Systems Biology in ELIXIR: modelling in the spotlight
F1000Research, vol. 11, pp. 1265
Abstract
In this white paper, we describe the founding of a new ELIXIR Community - the Systems Biology Community - and its proposed future contributions to both ELIXIR and the broader community of systems biologists in Europe and worldwide. The Community believes that the infrastructure aspects of systems biology - databases, (modelling) tools and standards development, as well as training and access to cloud infrastructure - are not only appropriate components of the ELIXIR infrastructure, but will prove key components of ELIXIR's future support of advanced biological applications and personalised medicine. By way of a series of meetings, the Community identified seven key areas for its future activities, reflecting both future needs and previous and current activities within ELIXIR Platforms and Communities. These are: overcoming barriers to the wider uptake of systems biology; linking new and existing data to systems biology models; interoperability of systems biology resources; further development and embedding of systems medicine; provisioning of modelling as a service; building and coordinating capacity building and training resources; and supporting industrial embedding of systems biology. A set of objectives for the Community has been identified under four main headline areas: Standardisation and Interoperability, Technology, Capacity Building and Training, and Industrial Embedding. These are grouped into short-term (3-year), mid-term (6-year) and long-term (10-year) objectives.
Authors 37
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Vítor A. P. Martins dos Santos corresponding
Wageningen University & Research
Affiliation as printed
Laboratory of Bioprocess Engineering, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands
Laboratory of Bioprocess Engineering, Wageningen University & Research, Wageningen, 6708 PB
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Mihail Anton corresponding
Science for Life Laboratory · National Bioinformatics Infrastructure Sweden · Chalmers University of Technology
Affiliation as printed
Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Gothenburg, SE-41258, Sweden
Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Gothenburg, SE-41258
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Barbara Szomolay corresponding
Affiliation as printed
Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff
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Marek Ostaszewski corresponding
University of Luxembourg · Luxembourg Centre for Systems Biomedicine
Affiliation as printed
Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, L-4367, Luxembourg
Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, L-4367
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Ilja C.W. Arts corresponding
Affiliation as printed
Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6200 MD, The Netherlands
Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6200 MD
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Rui Benfeitas corresponding
Stockholm University · Science for Life Laboratory · National Bioinformatics Infrastructure Sweden
Affiliation as printed
National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm
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Victoria Domínguez Del Angel corresponding
Affiliation as printed
Research and Platforms Department, Genopole, Evry-Courcouronnes, 91030, France
Research and Platforms Department, Genopole, Evry-Courcouronnes, 91030
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Elena Domínguez-Romero corresponding
Affiliation as printed
Department of Bioinformatics, Maastricht University, Maastricht, The Netherlands
Department of Bioinformatics, Maastricht University, Maastricht
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Polonca Ferk corresponding
Affiliation as printed
Faculty of Medicine, Institute for Biostatistics and Medical Informatics, Centre ELIXIR-SI, University of Ljubljana, Ljubljana, SI-1000, Slovenia
Faculty of Medicine, Institute for Biostatistics and Medical Informatics, Centre ELIXIR-SI, University of Ljubljana, Ljubljana, SI-1000
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Dirk Fey corresponding
Affiliation as printed
Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, 4, Ireland
Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, 4
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Carole Goble corresponding
Affiliation as printed
Department of Computer Science, The University of Manchester, Manchester, M13 9PL, UK
Department of Computer Science, The University of Manchester, Manchester, M13 9PL
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Martin Golebiewski corresponding
Heidelberg Institute for Theoretical Studies
Affiliation as printed
Heidelberg Institute for Theoretical Studies - HITS, Heidelberg, 69118, Germany
Heidelberg Institute for Theoretical Studies - HITS, Heidelberg, 69118
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Kristina Gruden corresponding
Affiliation as printed
Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, SI-1000, Slovenia
Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, SI-1000
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Katharina F. Heil corresponding
Affiliation as printed
ELIXIR Hub, Hinxton, Cambridge, CB10 1SD, UK
ELIXIR Hub, Hinxton, Cambridge, CB10 1SD
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Henning Hermjakob corresponding
European Bioinformatics Institute
Affiliation as printed
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, UK
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD
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Pascal Kahlem corresponding
Affiliation as printed
Scientific Network Management SL, Barcelona, 08015, Spain
Scientific Network Management SL, Barcelona, 08015
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Maria I. Klapa corresponding
FORTH Institute of Chemical Engineering Sciences · Foundation for Research and Technology Hellas
Affiliation as printed
Metabolic Engineering & Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology - Hellas (FORTH/ICE-HT), Patras, 26504, Greece
