Programmatic modeling for biological systems.
Journal
Current opinion in systems biology
ISSN: 2452-3100
Titre abrégé: Curr Opin Syst Biol
Pays: England
ID NLM: 101698476
Informations de publication
Date de publication:
Sep 2021
Sep 2021
Historique:
entrez:
6
9
2021
pubmed:
7
9
2021
medline:
7
9
2021
Statut:
ppublish
Résumé
Computational modeling has become an established technique to encode mathematical representations of cellular processes and gain mechanistic insights that drive testable predictions. These models are often constructed using graphical user interfaces or domain-specific languages, with community standards used for interchange. Models undergo steady state or dynamic analysis, which can include simulation and calibration within a single application, or transfer across various tools. Here, we describe a novel programmatic modeling paradigm, whereby modeling is augmented with software engineering best practices. We focus on Python - a popular programming language with a large scientific package ecosystem. Models can be encoded as programs, adding benefits such as modularity, testing, and automated documentation generators, while still being extensible and exportable to standardized formats for use with external tools if desired. Programmatic modeling is a key technology to enable collaborative model development and enhance dissemination, transparency, and reproducibility.
Identifiants
pubmed: 34485764
doi: 10.1016/j.coisb.2021.05.004
pmc: PMC8411905
mid: NIHMS1708200
pii:
doi:
Types de publication
Journal Article
Langues
eng
Subventions
Organisme : NCI NIH HHS
ID : U01 CA215845
Pays : United States
Organisme : NCI NIH HHS
ID : U54 CA217450
Pays : United States
Références
Bioinformatics. 2011 Sep 1;27(17):2457-8
pubmed: 21727139
Nat Methods. 2011 Feb;8(2):177-83
pubmed: 21186362
Nature. 2018 Nov;563(7729):145-146
pubmed: 30375502
Bioinformatics. 2009 Sep 15;25(18):2452-4
pubmed: 19578039
J Integr Bioinform. 2020 Jul 24;17(2-3):
pubmed: 32759406
PLoS Comput Biol. 2021 Jan 28;17(1):e1008208
pubmed: 33507922
Bioinformatics. 2017 Nov 1;33(21):3492-3494
pubmed: 28666314
Endocr Relat Cancer. 2019 Jun;26(6):R345-R368
pubmed: 30965282
J R Soc Interface. 2009 Mar 6;6(32):257-70
pubmed: 18647734
Prog Biophys Mol Biol. 1977;32(1):1-82
pubmed: 343173
PLoS Comput Biol. 2018 Feb 23;14(2):e1005991
pubmed: 29474446
BMC Syst Biol. 2013 Aug 08;7:74
pubmed: 23927696
Annu Rev Biophys. 2020 May 6;49:1-18
pubmed: 31913665
Dev Dyn. 2020 Mar;249(3):383-409
pubmed: 32034817
Mol Syst Biol. 2020 Aug;16(8):e9110
pubmed: 32845085
Bioinformatics. 2019 Jan 1;35(1):167-169
pubmed: 30561545
Mol Syst Biol. 2013;9:646
pubmed: 23423320
Annu Rev Phys Chem. 2007;58:35-55
pubmed: 17037977
Cell Syst. 2020 Aug 26;11(2):109-120
pubmed: 32853539
PLoS Comput Biol. 2007 Oct;3(10):1871-78
pubmed: 17922568
Bioinformatics. 2010 Jul 15;26(14):1797-9
pubmed: 20591907
Bioinformatics. 2016 Nov 1;32(21):3366-3368
pubmed: 27402907
PLoS Comput Biol. 2020 Dec 28;16(12):e1008492
pubmed: 33370258
Eur J Biochem. 1974 Feb 15;42(1):89-95
pubmed: 4830198
BMC Bioinformatics. 2010 Jul 30;11:404
pubmed: 20673321
Bioinformatics. 2006 Dec 15;22(24):3067-74
pubmed: 17032683
PLoS Comput Biol. 2015 Aug 27;11(8):e1004321
pubmed: 26313928
Curr Opin Syst Biol. 2018 Feb;7:8-15
pubmed: 29806041
PLoS One. 2017 May 11;12(5):e0177459
pubmed: 28494014
Nat Protoc. 2019 Mar;14(3):639-702
pubmed: 30787451
Proc Natl Acad Sci U S A. 1991 Aug 15;88(16):7328-32
pubmed: 1831270
Nat Methods. 2020 Mar;17(3):261-272
pubmed: 32015543
J Integr Bioinform. 2020 Jul 6;17(2-3):
pubmed: 32628633
Mol Syst Biol. 2017 Nov 24;13(11):954
pubmed: 29175850
Curr Opin Biotechnol. 2008 Aug;19(4):389-95
pubmed: 18620054
Bioinformatics. 2021 Jul 14;:
pubmed: 34260697
Nat Methods. 2012 Jan 29;9(3):283-9
pubmed: 22286385
iScience. 2019 Sep 27;19:1012-1036
pubmed: 31522114
Bioinformatics. 2018 Feb 15;34(4):695-697
pubmed: 29028896
Curr Opin Syst Biol. 2019 Dec;18:9-18
pubmed: 32719822
Bioinformatics. 2017 Mar 1;33(5):710-717
pubmed: 28365760
Bioinformatics. 2018 Jul 1;34(13):i583-i592
pubmed: 29950016
Wiley Interdiscip Rev Syst Biol Med. 2014 Sep-Oct;6(5):353-69
pubmed: 25269159
NPJ Syst Biol Appl. 2019 Jul 18;5:23
pubmed: 31341635
iScience. 2020 Jan 24;23(1):100748
pubmed: 31884165
Bioinformatics. 2020 Aug 1;36(15):4377-4378
pubmed: 32437515
Mol Syst Biol. 2009;5:239
pubmed: 19156131
Bioinformatics. 2015 Oct 15;31(20):3315-21
pubmed: 26085503
Syst Biol (Stevenage). 2006 Sep;153(5):375-8
pubmed: 16986321
J Integr Bioinform. 2018 Mar 19;15(1):
pubmed: 29550789
Sci Rep. 2016 Jul 15;6:29635
pubmed: 27417285
Front Genet. 2020 Jul 10;11:686
pubmed: 32754196
Science. 2020 Jan 24;367(6476):392-396
pubmed: 31974245
Curr Opin Biotechnol. 2021 Feb;67:35-41
pubmed: 33360621
PLoS Comput Biol. 2016 Dec 8;12(12):e1005220
pubmed: 27930676
Nature. 2019 Aug;572(7771):586
pubmed: 31455911
SIAM J Sci Comput. 2016;38(3):C179-C202
pubmed: 28190948
Symp Soc Exp Biol. 1973;27:65-104
pubmed: 4148886
Nat Biotechnol. 2020 Mar;38(3):272-276
pubmed: 32123384
Bioinformatics. 2016 Jan 15;32(2):309-11
pubmed: 26415722
Bioinformatics. 2005 Feb 15;21(4):560-1
pubmed: 15454409