Journal of integrative bioinformatics

Welcome to JIB.tools!

The official bioinformatics tool list for the Journal of Integrative Bioinformatics (JIB).


All bioinformatics tools published in JIB are automatically added to JIB.tools with first authors having the ability to edit their entries and directly import the tools information to bio.tools.


SBMLToolkit.jl

Library 
Julia is a general purpose programming language that was designed for simplifying and accelerating numerical analysis and computational science. In particular the Scientific Machine Learning (SciML) ecosystem of Julia packages includes frameworks for high-performance symbolic-numeric computations. It allows users to automatically enhance high-level descriptions of their models with symbolic preprocessing and automatic sparsification and parallelization of computations. This enables performant solution of differential equations, efficient parameter estimation and methodologies for automated model discovery with neural differential equations and sparse identification of nonlinear dynamics. To give the systems biology community easy access to SciML, we developed SBMLToolkit.jl. SBMLToolkit.jl imports dynamic SBML models into the SciML ecosystem to accelerate model simulation and fitting of kinetic parameters. By providing computational systems biologists with easy access to the open-source Julia ecosystevnm, we hope to catalyze the development of further Julia tools in this domain and the growth of the Julia bioscience community. SBMLToolkit.jl is freely available under the MIT license. The source code is available at https://github.com/SciML/SBMLToolkit.jl.

JIB Publications
  • Lang PF, Jain A, Rackauckas C. SBMLToolkit.jl: a Julia package for importing SBML into the SciML ecosystem.. J Integr Bioinform. 2024;. doi 10.1515/jib-2024-0003; PubMed 38801698
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