[Socbin] Call for participation: Workshop on Mass Spectrometry Informatics in Systems Biology

Juho Rousu juho.rousu at cs.helsinki.fi
Sun Sep 19 11:30:43 CEST 2010


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Call for participation

Workshop on Mass Spectrometry Informatics in Systems Biology

Helsinki, Finland
October 28-29, 2010

Workshop web site:
http://www.cs.helsinki.fi/u/mqheinon/msib.html

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Motivation

Mass spectrometry (MS) has become a standard tool for identifying  
metabolites in biological tissues, and metabolomics is slowly  
acknowledged as a legitimate research discipline for characterizing  
biological conditions. The computational analyses of metabolomics,  
however, lag behind compared with the rapid advances in analytical  
aspects for two reasons. First is the lack of standardized data  
repository for mass spectra: each research institution is flooded with  
gigabytes of mass-spectral data from its own analytical groups and  
cannot host a world-class repository for mass spectra. The second  
reason is the lack of informatics experts that are fully experienced  
with spectral analyses. The two barriers must be overcome to establish  
a publicly free data server for MS analysis in metabolomics as does  
GenBank in genomics and UniProt in proteomics.

The workshop brings together bioinformaticians working on mass  
spectral analyses and establishes a consortium to freely exchange and  
publicize
* mass spectra of metabolites measured on various platforms
* computational tools to analyze spectra
* spectral knowledge that are computationally predicted from  
standardized data
Since most spectral data are only commercially available, research  
collaboration to provide a free archive to the community is extremely  
important.

The workshop is organized as a joint effort between the MassBank  
consortium (http://massbank.jp/), an internationally leading effort  
towards providing a publicly available center of mass spectral data  
and analysis, and Computational Systems Biology and Bioinformatics  
group (http://www.cs.helsinki.fi/group/sysfys/) from University of  
Helsinki.

The workshop is funded by Japan Society for the Promotion of Science  
and Academy of Finland as part of the Japan-Finland joint seminar  
programme, Finnish Center of Excellence in Algorithmic Data Analysis  
and Department of Computer Science, University of Helsinki.


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Registration

The workshop is open to any researchers interested in the topic,
but the number of participants is limited. Participants are accepted on
first come - first served principle.

To register for the workshop, please send a notification email  
containing your
contact details to
msinformatics2010 at cs.helsinki.fi.

Registration is free of charge.

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Workshop Programme

Thursday, October 28

09:00 - 09:30 Registration & coffee
09:30 - 09:45 Opening of the workshop

09:45 - 12:30 Session 1
Chair: Juho Rousu
09:45 - 10:15. Takaaki Nishioka: MassBank: A public repository of mass  
spectral data
10:15 - 10:45. Markus Heinonen: Energy-based identification of  
molecular fragments in tandem mass spectrometry
10:45 - 11:15. Break & discussion
11:15 - 11:45. Masanori Arita: Circulating information and knowledge  
through a cyber-infrastructure
11:45 - 12:30. Invited Talk
Nicola Zamboni: TBA
12:30 - 14:30 Lunch break

14:30 - 17:00 Session 2
Chair: Masanori Arita
14:30 - 15:00. Juho Rousu: Algorithms and Machine Learning for Small  
Molecules
15:00 - 15:30. Kensuke Nakamura: Species-metabolite relation database  
KNApSAcK and its multifaceted retrieval system KNApSAcK Family
15:30 - 16:00. Coffee break & discussion
16:00 - 16:45. Invited Talk
Matej Oresic: Processing of mass spectrometry based molecular profile  
data
16:30 - 17:00. Open discussion
19:00 Speakers' dinner

Friday, October 29

09:00 - 09:30 Registration & coffee

09:30 - 13:00 Session 3
Chair: Markus Heinonen
09:30 - 10:15. Invited Talk
Steffen Neumann: Spectral libraries and computational mass  
spectrometry - A symbiosis?
10:15 - 10:45. Ken Tanaka: Analysis of biosynthetic fluctuations of  
cultured Taxus seedlings using LC-IT-TOF MS and a metabolomic approach
10:45 - 11:15. Break & discussion
11:15 - 11:45. Masahiro Sugimoto: Non-targeted analysis for CE-MS data
11:45 - 12:30. Invited Talk
Merja Penttilä: TBA
12:30 - 13:00 Open discussion
13:00 - 14:30. Lunch break

14:30 - 16:30 Technical meeting on the MassBank server

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Organizers

Masanori Arita (University of Tokyo and RIKEN Plant Science Center,  
Japan)
Markus Heinonen (Department of Computer Science, University of  
Helsinki, Finland)
Juho Rousu (Department of Computer Science, University of Helsinki,  
Finland)

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Sponsors

The workshop is funded by Academy of Finland (grants 139203 and 118653),
Japan Society for the Promotion of Science (JSPS Japan-Finland Bilateral
Seminar Program 2010) and  Department of Computer Science, University  
of Helsinki.









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