|
Constraint-based Analysis Softwares |
| Name |
Description |
Reference |
COBRA
(Homepage)
|
The COnstraints Based Reconstruction and Analysis (COBRA) approach focuses on
employing physicochemical constraints to define the set of feasible states for a
biological network in a given condition based on current knowledge. These constraints
include compartmentalization, mass conservation, molecular crowding, and thermodynamic
directionality. Although this methods may not provide a unique solution, it provides a
reduced set of solutions that may be used to guide biological hypothesis development.
|
PMID:
21886097
&
17406635
|
ORCA
(Homepage)
|
ORCA is a Matlab package extending the scope of established COBRA metabolic
modelling and integrates three unique functionalities: 1) a framework method
integrating three analyses of multi-objective optimization, robustness analysis
and fractional benefit analysis, 2) metabolic pathways identification with futile
loop elimination, and 3) a dynamic flux balance analysis framework (dFBA) incorporating
kinetic constraints.
|
PMID:
24336807
|
COBRApy
(Homepage)
|
COBRA for Python (COBRApy), is a Python package that provides support for basic
COBRA methods. It is designed in an object-oriented fashion that facilitates the
representation of the complex biological processes of metabolism and gene expression.
COBRApy does not require MATLAB to function; however, it includes an interface to the
COBRA Toolbox for MATLAB to facilitate use of legacy codes. For improved performance,
COBRApy includes parallel processing support for computationally intensive processes.
|
PMID:
23927696
|
VANTED
(Homepage)
|
Visualization and Analysis of Networks containing Experimental Data (VANTED) is a
tool for the visualization and analysis of networks with related experimental data.
Data from large-scale biochemical experiments is uploaded into the software via a
Microsoft Excel-based form. Then it can be mapped on a network that is either drawn
with the tool itself, downloaded from the KEGG Pathway database, or imported using
standard network exchange formats.
Transcript, enzyme, and metabolite data can be presented in the context of their
underlying networks. Visualization and navigation methods support the visual exploration
of the data-enriched networks.
|
PMID:
16519817
|
MetaFluxNet
(Homepage)
|
It is a program package for managing information on the metabolic reaction network and
for quantitatively analyzing metabolic fluxes in an interactive and customized way,
which allows users to interpret and examine metabolic behavior in response to genetic
and/or environmental modifications.
|
PMID:
14594721
|
SurreyFBA
(Homepage)
|
It provides constraint-based simulations and network map visualization in a free,
stand-alone software. In addition to basic simulation protocols, the tool also implements
the analysis of minimal substrate and product sets, which is useful for metabolic
engineering and prediction of nutritional requirements in complex in vivo environments.
It is based on a command line interface to the GLPK solver distributed as binary and
source code for the three major operating systems.
The command line tool, implemented in C++, is easily executed within scripting languages
used in the bioinformatics community and provides efficient implementation of tasks
requiring iterative calls to the linear programming solver.
It includes JyMet, a graphics user interface allowing spreadsheet-based model
presentation, visualization of numerical results on metabolic networks represented in
the Petri net convention, as well as in charts and plots.
|
PMID:
21148545
|
WEbcoli
(Homepage)
|
It is a WEb application for in silico designing, analyzing and engineering
Escherichia coli metabolism. It is devised and implemented using advanced web
technologies, thereby leading to enhanced usability and dynamic web accessibility.
As a main feature, this system provides a user-friendly rich web interface, allowing
users to virtually design and synthesize mutant strains derived from the genome-scale
wild-type E.coli model and to customize pathways of interest through a graph editor.
In addition, constraints-based flux analysis can be conducted for quantifying metabolic
fluxes and charactering the physiological and metabolic states under various genetic
and/or environmental conditions.
|
PMID:
19689960
|
BioMet Toolbox
(Homepage)
|
It is a web-based resource for analysis of high-throughput data, together with
methods for flux analysis and integration of transcriptome data exploiting the
capabilites of metabolic networks described in genome scale models. It also includes
genome scale metabolic models of various cell factories used both in industrial
biotechnology and in fundamental research.
|
PMID:
20483918
|
BioOpt
(Homepage)
(sub-tool of biomet toolbox)
|
It is a software application running on Windows command prompt. The program focuses
on the flux balance analysis, using linear programming as the mathematical support.
