Topic: sbml Goto Github
Some thing interesting about sbml
Some thing interesting about sbml
sbml,Advanced Multilanguage Interface to CVODES and IDAS
Organization: amici-dev
Home Page: https://amici.readthedocs.io/
sbml,A collection of mathematical models with experimental data in the PEtab format as benchmark problems in order to evaluate new and existing methodologies for data-based modelling
Organization: benchmarking-initiative
sbml,A platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results
Organization: biosimulations
Home Page: https://biosimulations.org
sbml,Registry of containerized biosimulation tools that support a standard command-line interface
Organization: biosimulators
Home Page: https://biosimulators.org
sbml,Tool for validating that biosimulation software tools implement the BioSimulators standards for simulators
Organization: biosimulators
Home Page: https://docs.biosimulators.org/Biosimulators_test_suite/
sbml,Python package for managing systems and subsystems of SBML models
Organization: buildacell
sbml,SBML parser + bindings to python
User: carrascomj
Home Page: https://docs.rs/rust_sbml
sbml,An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!
Organization: cnapy-org
Home Page: https://cnapy-org.github.io/CNApy-guide/
sbml,Documentation, models and code relating to the 3rd edition of the textbook Stochastic Modelling for Systems Biology
User: darrenjw
Home Page: https://darrenjw.github.io/work/smfsb/3e/
sbml,A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.
Organization: draeger-lab
Home Page: https://draeger-lab.github.io/EscherConverter/
sbml,A Java-based software for visualizing and translating the KEGG PATHWAY database. Conversion of KGML files into BioPAX, SBML, GraphML, GML, and various other formats.
Organization: draeger-lab
sbml,ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.
Organization: draeger-lab
sbml,Encoding ME models in SBML
Organization: draeger-lab
sbml,The Systems Biology Simulation Core Library (SBSCL) provides an efficient and exhaustive Java implementation of methods to interpret the content of models encoded in the Systems Biology Markup Language (SBML) and its numerical solution.
Organization: draeger-lab
Home Page: https://draeger-lab.github.io/SBSCL/
sbml,Cross platform highly-extensible JavaFx based application which provides functions for reading, writing, manipulating, and validating SBML files.
Organization: draeger-lab
Home Page: https://draeger-lab.github.io/SBTabEditor/
sbml,The Systems Biology Ontology (SBO) is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modeling.
Organization: ebi-biomodels
sbml,libraries & tools for spatial simulation of SBML models
User: fbergmann
sbml,A simulator for biological and physiological models
Organization: flintproject
Home Page: https://flintsimulator.org
sbml,Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease of the adult, characterized by degeneration of motor neurons in the spinal cord, brain stem and motor cortex. There is no bio-informatic model of ALS.
User: hjertesvikt
sbml,Parameter estimation for dynamical models using high-performance computing, batch and mini-batch optimizers, and dynamic load balancing.
Organization: icb-dcm
sbml,A web application to visualize and edit pathway models
Organization: ivis-at-bilkent
Home Page: http://newteditor.org
sbml,Julia interface to the Systems Biology Markup Language (SBML) library
Organization: lcsb-biocore
Home Page: https://lcsb-biocore.github.io/SBML.jl/stable
sbml,LibSBMLSim: A library for simulating SBML models
Organization: libsbmlsim
Home Page: http://fun.bio.keio.ac.jp/software/libsbmlsim/
sbml,mergem is a python package and command-line tool for merging, comparing, and translating genome-scale metabolic models
Organization: lobolab
Home Page: https://lobolab.umbc.edu/mergem/
sbml,Jupyter widget for the dynamic and static visualizations of systems biology models written in PySB, BNGL, and SBML
Organization: lolab-msm
sbml,cy3sbml: SBML for Cytoscape 3
User: matthiaskoenig
sbml,Encoding Dynamic Flux Balance Analysis in SBML
User: matthiaskoenig
sbml,FROG analysis in python for the reproducibility of FBC models
User: matthiaskoenig
Home Page: https://runfrog.de
sbml,Python utilities for SBML
User: matthiaskoenig
Home Page: https://sbmlutils.readthedocs.io/en/stable/
sbml,Export from NeuroML & LEMS
Organization: neuroml
Home Page: http://neuroml.org
sbml,COBRApy is a package for constraint-based modeling of metabolic networks.
Organization: opencobra
Home Page: http://opencobra.github.io/cobrapy/
sbml,memote – the genome-scale metabolic model test suite
Organization: opencobra
Home Page: https://memote.readthedocs.io/
sbml,Python package for working with PEtab files
Organization: petab-dev
Home Page: https://libpetab-python.readthedocs.io
sbml,PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology
Organization: petab-dev
Home Page: https://petab.readthedocs.io
sbml,The official PySCeS project source code repository.
Organization: pysces
Home Page: https://pysces.github.io
sbml,JSBML is a community-driven project to create a free, open-source, pure Java™ library for reading, writing, and manipulating SBML files (the Systems Biology Markup Language) and data streams. It is an alternative to the mixed Java/native code-based interface provided in libSBML.
Organization: sbmlteam
Home Page: https://sbml.org/software/jsbml/
sbml,LibSBML is a native library for reading, writing and manipulating files and data streams containing the Systems Biology Markup Language (SBML). It offers language bindings for C, C++, C#, Java, JavaScript, MATLAB, Perl, PHP, Python, R and Ruby.
Organization: sbmlteam
Home Page: https://sbml.org/software/libsbml
sbml,MOCCASIN translates basic ODE-based MATLAB models of biological processes into SBML format.
Organization: sbmlteam
Home Page: http://sbml.org/Software/MOCCASIN
sbml,Standalone Python package containing libSBML with support for SBML Level 3 Core and accepted SBML Level 3 packages.
Organization: sbmlteam
Home Page: https://sbml.org/software/libsbml/
sbml,The source code and issue tracker for the SBML.org website.
Organization: sbmlteam
Home Page: https://sbml.org
sbml,Repository of models to test exchange of sbml-spatial models.
Organization: sbmlteam
sbml,The SBML Test Suite is a conformance testing system. It allows developers and users to test the degree and correctness of the SBML support provided in a software package.
Organization: sbmlteam
Home Page: https://sbml.org/software/sbml-test-suite/
sbml,SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit
Organization: sciml
Home Page: https://docs.sciml.ai/SBMLToolkit/stable/
sbml,INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.
Organization: sorgerlab
Home Page: http://indra.bio
sbml,Spatial bio-chemical reaction model editor and simulator
Organization: spatial-model-editor
Home Page: https://spatial-model-editor.github.io
sbml,XitoSBML - the spatial SBML plugin for ImageJ
Organization: spatialsimulator
sbml,Python package for building SBML models without needing to use libSBML.
Organization: sys-bio
Home Page: http://simplesbml.readthedocs.io/en/latest/
sbml,CBMPy is a Python based platform for constraint based modelling and analysis.
Organization: systemsbioinformatics
Home Page: https://systemsbioinformatics.github.io/cbmpy/
sbml,Tool to convert an ODE model specified in the YAML format to SBML.
Organization: yaml2sbml-dev
Home Page: https://yaml2sbml.readthedocs.io/en/latest/
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