[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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