|
Annotation Databases |
| Name |
Description |
Reference |
RAST
(Homepage)
|
Rapid Annotation using Subsystem Technology (RAST) is a
fully-automated service for annotating bacterial and
archaeal genomes. It provides high quality genome
annotations for these genomes across the whole phylogenetic
tree.
|
PMID:
18261238
|
KAAS
(Homepage)
|
KEGG Automatic Annotation Server (KAAS) provides functional annotation of genes
by BLAST comparisons against the manually curated KEGG GENES database.
The result contains KO (KEGG Orthology) assignments and automatically generated KEGG pathways.
|
PMID:
17526522
|
GeneMarkS
(Homepage)
|
utilizes a non-supervised training procedure and can be used for a newly sequenced prokaryotic
genome with no prior knowledge of any protein or rRNA genes.
|
PMID:
11410670
|
ZCURVE
(Homepage)
|
It is a system for recognizing protein coding genes in
bacterial and archaeal genomes with
highly accurate gene start prediction. The program is based on
the Z curve theory of DNA sequence.
|
PMID:
12626720
|
CRITICA
(Homepage)
|
Coding Region Identification Tool Invoking Comparative Analysis (CRITICA)
is a suite of programs for identifying likely protein-coding sequences in
DNA by combining comparative analysis of DNA sequences with more common noncomparative
methods. It provides quality-controlled, aligned and annotated Bacterial
and Archaeal 16S rRNA sequences, and Fungal
28S rRNA sequences, and a suite of analysis tools to the scientific community.
|
PMID:
10331277
|
IdentiCS
(url is not available)
|
Identification of Coding Sequences from Unfinished Genome Sequences
(IdentiCS) combines the identification of coding sequences (CDSs)
with the reconstruction, comparison and visualization of metabolic
networks.
|
PMID:
15312235
|
metaSHARK
(url is not available)
|
The metabolic SearcH And Reconstruction Kit (metaSHARK) is a
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.
|
PMID:
15745999
|
PRIAM
(Homepage)
|
This is a method for automated enzyme detection in a fully
sequenced genome, based on the classification of enzymes in the
ENZYME database. It relies on sets of position-specific scoring
matrices automatically tailored for each ENZYME entry.
|
PMID:
14602924
|
MaGe
(Homepage)
|
Magnifying Genomes (MaGe) is a microbial
genome annotation system based on a relational database containing
information on bacterial genomes, as well as a web interface to
achieve genome annotation projects.
|
PMID:
16407324
|
AUTOGRAPH-method
(url is not available)
|
This methodology could be applied to accelerate the reconstruction
of genome-scale metabolic networks by taking optimal advantage of
existing, manually curated networks. Only the translated open reading
frames (ORFs) of a newly sequenced genome are necessary to reconstruct
a metabolic network.
|
PMID:
16772023
|
Genome Knowledgebase
(url is not available)
|
It is a resource for biologists and bioinformaticists in which
estimates on the number and nature of most of the proteincoding
genes.
|
PMID:
15338623
|
CycADS
(Homepage)
|
Cyc Annotation Database System is an automated annotation
management system that allows the seamless integration of the
latest sequence information into metabolic networks reconstruction.
|
PMID:
21474551
|
Vertebrate Genome Annotation
(Homepage)
|
A repository for high-quality gene models produced by the manual
annotation of vertebrate genomes.
|
PMID:
15608237
|
IMG
(Homepage)
|
Integrated Microbial Genomes (IMG) system tries to support the annotation,
analysis and distribution of microbial genome and metagenome
datasets sequenced.
|
PMID:
22194640
|
H-InvDB
(Homepage)
|
It provides curated annotations of human genes
and transcripts that include gene structures, alternative
splicing variants, non-coding functional RNAs, protein functions,
functional domains, sub-cellular localizations, metabolic pathways,
protein 3D structure, genetic polymorphisms (SNPs, indels and
microsatellite repeats), relation with diseases, gene expression
profiling, and molecular evolutionary features, protein-protein
interactions and gene families.
