Biological data; Biomolecular Models; Biotechnology; ELIXIR Communities; FAIR; Network Biology; Systems Biology; Systems Medicine; Europe; Databases, Factual; Biochemistry, Genetics and Molecular Biology (all); Immunology and Microbiology (all); Pharmacology, Toxicology and Pharmaceutics (all); General Pharmacology, Toxicology and Pharmaceutics; General Immunology and Microbiology; General Biochemistry, Genetics and Molecular Biology; General Medicine
Abstract :
[en] 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.
Disciplines :
Life sciences: Multidisciplinary, general & others
Author, co-author :
Martins Dos Santos, Vitor; Laboratory of Bioprocess Engineering, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands
Anton, Mihail ; Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Gothenburg, SE-41258, Sweden
Szomolay, Barbara; Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
Ostaszewski, Marek; Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, L-4367, Luxembourg
Arts, Ilja; Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6200 MD, The Netherlands
Benfeitas, Rui; National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
Dominguez Del Angel, Victoria ; Research and Platforms Department, Genopole, Evry-Courcouronnes, 91030, France
Ferk, Polonca; Faculty of Medicine, Institute for Biostatistics and Medical Informatics, Centre ELIXIR-SI, University of Ljubljana, Ljubljana, SI-1000, Slovenia
Fey, Dirk; Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, 4, Ireland
Goble, Carole; Department of Computer Science, The University of Manchester, Manchester, M13 9PL, UK
Golebiewski, Martin ; Heidelberg Institute for Theoretical Studies - HITS, Heidelberg, 69118, Germany
Gruden, Kristina; Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, SI-1000, Slovenia
Heil, Katharina F ; ELIXIR Hub, Hinxton, Cambridge, CB10 1SD, UK
Hermjakob, Henning; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, UK
Klapa, Maria I ; Metabolic Engineering & Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology - Hellas (FORTH/ICE-HT), Patras, 26504, Greece
Koehorst, Jasper; Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708WE, The Netherlands
Kolodkin, Alexey ; ISBE.NL, VU University of Amsterdam, Amsterdam, The Netherlands ; Competence Center for Methodology and Statistics, Transversal Translational Medicine, Translational Medicine Operations Hub, Luxembourg Institute of Health, Strassen, L-1445, Luxembourg
Kutmon, Martina ; Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6200 MD, The Netherlands ; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6200 MD, The Netherlands
Leskošek, Brane; Faculty of Medicine, Institute for Biostatistics and Medical Informatics, Centre ELIXIR-SI, University of Ljubljana, Ljubljana, SI-1000, Slovenia
Moretti, Sébastien ; SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
Müller, Wolfgang; Heidelberg Institute for Theoretical Studies - HITS, Heidelberg, 69118, Germany
Pagni, Marco; SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
Rezen, Tadeja; Faculty of Medicine, University of Ljubljana, Ljubljana, SI-1000, Slovenia
Rocha, Miguel; Centre of Biological Engineering, University of Minho, Braga, Portugal
Rozman, Damjana; Faculty of Medicine, University of Ljubljana, Ljubljana, SI-1000, Slovenia
Šafránek, David ; Faculty of Informatics, Masaryk University, Brno, 602 00, Czech Republic
Sheriff, Rahuman S Malik ; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, UK
Suarez Diez, Maria ; Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708WE, The Netherlands
Van Steen, Kristel ; Université de Liège - ULiège > Département d'électricité, électronique et informatique (Institut Montefiore) > Bioinformatique ; BIO3 - Laboratory for Systems Medicine, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
Westerhoff, Hans V ; ISBE.NL, VU University of Amsterdam, Amsterdam, The Netherlands
Wittig, Ulrike ; Heidelberg Institute for Theoretical Studies - HITS, Heidelberg, 69118, Germany
Wolstencroft, Katherine ; Leiden Institute of Advanced Computer Science, Leiden University, Leiden, 2333 CA, The Netherlands
Zupanic, Anze ; Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, SI-1000, Slovenia
Evelo, Chris T ; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6200 MD, The Netherlands
Hancock, John M ; Faculty of Medicine, University of Ljubljana, Ljubljana, SI-1000, Slovenia
We thank ELIXIR for financial and administrative support during the development of this white paper and its support of the ELIXIR Systems Biology Focus Group.
Commentary :
Updated version 2024: https://doi.org/10.12688/f1000research.126734.2
