Evidence map›Paper›PMID 36742342›Full record

ArticleF1000Research2022

Systems Biology in ELIXIR: modelling in the spotlight.

Vitor Martins Dos Santos, Mihail Anton, Barbara Szomolay, Marek Ostaszewski, Ilja Arts, Rui Benfeitas, Victoria Dominguez Del Angel, Elena Domínguez-Romero, Polonca Ferk, Dirk Fey and 28 more

Abstract read
In one paragraph

Article in F1000Research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed.

  1. AI-powered in silico twins: redefining precision medicine through simulation, personalization, and predictive healthcare.Saudi pharmaceutical journal : SPJ : the official publication of the Saudi Pharmaceutical Society · 2025
    Review
  2. Article
  3. Making PBPK models more reproducible in practice.Briefings in bioinformatics · 2024
    Article
  4. Article
  5. What's next for computational systems biology?Frontiers in systems biology · 2023
    Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

38 authors.

Vitor Martins Dos SantosLaboratory of Bioprocess Engineering, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands.
Mihail AntonDepartment of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Gothenburg, SE-41258, Sweden.ORCID https://orcid.org/0000-0002-7753-9042
Barbara SzomolayDivision of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK.
Marek OstaszewskiLuxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, L-4367, Luxembourg.
Ilja ArtsMaastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6200 MD, The Netherlands.
Rui BenfeitasNational Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
Victoria Dominguez Del AngelResearch and Platforms Department, Genopole, Evry-Courcouronnes, 91030, France.
Elena Domínguez-RomeroDepartment of Bioinformatics, Maastricht University, Maastricht, The Netherlands.
Polonca FerkFaculty of Medicine, Institute for Biostatistics and Medical Informatics, Centre ELIXIR-SI, University of Ljubljana, Ljubljana, SI-1000, Slovenia.
Dirk FeySystems Biology Ireland, School of Medicine, University College Dublin, Dublin, 4, Ireland.
Carole GobleDepartment of Computer Science, The University of Manchester, Manchester, M13 9PL, UK.
Martin GolebiewskiHeidelberg Institute for Theoretical Studies - HITS, Heidelberg, 69118, Germany.ORCID https://orcid.org/0000-0002-8683-7084
Kristina GrudenDepartment of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, SI-1000, Slovenia.
Katharina F HeilELIXIR Hub, Hinxton, Cambridge, CB10 1SD, UK.ORCID https://orcid.org/0000-0003-3341-3736
Henning HermjakobEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, UK.
Pascal KahlemScientific Network Management SL, Barcelona, 08015, Spain.ORCID https://orcid.org/0000-0002-8810-444X
Maria I KlapaMetabolic Engineering & Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology - Hellas (FORTH/ICE-HT), Patras, 26504, Greece.ORCID https://orcid.org/0000-0002-2047-3185
Jasper KoehorstLaboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708WE, The Netherlands.
Alexey KolodkinCompetence Center for Methodology and Statistics; Transversal Translational Medicine, Translational Medicine Operations Hub, Luxembourg Institute of Health, Strassen, L-1445, Luxembourg.ORCID https://orcid.org/0000-0002-7466-5027
Martina KutmonMaastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6200 MD, The Netherlands.ORCID https://orcid.org/0000-0002-7699-8191
Brane LeskošekFaculty of Medicine, Institute for Biostatistics and Medical Informatics, Centre ELIXIR-SI, University of Ljubljana, Ljubljana, SI-1000, Slovenia.
Sébastien MorettiSIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.ORCID https://orcid.org/0000-0003-3947-488X
Wolfgang MüllerHeidelberg Institute for Theoretical Studies - HITS, Heidelberg, 69118, Germany.
Marco PagniSIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Tadeja RezenFaculty of Medicine, University of Ljubljana, Ljubljana, SI-1000, Slovenia.
Miguel RochaCentre of Biological Engineering, University of Minho, Braga, Portugal.
Damjana RozmanFaculty of Medicine, University of Ljubljana, Ljubljana, SI-1000, Slovenia.
David ŠafránekFaculty of Informatics, Masaryk University, Brno, 602 00, Czech Republic.ORCID https://orcid.org/0000-0002-0713-2431
William T ScottLaboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708WE, The Netherlands.ORCID https://orcid.org/0000-0002-4029-2998
Rahuman S Malik SheriffEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, UK.ORCID https://orcid.org/0000-0003-0705-9809
Maria Suarez DiezLaboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708WE, The Netherlands.ORCID https://orcid.org/0000-0001-5845-146X
Kristel Van SteenBIO3 - Laboratory for Systems Medicine, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium.
Hans V WesterhoffISBE.NL, VU University of Amsterdam, Amsterdam, The Netherlands.ORCID https://orcid.org/0000-0002-0443-6114
Ulrike WittigHeidelberg Institute for Theoretical Studies - HITS, Heidelberg, 69118, Germany.ORCID https://orcid.org/0000-0002-9077-5664
Katherine WolstencroftLeiden Institute of Advanced Computer Science, Leiden University, Leiden, 2333 CA, The Netherlands.ORCID https://orcid.org/0000-0002-1279-5133
Anze ZupanicDepartment of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, SI-1000, Slovenia.ORCID https://orcid.org/0000-0003-3303-9086
Chris T EveloDepartment of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6200 MD, The Netherlands.ORCID https://orcid.org/0000-0002-5301-3142
John M HancockFaculty of Medicine, University of Ljubljana, Ljubljana, SI-1000, Slovenia.ORCID https://orcid.org/0000-0003-2991-2217

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

Biological dataBiomolecular ModelsBiotechnologyELIXIR CommunitiesFAIRNetwork BiologySystems BiologySystems Medicine

Identifiers

PMID36742342
PMCPMC9871403

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.