|
PMID:
23245335
|
Genome Reviews
(Homepage)
|
This database provides an up-to-date, standardized and
comprehensively annotated view of the genomic sequence of
organisms with completely deciphered genomes.
|
PMID:
16901215
|
|
Metabolic Pathways Databases |
| Name |
Description |
Reference |
Pathguide
(Homepage)
|
It contains information about biological pathway related
resources and molecular interaction related databases.
|
PMID:
16381921
|
KEGG
(Homepage)
|
Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database
resource for understanding various biological systems, such as
the cell, the organism and the ecosystem.
|
PMID:
10592173
|
The SEED
(Homepage)
|
This database focuses on the development of the comparative
genomics environment and, more importantly, on the development of
curated genomic data. The original SEED Project was started in 2003.
|
PMID:
16214803
|
MetRxn
(Homepage)
|
MetRxn is a comprehensive collection of consistent metabolite and
reaction entities for use in metabolic analysis and model construction.
|
PMID:
22233419
|
BRENDA
(Homepage)
|
It represents a comprehensive collection of enzyme and metabolic
information, based on literature.
|
PMID:
14681450
|
IntEnz
(Homepage)
|
the Integrated relational Enzyme database (IntEnz) is the
official version of the Enzyme Nomenclature.
|
PMID:
14681451
|
UMBBD
(Homepage)
|
This database contains information on microbial
biocatalytic reactions and biodegradation pathways for primarily
xenobiotic, chemical compounds.
|
PMID:
19767608
|
BKM-react
(Homepage)
|
It is an integrated and non-redundant biochemical reaction
database containing known enzyme-catalyzed and spontaneous reactions.
|
PMID:
21824409
|
MPW
(Homepage)
|
It is the collection of metabolic diagrams curated since the 1980s. |
PMID:
9407141
|
BioSilico
(Homepage)
|
It is a web-based database system that facilitates the search and
analysis of metabolic pathways. Heterogeneous metabolic
databases including LIGAND, ENZYME, EcoCyc and MetaCyc are
integrated in a systematic way, thereby allowing users to
efficiently retrieve the relevant information on enzymes,
biochemical compounds and reactions.
|
PMID:
15201189
|
SABIO-RK
(Homepage)
|
It is a curated database that contains information about
biochemical reactions, their kinetic rate equations with
parameters and experimental conditions.
|
PMID:
22102587
|
Reactome
(Homepage)
|
It is a free, open-source, curated and peer reviewed
pathway database.
|
PMID:
15608231
|
BNDB
(url is not available)
|
The Biochemical Network Database (BNDB) is a
powerful relational database platform allowing a
complete semantic integration of an extensive
collection of external databases. It is built
upon a comprehensive and extensible object model
called BioCore.
|
PMID:
17910766
|
EMP
(url is not available)
|
The Enzymes and Metabolic Pathways database (EMP) is
an encoding of the contents of over 10,000 original
publications on the topics of enzymology and metabolism.
Downloadable demo versions of EMP are available
via anonymous FTP.
|
PMID:
8594593
|
PathDB
(Homepage)
|
Pathways Database System including PathCaseSB,
PathCaseMAW, PathCaseKEGG, PathCaseRCMN, and
PathCasealpha is an integrated system with a set
of software tools for modeling, storing, analyzing,
visualizing, and querying biological pathways data at
different levels of genetic, molecular, biochemical
and organismal detail.
|
PMID:
12761054
|
BioCarta
(Homepage)
|
It is a commercial resource for study metabolic pathways.
|
PMID:
Not Available
|
Bioreaction DB
(url is not available)
|
Metabolic networks of 80 fully sequenced organisms are
reconstructed. The reaction database in excel format and
the programs in Visual Basic are available upon request.
|
PMID:
12538249
|
PMN
(Homepage)
|
The Plant Metabolic Network (PMN) provides a broad
network of plant
metabolic pathway databases that contain curated
information from the literature and computational
analyses about the genes, enzymes, compounds, reactions,
and pathways involved in primary and secondary metabolism
in plants.
