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Tuesday, January 12, 2010

Post-Mortem of Cheminfo Retrieval class FA09

In the fall of 2009 I taught Chemical Information Retrieval at Drexel as sole instructor for the first time. Last year Kevin Owens showed me ropes by co-teaching it with me. Here are some things I learned over the term:

1) Research Logs work. In analogy to the Open Notebook Science approach I use in my research lab, I wondered if there was some benefit to having students keep a log of what they were doing to research the topic for their paper in chemistry. That way, using the wiki I could comment in bracketed bold text to either answer a question directly or make suggestions for which resources or directions might be fruitful. (see example) This certainly did not replace the weekly face to face interaction but it was useful for the days we did not meet.

An unintended benefit of this is that as soon as students starting keeping a log our Sitemeter would show hits from Google searches that were effectively answered by even the limited content already there, with links to relevant papers. Even though as scientists we are trained to only expose our final comprehensive work to the public, the reality is that most people are looking for very specific information that does not require a massive compilation to answer.

2) Student generated content can work. I wanted for the class to cover the absolute latest developments in chemical information retrieval so I experimented by creating an FAQ of questions on hot topics of the day, many of which I didn't know the answer to. The students were assigned to answer one question each -and even suggest a new question if desired. I think this worked even better than I imagined, although it did take a significant amount of time for me to iteratively give feedback by pointing out inconsistencies with the information in cited sources or suggesting additional documents to research to properly address the questions. After the due date for the FAQ assignment, I did complete a few answers myself since this the final exam was based on this content.

In another assignment the students had to find 5 different sources for 5 experimental properties of compounds of their choice. A major objective of this was to make students appreciate how difficult it is to find reliable data - even with access to the best commercial databases. But as an additional benefit, these aggregated results provided valuable information to the chemistry community about the state of online chemistry information today. It can serve as a benchmark to compare in the coming years to see if things are getting better or worse. Some of the results even uncovered errors that were corrected in ChemSpider and CAS. For extra credit, Tony Williams provided some particularly difficult stereochemical incorrect assignments in ChemSpider and two students provided solutions that were corrected in the database.

3) Students are shy. Some of the FAQ questions were tricky to research because they involved very recent issues that might not yet have been covered in traditional journal articles. I suggested contacting librarians, authors or editors either directly or via social networking sites but most students were reluctant to do so, even if it meant saving a lot of research time. An example of a tricky question is the current ACS policy on self-archiving. It was difficult to find a complete answer just searching the web while a quick post on FriendFeed gave me the information I was looking for with the appropriate reference (by way of Dorothea Salo and Graham Steel).

Thinking back to my own mindset as an undergraduate I can certainly identify with my students' reluctance to interact. But over time I am becoming even more convinced that this skill is one of the most important for future success in science. This is especially true in world where the barrier for communication is as low as it is diverse. There are individuals whom I have come to know and respect on social networking sites. In some cases I was shocked to discover much later on that these were graduate students when I had assumed that they were established professionals - or at least postdocs. I have come to know many of them well enough to be able to write strong and detailed letters of recommendation. (In some rare cases as well I was surprised to learn that some particularly immature individuals were actually faculty.)

I don't know how much of this type of productive participation in scientific networks can be learned. Even if there is a personality trait that predisposes someone to take naturally to it, certainly a proper etiquette and ways of finding specific networking platforms and groups can be taught. It is in this spirit that I have assigned my students in previous terms (and my current course) assignments to interview and interact with scientists on FriendFeed and Second Life - and this term at a student's suggestion we'll try FaceBook. I don't feel comfortable making this mandatory but I do think that students who take advantage of this opportunity stand to gain a significant competitive edge over their classmates if they continue to make use of these resources.

4) Privacy not popular. Students were asked to write their assignments on a public wiki. I always want to be sensitive to the fact that some students may not want their names to be associated with work that is open. As I always do I gave students the option of using their real names, initials or pseudonyms. All but one chose to use their real names. This seems a little counter-intuitive given their reluctance to participate in social networks.

With public work the instructor has to be careful about providing feedback. Although I did point out simple errors or discrepancies and make suggestions online, I made more critical comments in private either by email or in person. In the end I think the students can be proud of the work that they accomplished. A month after the course ended the wiki still gets about a dozen hits a day from around the world.

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Wednesday, January 06, 2010

VLC saves the day - iTunes RIP

My first organic chemistry class (CHEM242) took place on Monday. That was the introductory lecture where I explained how my online-optional class works. The fundamental building blocks of this course are my recorded lectures.

That's why it was a particularly unpleasant experience to find that my m4v files just played static to my understandably skeptical audience. I had never had this problem before. I tried re-installing iTunes but neither that nor the simple QuickTime player worked. Some of my students were able to view the files ok through iTunes so it must be some configuration issue with my laptop.

I was expecting the worst at this morning's workshop when a student suggested using VLC. Not only did it work but I could swear the resolution was far better than when viewing on iTunes.

The fact that VLC is Open Source is very exciting. That should make it easier for developers to create OS educational multimedia applications.

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