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biomodelsed

A graphical editor for systems biology models.

bofdat

Generate biomass objective function stoichiometric coefficients for genome-scale models from experimental data

c_striatum_gems

This repository contains all changes made to the strain specific models of Corynebacterium striatum.

c_striatum_wetlab

This repository contains data generated in the wet lab need for characterization and validation of strain specific GEMs

escherconverter

A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.

fern

FERN (Framework for Evaluation of Reaction Networks) is an extensible and comprehensive framework for efficient simulations and analysis of chemical reaction networks written in Java.

incromap

Integrated analysis of Cross-platform MicroArray and Pathway data

insilico

InSilico

insilico-docs

InSilico Docs

insilico-lab-pages

keggtranslator

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.

krayon4insilico

krayon4sbgn

A yFiles-based editor for SBGN diagrams written in Kotlin

modeleditingtools

A collection of tools for working with models in SBML format

modelpolisher

ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.

pymcadre

pymCADRE enables the reconstruction of tissue-specific metabolic models in Python using transcriptomic data and information of the network topology.

pymcadre-1

pymCADRE enables the reconstruction of tissue-specific metabolic models in Python using transcriptomic data and information of the network topology.

r-drugs

Rationalized Discovery of Robust antiviral targets Using Genome-scale model Systems

refinegems

refineGEMs is a python package inteded to help with the curation of genome-scale metabolic models (GEMS).

sabine

Prediction of the binding specificity of transcription factors using support vector regression

sbml2latex

SBML2LATEX is a tool to convert files in the System Biology Markup Language SBML) format into LATEX files. A convenient online version is available, which allows the user to directly generate report from SBML in form of PDF or TeX, which can be further processed to various file types including DVI, PS, EPS, GIF, JPG, or PNG. SBML2LATEX can also be downloaded and used locally in batch mode or interactively with its Graphical User Interface or several command line options. The purpose of SBML2LATEX is to provide a way to read the contents of XML-based SBML files. This is helpful and important for, e.g., error detection, proofreading and model communication.

sbmlme

Encoding ME models in SBML

sbmlsimulator

An efficient Java™ solver implementation for SBML

sbmlsqueezer

Context-sensitive creation of kinetic equations in biochemical networks

sboannotator

SBOannotator: A Python tool for the automated assignment of Systems Biology Onotology terms

sbscl

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.

sbscl-demo

A demo repository with example code for using the Systems Biology Simulation Core Library (SBSCL).

sbtabeditor

Cross platform highly-extensible JavaFx based application which provides functions for reading, writing, manipulating, and validating SBML files.

sbvc

Systems Biology Visualizer and Converter

specimen

Automated pipeline for strain-specific metabolic modeling based on a high-quality template model.