|
PMID:
20522724
|
PlantDB
(Homepage)
|
It is a Microsoft Office Access database with a
user-friendly front-end feature for managing information
relevant for experimental plants
|
PMID:
18182106
|
MetaCrop
(Homepage)
|
It is a database that summarizes diverse information about
metabolic pathways in crop plants and
allows automatic export of information for the creation
of detailed metabolic models.
|
PMID:
17933764
|
PUMA2
(url is not available)
|
It is an interactive, integrated bioinformatics environment
for high-throughput genetic sequence analysis and metabolic
reconstructions from sequence data. It provides a framework
for comparative and evolutionary analysis of genomic data
and metabolic networks in the context of taxonomic and
phenotypic information.
|
PMID:
16381888
|
ERGO
(Homepage)
|
This genome analysis and discovery suite is an integration
of biological data from genomics, biochemistry,
high-throughput expression profiling, genetics and
peer-reviewed journals to achieve a comprehensive analysis
of genes and genomes. It combines pattern-based analysis
with comparative genomics by visualizing genes within
the context of regulation, expression profiling,
phylogenetic clusters, fusion events, networked
cellular pathways and chromosomal neighborhoods of
other functionally related genes.
|
PMID:
12519973
|
SoyBase
(Homepage)
|
It is the Metabolic Pathways Database for SoyBean
|
PMID:
Not Available
|
TransportDB
(Homepage)
|
It is a relational database designed for
describing the predicted cellular membrane
transport proteins in organisms whose complete
genome sequences are available. For each
organism, the complete set of membrane
transport systems was identified and classified
into different types and families according to
putative membrane topology, protein family,
bioenergetics and substrate specificities.
It is the Metabolic Pathways Database for
SoyBean
|
PMID:
14681414
|
Roche Biochemical Pathways
(Homepage)
|
It provides an overview of the chemical reactions of
cells in various species and organs.
(Ref.: Michal, Gerhard, and Dietmar Schomburg, eds.
Biochemical pathways: an atlas of biochemistry and
molecular biology. John Wiley & Sons, 2013)
|
PMID:
Not Available
|
OMMBID
(Homepage)
|
It includes the metabolic and molecular bases of inherited
diseases.
|
PMID:
Not Available
|
HPD
(Homepage)
|
It is an integrated human pathway database
providing comprehensive and combined view connecting
human proteins, genes, RNAs, enzymes, signaling,
metabolic reactions and gene regulatory events.
|
PMID:
19811689
|
Metabolic disease database
(Homepage)
|
It contains different tissues with totally different
metabolisms, such as liver, brain, and others.
|
PMID:
Not Available
|
RAMEDIS
(Homepage)
|
It is a platform independent, web-based information system
for rare metabolic diseases based on filed case reports.
It was developed in close cooperation with clinical partners
to allow them to collect information on rare metabolic
diseases with extensive details, e.g. about occurring
symptoms, laboratory findings, therapy and molecular data.
In addition, a convenient graphical user interface is
provided to the user accessible by every common web browser.
|
PMID:
16722776
|
HMDB
(Homepage)
|
The Human Metabolome Database (HMDB) is a freely available
electronic database containing detailed information about
small molecule metabolites found in the human
body.
|
PMID:
17202168
|
ExplorEnz
(Homepage)
|
It is a way to access the data of the IUBMB Enzyme
Nomenclature List. The enzymes are classifies in 6 different
groups (Oxidoreductases, Transferases, Hydrolases,
Lyases, Isomerases, Ligases)
|
PMID:
17662133
|
|
Softwares for GEM Reconstruction |
| Database |
Description |
Reference |
Pathways Tools
(Homepage)
|
It supports creation, editing, querying, visualization,
and analysis of Pathway/Genome Database (PGDB).
