Search Results for "metabolic pathway"

There is a scarcity of user-friendly tools that can be used in daily routine, providing insights about the metabolic network of a target organism for researcher’s groups. Here we present a novel tool, Chimera, which combines the most efficient tools in model reconstruction, prediction, and visualization and also implements new in-house algorithms for database integration and data manipulation. Our goals: Produce an organism-specific model based on the CarveMe algorithm Manage the model and perform growth predictions with COBRApy Create visualization for the metabolic network using PSAMM and Escher Add pathway information to metabolic maps using in house algorithm Perform single and double, gene and reaction, knockout in the organism

ASGARD is software for metabolic pathway reconstruction, but it can also generate other types of biological sequence annotation (EC and GO numbers, BLAST reports). This program is intended to be run in UNIX-like systems, and supports SGE or PBS.

This package includes a few programs for rapid functional annotation for metagenomic sequences, including, 1) Gene prediction by FragGeneScan; 2) Similarity search by RAPSearch2; 3) Functional annotation in GO (Gene Ontology) and EC (Enzyme Commission) based on similarity search results; 4) From EC to metabolic pathway reconstruction by MinPath. Inputs: Just sequencing reads (or assemblies) Outputs: Protein-coding genes (or gene fragments); similarity search; functional annotations (in GO and EC); metabolic pathways.

...For more information about execution access the README file. ## FUNCTIONAL AND TAXONOMIC ANALYSIS There is another version of the FUNN-MG pipeline with option of taxonomic analysis of each metabolic pathway identified from the results of the KAIJU tool (Menzelet al., 2016). You can access this version at this address: https://github.com/hscleandro/FUNN-MG

This project implements a Cytoscape plugin for viewing and manipulating pathway maps for metabolic models created by the Model SEED (http://www.theseed.org/models). See the "Files" area for README. See Project Homepage for Tutorial.

...This provides an alternative to pathway/gene set enrichment analyses which is simultaneously more flexible and more specific.

The Cell System Markup Language (CSML) is an XML format for modeling, visualizing and simulating biopathways. CSML supports to represent several pathway types including metabolic, signaling, genetic regulatory pathways, and cell-cell interactions.

The Katsura tool overlays microarray gene expression data, proteomics, and similar biological data onto metabolic pathways. [Pathogen Functional Genomics Resource Center (PFGRC) @ J. Craig Venter Institute (JCVI)]

This project is aimed at providing useful thermodynamic tools for biochemists, including formation energy estimation of virtually every biochemical compound and metabolic pathway analysis and profiling.

SBMLforge is a tool that enables the user to convert and merge KEGG metabolic and signaling pathways (KGML format) to create a single SBML pathway model.

We propose a metabolic pathway drawing algorithm for reducing the number of edge crossings by considering the fact that metabolic pathway graph is scale-free network.

Genome Expression Pathway Analysis Tool - Analysis and Visualization of Microarray Gene Expression Data under Genomic, Proteomic and Metabolic Context

GSCope3 performs microarray data analysis to find correlations between BLSOM clusters and any form of omic knowledge expressed in OSML. Includes example metabolic pathway, gene ontology, genome position, transcription and PPI knowledge in OSML format.

GeXpert is an expert system that can be used for genetics and metabolic pathway analysis. GeXpert can help Biotechnologists do their work faster, reducing the time required for performing, analyzing and storing the results of Bioinformatics research.

Crude Metabolic Pathway Analysis visualization software. For a software engineering class.

PNE provides an environment for modeling, simulating, and optimizing biological networks including regulatory and metabolic networks.

PathwayPointer is a software that can draw omics data on to metabolic pathway map.