UsefulChem put info into a wiki. Science isn't used to this, says Timo, because "it's like doing science in the nude": It exposes scientists to embarrassment because what they're posting may not be finished, perfect or right.

The question of embarrassment is really related to the expectation of the audience for a particular vehicle. When I pick up Nature magazine I expect to find complete thoughts, no spelling or grammatical mistakes and a minimum of speculation. If I were to attend a talk given by a researcher on the same material, I would not be thrown off if bullet points were used instead of full sentences or if the speaker discussed failed experiments and speculations or even used humor. And if I were to go to the researcher's lab and read their laboratory notebooks I would expect accuracy and clarity but not much else in terms of format.

I know what to expect in these situations because I have seen enough examples of papers, talks and lab notebooks. As science bloggers (especially data bloggers) we have an opportunity to set the expectations of these new data dissemination vehicles.

In the case of UsefulChem, the project has evolved into a collection of blogs and a wiki. The part that houses the raw experimental data generated in my lab serves as a collective laboratory notebook. But because of the added functionality of a wiki (such as versioning) it enables me to also use it as a pedagogical tool. For example, in this version of an experiment to synthesize DOPAL, I had reminded the researcher that the procedure was incomplete (in red) and it was subsequently corrected (in green). This is an especially useful way to guide students to formulate discussion points and ultimately conclusions based on their results. This format also provides a convenient mechanism to expose the undergraduates in my organic chemistry class to real research.

So what expectations should a visitor have for such a vehicle with the dual purpose of scientific information dissemination and pedagogy? They should be able to decipher how an experiment was carried out and analyzed, to a degree sufficient to reproduce any part of it. But since it is a work in progress and done by students with a wide range of laboratory experience it might not be pretty.

Open Access for Authors and Readers

The Directory of Open Access Journals just got a whole lot more useful by including information about author fees for Open Access journals. Indeed, it correctly lists the Beilstein Journal of Organic Chemistry and ARKIVOC as the two fully open organic chemistry journals.

As I mentioned before, I don't think that moving the financial hurdle from the readers to the authors is sufficient to really free up scientific dissemination.

What would be really interesting is for these publishers to make their budgets open to see how it is possible to run Open Access journals for free (or $100) while others are losing money charging over $1000/article.

Thanks to Andrew Waller from OA Librarian for the post.

Start of Fall Term 06

We have now entered the third week of our Fall 06 term at Drexel. This is usually a good time to take stock of how things are taking shape. I am teaching the CHEM 241 introductory organic chemistry class with 170 students and some special online only sections of CHEM242 and CHEM243 to about a dozen more students.

1) Basically things are proceeding about as well as the Spring term. Most students got their technical issues resolved quickly in the first week either by coming to the workshops or through email. With the lecture vodcast now available via a "subscribe through iTunes" button, it is easier than ever to get everybody on board quickly.

2) Based on talking with my colleagues over the summer, I decided to add questions in the quizzes and tests that evaluate the student's grasp of curly arrows. This is one of the very basic concepts in organic chemistry that is needed to make sense of chemical reactions. I had already started to do this in the Unreal Tournament races in the Spring but I had not yet used these in tests. I tried using the bitmaps used in UT directly into WebCT quizzes but, at 66K a piece, there were problems with displaying all the pics in the multiple choice. After experimenting with number of colors and picture size, I found that simply saving the bitmaps as jpegs from Paint reduced the file size to an average of 10K. These loaded quickly and without problem in WebCT. This is good news because it means that we have a simple and general mechanism to import existing UT doors from any subject area.

SlideShare

I just came across SlideShare from Christina's LIS Rant. This is a free hosted service that allows you to embed your Powerpoint slides directly on your blog in a format that permits a quick click-through without leaving the blog or requiring Powerpoint.

The site also extracts text from the Powerpoint to create a transcript that is searchable.

Here is an example from my recent talk at ACS.

