Sunday, April 27, 2008

UsefulChem on ChemSpider

As Antony Williams mentions in his blog, UsefulChem molecules now have their own url on ChemSpider:

This is important on so many levels. I've been talking about using ChemSpider as an integral part of our research for some time now and we've been steadily migrating content as new functionalities became available. We still have a lot to do to complete the process but the path is clear.

The ability to upload spectra of all types (IR, H NMR, C NMR, MS, etc) in JCAMP-DX format allows for anyone with a browser to drill down to any desired expansion using JSpecView. It just makes sense to upload the NMRs of our starting materials and our fully characterized products so that we can always be just a click away from the online lab notebook when discussing our chemistry.

The value of being able do substructure searching for our compounds is immense. Most organic chemistry students are not interested in learning how to run and maintain software on a lab server to keep track of their molecules. They also don't want to learn SMARTS. ChemSpider has a very familiar graphic interface for drawing molecule fragments to do substructure searching. For a free and hosted solution, the energy of activation for using ChemSpider has become very low indeed, especially for Open Notebook Science applications.

As we approach 200 experiments it is becoming clear that the ability to retrieve information is just as important as doing the experiments. Systematic tagging of experiment pages with InChIKeys and InChIs is a simple way to automatically allow for direct links from ChemSpider to UsefulChem pages via Google.

We've come a long way from using a blog to track our molecules :)

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Friday, April 18, 2008

Scholar2Scholar Webcast and Report

The webcast from the Scholar2Scholar conference on April 16, 2008 is now available here. The general introductions start at 15:30, my intro by Jane Bryan starts at 19:08, my talk on "Enhancing Scientific Communication through Open Notebook Science" at 23:28 and the panel at 51:40 (after several minutes of dead audio unfortunately).

The panel consisted of Jean-Claude Bradley, Andre Brown, Nicole Engard, James Mitchell, Banu Onaral, Beth Ritter-Guth, and Scott Warnock.

Small round-table discussions followed and were diligently documented by the library folks. Their notes will be posted here on the wiki.

Overall it was a very well organized and productive event. I was impressed by the level of engagement by the participants at my round table and I expect future projects to evolve from these discussions.

I especially thank Jay Bhatt and Anita Chiodo for setting the process in motion a few months ago!

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Thursday, April 17, 2008

Cell Article on Open Drug Discovery

Seema Singh wrote a review "India Takes an Open Source Approach to Drug Discovery" which just appeared in Cell: Volume 133, Issue 2, 18 April 2008, Pages 201-203. (The doi doesn't work yet but try this link in the meantime). You'll need a subscription to view it, an increasingly familiar irony of much of the Open Science discussion these days.

UsefulChem and our collaborators got a nice mention:
A related initiative is UsefulChem (, set up by Drexel University chemist Jean-Claude Bradley. Bradley has pioneered Open Notebook Science in which lab notebooks and raw research data are posted on the web for anyone to see and respond to ( As for success, Bradley says, “Probably the best example of a positive outcome from UsefulChem is finding two compounds that are somewhat active against malaria [in vitro],” blocking the activity of falcipain-2, a Plasmodium falciparum cysteine protease. “This demonstrates that a team of researchers can work together in the open—Rajarshi Guha from Indiana University did the docking calculations, my group at Drexel did the syntheses and Phil Rosenthal's group at UCSF did the testing.”

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Tuesday, April 15, 2008

NMR viewer in Second Life

Andrew Lang just finished coding this nifty little JCAMP-DX viewer in Second Life. The video shows that you can expand any area of the spectrum by typing zoom followed by the desired range in the chat box.

You can also type "back" and "reset" commands. It essentially functions like Robert Lancashire's JSpecView if it were running in Second Life (although integration is not yet implemented).

There are still a few kinks to iron out but it should work with any spectrum that can be represented in JCAMP-DX format: IR, CNMR, HNMR, UV-vis, MS, etc.

