Chemistry Wide Open

Heather Piwowar has collected an impressive set of notes on Open Notebook Science. From her blog post:

In anticipation of the ISMB BoF session on Open Notebook Science (ONS),I’m trying to come up to speed on ONS discourse. In between ISMBsessions, I’ve started consolidating snippets of blogposts and articles discussing ONS into a single document (in the open here).

This post provides an update of our CombiUgi project. From a larger perspective I think that this can be useful to people interested in how collaborative Open Science actually works.

For those who have not been following the progress of the CombiUgi project on our mailing list, here is a brief update.

The basic idea is to generate libraries of compounds that can be made quickly in the lab. The compounds in these virtual libraries are then prioritized according to potential usefulness (anti-malaria, anti-tumor, etc.).

As I've recently commented, there has been media interest in the use of the virtual online world Second Life for chemistry. We also recently demonstrated on Drexel Island that it was possible to visualize molecular docking using the molecular rezzer developed by Andrew Lang.

Nature Island also hosts several common molecules, including buckyballs.

Sarah Everts from Chemical and Engineering News has just published an article about chemistry activities in Second Life. Drexel Island got a mention:
My avatar was then deposited at a place in Second Life called Orientation Island. As I walked my avatar into a geodesic information dome, I happened to notice the "Fly" button. Intrigued, I wasted no time pressing it—and I shot up into the air, hitting the ceiling of the information dome like a clumsy goth-bird.

Rich Apodaca wrote about using his InChIMatic service to track molecules in UsefulChem.

Because we use InChIs in blog posts and HTML pages generated automatically from the molecules blog, doing an InChI search in Google is a pretty good way to find molecules of interest to UsefulChem.

Following up on my initial comments, my first two posts in Nature Precedings have appeared.

Most people have been posting Powerpoint presentations so I started there with a recent presentation at the American Chemical Society about Open Notebook Science.

Open Notebook Science Using Blogs and Wikis (doi:10.1038/npre.2007.39.1)

Next, I posted an update on the CombiUgi project by basically combining two blog posts (one and

Egon has just posted about Nature Precedings, which looks like a no-brainer as an additional publication outlet for UsefulChem. I've requested an account and we'll see how it works.

In my view, producing knowledge in a Science 2.0 world is about communicating through redundancy, making it easy to prove who-knew-what-when. That is difficult to do with the traditional scientific publication system of giving away copyright. (Not impossible, because concepts and results can be rewritten using different words, but still difficult).

This should be interesting.

There was quite a spike in our traffic to UsefulChem today.

The fact that Alicia's masters thesis "Synthesis of Diketopiperazines, Possible Malaria Enoyl Reducatase Inhibitors Using Open Source Science" is being written on a wiki was noted by Pharyngula,

This has been a productive week with setting up Drexel Island on Second Life. We have settled on a pod tree structure to house departments and faculty in the College of Arts and Sciences. Eloise helped with the pods and Beth and I selected most of the content.

We met with the librarians today and Beth gave them movie screens that play on Second Life. I also got to put a few of my lectures from CHEM241, introductory organic chemistry in the chemistry area.

Since I already have a blog used for vodcasting with files in m4v format, all I had to do is put links to those files in Second Life. The screen is placed between the quiz obelisks on the left and the UsefulChem project on the right.

Based on a suggestion by Beth and a rapid implementation by Eloise, the terrain of Drexel Island on Second Life is now shaped like the Drexel dragon mascot. That makes it pretty convenient to specify where things are located.

I started with the dragon's head to create a little section for the chemistry department, showing a picture of our building and adding some info as a note attached to the image.

I just got an invitation to attend Science Foo Camp in August 07, a unique meeting organized by Nature, O'Reilly and Google. Based on what I heard from last year's attendees this will be an amazing opportunity to bounce ideas around.

I'd like to hear more from others who are going or who attended last year.
As before, we will be inviting around 200 people who are doing particularly interesting work in a wide range of scientific disciplines, as well as in areas of technology and culture that influence, and are influenced by, science. The aim is to encourage cross-fertilization of ideas, creating a unique opportunity to explore topics that transcend traditional boundaries.