Thursday, October 29, 2009

Chemistry in Second Life paper in Chemistry Central Journal

Andrew Lang and I just published a review article on the chemistry content in Second Life:
Andrew SID Lang and Jean-Claude Bradley Chemistry in Second Life, Chemistry Central Journal 2009, 3:14.
This review will focus on the current level on chemistry research, education, and visualization possible within the multi-user virtual environment of Second Life. We discuss how Second Life has been used as a platform for the interactive and collaborative visualization of data from molecules and proteins to spectra and experimental data. We then review how these visualizations can be scripted for immersive educational activities and real-life collaborative research. We also discuss the benefits of the social networking affordances of Second Life for both chemists and chemistry students.
This is gratifying on many levels:

1. Andy and I met in Second Life a few years ago and it is fitting that we should finally have a paper highlighting our collaboration and the work of others doing chemistry in Second Life. In fact, our meeting and the resulting projects both inside and outside of Second Life is listed under the networking section of this paper.

2. We found a very appropriate Open Access journal to publish this work. We wanted this review to offer concrete examples of what can be done with chemistry in Second Life and it is loaded with images to illustrate as clearly as possible what these options look like.

Even though it has many educational components we did not want to submit it to a "chemical education" journal. Generally these types of journals require framing the work within a pedagogical theory. We have been through prolonged debates with reviewers around this issue on other papers and did not want to repeat the experience. There is an expectation in some circles that progress in education can only come about when built within the context of testable theories. At least the scope of many educational journals is tied to this viewpoint - and that is absolutely appropriate.

But it is interesting that we have had to rewrite sections of papers - not because the content was incorrect in any way - but because it did not conform to a conceptual format. It makes me realize how much scientific discourse is directed by the expectation of editors and reviewers, when the authors themselves might have preferred to present their content differently.

3. There is lots of useful content that is never published in peer-reviewed publications because it does not fit the mold. The example above fits in the category of describing tools without evaluating them in some quantitative way. So the third point of gratification is that we managed to zip up a number of small developments that might be useful to someone but by themselves were not the right size and shape to publish in the peer-reviewed system. This included the ChemTiles game and the EduFrag project, initiatives that were converted to or from a Second Life format.

Of course, the mechanism of using a review to assemble such content can't be used very often.

In the experimental sciences there are two other types of useful content that are difficult to publish formally: "failed" experiments and lab techniques. I've repeatedly discussed the importance of sharing the results of experiments with disappointing results as a strong motivation behind Open Notebook Science.

But just as important are the details of laboratory techniques - completely separate from the results they provide. In our lab, the measurement of solubility has proven to be far from trivial and we have reported several pitfalls, as well as some techniques which I think could save others much wasted effort.

When I was a graduate student at the University of Ottawa I found a way of visualizing column chromatography that I thought could be helpful to others in speeding up separations. The only mechanism available back in 1992 for wide dissemination of chemical information was peer-reviewed publication so that is what I did (Tet. Lett. 33(50) 7733).

In order to publish using that channel I had to format my communication accordingly. Instead of just reporting on the method (use a quartz column and an insoluble fluorescent agent mixed with silica gel), I had to evaluate the method systematically testing different solvents, stationary phases and specifications. It was a hassle and completely unnecessary to simply share the technique.

If I were doing this today I would just blog about it and record the details in my open notebook as I was experimenting with the technique. There is a good chance that someone else would have given me useful tips as well.

As it turned out, the feedback I did receive was a letter from a chemist who had been using the technique for many years. His use escaped our literature search because it only appeared in the experimental sections and thus did not show up on keyword searches - keep in mind this was before the era of computerized searching - and none of the reviewers knew about it either.

We published a Corrigendum accordingly and that was the full extent of the public scientific discourse. By any standard the new communication tools we have today are far more versatile for quickly and easily communicating this type of information.

4. Once again (here and here), we had no trouble using blog posts and wiki pages as references. The key consideration is: what is the most relevant document to link to. If you are blogging your work it is likely that blog posts will be the only citable option in many cases. In this instance we also wrote the article on a public wiki page, which limited our selection of peer-reviewed journals to those that allowed pre-prints.

I don't know how many journals that don't allow pre-prints would take articles that are based substantially on work that has appeared in public blogs and wikis. Since the article would require re-integration and re-writing of the work there wouldn't be any copyright issues.

Tuesday, October 20, 2009

Fourth Cheminfo Retrieval class: ChemSpider and Beilstein Databases

Peggy Dominy, our chemistry librarian at Drexel, was kind enough to teach my third class while I was at NERM. She demonstrated RefWorks - including how to copy and paste the proper formats to Wikispaces - and how to use our ILL (Inter-Library Loan) process.

