CASMI 2012 finished -- and CASMI 2013 has started !

Hi, The CASMI 2012 special issue in Metabolites is finally finished! Emma Schymanski and I will continue to present the results of CASMI 2012 at different occasions, e.g. the ASMS conference in Minneapolis (June 2013) and the upcoming Water Forum in Langenau in November this year.

The organisation of the contest and special issue was a lot of work, but also a lot of fun. We'd like to thank all of our participants and our advisory board, but also everyone who expressed interest or engaged us in discussions at meetings.

And CASMI keeps going: CASMI 2013 is currently being organised by a team of Japanese mass spectrometry experts headed by Prof. Nishioka, and the challenge data has already been opened up.

In addition to the CASMI specific mailing lists, the Metabolomics' society is also hosting the Metabolite Identification Interest group.

The small molecule analytical chemistry and computational mass spectrometry world is quite small, we're looking forward to bumping into you at some time in the future!

Call for Papers: CASMI proceedings

The special issue will contain a summary where Emma and Steffen give details about the challenge compounds, the evaluation measures and comment on the submissions.

But the main content will be your articles about your participation: we are really interested in descriptions of how you actually tackled the challenges, which steps were automagic and, if necessary, where manual intervention was required.

If your approach was published previously, please focus on what is relevant for the CASMI challenges, and improvements that have been made since the last publication. All articles will be peer-reviewed by at least two reviewers from the community. There is no actual page limit, but the reviews will check that the length is adequate.

We ask you to send us your intent to submit an article to the special issue (including a preliminary title and author list), before heading into the holiday season.

Note that there is an Early-Bird-Bonus: MDPI will waive the article processing charges if you send us a reply with your submission intent by the end of this year! For articles announced after 01.01.2013 it will be the regular 300 CHF charge for the Metabolites journal.

For more details on the special issue see the journal's pages at MDPI. Please visit the Instructions for Authors before submitting a manuscript. Manuscripts should be submitted through the online manuscript submission and editorial system.

Important Dates for the proceedings:
31.03.2013    Submission deadline for full papers in the journal Metabolites.
31.12.2012    Last day of early-bird article pre-registration

CASMI published first challenges

In the Critical Assessment of Small Molecule Identification (CASMI) contest we are publishing a set of LC/MS and GC/MS spectra on www.casmi-contest.org, and call the community to identify the underlying compounds. In different categories we ask for the molecular formula and/or for the molecular structure.

We now have deposited a first round of challenge spectra, and will add more over the course of the next weeks. If you are doing computational mass spectrometry, or you are an expert in spectral interpretation, or just started to learn mass spectrometry: these spectra help to "show off" your skills.

Early in 2013, we will reveal the compounds, evaluate the submissions and call for papers in a special issue of the journal Metabolites, where the participants describe their efforts.

If you have any questions, don't hesitate to contact us at casmi2012(at)ipb-halle.de, or join the mailing lists.

Chemical Systems Biology Meeting, Philidelphia, August 17-21, 2008

Rajarshi Guha wrote on the Chemical Computation List:

Chemical Systems Biology: Integrating Chemistry and Biology for
Network Models
236th ACS National Meeting
Philadelphia, August 17-21, 2008
CINF Division
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Dear Colleagues,
Josef Scheiber and I are organizing a symposium focusing on the use of biological networks and their models for the purposes of drug discovery. Traditionally, such models have been applied to large scale biological systems such as protein-protein interaction networks. Recently, there has been increased interest in the study of these networks to gain a global understanding of biological systems and the impact of small molecules to them in the context of drug discovery. As a result, it has become important that such models integrate small molecules with the usual biological systems. By leveraging the power of established cheminformatics methods along with the network models we get closer to the goal of "chemical systems biology", the full integration of chemical and biological data in the development of better in silico-methods for drug discovery.

We invite you to submit contributions that address various computational aspects of this approach including, but not limited to: network construction, integration of multiple data sources in network models, drug repurposing, target identification, polypharmacology, incorporation of chemical structure/similarity into network models, bridging chemical structure and biological structure based network models. Case studies where computational network models have provided experimental insight are also welcome.

We would also like to point out that sponsorship opportunities are available.

Please use the on-line abstract submission system (OASYS) for submitting your abstract (http://oasys.acs.org/oasys.htm). OASYS will be accepting abstracts between 28th January and 24th March, 2008.

Please contact Josef or myself if you have any questions.

Thanks,

Josef Scheiber Rajarshi Guha
Novartis Indiana University

The CINF division of the American Chemical Society is oriented at chemical information (molecular really, so including metabolites) and includes chemoinformatics, and increasingly bioinformatics.