Preprint Technical Note Version 1 Preserved in Portico This version is not peer-reviewed

The Systems Biology Simulation Core Library

Hemil Panchiwala
ORCID logo ,
Shalin Shah
,
Hannes Planatscher
,
Mykola Zakharchuk
,
Matthias König
ORCID logo ,
Andreas Dräger
* ORCID logo
Version 1 : Received: 11 December 2020 / Approved: 11 December 2020 / Online: 11 December 2020 (19:41:58 CET)

A peer-reviewed article of this Preprint also exists.

Hemil Panchiwala, Shalin Shah, Hannes Planatscher, Mykola Zakharchuk, Matthias König, Andreas Dräger, The Systems Biology Simulation Core Library, Bioinformatics, 2021;, btab669, https://doi.org/10.1093/bioinformatics/btab669 Hemil Panchiwala, Shalin Shah, Hannes Planatscher, Mykola Zakharchuk, Matthias König, Andreas Dräger, The Systems Biology Simulation Core Library, Bioinformatics, 2021;, btab669, https://doi.org/10.1093/bioinformatics/btab669

Abstract

Summary: Studying biological systems generally relies on computational modeling and simulation, e.g., for model-driven discovery and hypothesis testing. Progress in standardization efforts led to the development of interrelated file formats to exchange and reuse models in systems biology, such as SBML, the Simulation Experiment Description Markup Language (SED-ML), or the Open Modeling EXchange format (OMEX). Conducting simulation experiments based on these formats requires efficient and reusable implementations to make them accessible to the broader scientific community and to ensure the reproducibility of the results. The Systems Biology Simulation Core Library (SBSCL) provides interpreters and solvers for these standards as a versatile open-source API in Java™. The library simulates even complex bio-models and supports deterministic Ordinary Differential Equations (ODEs); Stochastic Differential Equations (SDEs); constraint-based analyses; recent SBML and SED-ML versions; exchange of results, and visualization of in silico experiments; open modeling exchange formats (COMBINE archives); hierarchically structured models; and compatibility with standard testing systems, including the Systems Biology Test Suite and published models from the BioModels and BiGG databases. Availability and implementation: SBSCL is freely available at https://draeger-lab.github.io/SBSCL/.

Supplementary and Associated Material

https://draeger-lab.github.io/SBSCL/: Website of the Systems Biology Simulation Core Library

Keywords

Systems Biology; Numerical Solver; Java™; API Library; SBML; SED-ML; OMEX; Constraint-Based Modeling; Stochastic Simulation; Ordinary Differential Equation Systems

Subject

Computer Science and Mathematics, Algebra and Number Theory

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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