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Saturday, December 31, 2005


I thought Chmoogle was nice when I blogged about it a few weeks ago.
But QueryChem takes open content chemical searching to the next level and here is why:

1) Just like Chmoogle, you can use an editor to draw the a molecule or type the SMILES code as input. But you can also add text queries to fine tune the results. For example, typing "CAS" in the text box pulls up only those hits where the CAS number is likely to be listed.

2) This is the big one: the results in QueryChem take you directly to the pages of the commercial suppliers. In a Chmoogle search, the results only take you to the general company URL, where you have to do the search over again.

3) A QueryChem search does a lot of work for you. It figures out the possible names for a compound then throws that back into Google or Google Scholar and then shows where those names appear in the results. That saves a lot of manual labor.

4) Compound analogs also show up and the threshold of similarity can be set in the search.

With all of these advantages, QueryChem is now my first choice for single search open content chemical information. For ongoing monitoring of our UsefulChem project I am still going to use CAS number searches in MSN (exportable via OPML) because QueryChem does not yet provide RSS feeds for searches.

Another feature that I would love to see in QueryChem is the ability to form a URL of a given search.

Update: Justin Dale Klekota from QueryChem has just enabled forming a URL for a search. For example the search below formed by searching the SMILES code for glycoaldehyde and "CAS" can be called up by clicking on this link. He also informs me that they are working on RSS feeds for searches. How is that for responsive!

Thursday, December 29, 2005

The online textbook is here

I finally came across a full free 1200 page textbook for undergraduate level organic chemistry from Daley & Daley. This is not a collection of Wikipedia articles but a full textbook of equal quality to any of the other currently used major orgo textbooks. In fact there is even a table to lookup the corresponding chapters of various textbooks! It looks like it covers about 80% of the material I am going to cover this fall. I have added it to my list online resources for my class.

The story behind this is very interesting. Apparently they were writing the textbook for a publisher, who decided not to publish it at the last minute. This is another example of open source removing the publisher from the equation in a natural way simply because the model does not work anymore. I think there are tremendous opportunities for publishers but they have to adapt.

Remember it only takes one person in the world to create a high quality open source product in a given field to change everything.

The problem sets, however, are not freely available. But they are provided at a reasonable price. The paper version of the book can also be ordered for a fee.

I don't think it will take long to find comprehensive high quality open source problem sets in organic chemistry. In my own courses I have made my problems and full screencast solutions openly available. Here is another great organic chemistry resource with plenty of good questions.

Thanks to Heather Morrison, who provided a link to the Textbook Revolution.

Monday, December 26, 2005

OPML vs RSSmix

A few days ago, I blogged about using an RSS merging tool (like RSSmix) to automatically track a chemist's research sphere, such as the reporting of the use or commercial availability of certain chemicals. I suggested using an RSS merging tool to convert several separate RSS search feeds into one for the convenience of subscribing. However, one drawback of this approach is that when there are new hits, it can be hard to tell which searches triggered them. For example the compound may show up burried in a long catalogue page and it might not be obvious where to look.

Another way to track several RSS feeds is to subscribe to a blogroll using OPML (Outline Processor Markup Language). I was trying to avoid doing this because I can't distribute my feeds via a one-click subscription process this way (which was possible with RSSmix).

However, although not one-click, the procedure is not that difficult. I created a blogroll using Bloglines simply by making certain feeds public and the rest private. Right click this link and select "save link as" (Firefox) or "save target as" (IE) to save the OPML file as "export.htm". You can then import this file into your favorite RSS reader. For Bloglines you do this by logging in to your account, click on the Edit tab on the top left then click on "Import Subscriptions" on the bottom left. Browse to the export.htm file you just saved and you are done. (Note: if you wish to export your own OPML file from Bloglines, make sure that you select feeds in the Top Folder - otherwise it won't import properly)

The OPML file that I just used in my example above consists of the CAS numbers of the compounds in our UsefulChem project. If one of these compounds shows up in a catalogue somewhere, the corresponding feed with become bold in Bloglines. However you can use this type of alerting system with any keyword search. I suggest that you use MSN because it has a "Subscribe with Bloglines" button for any regular search upon clicking the RSS button at the bottom of every search. MSN will cover blogs as well as regular internet pages so it beats Google's Blogsearch on coverage and convenience.