I'm including a recording of the fourth class on Chemical Information Retrieval on Oct 15, 2009 at Drexel University. It starts with some tips on removing formatting from Wikispaces pages, the Drexel Cisco VPN client for accessing paid subscriptions off campus and how to link to a DOI. The first two assignments for the class are then described. The first involves summarizing each paragraph of an article and an option to use AcaWiki is demonstrated. The second involves filling in an FAQ for publishing in chemistry. FriendFeed is then presented as a resource to help answer questions followed by an extensive overview of available information on ChemSpider, covering SMILES, InChIs, InChIKeys, experimental and predicted properties, linked databases and contributed spectra. Finally a demonstration of Beilstein Crossfire/DiscoveryGate is presented with an emphasis on doing substructure searching.

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Monday, October 19, 2009

Interactive 3D Visualisations of Biological Molecules Integrated into the Scholarly Literature

The embargo has now been lifted on the announcement from PLoS ONE - partially reproduced here:
On October 20th 2009, PLoS ONE will feature an impressive new 3D molecular animation technology on five newly published articles. This represents the start of a new PLoS ONE collection entitled “Structural Biology and Human Health: Medically Relevant Proteins from the SGC” (also known as the ‘Structural Genomics Consortium’).

These peer-reviewed articles, which include some of the research highlights from the SGC, describe new protein structures, including a protein involved in the survival and proliferation of cancer cells, a protein associated with hereditary paraplegia, and a protein involved in degrading foreign compounds and pollutants in the body.

Readers of these enhanced articles will first need to download a free plug-in for their browser but will then be able to click on hyperlinked text within the article to ‘fly’ to the relevant position within the molecule, and to then interact with it at will (by zooming, rotating and exploring). The functionality, whereby the text of an academic article is tightly integrated with an animated and interactive molecular structure, provides an entirely new and enhanced experience with a significant “wow” factor.
The first enhanced articles are available here. I've been trying to evaluate these but I'm having trouble downloading the required plug-in: it is very slow and has just stalled on me. Maybe the problem is on my side so I'm asking the community to give these a spin and report. I am especially curious about the comparison with Jmol. This particular plug-in does not use Java at all from what I can glean from the press release.

Notwithstanding these probably temporary issues I think this is a very exciting development for scientific publication in the life sciences.

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Thursday, October 15, 2009

NERM 09 session on Chemistry on the Web

Last week, on October 9, 2009 I presented at the ACS NERM conference. Martin Walker hosted a session on Publishing and Promoting Chemistry in the Internet Age. All of the talks were quite interesting and fit perfectly with the topic:
Martin Walker Chemistry on the Internet
Elizabeth Brown The Chemist's Toolkit for Publishing and Promoting Your Work On the Internet
Antony Williams Navigating the Complex Web of Chemistry Using ChemSpider
Jean-Claude Bradley Leveraging Transparency and Crowdsourcing in Chemistry Using Open Notebook Science
My talk consisted of an overview of Open Notebook Science with some new content on solubility prediction algorithms written by Andrew Lang and a few example of students taking a Chemical Information Retrieval class at Drexel University using research logs on a wiki to flesh out their projects.

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Tuesday, October 06, 2009

Second ChemInfo Retrieval Class

We had our second class on Chemical Information Retrieval on October 1, 2009 (see screencast here). I spent some time on technical aspects of Wikispaces then introduced topics relating to publishing in chemistry - and science in general. This included primary and secondary/tertiary sources, Open Access, copyright and Web2.0. The associated wiki page is currently just an outline and will get filled with details as students do assignments.

The student projects are coming along nicely. They have been recording the progress of their research on log pages, which I'm finding useful to give feedback. Among the interesting projects being fleshed out are green tea, DMT and trace amine receptors, caffeine, cytochrome C and liposome binding, beer and the psychoactive ingredients in chocolate. I love classes where the instructor learns as much as the students!

If anyone has suggestions for good information sources on these topics please feel free to leave comments.

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Monday, October 05, 2009

Chemistry MiniSymposium FA09: Bradley Lab

Every fall the faculty in the chemistry department at Drexel present the ongoing work in their lab, mainly for the benefit of the new students. The challenge is to fit a meaningful overview in a 15 minute slot. I think this is a useful exercise and it gives me a recording I can use for more general audiences that matches most people's attention span.

My talk was entitled "The synthesis of Anti-Malarial Compounds using the Ugi reaction and Collaboration using Social Software". The NaH oxidation story is a perfect way to introduce the application of Web2.0 tools to current research.

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