Visualizing Chemistry in Second Life ACS Talk Recording

The American Chemical Society has processed the recording of the talk that Andrew Lang and I gave at the Spring 2010 ACS meeting in San Francisco on March 23, 2010:
Visualizing Chemistry in Second Life

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.

Leveraging Transparency and Crowdsourcing in Chemistry Using Open Notebook Science

View more presentations from Jean-Claude Bradley.

Wendy Warr report on ONS from Fall 08 ACS meeting

Wendy Warr has provided a thorough report from the Fall 2008 American Chemical Society meeting in Philadelphia. My talk "Processing drug discovery raw data collaboratively and openly using Open Notebook Science" is summarized on p.10 as part of a special extract of talks and companies.

Wendy has covered a lot of material related to cheminformatics in the full report and is worth looking over if you missed the conference.

The Fall 2008 ACS meeting ends

It is always nice for a major conference to happen on home turf. Last week the American Chemical Society held its fall meeting in Philadelphia.

I finally got to meet my Second Life collaborator Andrew Lang during our first talk on Monday August 18, 2008. We presented on what is now possible to do for chemistry in Second Life. There are now several easy to use tools for chemistry and molecular biology. For example, Andy has created a tool to display protein surfaces using a lightweight sculpted prim from a PDB file. Take a look at the slides from the presentation for a quick overview.


I gave another talk on Monday about Second Life and Social Media: Networking Goldmine or Time Sink? It was a nice opportunity for me to talk about major success stories (Bora Zivkovic, Beth Ritter-Guth and Deepak Singh) as well as specific examples from my own experience. Sandy Adam from Sigma-Aldrich and Andy Lang contributed their own stories at the end. The take home message was that if you treat these platforms as a means of participating with your scientific community you're likely to get out of it more than you put in.

On Wednesday I spoke about Open Notebook Science and the value of raw data in drug discovery. The timing was perfect, since I had just finished analyzing the correlation of our docking predictions with biological assays against falcipain-2 and Plasmodium falciparum. (data here)

Back from Spring08 ACS

The American Chemical Society meeting in New Orleans proved to be as hectic as usual. I didn't get to spend as much time with everyone I was hoping to touch base with but I did get some useful things done:

1) I presented on the use of Cheminformatics in Open Notebook Science and Teaching Chemistry with Second Life. Since the ACS oral sessions are so short (15-20 mins before questions) this is a good opportunity to get our work recorded in a concise format. Speakers like to complain that they need a full hour to do justice to their elaborate projects but the shorter format seems to match the attention span of most attendees.

2) The Sci-Mix session on Monday was very hectic. I presented two posters related to my talks and helped out with the opening of the poster session on ACS island. We had 20 posters in Second Life and it was great to finally meet a few of the presenters and the organizer Kate Sellar (Finola Graves) in person. Kate was running Second Life on a large screen right at the poster entrance and giving out t-shirts. Andy Lang (Hiro Sheridan) was also helping out remotely from within Second Life. By all accounts it was well received. The posters will remain up on ACS island for the next few months and it will be possible to contact presenters via bells next to their posters.

3) I also finally met several people that I have known only virtually for some time: Rajarshi Guha, David Wild, Rich Apodaca, Noel O'Boyle and Warren DeLano. Rajarshi, Rich, Noel, Warren, Geoff Hutchison and I went out for the Blue Obelisk dinner on Tuesday night.

4) I had a good brainstorming session with Rajarshi about representing experimental workflows in XML. He suggested using Taverna to create "null" workflows - since our lab experiments are physical rather than executing code. Noel suggested using Knime. The idea is to represent experimental steps leading to a result in a standard machine readable (and thus minable) format. We're going to start very simply by limiting the workflow space to Ugi reactions.