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Related Experiment Video

Updated: May 12, 2026

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

Published on: April 3, 2026

LibSBMLSim: a reference implementation of fully functional SBML simulator.

Hiromu Takizawa¹, Kazushige Nakamura, Akito Tabira

¹Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama, Japan.

Bioinformatics (Oxford, England)

|April 9, 2013

Summary

This summary is machine-generated.

A new library, libSBMLSim, supports all Systems Biology Markup Language (SBML) features for simulating ordinary differential equation (ODE) models. This language-neutral tool enhances computational biology platforms with its portable, platform-independent design.

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A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

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Published on: April 3, 2026

Area of Science:

Computational Biology
Systems Biology
Bioinformatics

Background:

Systems Biology Markup Language (SBML) is a standard for biochemical models, with over 230 supporting tools.
160 SBML-compatible tools support numerical integration of ordinary differential equation (ODE) models.
A need exists for a language-neutral library supporting all SBML features for ODE model simulation.

Purpose of the Study:

To develop a simple, portable numerical integration library for SBML.
To enhance the development of computational platforms for systems biology.

Main Methods:

Implemented libSBMLSim in C, relying only on libSBML for SBML document handling.
Developed explicit and implicit numerical integration methods from scratch.
Ensured support for all SBML features, including Events, AlgebraicRules, 'fast' attribute, and Delay.

Main Results:

libSBMLSim supports all SBML features and passes the SBML test suite.
The library is platform-independent, running on Windows, MacOSX, and Linux.
Multiple language bindings (Java, C#, Python, Ruby) are provided.

Conclusions:

libSBMLSim offers a comprehensive, language-neutral solution for SBML-based ODE model simulation.
The library's portability and broad feature support facilitate systems biology research.
libSBMLSim enhances the development of computational platforms in systems biology.