Back from ACS San Francisco Meeting 2010

Last week I co-hosted a symposium with Noel O'Boyle and Andrew Lang on "Visual Analysis of Chemical Data" at the American Chemical Society meeting in San Francisco (March 22-23, 2010). The ACS recorded almost every talk in our symposium and I'll provide the link here when available (they tell me mid April).

Liz Dorland kicked off the symposium with a great keynote presentation covering effective visualization in a number of fields and the special challenges faced in chemistry. There were several talks about QSAR and I particularly enjoyed Edmund Chapness who incorporated the visualization of confidence in predictions with an intuitive colored molecule map. Geoff Hutchison gave an informative overview of Avogadro.

Perhaps the biggest revelation was the "iTunes for Cheminformatics" project by NIH researcher Ajit Jadhav (leading the team which includes Rajarshi Guha). The alpha version will be available for testing on April 5, 2010 and many of us are eagerly anticipating being able to give it a spin. From what I understand the system will automatically be able to identify scaffolds (fragments) in a collection of molecules and make it easy to search for and filter assay results.

Carmen Drahl covered in minute by minute detail announcements about new drug candidates on Twitter. Following the FriendFeed feed for the conference flagged a very interesting post about a Cold Fusion Symposium that was being held. In spite of the notorious lack of wireless availability at ACS conferences, attendees seem to be making due with accessing their social networks via their cell phone devices.

Andrew Lang and I spoke about Visualizing Chemistry in Second Life - our slides are here - hopefully I'll be able to post the recordings as well soon.

Visualizing Chemistry in Second Life ACS SP2010

View more presentations from Jean-Claude Bradley.

Spectral Game paper live on the Journal of Cheminformatics

Our paper on the Spectral Game is now published:

Jean-Claude Bradley, Robert J Lancashire, Andrew SID Lang and Antony J Williams The Spectral Game: leveraging Open Data and crowdsourcing for education Journal of Cheminformatics 2009, 1:9 doi:10.1186/1758-2946-1-9

This has been an especially gratifying collaboration because of the enthusiasm and vision of my co-authors. The philosophy behind the game is deeply rooted in openness and as a result it is an open ended evolving project. Any new NMR spectra uploaded to ChemSpider and marked as Open Data will continue to be automatically incorporated into the pool of problems. Teachers and students from around the world can play the game and flag problems or errors as they arise. This blurs the line between content creators and consumers and I think reflects a powerful trend that is occurring in education.

Another aspect of openness relating to this endeavor is the communication of our progress. Our paper was written on a public wiki. Not only were we able to discuss our progress on recorded talks and blog posts, but we were also able to cite these as regular references in the paper. And of course the Journal of Cheminformatics is itself an Open Access peer-reviewed publication so there is no limitation to sharing the final product.

Controversy still rages in the blogosphere about the wisdom of blogging research results prior to publication in peer-reviewed journals. It is true that this practice limits where articles can be submitted. Since many of our references are from the Journal of Chemical Education, we contacted the editors to see if they would accept our paper. Unfortunately their current pre-print policy did not allow them to do so.

If more authors begin to see the value of early disclosure it may just start to tip the balance towards journals such as the Journal of Cheminformatics.

Andrew Lang and I have just completed another paper on Chemistry in Second Life - written in the same way - that one just got submitted to Chemistry Central Journal.

ONS Solubility Challenge in Teaching Lab

Last year Brent Friesen started to experiment with using his organic chemistry teaching lab at Dominican University to carry out new reactions in the pursuit of making new anti-malarial agents, as part of the UsefulChem project.

This year, Brent is involving his class in the Open Notebook Science Challenge to measure the solubility of a variety of organic compounds in non-aqueous solvents (CHEM254). He took the time to write up a comprehensive laboratory handout on the topic so I'm hopeful that this exercise will go smoothly.

As we've discussed repeatedly during the past year the potential for university teaching labs to contribute real new science while training students is immense. It only requires instructors like Brent to take the time to make appropriate changes in the curriculum.

The lab is scheduled to run Jan 21-23, 2009.

Journal of Cheminformatics

Set to come out within the next few months, the Journal of Cheminformatics has it all for the Open Access hungry mob:

Editor-in-Chief
Dr David J Wild, Assistant Professor of Informatics at Indiana University, USA

Chemistry Central announces the imminent launch of the Journal of Cheminformatics.

The Journal of Cheminformatics is devoted to the dissemination of new and original knowledge in all branches of cheminformatics and molecular modelling including:

• chemical information systems, software and databases, and molecular modelling
• chemical structure representations and their use in structure, substructure, and similarity searching of chemical substance and chemical reaction databases
• computer and molecular graphics, computer-aided molecular design, expert systems, QSAR, and data mining techniques

Chemistry Central publishes peer-reviewed open access research in chemistry.

All research articles published by Chemistry Central are made freely and permanently accessible online immediately upon publication to ensure effective communication of research findings.

High standards are maintained through full and stringent peer review.

Authors who publish original research in Chemistry Central retain copyright over their work.

Chemistry Central is an independent publishing service operated by BioMed Central - the leading life science open access publisher.

Chemistry Tenure-Track Position 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.

Older Males Prefer NMR of Ester

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.

Chemical Heritage Foundation Talk on Second Life

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.