The Systems Biology Simulation Core Library (SBSCL)[1][2] is an open-source, cross-platform pure Java™ programming library that supports the simulation and analysis of computational models encoded in SBML (Systems Biology Markup Language) and SED-ML (Simulation Experiment Description Markup Language) formats. SBSCL offers a robust and extensible Java-based implementation of numerical solvers and simulation algorithms, making it a valuable tool for researchers and developers in systems biology.
SBSCL, built on top of another open-source library, JSBML,[3][4] enables platform-independent model simulation across any environment supporting the Java Virtual Machine. It includes a comprehensive suite of numerical methods for solving ordinary differential equations and other dynamic behaviors described in biological models.
SBSCL is designed as a reusable software library and does not come with a GUI or a CLI by default. Instead, it is intended to be embedded into larger software projects where custom user interfaces can be developed as needed. Researchers can also integrate SBSCL directly into their Java projects via its Apache Maven or Gradle dependency to programmatically simulate SBML models.
Capabilities
SBSCL offers a wide range of features for simulating and analyzing computational models in systems biology.
1. Numerical simulation in an ordinary differential equation framework
LSODA-Integrator (Livermore Solver for Ordinary Differential Equation Automatic) for the simulation of models containing general ODEs
Rosenbrock solver for the integration of stiff differential equation systems
Support of models from the Stochastic Test Suite for all levels and versions
3. Linear optimization framework
Incorporation of external implementations of the simplex algorithm in libraries, such as Gurobi, CPLEX, and many more, supports simulating models via linear optimization.
All models from the SBML Test Suite and the BiGG models database
All models from the Stochastic Test Suite
Application
SBSCL has been part of the systems biology community for several years and its adoption has also increased widely with time, primarily in research environments for the simulation of SBML models.
It also hosts different SBML-related software like SBMLsimulator[6] and CellDesigner.[7]
It has also been used to model zinc transportation in Bacillus spp.[8] and to conduct research on engineering the non-oxidative glycolytic pathway in Streptomyces toxytricini[9]
↑Funahashi, Akira; Morohashi, Mineo; Kitano, Hiroaki; Tanimura, Naoki (November 2003). "CellDesigner: a process diagram editor for gene-regulatory and biochemical networks". Biosilico. 1 (5): 159–162. doi:10.1016/S1478-5382(03)02370-9.
↑Bhatt, Kalpana; Maheshwari, Dinesh Kumar (22 January 2022). "Insights into zinc-sensing metalloregulator 'Zur' deciphering mechanism of zinc transportation in Bacillus spp. by modeling, simulation and molecular docking". Journal of Biomolecular Structure and Dynamics. 40 (2): 764–779. doi:10.1080/07391102.2020.1818625. PMID32924811.
↑Jatain, Indu; Yadav, Karuna; Nitharwal, Ram Gopal; Arora, Devender; Dubey, Kashyap Kumar (September 2022). "A system biology approach for engineering non-oxidative glycolysis pathway in Streptomyces toxytricini for high lipstatin biosynthesis". Bioresource Technology Reports. 19 101188. Bibcode:2022BiTeR..1901188J. doi:10.1016/j.biteb.2022.101188.
