Sunday, April 29, 2007

Blogs That Make Me Think

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.

1. Beth's Second Life Beth Ritter-Guth has been a huge inspiration for me and she is the main reason I pulled the trigger on getting involved with Second Life for my teaching and research. We have collaborated on many other projects involving social software and new approaches to education - Google her name for many more goodies.

2. Chem-bla-ics Egon Willighagen has been instrumental to the cheminformatics community. From the description on his blog: "chemblaics only uses open source software, making experimental results reproducable and validatable". What I like about his blog is that he posts or links to real usable code (like chemistry enhancing GreaseMonkey scripts) or implements simple but powerful tools that can be used immediately (like making Chemical Blogspace more semantically aware).

3. Peter Murray-Rust's blog - Peter is a pioneer of cheminformatics, including the creation of Chemical Markup Language (CML) with Henry Rzepa. For anyone working in any area of cheminformatics and Open Chemistry, his blog is indispensable.

4. Open Reading Frame Bill Hooker is one of the strongest champions of Open Science that I know and has written probably the most comprehensive series of articles on the topic that I have seen.

5. business/bytes/genes/molecules
Deepak Singh tends to write about stuff that interests me. Although there are many bioinformatics blogs out there, most of them don't have a high enough signal to noise ratio to make it to my most frequently checked list.

I didn't include several other blogs that I also follow closely - I'll add these to my blogroll shortly (which I have been meaning to do for a while).

Instructions for the next group, copied from Hari's post:

(1) If, and only if, you get tagged, write a post with links to 5 blogs that make you think; (2) Link to this post so that people can easily find the exact origin of the meme; and (3) Optional: Proudly display the ‘Thinking Blogger Award’ with a link to the post that you wrote.

Saturday, April 28, 2007

Nature Island Review

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.

The Blue Obelisk Cemetery, where I give my students quiz races on Fridays was featured (only possible through help from Beth and Eloise - thanks again!). Another fun place is Mary Anne Clark's biological cell that you can enter and float amongst the mitochondria.

Nature Island has really become a very interesting place to hang out, meet smart people and learn and share.

Assignment Zero and Open Source Science

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.

The investigation takes place in the open, not behind newsroom walls. Participation is voluntary; contributors are welcome from across the Web. The people getting, telling and vetting the story are a mix of professional journalists and members of the public -- also known as citizen journalists. This is a model I describe as "pro-am."

The "ams" are simply people getting together on their own time to contribute to a project in journalism that for their own reasons they support. The "pros" are journalists guiding and editing the story, setting standards, overseeing fact-checking, and publishing a final version.
There is a page for crowdsourcing science, where I added some info about Open Source Chemistry. The existing info on that page is pretty sparse - maybe Bill Hooker can pick out a few gems from his comprehensive reports on Open Science in 3QuarksDaily.

The site functions like a wiki in that information from anyone is sought but it looks like only an editor can include the contributions in the main content pages. There is no edit button - in order to submit you have to find an existing open item and respond to it, just like in a forum.

The final article will be published in Wired magazine.

More info about crowdsourcing from Jeff Howe

Tuesday, April 24, 2007

First DTP-NCI Compound Submission

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.

This is good timing because it really is time to gather up all of the isolated and characterized compounds in UsefulChem on one page, which is now linked on the left navigation bar on the wiki. This page should also be used by other people interested in screening who want to quickly see what we have on hand. Right now we have a few boc protected and deprotected Ugi products, and these will be added to the page shortly.

Dan has also joined the wiki and created a page to detail the DTP-NCI process. He is inviting us to comment on the process there to understand and improve it.

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Funding UsefulChem

I have talked to a number of people lately about funding sources for UsefulChem. I have also been working with our Institutional Advancement Office at Drexel to contact appropriate foundations. At this point it probably makes sense to put my proposal summary sheet on the blog to get some additional suggestions. Also please forward to anyone who might be interested.

UsefulChem and Open Notebook Science Proposal Summary
contact: Jean-Claude Bradley (

The communication of scientific information is undergoing a substantial shift towards openness. There is much discussion about providing Open Access (OA) to journal articles and several publishers are providing an OA option for authors willing to pay for the publication costs. A few publishers are even supporting free access for both authors and readers.

As another step towards a more open system, some forms of open peer review are undergoing experimentation. In one trial, some Nature article submissions were posted for review by the community at large first then submitted for standard peer review. Another longer term and successful open peer review system, ArXiv, has been extensively used mainly by physicists as a pre-print system. Others, like PLoS ONE, are changing the traditional criteria used to evaluate the merit of submitted articles.