Given a biological system model, which includes a set of metabolic reactions, the
program is able to calculate all internal mass balance fluxes, reduced costs and
shadow prices depending on the constraints and objective defined by the user.
|
Not Available
|
Acorn
(Homepage)
|
It is a web server for constraint based modeling of genome scale metabolic reaction networks.
After signing in, users can run Flux Balance Analysis simulations on multiple models loaded
by an administrator from SBML files.
Initial conditions of computer simulations (reaction bounds, objective function) are stored
and can be shared with other users.
Models and results are displayed in tables with genes linked to genome information portals,
but pathway visualisation will soon be implemented.
The server is capable of handling multiple users and iterative FBA simulations by using
clusters set up in GlassFish environment.
|
PMID:
21609434
|
PathwayAnalyser
(Homepage)
|
It is a software for systems biologists who want to perform flux based analyses and
simulations on SBML Models.
It affords FBA as well as interfacing with Taylor software for high precision simulations of ODEs.
|
Not Available
|
FluxAnalyzer
(url is not available)
|
It is a MATLAB package which facilitates integrated pathway and flux analysis for metabolic
networks within a graphical user interface.
Arbitrary metabolic network models can be composed by instances of four types of network elements.
The abstract network model is linked with network graphics leading to interactive flux maps which
allow for user input and display of calculation results within a network visualization.
Therein, a large and powerful collection of tools and algorithms can be applied interactively
including metabolic flux analysis, flux optimization, detection of topological features
and pathway analysis by elementary flux modes or extreme pathways.
|
PMID:
12538248
|
CellNetAnalyzer
(Homepage)
|
It is a MATLAB package which provides a comprehensive and user-friendly environment
for structural and functional analysis of biochemical networks.
It facilitates the analysis of metabolic as well as signaling and regulatory networks
solely on their network topology, i.e. independent of kinetic mechanisms and parameters.
It provides a powerful collection of tools and algorithms for structural network
analysis which can be started in a menu-controlled manner within interactive network maps.
|
PMID:
17408509
|
MOMA
(Homepage)
|
Minimization of Metabolic Adjustment (MOMA) predicts the immediate sub-optimal flux
distribution following the perturbation by minimizing the distance (Euclidean)
between the wild-type FBA flux distribution and the mutant flux distribution
using quadratic programming.
It employs quadratic programming to identify a point in flux space, which is
closest to the wild-type point, compatibly with the gene deletion constraint.
|
PMID:
12415116
|
FAME
(Homepage)
|
The Flux Analysis and Modeling Environment (FAME) is a 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.
It is written in PHP and uses the Python-based PySCeS-CBM for its linear solving capabilities.
|
PMID:
22289213
|
ROOM
(url is not available)
|
Regulatory onoff minimization (ROOM) is a constraint-based algorithm for predicting the
metabolic steady state after gene knockouts.
It aims to minimize the number of significant flux changes with respect to the wild type.
It attempts to improve the prediction of the metabolic state of an organism after a gene knockout.
It follows the same premise as MOMA that an organism would try to restore a flux distribution
as close as possible to the wild-type after a knockout.
However it further hypothesizes that this steady state would be reached through a series
of transient metabolic changes by the regulatory network and that the organism would try
to minimize the number of regulatory changes required to reach the wild-type state.
Instead of using a distance metric minimization however it uses a Mixed Integer Linear Programming method.
|
PMID:
15897462
|
PySCeS
(Homepage)
|
The Python Simulator for Cellular Systems (PySCeS) is an extendable research tool for the
numerical analysis and investigation of cellular systems.
It includes a selection of non-linear root-finding algorithms that can quickly and efficiently
be used to calculate steady state solutions.
It includes Metabolic Control Analysis, structural analysis, bifurcation analysis, parameter scans,
Visualise the results of simulations, SBML import and export capability.
|
PMID:
15454409
|
OpenFLUX
(Homepage)
|
It is a MATLAB-based modelling software for 13C metabolic flux analysis (MFA).
