Systems Biology in ELIXIR: modelling in the spotlight.
Biological data
Biomolecular Models
Biotechnology
ELIXIR Communities
FAIR
Network Biology
Systems Biology
Systems Medicine
Journal
F1000Research
ISSN: 2046-1402
Titre abrégé: F1000Res
Pays: England
ID NLM: 101594320
Informations de publication
Date de publication:
2022
2022
Historique:
accepted:
24
10
2022
entrez:
6
2
2023
pubmed:
7
2
2023
medline:
8
2
2023
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 36742342
doi: 10.12688/f1000research.126734.1
pmc: PMC9871403
pii:
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
Copyright: © 2022 Martins dos Santos V et al.
Déclaration de conflit d'intérêts
No competing interests were disclosed.
Références
Mol Syst Biol. 2015 Dec 23;11(12):851
pubmed: 26700851
Nucleic Acids Res. 2020 Jan 8;48(D1):D445-D453
pubmed: 31586394
Bioinformatics. 2016 Feb 15;32(4):563-70
pubmed: 26490504
Nat Biotechnol. 2010 Dec;28(12):1248-50
pubmed: 21139605
Nucleic Acids Res. 2022 Jan 7;50(D1):D687-D692
pubmed: 34788843
Sci Data. 2016 Mar 15;3:160018
pubmed: 26978244
Sci Data. 2018 May 08;5:180029
pubmed: 29737976
Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50
pubmed: 16199517
FEBS J. 2022 Jan;289(1):90-101
pubmed: 33755310
Bioinformatics. 2016 Feb 15;32(4):638-40
pubmed: 26508761
Nucleic Acids Res. 2019 Jan 8;47(D1):D330-D338
pubmed: 30395331
Science. 2009 Apr 3;324(5923):85-9
pubmed: 19342587
Nucleic Acids Res. 2019 Jan 8;47(D1):D1038-D1043
pubmed: 30445645
Methods Mol Biol. 2009;500:17-59
pubmed: 19399433
Pharm Res. 2005 Sep;22(9):1432-7
pubmed: 16132354
Nucleic Acids Res. 2021 Jan 8;49(D1):D570-D574
pubmed: 33156326
CPT Pharmacometrics Syst Pharmacol. 2017 Feb;6(2):71-72
pubmed: 28035755
Sci Signal. 2020 Mar 24;13(624):
pubmed: 32209698
Bioinformatics. 2017 May 15;33(10):1589-1590
pubmed: 28130238
Cell Death Differ. 2018 Nov;25(11):1952-1966
pubmed: 29500433
F1000Res. 2018 Jun 29;7:
pubmed: 30271575
Nucleic Acids Res. 2018 Jan 4;46(D1):D1266-D1270
pubmed: 29069414
Nucleic Acids Res. 2021 Jan 8;49(D1):D498-D508
pubmed: 33211880
Nucleic Acids Res. 2020 Jan 8;48(D1):D407-D415
pubmed: 31701150
Nucleic Acids Res. 2001 Jan 1;29(1):308-11
pubmed: 11125122
Trends Microbiol. 2019 Jun;27(6):524-537
pubmed: 30819548
BMC Syst Biol. 2015 Jul 11;9:33
pubmed: 26160520
J Pers Med. 2022 Jan 26;12(2):
pubmed: 35207655
Sci Signal. 2015 Dec 22;8(408):ra130
pubmed: 26696630
Nat Biotechnol. 2010 Sep;28(9):935-42
pubmed: 20829833
Nucleic Acids Res. 2019 Jan 8;47(D1):D711-D715
pubmed: 30357387
Bioinformatics. 2017 Aug 15;33(16):2580-2582
pubmed: 28379341
IEEE Trans Biomed Eng. 2016 Oct;63(10):2007-14
pubmed: 27305665
PLoS Comput Biol. 2021 Jan 28;17(1):e1007900
pubmed: 33507915
Nucleic Acids Res. 2021 Jan 8;49(D1):D516-D522
pubmed: 33174603
Nat Biotechnol. 2013 May;31(5):419-25
pubmed: 23455439
Nucleic Acids Res. 2018 Jan 4;46(D1):D656-D660
pubmed: 29092055
ACS Chem Neurosci. 2018 Jan 17;9(1):118-129
pubmed: 28950062
NPJ Syst Biol Appl. 2016 Sep 22;2:16020
pubmed: 28725475
Environ Res. 2020 Mar;182:108948
pubmed: 31841869
Big Data. 2016 Jun;4(2):97-108
pubmed: 27441714
Nucleic Acids Res. 2021 Jan 8;49(D1):D613-D621
pubmed: 33211851
Mol Syst Biol. 2021 Oct;17(10):e10387
pubmed: 34664389
Genome Res. 2003 Nov;13(11):2498-504
pubmed: 14597658
Cell. 2018 Apr 5;173(2):283-285
pubmed: 29625045
J Pharm Sci. 1992 Jun;81(6):605-10
pubmed: 1355792
Curr Opin Syst Biol. 2017 Apr;2:67-73
pubmed: 28989987
J Integr Bioinform. 2020 Jun 29;17(2-3):
pubmed: 32598315
Nucleic Acids Res. 2017 Jan 4;45(D1):D945-D954
pubmed: 27899562
Nucleic Acids Res. 2021 Jan 8;49(D1):D605-D612
pubmed: 33237311
Bioinformatics. 2020 Nov 1;36(17):4649-4654
pubmed: 32573648
Bioinform Biol Insights. 2020 Jan 31;14:1177932219899051
pubmed: 32076369
Netw Syst Med. 2021 Feb 25;4(1):2-50
pubmed: 33659919
Mol Syst Biol. 2020 Feb;16(2):e8664
pubmed: 32073727
Mol Syst Biol. 2021 Feb;17(2):e9982
pubmed: 33620773
Cell Syst. 2018 Dec 26;7(6):567-579.e6
pubmed: 30503647
Pharmacol Ther. 2020 Aug;212:107555
pubmed: 32320730
Bioinformatics. 2017 Jul 15;33(14):i311-i318
pubmed: 28881985
Bioinformatics. 2020 May 1;36(10):3290-3291
pubmed: 32044952
NPJ Syst Biol Appl. 2018 Jun 2;4:21
pubmed: 29872544
J Integr Bioinform. 2020 Jun 29;17(2-3):
pubmed: 32598316
Interface Focus. 2016 Apr 6;6(2):20150103
pubmed: 27051515
BMC Bioinformatics. 2010 Jan 04;11:5
pubmed: 20047655
J Cheminform. 2017 Jun 6;9(1):33
pubmed: 29086040
Nucleic Acids Res. 2017 Jan 4;45(D1):D404-D407
pubmed: 27899646
Nucleic Acids Res. 2008 Jan;36(Database issue):D480-4
pubmed: 18077471
Nat Biotechnol. 2020 Mar;38(3):272-276
pubmed: 32123384
Front Bioeng Biotechnol. 2015 Feb 24;3:19
pubmed: 25759811
Nucleic Acids Res. 2016 Jan 4;44(D1):D38-47
pubmed: 26538599
Nucleic Acids Res. 2020 Jan 8;48(D1):D489-D497
pubmed: 31647099
Nucleic Acids Res. 2020 Jan 8;48(D1):D440-D444
pubmed: 31691833
Methods Mol Biol. 2019;2049:285-314
pubmed: 31602618