Science Blogging Conference

Mark your calendars for the North Carolina Science Blogging Conference on Jan 20, 2007 in Chapel Hill.

This is a free, open and public event for scientists, educators, students, journalists, bloggers and anyone interested in discussing science communication, education and literacy on the Web.

I will be leading breakout session in the afternoon on Open Source/Open Notebook Science.
If this is anything like last year's PodcasterCon event, it is going to be awesome.

Subscribe to the Blogging Together Blog for updates.

sciencebloggingconference

Scientific Journals International

The first issue of SJI has just come out. This is an Open Access online journal open to all areas of science. Although not free for authors, the $100 fee is an order of magnitude more affordable than most other scientific Open Access journals.

SJI welcomes papers from researchers, writers and artists in all disciplines. All submissions will be sent to three reviewers with final decisions reported to the author within four weeks. If your paper is accepted for publication, you will be asked to submit the License to Publish agreement along with a processing fee of $99.95.

The copyright notice is a little strange. They claim that authors retain the copyright but then list the ways that authors may or may not use their intellectual property :)

Copyright remains yours, and you retain the right to use your own article (provided you acknowledge the published original in standard bibliographic citation form) in the following ways, as long as you do not sell it in ways which would conflict directly with our interests. You are free to use your article for the internal educational or other purposes of your own institution or company; mounted on your own or your institution's website, posted to free public servers of preprints and/or articles in your subject area or in whole or in part, as the basis for your own further publications or spoken presentations.

What Good Science Looks Like

Yet another article appeared yesterday on Excite News on how Web Journals Threaten Peer-Review System. (For another view see Deepak Singh.) There were some good points made. For example, on tenure and evaluation:

Researchers whose work appear in traditional journals are often more highly regarded. That attitude appears to be slowly changing. In 2002, the reclusive Russian mathematician Grigori Perelman created a buzz when he bypassed the peer-review system and posted a landmark paper to the online repository, arXiv.
Perelman later won the Fields Medal this year for his contribution to the Poincare conjecture, one of mathematics' oldest and puzzling problems.

On quality control:

Editors of traditional, subscription-based journals say the peer-review system weeds out sloppy science. The traditional process isn't designed to detect fraud (referees rarely look at a researcher's raw data), and prestigious journals have unwittingly published bogus work. Last year, for example, Science retracted papers on embryonic stem cell research by a South Korean cloning scientist who admitted falsifying his results.

I think we need to highlight good Open Science when we find it. Org Prep Daily is a nice recent example. It is a blog with synthetic procedures. From the way it is written, any competent organic chemist can tell that the information is self-consistent and of high quality, with enough information to repeat the experiment and confirm that it worked. Those who can't tell have no business doing the chemistry. And those who want to learn need to discuss it with peers and mentors to try to understand how to tell if it makes sense, just like they would with any other type of publication.

Org Prep Daily is very similar in scope to Synthetic Pages. Both provide recipes for making chemicals at a similar level of detail. However, they differ in some important respects. Synthetic Pages is organized in a central database and users must abide by the website's terms. For the authors, the copyright is relatively friendly, at least compared with standard journals:

Can I publish after submitting a procedure to SyntheticPages?

Yes. Although you transfer copyright of the SyntheticPage to us, you may also incorporate the information into a paper (subject of course to the third party's terms and conditions) or elsewhere. For this, no copyright notice is required. You should, however, consider that submitting a SyntheticPages may affect your right to claim a patent on the material at a later date.

But for users, no re-mixing with attribution allowed:

You are not authorized to:

* alter the material in any way
* reproduce or store any part of this web site in any other public or private storage medium, electronic or otherwise, without written permission from SyntheticPages.

In contrast, using a blog like Org Prep Daily enables the authors to set their own format and copyright terms. Since they control the blog, in principle they could selectively remove negative comments, which would not be the case with Synthetic Pages. However, it is hard to unlink things in the Blogoshere and if someone really wanted to indicate that something was seriously wrong with a procedure they could do so on another easily found forum. One advantage of the Synthetic Pages approach is that it offers a third party time stamp, which is more difficult to do on a blog. Using a hosted wiki solves that problem.

