Dräger Lab
Computational Systems Biology Lab within the Institute for Bioinformatics and Medical Informatics (IBMI) of the University of Tübingen
Sand 14, 72076 Tübingen
Pinned Repositories
EscherConverter
A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.
insilico
InSilico
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.
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.
refinegems
refineGEMs is a python package inteded to help with the curation of genome-scale metabolic models (GEMS).
SBMLme
Encoding ME models in SBML
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.
SBTabEditor
Cross platform highly-extensible JavaFx based application which provides functions for reading, writing, manipulating, and validating SBML files.
Dräger Lab's Repositories
draeger-lab/ModelPolisher
ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.
draeger-lab/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.
draeger-lab/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.
draeger-lab/EscherConverter
A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.
draeger-lab/pymCADRE
pymCADRE enables the reconstruction of tissue-specific metabolic models in Python using transcriptomic data and information of the network topology.
draeger-lab/refinegems
refineGEMs is a python package inteded to help with the curation of genome-scale metabolic models (GEMS).
draeger-lab/SBTabEditor
Cross platform highly-extensible JavaFx based application which provides functions for reading, writing, manipulating, and validating SBML files.
draeger-lab/insilico
InSilico
draeger-lab/SBMLme
Encoding ME models in SBML
draeger-lab/SBOannotator
SBOannotator: A Python tool for the automated assignment of Systems Biology Onotology terms
draeger-lab/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.
draeger-lab/TFpredict
Identification and structural characterization of transcription factors based on supervised machine learning
draeger-lab/S_aureus_GEMs_Collection
In this resporitory, all modifications made within the publication "Curating and comparing 114 Strain-Specific Genome-Scale Models of Staphylococcus aureus" are documented.
draeger-lab/SBMLsqueezer
Context-sensitive creation of kinetic equations in biochemical networks
draeger-lab/ModelEditingTools
A collection of tools for working with models in SBML format
draeger-lab/SABINE
Prediction of the binding specificity of transcription factors using support vector regression
draeger-lab/SBMLsimulator
An efficient Java™ solver implementation for SBML
draeger-lab/R-DRUGS
Rationalized Discovery of Robust antiviral targets Using Genome-scale model Systems
draeger-lab/VisSim
Easily usable JavaFx-based inSilico module for dynamic Systems Biology Markup Language (SBML) model simulation visualization. Provides an intuitive Graphical User Interface for dynamic processing based on SBSCL.
draeger-lab/C_striatum_GEMs
This repository contains all changes made to the strain specific models of Corynebacterium striatum.
draeger-lab/C_striatum_wetlab
This repository contains data generated in the wet lab need for characterization and validation of strain specific GEMs
draeger-lab/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.
draeger-lab/krayon4insilico
draeger-lab/krayon4sbgn
A yFiles-based editor for SBGN diagrams written in Kotlin
draeger-lab/SBVC
Systems Biology Visualizer and Converter
draeger-lab/SysBio
A convenient library that greatly simplifies application development with Java™
draeger-lab/insilico-docs
InSilico Docs
draeger-lab/pymCADRE-1
pymCADRE enables the reconstruction of tissue-specific metabolic models in Python using transcriptomic data and information of the network topology.
draeger-lab/SBSCL-demo
A demo repository with example code for using the Systems Biology Simulation Core Library (SBSCL).
draeger-lab/Table2Model
A parser for systems biology models published in a table form that produces standardized files, such as SBML.