Dräger Lab

Dräger Lab's repositories

ModelPolisher

ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.

Language:JavaMIT22 15 83

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.

Language:HTMLLGPL-3.020 9 54

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.

Language:JavaLGPL-3.017 6 10

EscherConverter

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

Language:JavaMIT15 7 34

pymCADRE

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

Language:Jupyter NotebookGPL-3.012 3 4

refinegems

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

Language:PLpgSQLMIT9 1 68

SBTabEditor

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

Language:JavaMIT9 11 42

insilico

InSilico

Language:JavaMIT7 5 9

SBMLme

Encoding ME models in SBML

Language:JavaMIT7 60

SBOannotator

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

Language:PythonGPL-3.07 4 1

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.

Language:TeXGPL-3.05 4 4

TFpredict

Identification and structural characterization of transcription factors based on supervised machine learning

Language:JavaGPL-3.05 3 3

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.

Language:Jupyter Notebook4 3 2

SBMLsqueezer

Context-sensitive creation of kinetic equations in biochemical networks

Language:HTMLGPL-3.04 6 12

ModelEditingTools

A collection of tools for working with models in SBML format

Language:JavaMIT3 30

SABINE

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

Language:JavaGPL-3.03 3 2

SBMLsimulator

An efficient Java™ solver implementation for SBML

Language:JavaLGPL-3.03 4 2

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.

Language:JavaMIT2 30

C_striatum_GEMs

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

Language:HTMLMIT1 1 7

C_striatum_wetlab

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

Language:Jupyter Notebook1 2 8

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.

Language:JavaLGPL-3.01 4 1