This basically boils down to a top-down vs. bottom-up approach. Which is better? For me it comes down to findability. Unless you had heard of Synthetic Pages, you probably would not search on their database. However searching for a compound's name on Google pulled up the relevant posts on both Synthetic Pages and Org Prep Daily. If they are both equally findable, which one to use?

When in doubt duplicate. Post on both. That's why it is so important to retain the right to republish, which is almost always given away when publishing in a journal.

Reference to the compounds in redundant formats (i.e. InChI, SMILES, CAS number, etc) would also make the information much more findable. Read some Peter Murray Rust for more details on that.

Open Notebook Science

Thanks to Beth Ritter-Guth's efforts to clarify the definition of terms relating to Open Source Science, a good discussion has evolved on the Blue Obelisk mailing list. Peter Murray-Rust has made the point that this term may be confused with Open Source Software. However, as Peter notes in a follow-up post, Jamais Cascio from WorldChanging has used this definition of Open Source Science, which is fairly consistent with our use of it in UsefulChem:

...research already in progress is opened up to allow labs anywhere in the world to contribute experiments. The deeply networked nature of modern laboratories, and the brief down-time that all labs have between projects, make this concept quite feasible. Moreover, such distributed-collaborative research spreads new ideas and discoveries even faster, ultimately accelerating the scientific process.

In Open Source Software, the code is made available to anyone to modify and repurpose. What we have been trying to do with UsefulChem is to provide the analogous entity for chemical research, which is raw experimental data along with the researcher's interpretation in a format that anyone can easily re-analyze, re-interpret and re-purpose. A good example of re-purposing is using some results and observations from a failed experiment in a way that was never intended by the original researcher. This just doesn't happen regularly in science because failed experiments are almost never included in publications.

Unfortunately, in addition to the confusion with Open Source Software, others are using the term Open Source Science to mean discussions about pre-prints of regular journal articles.

To clear up confusion, I will use the term Open Notebook Science, which has not yet suffered meme mutation. By this I mean that there is a URL to a laboratory notebook (like this) that is freely available and indexed on common search engines. It does not necessarily have to look like a paper notebook but it is essential that all of the information available to the researchers to make their conclusions is equally available to the rest of the world. Basically, no insider information.

Linking to a Blogger Post

One of the advantages of using a blog is to be able to create a link to a specific post. For recent posts in Blogger you just need to click on one of the links under "Previous Posts" on the right of the page.

However, for posts that are very old, it is not so obvious. On the bottom right of every Blogger post is a link called "links to this post". Hover over it to reveal a URL that you can copy by right-clicking. Just remove the "#links" at the end and you have a link that will go directly to that post.

Note: in order for this to work the Backlinks options has to be activated, which is located under Settings->Comments.

Physics Views on Publishing

Not Even Wrong has a post on the future of scientific publication and open access with a good assessment of the costs involved. What makes this a particularly good read is the collection of over 50 comments mainly from the physics and math communities.

The point is made several times that the arXiv experiment in chemistry, the Elsevier Chemistry Preprint server, was a failure. I actually published multiple times using that vehicle and it was indeed a shame when they shut down. This was a totally free model - for authors and readers - and authors kept their copyright. Here is the explanation of why they shut it down.

Despite the wide readership of CPS preprints, the chemistry community has unfortunately not contributed articles or online comments to this service in sufficient numbers to justify further development. The decision has therefore been taken to stop the processing of any further submissions.

Book Chapter on Open Access

Taken from Knowledge Transfer Innovations:

Benkler addresses the forces affecting Scientific Publication in this chapter of his book, “The Wealth of Networks. (Click the link then scroll down through the chapter to the subhead Scientific Publication’.