The software also allows users to publish a PGDB on
the Web for access by the scientific community.
|
PMID:
19955237
&
12169551
|
metaSHARK
(url is not available)
|
The metabolic SearcH And Reconstruction Kit (metaSHARK)
is a 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.
|
PMID:
15745999
|
MetNetMaker
(Homepage)
|
It is a free software designed solely to create metabolic networks based on
the KEGG LIGAND database ready for Flux-Balance Analysis in the COBRA toolbox.
|
PMID:
20671147
|
SuBliMinaL Toolbox
(Homepage)
|
It comprises a number of independent tools that can be used to automate
steps in the development of genome-scale metabolic reconstructions.
|
PMID:
22095399
|
iMAT or MBA
(Homepage)
|
It is a computational method for integrating transcriptomic and proteomic
data with genome-scale metabolic network models to predict enzymes metabolic flux.
|
PMID:
18711341
&
21081510
|
Model SEED
(Homepage)
|
It is a resource for the generation, optimization, curation, and analysis of
genome-scale metabolic models.
|
PMID:
20802497
|
IdentiCS
(url is not available)
|
It combines the identification of coding sequences (CDSs) with the reconstruction,
comparison and visualization of metabolic networks.
It has been also mentioned in the Annotation Software Section.
|
PMID:
15312235
|
Bio-SPICE
(Homepage)
|
It is an open source framework and software toolset for Systems Biology,
which intends to assist biological researchers in the modeling
and simulation of spatio-temporal processes in living cells.
|
PMID:
14683613
|
PathFinder
(It is no longer available online.)
|
It is a tool for the dynamic visualization of metabolic pathways based on annotation data.
|
PMID:
11836220
|
GEM System
(Homepage)
|
The Genome-based Modeling (GEM) System tries to perform automatically prototyping
simulation models of cell-wide metabolic pathways from genome sequences and
other public biological information.
|
PMID:
16553966
|
PathoLogic
(url is not available)
|
This program predicts the metabolic pathways of an organism from its
annotated genome. It takes as input an annotated genome sequence for
an organism and produces a new Pathway/Genome Database (PGDB) containing
those pathways that it has computationally inferred to be present in the
organism. A PGDB describes the genes, proteins, and metabolic reactions
and pathways of an organism. The software is freely available
to academic users, and is available to commercial users for a fee.
|
PMID:
12050068
|
semi-automated methodology
(Software and protocol are available in Java source code In the manuscript, Additional file 9.)
|
This semi-automated methodology aimed at streamlining the process
of metabolic network reconstruction by enabling the integration of
different genome-wide databases of metabolic reactions.
|
PMID:
20712863
|
CycSim
(Homepage)
|
It is a web application dedicated to in silico experiments with genome-scale
metabolic models coupled to the exploration of knowledge from BioCyc and KEGG.
It supports the design of knockout experiments: simulation of growth phenotypes
of single or multiple gene deletions mutants on specified media, comparison of
these predictions with experimental phenotypes and direct visualization of both
on metabolic maps.
|
PMID:
19420054
|
WIT
(url is not available)
|
What Is There (WIT) system supports comparative analysis of sequenced genomes
and generate metabolic reconstructions based on chromosomal sequences and
metabolic modules from the EMP/MPW family of databases.
|
PMID:
10592199
|
ADOMET
(url is not available)
|
It is a useful tool for the Gap filling section. It could perform Identification of
candidates genes based on local structure of the metabolic network using gene
clustering, phylogentic information and others.
|
PMID:
16571130
|
BOSS
(url is not available)
|
Biological Objective Solution Search (BOSS) identifies candidate objective reaction
that can be an existing reaction, a combination of existing reactions,
or a previously uncharacterized reaction. However this reaction
must be linear and stoichiometric. The framework relies on a reconstructed
network and experimental data.
|
PMID:
18218092
|
GapFill
(see additional file 4)
|
It proposes changes or additions to the network to connect blocked metabolites to
the remainder of the network.
