draeger-lab/ModelPolisher

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Language
Java
License
MIT License
Created about 9 years ago
Updated 3 months ago

draeger-lab/ModelPolisher

draeger-lab

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ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.

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.

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.

EscherConverter

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

pymCADRE

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

Jupyter Notebook

refinegems

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

Jupyter Notebook

SBTabEditor

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

insilico

SBMLme

Encoding ME models in SBML

SBOannotator

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

TFpredict

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

SPECIMEN

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

Jupyter Notebook

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.

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.

Jupyter Notebook

SBMLsqueezer

Context-sensitive creation of kinetic equations in biochemical networks

ModelEditingTools

A collection of tools for working with models in SBML format

SBMLsimulator

An efficient Java™ solver implementation for SBML

SABINE

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

InCroMAP

Integrated analysis of Cross-platform MicroArray and Pathway data

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.

R-DRUGS

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

Jupyter Notebook

SBVC

Systems Biology Visualizer and Converter

BioModelsEd

A graphical editor for systems biology models.

SysBio

A convenient library that greatly simplifies application development with Java™

MPClient

Client library for the MPServer

krayon4insilico

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

Jupyter Notebook

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.