This is basically a summary of the clash between publishers, scientists and those who judge them.

Open Source Science in Class

Beth Ritter-Guth is currently running her English class with a very special assignment for her students: research and document the emerging role of Open Source Science. They are tackling this using multiple information sources, including blogs, articles and interviews.

They interviewed me this week and the podcast is now available.

Anyone with an interest in Open Source Science is free to comment on their work in progress posted on this wiki page. Also see Beth's Technical Writing class blog on OSS.

Another part of this assignment will involve understanding the larger context of the UsefulChem research projects on malaria, AIDS and arsenic in drinking water. They will be interviewing people involved in this type of research, including the students working in my lab, mainly on the malaria project.

Can Librarians Learn to Love Science Wikis?

The students in my lab have been posting their raw experimental data to a blog since February. Since that time we have evolved this process onto a wiki. This has been very useful for tracking the contributions of multiple students and editors. It has particularly convenient to annotate the text directly with temporary comments, such as, "dead link here" or "redo this analysis with these conditions" , etc. On a blog, the previous versions of a post are deleted, which makes comments inapplicable after revision.

However, the great flexibility of such a publication system has made many librarians uneasy, as I have learned through conversations with them.

One of the main issues is referenceability.

One of the advantages of using a wiki is that pages can be updated when new information becomes available. However, if that is the case, then how can morphing information sources be verified? Formal publications have already had to deal with this issue when citing websites for information that can only be found on the web. The current trend seems to be to state the time the website was accessed next to the hyperlink. This is a pretty weak form of referencing since there is no reliable way to verify what was on that site at that time. Of course, there is the Wayback Machine archiving the internet over time but that requires some forethought to submit the website and will only be updated about once a month.

Others have proposed services that freeze a copy of the web page on a third party site when making a citation. (I don't have a link for this - maybe someone can remind me of an example). The wiki (specifically Wikispaces) has both the third party time stamp and the version available automatically. If the publication time of a document is known, it should usually be possible to find the version of the wiki page available at that time. To make this explicit, one could just post the link to the version in addition to the current page.

Google Apps for Education

Google is now offering a service to educational institutions to permit branding and account management for Gmail, Google Calendar and Google Chat. Here are some of the applications Google suggests:

Gmail - Give students email with huge storage capacity, less spam, search tools to help them find information fast and built-in instant messaging.

Google Talk - Keep students in contact even when not on campus with instant messaging and voice calling over the Web.

Google Calendar - Help students stay on top of their schedules, share plans with others and keep up-to-date on campus events.

There is currently a beta period where institutions that sign up will get free access. This seems to imply that there will be a charge for latecomers.

Now if Google will just create an assessment module, Course Management Systems like WebCT will have trouble justifying their price tag.

Thanks to Stewart Mader for the link.

Chemistry Central and Fully Open Access

Hot off the presses from Sciencebase:

A new open access site for chemists - Chemistry Central - launches today as part of the newly announced Open Access Central group of sites from the makers of BioMedCentral.

CC collates peer-reviewed research from a range of open-access journals and makes available the original research articles as soon as they are published.

Deputy Publisher and former chemist Bryan Vickery explains the motivation, “We have seen increasing interest from chemists in the open access publishing model and, having launched two chemistry-specific titles in the last 18 months, the time seemed right for BioMed Central to create an open access publishing website to meet the needs of chemists,” he says.

On the CC roster are OA articles from Geochemical Transactions, the Beilstein Journal of Organic Chemistry, and chemistry-related articles from BMC Pharmacology, BMC Biochemistry, and BMC Chemical Biology.

It is hard to tell exactly what this will mean for Open Access chemistry research. Right now the vast majority of articles on Chemistry Central are better classified as bioinformatics related, although there are a few articles on analytical and organic chemistry.

