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Chemistry Wide Open

Chemistry in Second Life Article

Chemistry
1
peers

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. It was around this time that Horace Moody, the avatar of a real-life chemist at Drexel University named Jean-Claude Bradley, came to the rescue and offered to teleport me to Drexel Island. Horace has been experimenting with Second Life as a way to teach undergraduate organic chemistry, a topic he says can definitely benefit from 3-D visualization. Several of his students have met on Drexel Island to challenge each other's organic know-how by touching an obelisk, which then flashes a sequence of quiz questions on Newman projections and Lewis dot structures.

Storing and Finding Molecules on the Open Web with InChIs

Chemistry
1
peers

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. However, Rich makes the valid point that these pages do not always point to the experiments where they are used.

I was aware of the limitations of using a blog to track molecules when I set it up. Because we were limiting ourselves to a few hundred molecules, the blog served its purpose much as I expected it would.

But now, as we move to the manipulation of tens of thousands (and soon to millions) of molecules, we need to transition to a true database.

Nature Precedings Follow-Up

Science & Society
0
peers

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 two).

It took a lot longer to do this than I expected, experimenting with the format and trying to make it fairly self-contained. I ended up using Powerpoint, which I like for its modular nature and flexibility with image-rich materials. For example, it is easy to spin off as a SlideShare document (which I just noticed supports hyperlinks while embedded - nice!).

Nature Precedings

Science & Society
3
peers

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. Here is a description of Nature Precedings:

will enable researchers to share, discuss and cite their early findings. It provides a lightly moderated and relatively informal channel for scientists to disseminate information, especially recent experimental results and emerging conclusions. In this sense, it is designed to complement traditional peer-reviewed journals, allowing researchers to make informal communications such as conference papers or presentations more widely available and enabling them to be formally cited. This, in turn, allows them to solicit community feedback and establish priority over their results or ideas.

Thesis on a Wiki - More to Come?

Science & Society
3
peers

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, A Blog around the Clock and Pimm - Partial Immortalization.

City of Pods

Science & Society
6
peers

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. The chemistry pod has a list of recent student awards, some images of our equipment and a 3D Bunsen burner and molecule.

The faculty pods are arranged like leaves hovering above the departmental base pods. There are plenty of spaces that we'll populate as we get more faculty involved. For my pod, I have my picture, a link to my organic chemistry class wiki, my research wiki and an example of a quiz obelisk. Other pods have desks. I think that this would be a nice arrangement for virtual open houses where prospective students could visit a few professors from each department in their pods.

Organic Chemistry Lectures on Second Life

Chemistry
4
peers

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.

Chemistry on Drexel Island

Chemistry
3
peers

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.

Science Foo Camp 07

Science & Society
6
peers

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.

Five Blogs That Make Me Think

Science & Society
5
peers

Hari Jayaram just listed my blog as one that makes him think. Keeping the meme going, I'll list 5 that have had an impact on me.

Nature Island Review

Physical Science
3
peers

Joanna Scott just wrote a nice little review of what is going on at Nature Island (slurl) on Nature's Nascent blog since her return from the American Chemical Society meeting in Chicago.

Assignment Zero

Physical Science
4
peers

Fans of Open Source Science (or just the open source concept in general) should take a look at Assignment Zero. Jay Rosen writes on the About page:

Inspired by the open-source movement, this is an attempt to bring journalists together with people in the public who can help cover a story. It's a collaboration among NewAssignment.Net, Wired, and those who choose to participate.

First Compound Submitted to DTP-NCI

Physical Science
1
peers

As I mentioned earlier, we were interested in getting our compounds screened by the Developmental Therapeutics Program (DTP) at the National Cancer Institute. The first entry is now done and from what I understand it will be 8-10 business days before we get a request for the compound after they check for uniqueness.

Social Software in Chemical Education Article

Chemistry
10
peers

The April 23, 2007 Chemistry and Engineering News article on the Social Software in Education symposium at the American Chemical Society spring meeting in Chicago has come out. I gave a talk there on using blogs and wikis to teach organic chemistry.

NCI - UsefulChem Open Science Link

Chemistry
2
peers

Earlier this week, I was contacted by Daniel Zaharevitz, Chief of the Information Technology Branch of the Developmental Therapeutics Program at the National Cancer Institute. He is also involved with the NIH Roadmap Molecular Libraries Initiative. We had a very interesting talk about Open Science and what kind of further impact it could have in drug development. Lets just say that we are on the same page on this issue and I'm really impressed with what Dan is trying to achieve.

Edison Predicted Educational Podcasting?

Science & Society
3
peers

I often find that books on the history of science and technology are fun to read because they give me an opportunity to try to forget what I know about how things turned out and piece together an older worldview.

Getting the Hang of Quizzes in Second Life

Physical Science
2
peers

We just ran a quiz race in Second Life for the second time yesterday in my organic chemistry class. Two of the students were physically with me in the classroom and two were coming in remotely.

Scooped by a Blog

Science & Society
10
peers

The Scientist printed an article on the blogging of scientific data, with a focus on Reed Cartwright's inclusion as a co-author on a paper because of ideas that he shared on his blog. This is an impressive example of how social software can serve as a primary information source in science (whether intentionally or not).

Molecules on Second Life

Chemistry
5
peers

Thanks to Joanna Scott, we've been taking advantage of our invitation to contribute to the Nature island on Second Life. Beth made a copy of the Open Notebook Science building and created a cemetery filled with blue obelisks so that multiple students can take organic chemistry quizzes at the same time. I'll be testing that shortly in my class to see how many students can comfortably compete in a virtual race.

Searching for Molecules with ChemSpider

Chemistry
5
peers

There is a new kid on the cheminformatics block.

ChemSpider Beta went live on Saturday March 24, 2007 with over 10 million compounds. Anyone using other free online molecular databases (like eMolecules or Chemistry Search Lookup Service) should definitely give this one a spin.

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Science Pick-Up Lines

- Oooh, your IQ is 145? I like 'em beautiful and dumb!

- By looking at you I can tell you're 36-25-36 which, by the way, are all perfect squares.

- According to the second law of thermodynamics, you're supposed to share your hotness with me.

- I wish I was your differential, because then I'd be touching all your curves.

- But enough about me, let's talk about mu.

- What say we skip this nerd-fest and hit an all-night symposium on Euclidean Geometry?