This should extend considerably the set of tools available to chemistry teachers who use Second Life to interact with students.

Give it a try on Second Nature island: SLURL. (You'll need the most recent version of Second Life to run this and click the link from within IE, not Firefox)

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Scholar2Scholar Tomorrow

The Scholar2Scholar conference is upon us. Jay Bhatt and Anita Chiodo did an amazing job with organizing this from the start. I'll be giving the introductory talk on "Enhancing Scientific Communication through Open Notebook Science". Here are the slides - I'm starting with an introduction to Web2.0 using FriendFeed as an example.

date: April 16, 2008 8:30-1:30
location: Drexel University Bossone Lobby

Join us to discuss how Web2.0 is changing scholarship. Dr. Jean-Claude Bradley will give a presentation, followed by a panel discussion featuring: Andre Brown, Nicole Engard, James Mitchell, Banu Onaral, Beth Ritter-Guth, and Scott Warnock. Small round-table discussions will follow. An optional Dutch-treat lunch concludes the day.

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Thursday, April 10, 2008

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.

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Sunday, April 06, 2008

Attila Csordas writing his thesis on a blog

Attila is writing his thesis openly and is welcoming comments:

From now on I start every “thesis live” post with the standard introduction: In the live thesis building blogxperiment I edit (digest, compile, write, rewrite, delete) my ongoing doctoral thesis in blog posts and put the parts together on thesis live. The title: The physiologic role of stem cells in tissues with different regenerative potential

I am not aiming any perfection, my focus is clearly on getting things (the PhD) done here. Anyway, I found the idea of “writing” a complete, lengthy and formal thesis outdated and inefficient (after all, scientists should conduct nice experiments and publish their results in short, inforich and accessible research papers in order to share it ASAP with the research community, not in book-length, otherwise unaccessible PDFs) and so I try to keep myself motivated by

- doing this “thesis live” series as an open science experiment and getting useful feedback from my fellow scientists and readers

- trying to include as many systemic, whole body level material into it that could be relevant for systemic regmed approaches

- reminding myself every day that without a PhD it is hard to move further in science officially (that’s the least motivating factor though as it is official)

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Saturday, April 05, 2008

Data-Centric eScience Workshop Call for Papers

General Info: Call for Papers for the UK e-Science AHM2008
'Crossing Boundaries: Computational Science, E-Science and Global
8th - 11th September 2008 in Edinburgh, Scotland
Call for workshop papers for the workshop on
The Global Data Centric View of e-Science or “Data in Science, Arts and Medicine: getting it, testing it, using it, keeping it, and sharing it!”
Abstract Submission (Abstracts due 1 May)
Further details about the workshops and important information about the submission and review process, including guidelines for authors can be found at:
Submission Deadline: 1st May 2008
Enquiries: Please address any enquiries about abstract submission to

General Information:

This is the principal e-Science meeting in the UK and brings together researchers from all disciplines, computer scientists and developers to meet and exchange ideas. The meeting is in its seventh year and normally attracts between 500 and 600 participants. The theme for this year's meeting is 'Crossing Boundaries: Computational Science, E-Science and Global E-Infrastructures'. The appointment of Professor Peter Coveney (UCL) as Programme Chair, heralds a new approach. This year, for the first time, key papers will be published in two back to back editions of Philosophical Transactions of the Royal Society A in the early part of 2009, with the title 'Crossing Boundaries: Computational Science, E-Science and Global E-Infrastructures'. One of the central aims of this year's meeting is to promote the domain specific applications aspects of e-Science, as well as building bridges between the three communities of the theme title.

The general format of the meeting will include cross-community symposia (kicked off by invited key speakers) and workshops. The workshops are being championed by Programme Committee members in what are considered to be key areas of e-Science that need to be addressed, rather than by a call for workshops as has been done in the past. There will also be opportunities to present 20 minute talks.
Call for workshop papers for the workshop on
The Global Data Centric View of e-Science or “Data in Science, Arts and Medicine: getting it, testing it, using it, keeping it, and sharing it!”