There are certainly some intriguing opportunities laid out in the current system. For example, they are making their software and templates available for someone to start a new Open Access journal in a chemistry sub-field or interdisciplinary topic. That is actually really cool and I hope that this catalyzes the creation of novel useful information channels.

However, I am concerned that part of the model is based on author publishing fees on the order of $1000/article, similar to the PloS and PloS One models. Note that authors from institutions who are members can publish free of charge. Drexel is not a member as of yet.

Not all Open Access journals are funded by author fees. In the realm of organic chemistry the Beilstein Journal of Organic Chemistry and Arkivoc are funded using different mechanisms and provide what I would call Fully Open Access on the front as well as the back end. I think that this is where Open Access can really become a fully free and democratic process, with no barriers from the author and subscriber to share knowledge freely.

Notwithstanding all of these details and caution, this is a very important story for the chemical community to monitor.

Quality Control and Peer Review

Anyone following the current debate about Open Access scientific publication is well aware that peer review is a big factor in these discussions. For example, see Pedro Beltrao's recent discussion at Science Foo Camp.

I have found that this issue is of particular concern to librarians, who would like to be able to categorize all publications into two neat piles: reliable and unreliable. That makes it convenient to simply ignore anything that is not on the reliable list. Since librarians cannot be experts in every field, they have to rely on other criteria, such as a notice that a document has been peer reviewed.

Unfortunately, it is often assumed that peer reviewed information is reliable. This can be a dangerous assumption.

For example, in our research on the synthesis of anti-malarial compounds, we designed our experiments based on information found in peer-reviewed journal articles. Over time, we found some contradictory information in the literature about the solubility and spectroscopic properties of one of the compounds we were trying to make and this cost us some time.

I think that this was a great lesson for my students about how to use the chemical literature. The only way to confidence in science is to look for redundancy in independent reports. Peer review (from anonymous people who do not repeat experiments in a paper) cannot be used as a short cut to assessing reliability.

Of course if the papers that mislead us had links to the raw data of their experiments we would have been able to spot these errors much more quickly. This is a huge advantage of doing open source science.

With the proliferation of new forms of scholarship, it is no longer effective to teach our students that there is such a thing as reliable literature. There is uncertainty in every information source. We should teach them to find the same information from several different sources and then discuss the confidence we can derive from the aggregate results.

Finding the melting or boiling point of a compound is a great way to make that point. Use a company catalogue, Wikipedia, a textbook and Google and see if there is consensus. For example, the boiling point of ethanol is listed as 78.4 C in Wikipedia, 78.3 C on this website, 78.30 C on this website and 78.5 C here. Based on this we can be reasonably certain that the boiling point is between 78 C- 79 C and that may be all that we need for our application. Finding the accurate value for that first decimal place is going to require a lot more research.

Unfortunately most of these information sources do not reveal the details of the original experiments where the boiling point was determined, which would be extremely helpful in this case. However, before you start bashing Wikipedia and web pages as being inherently unreliable, take a look at the official information compilations that are out there. For example, MSDS (Material Safety Data Sheet) is considered by chemists to be the standard information source for chemical safety. In the course of our research, I was disturbed to find that benzene was listed as an incompatibility for sulfuric acid. This is the very first reaction I cover in the chemistry of aromatics!

I found this to be even more disturbing:

The quality and accuracy of MSDSs varies widely. One recent study showed that of 150 randomly selected MSDSs, information was accurately identified in Health Effects in 37%, in First Aid Procedures in 76%, in Personal Protective Clothing in 47%, and in Occupational Exposure Limits in 47%.

Unfortunately, there does not appear to be a simple way to get to the original experiments where the MSDS information was obtained. At least on Wikipedia you can ask the author directly for the source if it is not listed.

For a nice discussion on the issue of reproducibility in peer reviewed publications see Chris Surridge's post on the PLoS blog.

UsefulChem space of the month

From the August 2006 Wikispaces newsletter, here is a concise summary of the UsefulChem project:

August's Space of the Month is great blend of the principles of open
content and open source applied to science and education.