The OpenFLUX parser automatically generates MATLAB-readable metabolite and isotopomer
balances, thus strongly facilitating model creation. The model can be used to perform
experimental design, parameter estimation and sensitivity analysis either using the
built-in gradient-based search or Monte Carlo algorithms or in user-defined algorithms.
|
PMID:
19409084
|
OptFlux
(Homepage)
|
It is an open-source and modular software to support in silico metabolic engineering tasks aimed
at being the reference computational application in the field.
|
PMID:
20403172
|
SBRT
(Homepage)
|
The Systems Biology Research Tool (SBRT) tries to facilitate the computational aspects of systems biology.
It performs 35 methods for analyzing stoichiometric networks and 16 methods from fields such as
graph theory, geometry, algebra, and combinatorics. New computational techniques can
be added to the SBRT via process plug-ins, providing a high degree of evolvability and a
unifying framework for software development in systems biology.
|
PMID:
18588708
|
FASIMU
(Homepage)
|
It is a command line oriented software for the computation of flux distributions using a
variety of the most common FBA algorithms, including the first available implementation
of weighted flux minimization, fitness maximization for partially inhibited enzymes, and
usage of the concentration-based thermodynamic feasibility constraint.
It allows batch computation with varying objectives and constraints suited for network
pruning, leak analysis, flux-variability analysis, and systematic probing of metabolic
objectives for network curation. Input and output supports SBML.
FASIMU can work with free (lp_solve and GLPK) or commercial solvers (CPLEX, LINDO).
A new plugin (faBiNA) for BiNA allows to conveniently visualize calculated flux distributions.
|
PMID:
21255455
|
GEMSiRV
(Homepage)
|
It is an open-source software for building metabolic systems biology project.
It provides interactive features in model management, simulation, visualization and
integration of omics data.
Furthermore, all of the GEMSiRV-generated metabolic models and analysis results,
including projects in progress, can be easily exchanged in the research community.
It is a powerful integrative resource that may facilitate the development of systems biology studies.
|
PMID:
22563070
|
SNA
(Homepage)
|
It is a Mathematica toolbox for stoichiometric network analysis.
Among other things, it supports flux balance analysis and the enumeration of the
elementary vectors of the flux and the conversion cone.
|
PMID:
16533403
|
MetaFlux
(Homepage)
|
It is a multiple gap-filling method to accelerate the development of FBA models based on
mixed integer linear programming (MILP).
The method suggests corrections to the sets of reactions, biomass metabolites, nutrients and secretions.
The method generates FBA models directly from Pathway/Genome Databases. Thus, FBA models developed
in this framework are easily queried and visualized using the Pathway Tools software.
|
PMID:
22262672
|
MicrobesFlux
(Homepage)
|
It is a semi-automatic, web-based platform for generating and reconstructing metabolic
models for annotated microorganisms.
It is able to automatically download the metabolic network (including enzymatic reactions
and metabolites) from the KEGG database and then convert it to a metabolic model draft.
The platform also provides diverse customized tools, such as gene knockouts and the
introduction of heterologous pathways, for users to reconstruct the model network.
The reconstructed metabolic network can be formulated to a constraint-based flux model
to predict and analyze the carbon fluxes in microbial metabolisms.
The simulation results can be exported in the SBML format.
|
PMID:
22857267
|
FBA3
(Homepage)
|
the Flux Balance Optimization linear programming package that can be used to study metabolic systems.
|
PMID:
11175725
|
SimPheny
(url is not available)
|
It is an enterprise-level software platform developed by Genomatica that enables the development
of predictive computer models of organisms.
|
Commercial
|
RAVEN
(Homepage)
|
Reconstruction, Analysis, and Visualization of Metabolic Networks (RAVEN) toolbox is
a complete environment for reconstruction, analysis, simulation, and visualization
of GSMM and runs within MATLAB. The software has three main features:
1) automatic reconstruction of GSMMs based on protein homology,
2) network analysis, modeling and interpretation of simulation results,
and 3) visualization of GSMMs using pre-drawn metabolic network maps.
|
PMID:
23555215
|
libStructural
(Homepage)
|
The structural analysis library is a C/C++ portable software library for analyzing the
structural properties of stoichiometric networks.
