James C Schaff
Overview
Explore the profile of James C Schaff including associated specialties, affiliations and a list of published articles.
Author names and details appear as published. Due to indexing inconsistencies, multiple individuals may share a name, and a single author may have variations. MedLuna displays this data as publicly available, without modification or verification
Snapshot
Snapshot
Articles
21
Citations
934
Followers
0
Related Specialties
Related Specialties
Top 10 Co-Authors
Top 10 Co-Authors
Published In
Published In
Affiliations
Affiliations
Soon will be listed here.
Recent Articles
1.
Sauro H, Agmon E, Blinov M, Gennari J, Hellerstein J, Heydarabadipour A, et al.
ArXiv
. 2025 Mar;
PMID: 40034129
Guidelines for managing scientific data have been established under the FAIR principles requiring that data be Findable, Accessible, Interoperable, and Reusable. In many scientific disciplines, especially computational biology, both data...
2.
Smith L, Malik-Sheriff R, Nguyen T, Hermjakob H, Karr J, Shaikh B, et al.
bioRxiv
. 2025 Feb;
PMID: 39896466
The BioModels Repository contains over 1000 manually curated mechanistic models drawn from published literature, most of which are encoded in the Systems Biology Markup Language (SBML). This community-based standard formally...
3.
BioSimulators: a central registry of simulation engines and services for recommending specific tools
Shaikh B, Smith L, Vasilescu D, Marupilla G, Wilson M, Agmon E, et al.
Nucleic Acids Res
. 2022 May;
50(W1):W108-W114.
PMID: 35524558
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating...
4.
Keating S, Waltemath D, Konig M, Zhang F, Drager A, Chaouiya C, et al.
Mol Syst Biol
. 2020 Aug;
16(8):e9110.
PMID: 32845085
Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review...
5.
Hucka M, Bergmann F, Chaouiya C, Drager A, Hoops S, Keating S, et al.
J Integr Bioinform
. 2019 Jun;
16(2).
PMID: 31219795
Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in...
6.
Hucka M, Bergmann F, Drager A, Hoops S, Keating S, Le Novere N, et al.
J Integr Bioinform
. 2018 Mar;
15(1).
PMID: 29522418
Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in...
7.
Blinov M, Schaff J, Vasilescu D, Moraru I, Bloom J, Loew L
Biophys J
. 2017 Oct;
113(7):1365-1372.
PMID: 28978431
In rule-based modeling, molecular interactions are systematically specified in the form of reaction rules that serve as generators of reactions. This provides a way to account for all the potential...
8.
Schaff J, Gao F, Li Y, Novak I, Slepchenko B
PLoS Comput Biol
. 2016 Dec;
12(12):e1005236.
PMID: 27959915
Hybrid deterministic-stochastic methods provide an efficient alternative to a fully stochastic treatment of models which include components with disparate levels of stochasticity. However, general-purpose hybrid solvers for spatially resolved simulations...
9.
Schaff J, Vasilescu D, Moraru I, Loew L, Blinov M
Bioinformatics
. 2016 Aug;
32(18):2880-2.
PMID: 27497444
Unlabelled: Rule-based modeling is invaluable when the number of possible species and reactions in a model become too large to allow convenient manual specification. The popular rule-based software tools BioNetGen...
10.
Hucka M, Bergmann F, Drager A, Hoops S, Keating S, Le Novere N, et al.
J Integr Bioinform
. 2015 Nov;
12(2):271.
PMID: 26528569
Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in...