Our Space: UsefulChem is an Open Source Science project aiming to share real time results from the Bradley chemistry lab at Drexel University. The main objective right now is to make compounds to fight malaria.

Our Community: The main contributors currently are Khalid Mirza (grad student), James Giammarco (undergrad), Lin Chen (undergrad), David Strumfels (grad student), Alicia Holsey (grad student) and Jean-Claude Bradley (Principal Investigator).

Our Experience with Wikispaces: After evaluating several wiki solutions we settled on Wikispaces because it offered a clean simple interface, RSS feeds, rapid indexing on Google and a free hosted option. Our objective is not only to communicate our research work directly to the world but also to offer solutions that can be easily replicated by other scientists at minimal or no cost. The coupling of the organizing power of Wikispaces with the chronological recording of Blogger creates an optimal vehicle for the dissemination of Open Source Science.

Back from BCCE

Here are some notes on the BCCE 06, the Biennial Conferences on Chemistry Education at Purdue last week:

1. I gave two talks: one with Mark Ott on screencasting and podcasting chemistry courses and one on games specifically for organic chemistry.
2. I attended the sessions that I could find related to podcasting in chemistry. Alan Kiste talked about using enhanced podcasts to supplement his organic chemistry class.
3. Bob Hanson opened my eyes to the power of AJAX for chemistry. He had a demo where highlighting a word pulled up more info without having to reload the page. His first example was Google Suggest, where suggestions come up as the user types.
4. Richard Zare gave a very entertaining Keynote talk about general ways to solve problems. He demonstrated all kinds of brain teasers, both chemical and general. His basic point was that people don't solve problems in an organized way and that is ok. Let the students feel comfortable with the messiness of thinking. I agree.
5. I finally got to see a little demo of the First Person Shooter Critical Mass chemistry game (Gabriela Weaver). They used the gun to shoot some crates and to heat up a reactor. It will be interesting to play when they are done.
6. Zangyuan Own showed some pretty impressive data about delivering chemistry courses customized for different kinds of Multiple Intelligences. Unfortunately, the material was only available in Mandarin. He was also handing out handsome decks of playing cards with a different element showcased on each card.

Open Science Survey

An Open Access and Science Publishing survey is currently being distributed. Take a few minutes to contribute your viewpoint.

Can Open Source Science be too Open?

Pedro Beltrao brings up some good points on his post about re-thinking the scientific process. He proposes the use of black box modules as a way to make the scientific process partially more open:

Wouldn't it be great if we could find a way to make most of the scientific process public but at the same time guaranty some level of competition? What I think we could do would be to define steps in the process that we could say are independent, which can work as modules. Here I mean module in the sense of a black box with inputs and outputs that we wire together without caring too much on how the internals of the boxes work.

Although I don't agree that it is necessary to hide real-time information to be a productive scientist, I am glad to see that people are having this conversation. And the beauty of current web technologies is that each scientist can set up their own black boxes as they see fit.

We already see that with existing attempts - for example Nature Protocols discloses much more than a typical experimental section in an article, including troubleshooting tables. But we don't get to see the messy series of failed experiments that enabled those troubleshooting tables to be constructed.

Track Wikispaces Visitors

Before my CONFCHEM presentation was to start, I wanted to set up a counter on the Wikispaces page where my document was located. Wikispaces help replied that they do not support arbitrary HTML, which made it problematic to insert the javascript needed for the counter.

I was pleased to notice yesterday that, when editing a Wikispaces page in text mode, an option to embed media pops up on the right. This new feature does in fact allow introducing the script required for the counters like Sitemeter. The versatility of the Sitemeter tracker is such that I can use the same counter for my UsefulChem blog and wiki and tell where visitors landed from the Entry Page view. And the Referrals View shows how they found the site, including keywords used in Google, for example.

