Sunday, May 16, 2010

OpenSciNY Open Notebook Science Talk

On May 14, 2010 I presented on Open Notebook Science at the OpenSciNY conference at the New York University Bobst Library. I introduced the topic by telling a few stories about how new forms of communication are affecting how we think about concepts like "scientific precedent", "peer review", "scientific publishing" and "scientific scholarship". At the end I spoke about archiving Open Notebook Science projects and showed the physical copies of both the Reaction Attempts and ONS Solubility Challenge books.

Margaret Smith did a wonderful job of organizing the conference with a very interesting line-up of speakers: Heather Joseph, Antony Williams, Elizabeth Brown and David Hogg. We formed break-out sessions at the end to discuss with the attendees concepts around Open Science. I was part of the session on Promoting Open Science.

The tone at this and other similar conferences I have attended recently is probably best described as cautiously optimistic and focused on what is possible. The Open Science movement - at least as far as it is reflected by the people I know - does not seem to be driven by zealots or idealists trying to get everyone to drink the cool-aid. It is just a bunch of people who see opportunities to do things in better ways as new tools become available - and they can't find a credible reason not to do them.

Check here on FriendFeed for updates about links to recordings, slides, etc.

My presentation below:

Friday, May 07, 2010

The Scientist Article on Electronic Lab Notebooks

Amber Dance has written an article in The Scientist (2010-05-01) Digital Upgrade: How to choose your lab’s next electronic lab notebook. This is basically a quick overview of different Electronic Lab Notebooks (ELNs) that should be helpful for people researching what is currently available in that space.

There was some coverage of Open Notebook Science and Steve Koch and I were quoted. Ironically my contribution appeared in the "Cons" section :)


  • The format is unconstrained—you can set up any categories, and as many users and pages, as you want—and fast to set up.
  • Open notebooking attracts collaborators. Koch counts three collaborations that wouldn’t have happened if he weren’t on OpenWetWare. And his students build professional networks well before they author a paper.


  • Wikis were not designed with scientific data in mind. For example, it’s hard to make a table, Koch says.
  • Open notebook science “does limit where you can send your work,” says Jean-Claude Bradley, a chemist at Drexel University in Philadelphia, who also uses an open wiki notebook. His lab sticks to journals that accept preprints.
  • Posting online voids international patent rights, although US patents are still possible.
In my opinion, one of the biggest "Pros" wasn't listed in that section: the free cost. (That was mentioned elsewhere though) When you see the costs of some of these other commercial systems, that has to be a factor for many people trying to make a decision.

If privacy is an issue wikis can certainly be made private, although I'm not sure if that is possible on OpenWetWare. It can be done for $5/month on Wikispaces, the wiki we use for lab notebooks - although then it wouldn't be Open Notebook Science.

Concerning Steve's Con of wikis being difficult to use to store data, that is true. However combining the use of a wiki with Google Spreadsheets has completely resolved that issue for us. With our ability to automatically export an archive of the notebook (as HTML) and spreadsheets (as XLS) into an integrated archive, the two platforms operate essentially as if they were a single system.

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Tuesday, May 04, 2010

Visualizing Chemistry in Second Life ACS Talk Recording

The American Chemical Society has processed the recording of the talk that Andrew Lang and I gave at the Spring 2010 ACS meeting in San Francisco on March 23, 2010:
Visualizing Chemistry in Second Life

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Monday, May 03, 2010

ChemSpider SyntheticPages

I recently mentioned the Reaction Attempts project, which aims to collect organic chemistry experiments - especially those that are "failed", in progress or somehow incomplete.

For reactions where the desired product has been obtained and fully characterized, ChemSpider SyntheticPages also offers a very convenient publication vehicle. As I mentioned previously there is a need for enabling the publication of single experiments, especially when these are unlikely to become part of a traditional article.

We are in the process of submitting suitable reactions from the UsefulChem project to CS|SP. This will require some re-formatting of procedures and characterization data as they currently appear in the lab notebook.

Here is an example of one of our Ugi reactions: SyntheticPage 406 (UCEXP176C)

A nice feature of these pages is the automatic rendering of 2D structures upon hovering on top of chemical names.

Here are a few more reasons to use ChemSpider SyntheticPages:
* ChemSpider SyntheticPages takes you directly to a procedure. When you get a hit - you get a procedure.
* ChemSpider SyntheticPages provides information that may not generally be found elsewhere, such as frequently encountered problems, trouble-shooting tips, the number of times the reaction has been carried out, scale-variation etc.
* ChemSpider SyntheticPages is the only interactive chemistry database. Information is constantly updated and validated by comments from the user community (Peer Review in the Public Domain™).
* ChemSpider SyntheticPages can provide you with the most up-to-date method, we aim for 95% of submissions to be processed within 48 hours of submission.
* ChemSpider SyntheticPages is free of charge.
[Disclaimer: I am a member of the editorial group at CS|SP]

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Sunday, May 02, 2010

The Synaptic Leap Experiments on Reaction Attempts

Andrew Lang and I recently reported on the first edition of the Reaction Attempts book and database. Part of the motivation for this was to structure the experiments from the UsefulChem project in both a machine readable format and one that could be browsed as a physical copy. However, we also had in mind the easy integration of other open experiments, especially those labeled as "failed", since these are unlikely to be found by searching conventional reaction archives.

As a demonstration, we have added a series of experiments from The Synaptic Leap, which Michael Wolfle (working as a post-doc with Mat Todd) has posted. All of these reactions involve intermediates in the synthesis of praziquantel, which is a major focus of the Todd group. One group of these reactions involved the attempted synthesis of praziquanamine via a Pictet-Spengler cyclization. Most of these are failed attempts and one successful one.

Adding these experiments to Reaction Attempts was very simple - since the minimum information required is the ChemSpiderIDs (CSIDs) of all the reactants and the product, which a hyperlink to more details. We also added a few more details provided by Michael - such as the solvent, reaction conditions and outcome.

Andy has provided a simple mechanism to pull up all Reaction Attempts for a given reactant with the following url structure:
The number at the end is the CSID for the reactant. Multiple reactants can be pulled from the database by adding more CSIDs separated by commas.

Successful runs in Reaction Attempts are identified with a green check mark:

Again the main idea here is not to exhaustively abstract all pertinent information for an experiment. Rather it is to connect up researchers who are working on similar reactions. Since it requires so little effort to come up with the minimum required information we are hoping to get contributions from other sources.

We will focus next on coming up with more sophisticated ways to retrieve information - such as substructure searching or by reaction type, solvent, etc. We will also periodically publish hard copies of future Reaction Attempts editions.

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