The library supports the analysis of both flux balance and moiety conservation.
The library will accept models in the form of either standard SBML or raw stoichiometry matrices.
|
Not Available
|
MetaNET
(Homepage)
|
A web-accessible interactive platform for biological metabolic network analysis
|
Paper_Link
|
CBFA
(Homepage)
|
Phenotype prediction integrating metabolic models with constraints derived from experimental data
|
PMID:
25466481
|
|
EM and EP Calculators |
| Name |
Description |
Reference |
Metatool
(Homepage)
|
It is a program for computing the nullspace matrix, elementary modes and other structural
properties of biochemical reaction networks.
|
PMID:
10222413
&
16731697
|
BlockDiag
(Homepage)
|
This Program is for computing and block-diagonalizing the nullspace matrix to the
stoichiometriy matrix of a chemical reaction network.
|
Not Available
|
OptiMode
(Homepage)
|
It is a program for detecting the elementary mode with the highest molar yield for a
specified substrate - product pair from the output file of METATOOL.
|
Not Available
|
Reducing modes
(Homepage)
|
It is a program to calculate elementary modes for the complete variety of external and
internal metabolites and a program to calculate the approximated minimal number of modes.
|
Not Available
|
Separator
(Homepage)
|
This Program is for decomposing of large biochemical networks in to smaller ones.
|
Not Available
|
NAD+ metabolism
(Homepage)
|
It Visualizes all the elementary modes computed with Metatool 5.1 in the analysis of the
NAD+ metabolic network.
|
Not Available
|
Expa
(Homepage)
|
This program could compute the set of extreme pathways (a generating set for all possible
steady-state flux maps in a biochemical reaction network) from the stoichiometric matrix.
|
PMID:
15613397
|
YANA
(Homepage)
|
This is a toolbox for metabolic networks with a graphical user interface to calculate
(integrating METATOOL), edit (including support for the SBML format), visualize, centralize,
and compare elementary flux modes.
Further, it calculates expected flux distributions for a given Elementary Mode activity
pattern and vice versa.
|
PMID:
15929789
|
YANAsquare
(Homepage)
|
It provides a software framework for rapid network assembly (flexible pathway browser with
local or remote operation mode), network overview (visualization routine and YANAsquare editor),
and network performance analysis (calculation of flux modes as well as target and robustness tests).
It comes as an easy-to-setup program package in Java. It is fully compatible and integrates the
programs YANA and Metatool.
|
PMID:
17725829
|
ScrumPy
(Homepage)
|
It is a software package used for the definition and analysis of metabolic models.
It is written using the Python programming language that is also used as a user interface.
It has features for both kinetic and structural modelling, but the emphasis is on structural
modelling and those features of most relevance to analysis of genome-scale models.
|
PMID:
16986321
|
DFS Algorithm
(Additional file 3 Contains MATLAB scripts for the DFS algorithm.)
|
This depth-first search algorithm uses linear programming (LP) to enumerate elementary flux modes (EFMs)
in an exhaustive fashion.
Constraints can be introduced to directly generate a subset of EFMs satisfying the set of constraints.
It has a constant memory overhead. Using flux constraints, a large LP problem can be massively
divided and parallelized into independent sub-jobs for deployment into computing clusters.
Since the sub-jobs do not overlap, the approach scales to utilize all available computing
nodes with minimal coordination overhead or memory limitations.
|
PMID:
25074068
|
F2C2
(Homepage)
|
Flux coupling analysis (FCA) has become a useful tool in the constraint-based analysis of
genome-scale metabolic networks.
FCA allows detecting dependencies between reaction fluxes of metabolic networks at steady-state.
On the one hand, this can help in the curation of reconstructed metabolic networks by verifying
whether the coupling between reactions is in agreement with the experimental findings.
On the other hand, FCA can aid in defining intervention strategies to knock out target reactions.
F2C2 is a fast tool for the computation of flux coupling in genome-scale metabolic networks.
|
PMID:
22524245
|