I'll show a demo for this at our next RSS club meeting in early January and it will posted on the Drexel CoAS podcast/screencast.

Sunday, December 25, 2005


A few days ago I came across CastingWords, a podcast transcribing service. This is something I have been looking for a while now.

Earlier in the fall term I started posting the transcripts for the podcast of my organic chemistry class. They were available because I had a hearing impaired student in my class. That came in handy for me as well as other students for quickly finding out exactly what I said in class.

Because transcripts are extremely long, I put them in a separate blog that I cross-referenced with my class blog. I also added the the free site meter to the transcript blog to find out how others were finding the site.

I just basically did the same thing for my Drexel CoAS E-Learning podcast, creating a separate transcript blog and linking back to the podcast. My test podcast was an 18 minute demonstration of how to use Blogger and Feedburner to create a podcast. I would be interested to hear comments as to how the transcript is (or is not) useful. For me the indexing feature alone makes it worth it.

CastingWords charges about $25/hour. They say they have organic chemists on their team so we'll see how they do on one of my lectures.


Friday, December 23, 2005

RSS aware chemical research

Here is a way of leveraging a few free resources to automatically alert chemical researchers to new events in their sphere of interest.

1) Start with an open source repository of molecules of interest. For our UsefulChem project the molecules we wish to make or think we need for various syntheses we are contemplating are found here.

2) For each molecule create an RSS feed using an MSN search using a unique molecule identifier. The CAS number is particularly handy to do this. Make sure to put quotes around the number in the search. Scroll down to the bottom of the results page in MSN to find the RSS feed. Unfortunately Google does not yet have RSS feeds for general web searches yet, just for blogs or news.

3) Merge the RSS feeds into a master feed using RSS mix. I actually tried 4 or 5 other RSS merging services and none worked as claimed. There are probably some better ones out there and let me know if you come across a better service. One of the downsides of RSS mix is that it does not seem possible to modify an exising master feed without creating a new url.

For the UsefulChem project the result corresponds to the following master RSS feed, that I can just add to Bloglines. For a look in a normal web page see here.

The use of the CAS number in a general web search tends to pull a lot of catalogue entries, which is one of the most useful pieces of information for a particular molecule of interest. It will also pull blog entries, patents and other goodies usually with few false hits. At this point, this is a far better way to find commercial sources of chemicals compared to Chmoogle. But that may change as they increase their database coverage.

What this effectively means is that, with no further effort, all members of my research team will be alerted when our molecules of interest become of interest to other scientists carrying out open source research or are made commercially available.

Monday, December 19, 2005

More open source science sites

Here are some examples of web sites enabling more open collaboration between scientists.

1) Openwetware is an MIT project to share mainly molecular biology information through a wiki. So far most of the posted experimental data seems to be laboratory protocols. Our UsefulChem project is listed here.

2) MetaCollab is a wiki focusing on collaboration in general with an open source science section. Our UsefulChem project is listed in the open research section.

It is interesting to observe the evolution of all this. Both of these sites use MediaWiki and there appears to be no way of getting RSS feeds from sub sections, only the entire site (although I think it is possible to get email alerts for certain pages). One of the things I really liked about Wikispaces was the flexibility of using RSS to track either the whole site or certain pages or discussion posts.

But a general problem with wikis is the difficulty in following changes. The text in the RSS feed is usually marked up extensively and not reader friendly. This is one reason that I am sticking with the wiki/blog hybrid strategy. The blog is for reader friendly RSS feeds and fine detail; the wiki for high level organization linking back to more detailed blog posts.

Saturday, December 17, 2005

Archived lectures and workshops post-mortem

The 2005 fall term has just ended here at Drexel and it is time to report on my organic chemistry class, where I assigned recorded lectures (screencast and podcast) and ran workshops during class time instead.

