Databases, Software and Tools for metabolic pathway/network reconstructions

Here I am providing the details about the available tools and methods for the metabolic pathway reconstruction. 

1. The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model   for Penicillium chrysogenum:

RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox: a software suite that allows for semi-automated reconstruction of genome-scale models. It makes use of published models and/or the KEGG database, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. 

Available at: http://129.16.106.142/downloads.php

2. RAST/Model SEED genome-scale metabolic reconstruction pipeline:

RAST and the Model SEED framework were developed as a means of automatically producing annotations and draft genome-scale metabolic models. They break down the model reconstruction process into eight steps: submitting a genome sequence to RAST, annotating the genome, curating the annotation, submitting the annotation to Model SEED, reconstructing the core model, generating the draft biomass reaction, auto-completing the model, and curating the model. Each of these eight steps is documented in detail.

Availbale at: http://seed-viewer.theseed.org/seedviewer.cgi?page=ModelView (Standalone version not available)

3. MicrobesFlux: a web platform for drafting metabolic models from the KEGG database:

MicrobesFlux is an installation-free and open-source platform that enables biologists without prior programming knowledge to develop metabolic models for annotated microorganisms in the KEGG database. Our system facilitates users to reconstruct metabolic networks of organisms based on experimental information. Through human-computer interaction, MicrobesFlux provides users with reasonable predictions of microbial metabolism via flux balance analysis. This prototype platform can be a springboard for advanced and broad-scope modeling of complex biological systems by integrating other “omics” data or 13 C- metabolic flux analysis results. 

Available at: http://tanglab.engineering.wustl.edu/static/MicrobesFlux.html  (Standalone version not available)

4. FAME the Flux Analysis and Modeling Environment:

The Flux Analysis and Modeling Environment (FAME) is the first web-based modeling tool that combines the tasks of creating, editing, running, and analyzing/visualizing stoichiometric models into a single program. Analysis results can be automatically superimposed on familiar KEGG-like maps.

Available at: http://f-a-m-e.org/ajax/page1.php (Standalone version not available)

5. Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology:

Pathway Tools is a production-quality software environment for creating a type of model-organism database called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc integrates the evolving understanding of the genes, proteins, metabolic network and regulatory network of an organism.

Available at: http://bioinformatics.ai.sri.com/ptools/

6. BioModels Database:

BioModels Database serves as a huge repository of computational models of genomes and different biological processes. It hosts models described in peer-reviewed scientific literature and automatically generated models from pathway resources (Path2Models). Models collected from literature are manually curated and semantically enriched with cross-references from external data resources. The database resource allows scientific community to store, search and retrieve mathematical models of their interest. In addition, features such as generation of sub-models, online simulation, conversion of models into different representational formats, and programmatic access via web services, are also provided.

Available at: http://www.ebi.ac.uk/biomodels-main/

7. GEMSiRV: A software platform for GEnome-scale Metabolic model Simulation, Reconstruction and Visualization

GEMSiRV comes with downloadable, ready-to-use public-domain metabolic models, reference metabolite/reaction databases, and metabolic network maps, all of which can be input into GEMSiRV as the starting materials for network construction or simulation analyses. Furthermore, all of the GEMSiRV-generated metabolic models and analysis results, including projects in progress, can be easily exchanged in the research community. GEMSiRV is a powerful integrative resource that may facilitate the development of systems biology studies.

Available at: http://sb.nhri.org.tw/GEMSiRV/en/GEMSiRV

8. Metashark: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella.

The metabolic SearcH And Reconstruction Kit (metaSHARK) is a new fully automated software package for the detection of enzyme-encoding genes within unannotated genome data and their visualization in the context of the surrounding metabolic network.

Available at:

9. The SuBliMinaL Toolbox:  automating steps in the reconstruction of metabolic networks. 

The SuBliMinaL Toolbox (http://www.mcisb.org/subliminal/) facilitates the reconstruction process by providing a number of independent modules to perform common tasks, such as generating draft reconstructions, determining metabolite protonation state, mass and charge balancing reactions, suggesting intracellular compartmentalisation, adding transport reactions and a biomass function, and formatting the reconstruction to be used in third-party analysis packages. 

Available at: http://www.mcisb.org/resources/subliminal/