The code from Sitemeter that you need to put into the Embed Media text box will look something like this:



If you are using the Sitemeter code in your Blogger account, you will find it at the very end of your Template file.

The HTML for the counter is stored in a Wikispaces database and shows up like this in the Text view:

[[media type="custom" key="646"]]

Note that you can't simply copy this one line to all your Wikispaces pages. You'll need to use the Embed Media box on every page you wish to track.

All of this works with the free versions of Wikispaces and Sitemeter.

Poem about Science and the Web

I just came across Stevan Harnad's poem "Publish or Perish" on Christina's LIS Rant.

Open Source Science advocates, savor this stanza:

For showbiz being what it is today,
work's not enough, you've got to make it pay.
What ratings, sweeps and polls count for our actors,
no less than our elected benefactors,
for Science the commensurate equation
is not just publication but citation.
The more your work is accessed, read and used,
the higher then is reckoned its just dues.
Sounds crass, but there may be some consolation,
where there's still some residual motivation
to make a difference, not just make a fee:
the World Wide Web at last can make Science free.

UsefulChem in C&E News

Chemical & Engineering News is running a story on Open Source Science, with an emphasis on chemistry related projects. UsefulChem got a nice mention.

They also put a pic of me with my students James and Khalid. James is on the left next to the rotovap. Anyone familiar with our malaria research will wonder why there is a blue solution on the rotovap. The photographer wanted us to do something interesting and colorful so James made up a solution of methylene blue for effect. Trying to look serious talking about the blue solution gave everybody the giggles.

Nature Protocols

Nature Protocols is a definite step forward toward open source science. The protocols are peer-reviewed and open for comments. I really like the troubleshooting tables.

Nature Protocols is an interactive online resource for laboratory protocols for bench researchers. Protocols are presented in a 'recipe' style providing step-by-step descriptions of procedures that users can take to the lab bench and immediately apply in their own research. Protocols on the site are fully searchable and organized into logical categories to be easily accessible to researchers.

From The Sceptical Chymist

Dissertation on Translating Open Courseware

For those of you following the open courseware scene, Meng-Fen Grace Lin has just completed her thesis at the University of Houston:

Sharing Knowledge and Building Communities, a Narrative of the Formation, Development and Sustainability of OOPS

OOPS is the Opensource Opencourseware Prototype System involved in translating content from MIT's OpenCourseware.

This thesis offers an unusually candid look into the politics and personalities involved in an open source volunteer-based organization.

The cost of Open Access

Here is a nice little review from the Economist of the current state of Open Access to scientific publications. The financial burden on the author is detailed:

There are, however, a few thorns among the roses. Traditional publishers are often skeptical about the business models of their open-access rivals, and they sometimes have cause to be. The Public Library of Science (PLoS), an American organization regarded by many as the flagship of the open-access movement, lost almost $1m last year. As a result, it is about to increase its charge from $1,500 per article to as much as $2,500, depending on which of its journals an author publishes in.

Since anyone can make their research available for free by self-archiving, presumably the added value is the "blessing of peer-review". But if reviewers are not paid, where does that money go? Anyone out there know?

Thanks to Beth for the link.

LCTI/LCCC workshop

I just returned from doing a workshop at Lehigh Carbon County College (LCCC) and Lehigh Career and Technology Institute (LCTI) in the great Schnecksville, PA. There were about 50 attendees, mostly a mix of college and high school teachers.

In the morning, Beth and I gave some general talks introducing RSS and some applications of blogs, wikis, podcasting, vodcasting and games in education. The attendees were very active in asking questions and I didn't get to finish my slides. That's actually a good sign that there was some real interest and knowledge transfer.

In the afternoon the attendees split up and rotated between our workshops. Beth ran the one on blogging, Marc Bonanni did wikis and mine was on games. That was a lot of people to train in 2.5 hours and we were all exhausted afterwards.