Workshop Organizer - Jeremy Frey, School of Chemistry, University of Southampton
Workshop Programme Committee

Roger Barga, Microsoft Research, Redmond, USA

Colin Bird, IBM Labs, Hursley, UK

Jean-Claude Bradley, Department of Chemistry, Drexel University, USA

Simon Coles, University of Southampton, UK

Peter Dew, School of Computer Science, Leeds, UK

Lee Dirks, Microsoft Research, Redmond, USA

Jon Essex, University of Southampton, UK

Geoffrey Fox, Indiana, USA

Lee Giles, Penn State, USA

Jane Hunter, University of Queensland, Australia

Charles Laughton, Nottingham, UK

Liz Lyon, UKOLN, Bath,

Peter Murray-Rust, Unilever Centre, Cambridge, UK

Jim Myers, NSCA, Illinois, USA

Cameron Neylon, RAL, STFC, UK

Mike Pilling, School of Chemistry, Leeds, UK

Peter Turner, University of Sydney, Australia

Andrew Woolf, RAL, STFC, UK

Invited talks: TBA
Call for papers:

In this workshop we request papers (abstracts) contributing to the consistent or integrated treatment of data derived from laboratory processes, computational simulations, analyses, legacy systems and human annotation and that address one or more of the following:

  • Distributed Data Acquisition & Generation
  • Data Management, Migration and Curation
  • Data Models, Representations,
  • Metadata and Annotation
  • Data Flows & Access Services
  • Data Translation, Normalization and Integration
  • Data Evaluation, Error correction and Attribution of confidence
  • Data transparency: Approaches and Policies
  • Data Search, Open Data

We are particularly interested in papers that highlight and demonstrate the ways in which the data centric view provides a unifying approach to the handling and processing of information in multi- and interdisciplinary environments in ways that can satisfy the needs of small, medium and large-scale generators and consumers of data and for example the role of Web 2.0 and the “Cloud” in dealing with the topics listed.

Workshop Discussions
We are planning a blog/wiki/forum operation at the workshop so that the questions & discussion can be captured and 'published' along with the papers (a bit like Faraday Discussions for those who know the Royal Society Chemistry system). We should be able to do this in an efficient way making use of the fact that most people in the w/s will have a laptop open and be typing anyway!
Further details about the workshops and important information about the submission and review process, including guidelines for authors can be found at:
Submission Deadline: 1st May 2008

Thursday, April 03, 2008

Ugi Precipitation Predictions

Following a recent discussion about the Ugi Master Table, things got sorted out enough that Rajarshi has built a model to predict which of the top 100 molecules from his docking run against falcipain-2 (V2 receptor) are most likely to precipitate the Ugi product. He get 6 hits, 3 of which are part of the training set and 3 have not yet been attempted yet. The new ones are here:

Hit 87

Hit 83

Hit 72

As we get more information in the table, we can start formulating new hypotheses. One of the factors that I have suspected for a while is that the products that precipitated tended to come from less concentrated solutions. Now we are starting to get results from the same Ugi reactions at different concentrations, where this effect should be more obvious.

For example this compound precipitated from a 1 mmol scale reaction with 4 ml of methanol but remained in solution at a 0.25 mmol scale with 0.25 ml of methanol.

This seems counterintuitive because one would expect increasing the concentration should make it easier to precipitate. But I think those solutions are so concentrated that the reagents compete as role of solvent with methanol.

Rajarshi has not yet taken into account the role of concentration but we have discussed it and can more easily do so as we accumulate more results.

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Wednesday, April 02, 2008

ACS Island Party Tonight

As I mentioned previously, the American Chemical Society is gearing up for a poster session in Second Life on April 7, 2008 immediately following the New Orleans ACS meeting Sci-Mix session at 20:00 EDT. There are currently 16 presenters from diverse chemical fields.