1) At almost every workshop I was able to help every student who came on an individual level and answer all of their questions. This was probably most helpful to a hearing impaired student in my class. He not only had transcripts of the archived lectures but also my full attention much of time as we communicated through a transcriber.

2) The average class performance was slightly better than last term, when I held lectures in class. Since most students chose to take the class fully online, holding lectures or workshops should not have had much of an effect on the average and it didn't.

3) My initial plan to schedule workshop topics ahead of time and post them on the wiki was abandoned midway. Not a single student made a request. I just dealt with whatever topic that was causing them the most difficulty.

4) Some students came to the workshops and watched my screencasts, listening through earphones. I thought this was a clever way to simulate the experience of attending a lecture and being able to ask questions in person immediately. Of course, if I were giving the lecture during class time, I could not just stop, pull out a molecular model kit and talk with a student for 10 minutes until they understood.

5) Other students came to the workshops unprepared and did the assigned problems during the class time, asking me for help when necessary. That seemed to be a fairly efficient approach for many.

6) Aside from the odd pair, students did not spontaneously form groups with common questions. However, if I noticed that a student had many questions about the same topic, I would address the class and ask others with similar interest to form a group.

7) I had gone to some trouble to identify a computer classroom that we could use for the activities requiring that (such as games) but it turned out that most students had laptops and for the few that didn't I just lent them my tablet PC. We had a decent wireless connection most of the time. Being able to show them exactly what to do on their computers was also the best way to resolve confusion about the technical aspects of the class (subscribing to Bloglines, podcasts, etc.). Also this made it a lot easier to run the EduFrag races. I handed out molecular model sets and chemistry books as prizes.

8) For their 1% extra credit assignment, students could either create a map or 5 true and 15 false doors for the EduFrag project. One student who was a bit familiar with Unreal Tournament made very nice maps. A few other students created doors. An advantage of this constructivist approach is that the false doors gave me a very good insight into what they thought were common mistakes and thus how they conceptualized the material. Yet another opportunity to talk to them about some of the finer points. And, of course, all of these map quizzes will be available for the next group of students (or anyone) to help them learn.

9) Only one student chose to do a blog assignment (instead of a game map) for the 1% extra credit, finding one of the reactions covered in class in a real world application (she did ozone depletion). Just like the previous term this type of assignment was selected more from the higher level CHEM243 students than the introductory CHEM241.

10) For students who were completely on top of everything and wanted a challenge, I provided extra problems, many of which were taken from real world applications not yet solved (such as the synthesis of potential anti-malarial and anti-HIV agents). This was a chance to review class material in an applied context and to introduce some reactions that we don't have to time to cover in any of the undergraduate organic chemistry classes.

11) Contrary to other reports, I do not find that this generation of students is any more tech savvy than the faculty that I help. You cannot assume that they are familiar with podcasting, blogs, wikis or any RSS technology or even games. They can, however, learn quickly. Although I have used screencast tutorials and took an entire class to go over most of the technical aspects, there is nothing as effective as helping a student with their laptop in a workshop environment.

12)Overall I spent as much time in the classroom as I did when I gave lectures and this was sometimes exhausting, especially after our 2 hour sessions on Fridays. But it was more rewarding also. I felt more like a teacher because I observed the learning take place one student at a time.

Wednesday, December 14, 2005

Clickers and chemistry

Dan King from our Drexel Chemistry Department has a screencast showing his use of clickers in his introductory chemistry course. He posts a multiple choice question then asks students to vote their answer and displays the distribution of choices as students click a handheld device.

If the multiple choice questions are designed well this is a great way to get insight into how students are understanding and misunderstanding the class material.

If you would like to experiment with clickers in your class, contact Dan. I think he has some he could lend out at Drexel.

Sunday, December 11, 2005


Opinmind is a cool new service that reports on the relative positive to negative opinions expressed in blogs on specific topics.

Here are some fun results:

88% love kittens
84% love Christmas
76% love Drexel
34% love organic chemistry
33% love elearning
25% love taxes
25% love WebCT

Don't take this too seriously but it is interesting to read the comments on either side.

Thanks to LearnAndTeachOnline for the link!