However, these examples are still based on the traditional scientific article, a format that evolved within the context of paper based communication. When publication and retrieval costs (time and money) are high, it makes sense to package information as compactly as possible in few larger documents and use relatively few established vehicles. Consider the case of a chemist looking for the prior synthesis of a compound. Before computer assisted searching, finding relevant references was very time consuming and required searching through piles of books at the library. Deciding which references to then pursue was dictated by the availability of the physical document in the library and the likelihood of the information therein being reliable. It made sense to first look for information from a known source that had previously generated quality information and then, only as a last resort, request interlibrary loans or send a card to the author requesting a re-print from sources more difficult to obtain.

In the Google Age, the retrieval and sorting costs for a large number of documents are negligible. Even with pay document databases at university libraries, the costs are generally fixed so that additional searching, within reason, has no incremental additional cost. The reader, who has the most invested in assessing the validity of the work, is really in the best position to act as a reviewer. In the case of a chemistry researcher looking for methods or synthesizing a particular compound, if they are not competent enough to review the merits of the synthesis based on the evidence provided in the paper, they should not be performing the experiment without guidance from a mentor.

Thus, in the Google Age, the most important criterion for the usability of a document is immediate online availability. Articles and information sources that are not immediately available will only be pursued as a second choice, even if the vehicle is reputable.

With the advent of easy to use, free and hosted social software like blogs and wikis, and extremely efficient indexing by major databases such as Google, publication costs and learning curves are essentially zero. It is now possible to connect a researcher providing information with a researcher looking for that information very quickly with minimal technological obstacles.

Keeping the actual laboratory notebook of a research group in real time on a public wiki and holding discussions on a public blog is the natural extension of the openness concept leveraging today's technologies and global infrastructure. Operating with such transparency and demonstrating that science can be accomplished in this type of an environment is at the core of the UsefulChem project.

The UsefulChem project was started in the summer of 2005 by Jean-Claude Bradley, associate professor of chemistry at Drexel University. Initially, the project consisted of a single blog,, with the objective of carrying out chemistry research in areas that could benefit most from an Open Science model. In a process that was documented in the blog, the synthesis of anti-malarial compounds was identified as a worthwhile objective. Synthetic approaches were discussed and developed, and with new graduate and undergraduate students, lab work was started and recorded online from February 2006. Since then the project evolved to three graduate and three undergraduate students.

One of the graduate students is responsible for developing the automation components of the system. As often repeated by Peter Murray-Rust, a long time champion of Open Science in chemistry, cheminformatics still lags significantly behind bioinformatics, especially when comparing with the quantity and quality of open data in areas such as genomics. By representing molecules, reactions and results in a way that can be universally accessed and understood by machines as well as humans, there is great potential for accelerating progress in chemical research. This is especially true if "failed experiments" are routinely reported since they still provide valuable information to other researchers in designing their next experiments.

With the idea of creating an infrastructure that can be quickly and cheaply duplicated by other researchers, UsefulChem uses free and hosted services like Blogger (blogs), Wikispaces (wikis), YouTube (video), Google Video (video) and ManyEyes (data visualization). However, funding is still needed to purchase chemicals, equipment and support students.

One of the attractive features of funding Open Notebook Science is the built-in transparency of how resources are spent. Just like the rest of the world, a funding source has access to the daily work of the laboratory group and their collaborators and is free to provide feedback at any time.

Wiki Paper Experiment Started

Although we still have a few loose ends to tie up, I started writing up our work on the Ugi reaction on the wiki. So far I have abstract up.

Anatomy of the Ugi Reaction and Attempted Cyclization to Diketopiperazines

Reaction profiling using H NMR spectroscopy was used to elucidate the kinetics and progression of the 4-component Ugi reaction, involving an aldehyde, an amine, a carboxylic acid and an isonitrile. Aromatic aldehydes such as benzaldehyde, veratraldehyde and piperonal were found to react smoothly with 5-methylfurfurylamine and t-butylamine to yield imines in methanol. Phenylacetaldehyde led to intractable (product mixtures within minutes of adding to the amine component. The addition of boc-gly alone led to a reversal of the imine formation, while the addition of boc-gly with t-butyl isonitrile or benzyl isonitrile led to a more limited reversal to the aldehyde that peaked after about 30 min before diminishing again over several days. The Ugi products started to crystallize within hours or days. 2-morpholinoethyl isonitrile did not generate Ugi products, apparently due to its instability in the presence of boc-gly.

The experiment will consist in seeing which chemistry publishers will accept a paper written on a public wiki and the use of links to experiment pages on a laboratory notebook wiki as valid references. As I learned from a talk by one our librarians Jane Bryan a few weeks ago, publishers are really becoming tolerant of pre-prints hosted on institutional repositories. This is really not that different.

Who knows - it might even work for an ACS journal. We'll see.

And in the meantime, feedback is welcome on the drafts.

(Note that Alicia also started writing her Masters Thesis on the wiki.)

Monday, April 23, 2007

C&E News Article on Social Software and Chemistry

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.