In anticipation of this event there will be a little party on ACS island tonight (April 2) at 18:00 EDT. Everyone is welcome to attend.

Just type "ACS" in the Second Life map search function to find the island.


Tuesday, April 01, 2008

We're Gonna Ugi All Night!

Thus begins the CHEM254 lab manual for the week of April 7, 2008 at Dominican University:
“Ugi to the left, Ugi to the right. This is so fun, we’re gonna Ugi all night.”
As I discussed a few days ago, Brent has followed through in a big way in incorporating the UsefulChem project into his teaching lab:
This experiment represents the beginning of collaboration with the UsefulChem Bradley open notebook science group of graduate and undergraduate research at Drexel University. The goal of the UsefulChem project is to use the Ugi 4 component reaction to synthesize possible anti-malarial compounds. Open notebook science allows immediate dissemination of experimental results that invites advice and suggestions as well as complementary experiments that enhance and advance the project. We are going to reproduce some of the Drexel results as well as perform two complementary reactions that have not been done at Drexel.
The procedure is derived from our lab notebook with one interesting vortexing modification :)
Part I.
Add 0.33 g of your aldehyde to 8 mL methanol in a 20 mL scintillation vial.
Screw on a Teflon (green) cap on the vial. Vortex to mix and dissolve the aldehyde.
Add 1 mL of methylamine solution to the vial.
Vortex to mix. Sing the “Ugi song” while vortexing.
Obtain 0.34 g of the carboxylic acid. Add the carboxylic acid to the vial.
Vortex to mix.
Obtain 0.39 g of tosylmethylisocyanide. Add the tosylmethylisocyanide to the vial.
Vortex to mix.
Take a photo of your reaction mixture.
Label the vial and let the reaction mixture sit in the sealed vial.
By taking pictures his students can directly compare the progress of the reaction with our group. The questions for this lab are also excellent and may result in some useful ideas for my students to ponder (this may end up being a realistic way to foster chemistry crowdsourcing):
What could you do to isolate your product if after 7 days if there are no spontaneously formed crystals?

Refer to UsefulChem Experiment 171 . Which reaction most closely corresponds to our experiment? What were the results?

Consider the IR spectrum may reveal that there is unreacted isocyanide in your product mixture. Where does the isonitrile group appear in an IR spectrum? (Refer to appendix 2B in your textbook.)

Consider the possible 1H spectrum of your Ugi product. How many aromatic Hydrogens are there? How many methyl groups are there? Where would you expect to observe the methyl groups?

Consider the possible 13C spectrum of your Ugi product. How many aromatic Carbons are there? How many carbonyl carbons are there? How many methyl carbons are there? Where would you expect to observe the methyl carbons?

If you were given four different compounds for each type of Ugi reactant (16 compounds in all), how many different Ugi products could you attempt to make?

Safety Question: What is the safest way to transfer 1 mL of 2.0 M methamine in methanol from the stock bottle to your reaction vial? Give a reasonable explanation of your choice.
I also really like that he is exposing his students to some handy cheminformatics tools:
Look up “tosylmethyl isocyanide” in chemspider. What is the InChI code? What is an InChI code?
Since Brent and I started the discussion we have a few more precipitates involving the non-stinky tosylmethylisocyanide that may be suitable for his lab. Khalid has been doing some tedious but very necessary data checking and recording and the updated results are available on the Master Table of Ugi reactions.

There are currently 65 reactions, with 20 giving precipitates - and we are now including reactions where the starting materials fail to dissolve. Not all the precipitates have been characterized but they will be over time. In fact the Ugi product that Brent is trying to make in his lab for next week has not yet been fully characterized - all those phenolic groups seem to give rise to solubility issues in CDCl3.

That is a risk associated with using Open Notebook Science for a teaching lab. But it is also one that could pay off because his students could be contributing valuable results to an ongoing research project focussed on making anti-malarial compounds.

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