Wednesday, December 07, 2005

Chmoogle accommodates automation

I just received word from Craig James at Chmoogle that they will modify their Terms of Use to accommodate our request for automated queries:

"You may perform an unlimited number of searches on Chmoogle from a standard web browser application which is under your immediate personal control. If you use an automated system such as a script or program to search Chmoogle, you may only access the first one hundred pages (1000 compounds) for each distinct query, and you may not access more than one thousand pages (10000 compounds) in any twenty-four hour period."

This is very nice. Note, however, that they do not make an API available.

Also they will be incorporating the Sigma-Aldrich catalogue in a few weeks - that will take Chmoogle to a new level of usefulness for automated queries.

more chemistry lectures online

It is really interesting to see the wide variety of solutions that teachers are implementing to deliver recorded lectures.

In the chemistry world here are some recent additions:

1) Patricia Hogan teaches organic chemistry at Suffolk University. You will need to select CHEM212 from the left menu. She uses MediaSite that shows a recording of her face as well as a video of a piece of paper on which she writes. This brings back memories. Before I used Camtasia, all my recordings were done in MediaSite. The main reasons for moving to a Camtasia/TabletPC platform were being able to record in any classroom with a projector and the difficulty in getting high enough frame capture rates for rapid drawing with MediaSite. Also it seems that the links on that site don't work on Firefox. Thanks to the Chronicle for the link.

2) Robert Burk teaches Chemistry 101 at Carleton University. He is podcasting the video of his lectures using 2 video cameras controlled by himself or an assistant. A downside of this approach is the huge files for each 3 hour lecture. Thanks to Mark Ott for the link.

3) Justin Gallivan teaches Biochemistry at Emory University. He puts out a podcast enhanced with pictures of the board taken by a teaching assistant. Thanks to Dan Karleen for the link.

Sunday, December 04, 2005

Drexel ethics blog

Marti Smith teaches Information Ethics at Drexel and keeps an interesting blog detailing her projects and upcoming class in the winter term INFO679.

She gets extra points from me for listing cats as an interest in her profile :)

Friday, December 02, 2005

more on open source science

As I mentioned previously, I started an open source science blog to plan and execute on applied chemistry projects. A few problems were brought up, including specific issues involving arsenic in drinking water, malaria and HIV.

During the past week, I am happy to report that several people (mainly from the find-a-drug folks) have offered to help and one Russian programmer has written and posted useful code to process chemical information from Chemsketch. I have created a separate blog to collect information we will need (such as commercial availability and price) about specific molecules necessary for the synthesis of the anti-malaria candidates initially. We are getting close to getting the syntheses started.

I was also happy to find that open source science is getting more press. Read this Nature article for example.

Thursday, December 01, 2005

Philadelphia Area Educational Technology Conference

Here is a call for presentations for a regional conference that I am helping organize with Laura Blankenship, Sharon Strauss, Jeff White and Ben Johnston.

Philadelphia Area Educational Technology Conference
"Teaching the Millenials"
February 22, 2006
Haverford College
Haverford, PA

Bryn Mawr College, Drexel University, and Haverford College are organizing a Philadelphia area Educational Technology Conference to be held February 22 at Haverford College. We invite you to submit proposals for presentations and poster sessions. We will have several formats for the presentations. Some will be standard 15-20 minute per presenter panel sessions, but we would also like to see suggestions for shorter presentations with more time for discussion and perhaps longer presenations of 30 minutes or more. In addition, we will have a poster session. When submitting your proposal, please let us know what format you'd prefer. We also welcome submissions of entire panels. Some suggested topics include the following:

* Where are we going? What's new in ed tech?
* Web 2.0
* RSS, Blogs and Wikis
* Podcasting/Screencasting
* What are our future students like?
* What are area (or national) K-12 schools doing in terms of technology
and what does that mean for us?
* Technology Literacy/Fluency
* Video Games in Education
* The impact of sites like Facebook and MySpace

Please provide a brief description of your presentation and the type of format you think it would be best suited to. Deadline for submissions is January 9, 2006.

Please email submissions to lblanken@brynmawr.edu.

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