Metabolic Engineering & Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology - Hellas (FORTH/ICE-HT), Patras, 26504
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Jasper J. Koehorst corresponding
Wageningen University & Research
Affiliation as printed
Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708WE, The Netherlands
Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708WE
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Alexey N. Kolodkin corresponding
Luxembourg Institute of Health · Vrije Universiteit Amsterdam
Affiliation as printed
Competence Center for Methodology and Statistics; Transversal Translational Medicine, Translational Medicine Operations Hub, Luxembourg Institute of Health, Strassen, L-1445, Luxembourg
ISBE.NL, VU University of Amsterdam, Amsterdam, The Netherlands
Competence Center for Methodology and Statistics
ISBE.NL, VU University of Amsterdam, Amsterdam
Transversal Translational Medicine, Translational Medicine Operations Hub, Luxembourg Institute of Health, Strassen, L-1445
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Martina Kutmon corresponding
Affiliation as printed
Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6200 MD, The Netherlands
Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6200 MD, The Netherlands
Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6200 MD
Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6200 MD
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Brane L. Leskošek corresponding
Affiliation as printed
Faculty of Medicine, Institute for Biostatistics and Medical Informatics, Centre ELIXIR-SI, University of Ljubljana, Ljubljana, SI-1000, Slovenia
Faculty of Medicine, Institute for Biostatistics and Medical Informatics, Centre ELIXIR-SI, University of Ljubljana, Ljubljana, SI-1000
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Sébastien Moretti corresponding
SIB Swiss Institute of Bioinformatics
Affiliation as printed
SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
SIB Swiss Institute of Bioinformatics, Lausanne
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Marco Pagni corresponding
SIB Swiss Institute of Bioinformatics
Affiliation as printed
SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
SIB Swiss Institute of Bioinformatics, Lausanne
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Tadeja Režen corresponding
Affiliation as printed
Faculty of Medicine, University of Ljubljana, Ljubljana, SI-1000, Slovenia
Faculty of Medicine, University of Ljubljana, Ljubljana, SI-1000
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Miguel Rocha corresponding
Affiliation as printed
Centre of Biological Engineering, University of Minho, Braga, Portugal
Centre of Biological Engineering, University of Minho, Braga
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Damjana Rozman corresponding
Affiliation as printed
Faculty of Medicine, University of Ljubljana, Ljubljana, SI-1000, Slovenia
Faculty of Medicine, University of Ljubljana, Ljubljana, SI-1000
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David Šafránek corresponding
Affiliation as printed
Faculty of Informatics, Masaryk University, Brno, 602 00, Czech Republic
Faculty of Informatics, Masaryk University, Brno, 602 00
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William Taussig Scott corresponding
Wageningen University & Research
Affiliation as printed
Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708WE, The Netherlands
UNLOCK, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708WE
UNLOCK, Wageningen University & Research, 6708 PB Wageningen
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Rahuman S. Malik‐Sheriff corresponding
European Bioinformatics Institute
Affiliation as printed
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, UK
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD
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Maria Suarez Diez corresponding
Wageningen University & Research
Affiliation as printed
Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708WE, The Netherlands
Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708WE
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Kristel Van Steen corresponding
University of Liège · KU Leuven
Affiliation as printed
BIO3 - Laboratory for Systems Medicine, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
BIO3 - Systems Genetics, GIGA-R Medical Genomics, University of Liege, Liege, 4000, Belgium
BIO3 - Laboratory for Systems Medicine, Department of Human Genetics, KU Leuven, Leuven, 3000
BIO3 - Systems Genetics, GIGA-R Medical Genomics, University of Liege, Liege, 4000
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Hans Victor Westerhoff corresponding
Affiliation as printed
ISBE.NL, VU University of Amsterdam, Amsterdam, The Netherlands
ISBE.NL, VU University of Amsterdam, Amsterdam
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Ulrike Wittig corresponding
Heidelberg Institute for Theoretical Studies
Affiliation as printed
Heidelberg Institute for Theoretical Studies - HITS, Heidelberg, 69118, Germany
Heidelberg Institute for Theoretical Studies - HITS, Heidelberg, 69118
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Affiliation as printed
Leiden Institute of Advanced Computer Science, Leiden University, Leiden, 2333 CA, The Netherlands
Leiden Institute of Advanced Computer Science, Leiden University, Leiden, 2333 CA
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Anže Županič corresponding
Affiliation as printed
Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, SI-1000, Slovenia
Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, SI-1000
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Chris T. Evelo corresponding
Affiliation as printed
Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6200 MD, The Netherlands
Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6200 MD
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John M. Hancock corresponding
Affiliation as printed
Faculty of Medicine, University of Ljubljana, Ljubljana, SI-1000, Slovenia
Faculty of Medicine, University of Ljubljana, Ljubljana, SI-1000
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