The article is a pretty comprehensive report on the session and does a good job of summarizing the key technologies currently being tried without much hype. Podcasting, vodcasting, tagging and wikis were discussed from teachers and librarians using them in different ways. Of course the controversial issue of attendance was highlighted.

Although the session was primarily about education, UsefulChem got a nice plug.
Bradley posts his lectures and all other information for his class on a wiki with open access. He also has an open-access wiki for his research group (, where the students' lab notebooks are freely available to anyone in the world who wants to read them. His group will write and edit manuscripts using the wiki itself and invite any interested person to edit them.

Sunday, April 22, 2007

NCI - UsefulChem Link

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.

The first thing we are going to do is start shipping the compounds we make for an automatic screening of 60 cell lines for tumor inhibitory activity. No, these compounds were not designed for this purpose but the screening service Dan offers is free and we might just learn something.

Also, if someone has a model of tumor suppression and would like to make a suggestion (hint, hint), I would be happy to re-prioritize the order in which we make our molecules. The UsefulChem project is designed to be flexible that way.

The Ugi reaction we are using is very simple and amenable to combinatorial approaches from commercially available compounds. Many of these compounds have probably been made and tested by pharmaceutical companies but the results are sitting behind a firewall.

Dan will also be visiting me in Philly next week.

Thanks to Peter Murray-Rust for catalyzing this connection!

Saturday, April 21, 2007

UsefulChem and Skateboarding

I just came across Karl Bailey's blog, a chemistry teacher at Clark College who happens to teach virtually the same 3 organic chemistry classes that I do, in the same sequence following the Wade book. Clark has a quarter system like Drexel.

But what really caught my attention was his mention of UsefulChem and the image of skateboarders he used on the post. What a great representation of Open Source Science, at least the way that many of my friends and I conceive of it. I also get the same vibe from many of the young people that see me after I speak on the topic.

I suppose it represents a form of rebellion from the status quo, but not without standards for competence and dedication. Without that rebellion is just cynicism.

Thursday, April 19, 2007

Open Source Science Expands with Tan

A few months ago I posted a request for a docking collaborator to help us understand and reproduce our docking results with our targeted anti-malarial compounds. I've been contacted by a few people and I'll report on every one of those collaborations when it is possible.

Last week, Tan Tsu Soo from the Bioinformatics Group at Nanyang Polytechnic in Singapore informed me that he worked things out with his Director and was now in a position to collaborate with us openly. He has been busy docking uncyclized Ugi products and diketopiperazines using FlexX to compare with the results than Sean has obtained in D-EXP005.

He has not obtained identical results, partly because his search is not restricted to the same binding site that Sean used with THINK.

But the good news is that Tan also has managed to dock a good number of our molecules, including Ugi products that we have made and can start testing. He uploaded some of his results using Jmol to demonstrate the docking. Stay tuned for more data on the wiki.

The deprotected Ugi products (R and S) that Alicia prepared in EXP062 are shown below to dock in a similar fairly shallow location. (DRuncycltBu and DSuncycltBu from D-EXP005) Others, like the catechol derivative BRuncycltBu bind deep into the pocket. Check them out on Jmol.

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Saturday, April 07, 2007

Scooped by a Blog Article

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).

The part I enjoyed the most (referring to Bora):
Zivkovic concedes that he has had less luck in convincing people that he should post his dissertation on his blog before he publishes it. "But if and when I get to having my own lab I'd like to be completely open," he says, "having a live blog where everyone posts what happens in the lab every day."

I have had several people express the same sentiment to me in the past few months, including at the American Chemical Society a week ago. When they are in a position to do so I'll make sure to report it here.

UsefulChem got a mention as well.
Jean-Claude Bradley and his colleagues at Drexel University are already experimented with such a live lab-log. Their blog, Useful Chemistry, is being put forward as "an attempt at open source science in chemistry." They post their raw data and ideas for experiments on tropical diseases in an attempt to build collaborations, hoping it will spark pharmaceutical development on neglected diseases.

Thanks to Bora for alerting me.

Thursday, April 05, 2007

Chemistry on Nature Island in Second Life

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.

Today I met Andrew Lang (Hiro Sheridan on SL) who has built a molecule rezzer on Nature Island. He has a nice little area where he displays some molecules (like cholesterol) and gives information about them on a screen. Andrew's rezzer takes hin (Hyperchem) files as input and I gave him one of ours to render after converting from sdf using OpenBabel.

I think that being able to walk around a molecule can add valuable new insight to thinking about and doing chemistry. It should also make it easier to explain some ideas. In about a month we'll be looking at chirality in my class and I can see how this could be really useful.

The molecule that I chose was predicted by Sean to dock into enoyl reductase (molecule 4 in D-EXP005). If possible it would be nice to show how it docks in Second Life. Andrew's rezzer is limited to about 80 atoms so we'll have to see if we can show enough of the docking site on the protein to see clearly.

Come on over to the Nature Island and let me know what you think! (slurl)

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