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Systems biologists seek fuller integration of systems biology approaches in new cancer research programs.

ABSTRACT: Systems biology takes an interdisciplinary approach to the systematic study of complex interactions in biological systems. This approach seeks to decipher the emergent behaviors of complex systems rather than focusing only on their constituent properties. As an increasing number of examples illustrate the value of systems biology approaches to understand the initiation, progression, and treatment of cancer, systems biologists from across Europe and the United States hope for changes in the way their field is currently perceived among cancer researchers. In a recent EU-US workshop, supported by the European Commission, the German Federal Ministry for Education and Research, and the National Cancer Institute of the NIH, the participants discussed the strengths, weaknesses, hurdles, and opportunities in cancer systems biology.

SUBMITTER: Wolkenhauer O

PROVIDER: S-EPMC2802734 | biostudies-literature | 2010 Jan

REPOSITORIES: biostudies-literature

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Systems biologists seek fuller integration of systems biology approaches in new cancer research programs.

Wolkenhauer Olaf O Auffray Charles C Baltrusch Simone S Blüthgen Nils N Byrne Helen H Cascante Marta M Ciliberto Andrea A Dale Trevor T Drasdo Dirk D Fell David D Ferrell James E JE Gallahan Daniel D Gatenby Robert R Günther Ulrich U Harms Brian D BD Herzel Hanspeter H Junghanss Christian C Kunz Manfred M van Leeuwen Ingeborg I Lenormand Philippe P Levi Francis F Linnebacher Michael M Lowengrub John J Maini Philip K PK Malik Arif A Rateitschak Katja K Sansom Owen O Schäfer Reinhold R Schürrle Karsten K Sers Christine C Schnell Santiago S Shibata Darryl D Tyson John J Vera Julio J White Michael M Zhivotovsky Boris B Jaster Robert R

Cancer research 20091222 1

Systems biology takes an interdisciplinary approach to the systematic study of complex interactions in biological systems. This approach seeks to decipher the emergent behaviors of complex systems rather than focusing only on their constituent properties. As an increasing number of examples illustrate the value of systems biology approaches to understand the initiation, progression, and treatment of cancer, systems biologists from across Europe and the United States hope for changes in the way t ...[more]

PMID: 20028868

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Project description:Systems biology research typically involves the integration and analysis of heterogeneous data types in order to model and predict biological processes. Researchers therefore require tools and resources to facilitate the sharing and integration of data, and for linking of data to systems biology models. There are a large number of public repositories for storing biological data of a particular type, for example transcriptomics or proteomics, and there are several model repositories. However, this silo-type storage of data and models is not conducive to systems biology investigations. Interdependencies between multiple omics datasets and between datasets and models are essential. Researchers require an environment that will allow the management and sharing of heterogeneous data and models in the context of the experiments which created them.The SEEK is a suite of tools to support the management, sharing and exploration of data and models in systems biology. The SEEK platform provides an access-controlled, web-based environment for scientists to share and exchange data and models for day-to-day collaboration and for public dissemination. A plug-in architecture allows the linking of experiments, their protocols, data, models and results in a configurable system that is available 'off the shelf'. Tools to run model simulations, plot experimental data and assist with data annotation and standardisation combine to produce a collection of resources that support analysis as well as sharing. Underlying semantic web resources additionally extract and serve SEEK metadata in RDF (Resource Description Format). SEEK RDF enables rich semantic queries, both within SEEK and between related resources in the web of Linked Open Data.The SEEK platform has been adopted by many systems biology consortia across Europe. It is a data management environment that has a low barrier of uptake and provides rich resources for collaboration. This paper provides an update on the functions and features of the SEEK software, and describes the use of the SEEK in the SysMO consortium (Systems biology for Micro-organisms), and the VLN (virtual Liver Network), two large systems biology initiatives with different research aims and different scientific communities.

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Systems biologists seek fuller integration of systems biology approaches in new cancer research programs.

Publications

Systems biologists seek fuller integration of systems biology approaches in new cancer research programs.

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