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Tuesday, October 24, 2006

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.

Wednesday, October 18, 2006

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.

Monday, October 16, 2006

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.

Tuesday, October 10, 2006

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.

Thursday, October 05, 2006


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.

Tuesday, October 03, 2006

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.

Monday, October 02, 2006

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.

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