My objective was to have them learn to navigate one of the EduFrag mazes, create at least one bitmap door with Paint then import it into a room using the UnrealEditor (free version, no weapons). There were too many people for me to assist individually in that amount of time so after I trained the more tech savvy attendees I asked them to help the others. It was not possible to do it "lecture style" because people were rotating on their time. I think most attendees who were interested in creating games at least acquired an understanding of how the EduFrag system works to create their own content for their classes without much additional help. I also asked them to create true and false doors based on what they learned in the workshop. If I collect enough, I'll pool the best of these together in one common maze to teach educational web technologies.

Beth discussed a problem in her talk that I ran into directly during my workshop: the blocking of blogs in PA high schools. I was unable to access the EduFrag blog to show the attendees how to download other maps. Luckily, for now, access to Wikispaces was unobstructed and the computers in the workshop room were pre-loaded with the educational version of Unreal Tournament with Beth's grammar and one of my chemistry mazes.

Beth ran her workshop in LCCC, which is a college, and thus was not subject to the blog blocking.

Overall the response was very positive and I look forward to following up on the implementation of some of these technologies.

Here are the workshop blog and wiki.

Here are the recordings of Beth's and my talk.

CONFCHEM is on

This is the last week of the online CONFCHEM and my presentation is up there.

The conference is run by mailing list. If you have any interest in lurking or participating this week just sign up with the instructions at the bottom of this page.

Here is my abstract:

CONFCHEM 8C

Expanding the role of the organic chemistry teacher through podcasting, screencasting, blogs, wikis and games

Jean-Claude Bradley (Drexel University)

Technology is enabling new ways to channel the relationship between teacher and student. The ability to provide an archive of recorded lectures in rich and convenient formats like screencasts, podcasts and vodcasts enable an instructor to explore additional means to integrate class material through activities such as games, blogs and conversation. This presentation will describe the implementation of such technologies in a university level organic chemistry class. See http://chem241.wikispaces.com.

PLoS ONE

There has been a lot of talk lately about PLoS ONE, an open access online journal based on the existing Public Library of Science (PLoS) format. PLoS ONE aims to be more inclusive, aiming to publish reports that are scientifically sound, without assessing importance.

This seems like a step in the right direction towards the dissemination of laboratory results. However, it is uncertain exactly what this will cost the authors:

From an interview of Chris Surridge, the managing editor of PLoS ONE, Richard Poynder reports:

RP: Will the article processing charges for PLoS ONE be the same as those applying to the journals, which I understand have just risen from $1,500, to between $2,000 and $2,500 per paper?

CS: Hopefully the rate can be lower. One of the driving forces of PLoS ONE is that we want to be able to publish lots of papers. To that end we are setting up the system in a completely scaleable way so that we can cope with as many papers as people want to publish with us. One of the advantages of doing so is that we can start getting economies of scale, and this will keep author fees as low as possible.

I wonder if this model can really support the open sharing of scientific information, when the barrier to contribution excludes anyone who is not well funded. I know that I would much rather spend $2000 on chemicals, lab equipment and students. But I would be very interested in a breakdown of how that money is spent to better appreciate the model.

So, for now, I still maintain that self-archiving is the way to go for the lowest barriers on both the sender and receiver sides.

Thanks to Glyn Moody for the link.

Back from Frye

I just returned from an intense two weeks at the Frye Leadership Institute at Emory. There were about 50 participants, mainly from the IT and academic library domains. As a faculty member, it was really interesting to get a perspective of the university through other eyes.

There were a lot of talks but also some group work. Here is some work that my group did on our hypothetical university, Maverick U.

The main intersection with my interests revolved around social software and other non-traditional modes of communicating scholarship (especially scientific), including implications for tenure and promotion. The librarians were also very much interested in discussing their role in the archiving and retrieval of new forms of documents. Of course, nothing was resolved, but the dialogue is open and we'll continue to share our thoughts and experiments as we move forward.

The best part of all this was meeting and engaging with a group of terrific people, especially when we played Weboggle.