Wednesday, July 25, 2007

Open Interview

Bryan Vickery did his BSc in chemistry at Liverpool University, and then studied electrochemistry there for his PhD. He has never regretted his choice of university or city, but having ruined too many pairs of jeans and a laboratory fume cupboard opted for a desk instead of a bench job. He is currently Publisher at BioMed Central with special interest in Chemistry Central. I interviewed him for the Reactive Profile column recently and you can read his thoughts on online published and the open access movement there.

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Tuesday, July 24, 2007

Heather's Notes on Open Notebook Science

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). It obviously relies heavily on work from Bill Hooker and Jean-Claude Bradley: Thank you. Following the advice to“make a mess in your zero draft,” the current version isn’t very good reading. I have many more links to comb, and then I’ll start pulling it together and making a first-draft (aka human-readable version). I’ll post again once it gets to that state.

Wednesday, July 18, 2007

CombiUgi: Time for Synthesis

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.). The top hits are then synthesized and tested.

We chose the Ugi reaction because it is very simple experimentally - mix four components (an amine, an aldehyde, a carboxylic acid and an isonitrile) in methanol at room temperature. In the creation of the libraries we used only components that were commercially available.

In our first library of 68,000 compounds, although all starting materials were commercially available, one of the main components needed (2-naphthyl isonitrile) for predicted anti-tumor activity was not available to ship for 6 weeks.

Since it is important to keep this science loop as short as possible we reran the library generation with Rajarshi Guha's open web service using only compounds that were next-day shippable. We also used this opportunity to increase the number of compounds in the virtual library to 500,000.

Rajarshi has now provided the docking results of this library with malarial enoyl reductase (PfENR). Here is what the top hit looks like:

So far we have been doing Ugi reactions usually with intensive NMR monitoring of each step. This has been very useful in debugging experimental conditions and reagent choice. Now that we have a better understanding of how to do it, generating many products quickly is more important than close monitoring.

We will take advantage of our observation that most of our Ugi products simply precipitate from solution over the course of a day. Instead of looking into additional purification techniques, we will make this an additional requirement for a compound to be considered a suitable lead. Any reactions that fail to precipitate within a day will be noted and discarded (see protocol). This information could surely be of use to others looking for suitable compound libraries.

As for the testing phase of these potential anti-malarial agents, I have a few very promising leads now and I'll report shortly when I get confirmation of a collaborator.

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Monday, July 16, 2007

Jeremiah's Open Notebook

Jeremiah Faith, a graduate student at the Bioinformatics Program at Boston University has recently made the jump into Open Notebook Science. His motivations resonate with me. As he says very nicely in his blog:

Science typically builds on the body of available knowledge - the more knowledge available the faster science goes. It's striking when you visit other labs in person; you see all of their unpublished work, and you know that most of their results and data won't be available to the bulk of the scientific community until a year after each particular scientific project is finished. By the time papers are in print, it's old news to the insiders. More striking is when you visit labs whose work you've thought about replicating and expanding on. It's not too uncommon to find that only one person in the entire lab is able to get the technique to work, and even for him the technique only works on Wednesdays. This type of information would be useful to know before you embark on a useless three months trying to adapt their method. But scientific publications are covered in a thick coat of high-gloss finish, making these unacknowledged difficulties hard to detect.
His notebook is currently available as a 300 page PDF file.

Sunday, July 08, 2007

Indexing Molecules in Second Life

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. As more people start to experiment with representing chemicals and chemistry research in Second Life it would be nice if such examples were discovered by a simple Google search.

All that really needs to be done to accomplish this is to co-locate molecular descriptors with corresponding SLURLs (Second Life URLs) on the same web page. When clicked, the SLURL will automatically start Second Life and teleport the user to the location where the molecule can be found. If the user does not have Second Life, a page pops up explaining how to set up a free account and download the software. This could be a good way to introduce the mainstream chemical community to new modalities of communicating science.

As for descriptors, I am suggesting that we use InChIs and common names at the very least. Google does a fairly good job of finding molecules by InChI.

I created a wiki,
and seeded it with a molecule from our malaria research that I've used in several places and with caffeine, which is displayed on Nature Island. I invite anyone to contribute to the wiki and add information that could be useful. (The indexing on Google can take a few days for a new wiki)

There are several other ways of creating this index and I think the more redundancy the better. For example, we could make Second Life a "supplier" on ChemSpider. It might also be possible for Andrew's molecule rezzer to note the location of a molecule when it gets created in Second Life and automatically send off an email to a Blogger account to create a post.

Chemical Blogspace Tags


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Friday, July 06, 2007

Spectral Deconvolution with UsefulChem Data

Tom Shattuck from Colby College just emailed me with the following request:

I would like to request permission to use a part of one of your posted JCAMP spectra as an example spin-spin multiplet. I have set up a silent link to my proposed applet that you can check out for your reference. The applet downloads a JCAMP spectrum for an individual multiplet and does deconvolution and peak picking. I would like to use your spectrum as an example. The actual file is just a small portion of your spectrum. The applet is at
When complete the link to this applet will be available from my couse Web page:
First of all, all of our work is published with a Creative Commons Share-Alike with Attribution license so he didn't really have to ask to use it, as long as he linked to the source.

But I'm glad he did contact me because I was able to learn about the awesome open NMR resources (including spectrum prediction) he uses in his class and add them to our lab links.

I think this is a good example of the integration of research and teaching. This is a real spectrum taken strictly for research then re-purposed for an educational objective. And because the data are open and indexed on popular search engines, this integration was possible between people who did not have a prior collaboration.

This also makes a really good case for the value of Open Notebook Science and the availability of raw NMR data in JCAMP format, especially using a browser-based viewer like JSpecView. This type of information (the full spectrum of a starting material) would likely not have been included in a traditional publication, even in the supplementary information section.

I think we'll be seeing more of this type of re-mixing of scientific information as new vehicles like Nature Precedings get some traction.

Here is an example of Dr. Shattuck's deconvolution code at work:

Wednesday, July 04, 2007

UsefulChem Mailing List

We now have a mailing list for UsefulChem.

Although we currently have a wiki and blog to keep track of the UsefulChem project, there is a lot of valuable information not being captured.

The wiki records details of experiments (effectively serving mainly as the group laboratory notebook) and the blog serves to highlight milestones and key problems.

But the day to day interaction between the collaborators is lost in the email system that currently serves as our workhorse for getting things done.

This mailing list should help capture that process and everyone who is comfortable discussing in the open is welcome to contribute.

Creative Commons Attribution Share-Alike 2.5 License