11.08.2015   Biomass and Biofuels from Microalgae

Common Optimization Tools for Constraint-Based Models

Several integrated toolsets are available for constraint-based analysis. These include Pathway Tools, COBRA Toolbox, SNA, and MetaFluxNet (Table 10.1). The most widely used tools are Pathway Tools and COBRA Toolbox, with COBRA offering

Table 10.1 Software tools available to carry out constraint-based analysis

Software/tool

URL

Description/uses

Pathway tools

http://bioinformatics. ai. sri. com/

ptools/

Software includes tools including: model organism databases, flux balance analysis, visualization of metabolic network and omics datasets, and model refinement including dead-end metabolites

COBRA toolbox

http://opencobra. sourceforge. net/

openCOBRA/Welcome. html

MATLAB software package for extensive analysis of networks using; FBA, FVA, gene deletion, Monto Carlo sampling, metabolic network visualizations, and gap filling

MetaFluxNet

http://metafluxnet. kaist. ac. kr/Default.

aspx

Program package that allows users to interpret and examine metabolic behavior in response to genetic or environmental modifications

CellNetAnalyzer

http://www2.mpi-magdeburg. mpg. de/

projects/cna/cna. html

MATLAB software package for structural and functional analysis of cellular networks

SNA

http://www. bioinformatics. org/

project/?group_id=546

Mathematica toolbox for analyzing fluxes of metabolic network at steady state by linear programing

PathwayAnalyser

http://openwetware. org/wiki/Chandra:

Software_and_Databases:

PathwayAnalyser

Software for flux balance analyses and simulations on SBML models

the largest number of tools. A few of these tools (mostly available in COBRA) are described below (Fig. 10.5).