|
PMID:
17584497
|
GapFind
(see additional file 3)
|
It performs systematic identification of metabolites along blocked reactions
(blocked metabolites).
|
PMID:
17584497
|
GrowMatch
(url is not available)
|
It is an automated method for reconciling in silico/in vivo growth predictions.
|
PMID:
19282964
|
OptFind
(url is not available)
|
It uses experimental data, a reconstructed network and a scoring system to identify
a network reaction that is likely to be a component of the cellular objective function.
| PMID:
12673766
|
ReMatch
(Homepage)
|
It is a web-based, user-friendly tool that constructs stoichiometric network models
for metabolic flux analysis, integrating user-developed models into a database
collected from several comprehensive metabolic data resources, including KEGG, MetaCyc and CheBI.
| PMID:
20134058
|
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
|
rBioNet
(Homepage)
|
It is a COBRA toolbox extension which enables the construction of publication-level
biochemical networks while enforcing necessary quality control measures.
It has an intuitive user interface facilitating the reconstruction process for
novices and experts.
| PMID:
21596791
|
SMILEY
(url is not available)
|
It proposes possible missing functions given a metabolic model and physiological, growth data.
| PMID:
17088549
|
PathwayBooster
(url is not available)
|
A tool to support the curation of metabolic pathways
| PMID:
25887214
|
Pantograph
(Homepage)
|
It is a software toolbox to reconstruct, curate and validate genome-scale metabolic models.
It uses existing metabolic models as templates, to start its reconstructions process,
to which new, species-specific reactions are added. It uses an iterative approach to
improve reconstructed models, facilitating manual curation and comparisons between
reconstructed model's predictions and experimental evidence.
| PMID:
25572717
|
BiGGR
(Homepage)
|
Constraint based modeling in R using metabolic reconstruction databases
| PMID:
25806817
|
MOST
(Homepage)
|
It is a standalone software package that can be used to create constraint-based
models of metabolism, load existing models, export models, and run analyses on
these models to predict the production of desired compounds by microbes under genetic manipulations.
| PMID:
25677126
|
Merlin
(Homepage)
|
The Metabolic Models Reconstruction Using Genome-Scale Information (merlin) tool is an user-friendly
Java application that performs the reconstruction of genome-scale metabolic models for any organism
that has its genome sequenced. It performs the major steps of the reconstruction process,
including the functional genomic annotation of the whole genome and subsequent construction
of the portfolio of reactions. Moreover, it includes tools for the identification and
annotation of genes encoding transport proteins, generating the transport reactions
for those carriers. It also performs the compartmentalisation of the model, predicting the
organelle localisation of the proteins encoded in the genome, and thus the localisation of
the metabolites involved in the reactions promoted by such enzymes.
The gene to proteins to reactions (GPR) associations are automatically generated and
included in the model. Finally, merlin expedites the transition from genome-scale reconstructions
to draft metabolic models exported in the SBML standard format, allowing the user to have a
preliminary view of the biochemical network.
| PMID:
25845595
|
KBase
(Homepage)
|
You could use this App to generate a draft metabolic model for the genome and then gapfill the metabolic model.
| NA
|
|
Visual Editors |
There are some useful reviews which deal with visualization of biological networks:
Tools for visually exploring biological networks.
Visualization of omics data for systems biology.
Here are some useful editors for visualizing metabolic networks:
|
| Name |
Description |
Reference |
Paint4Net
(Homepage)
|
It is a novel COBRA Toolbox extension for automatic generation of a hypergraph layout of
defined scope with the steady state rates of reaction fluxes of stoichiometric models.
Directionalities and fluxes of reactions are constantly represented in the visualization
while detailed information about reaction (ID, name and synonyms, and formula) and
metabolite (ID, name and synonyms, and charged formula) appears placing the cursor on
the item of interest. Additionally Paint4Net functionality can be used to get lists
of involved metabolites and dead end metabolites of the visualized part of the network,
exclude particular metabolites from representation, find isolated parts of a network,
and find running cycles when all the substrates are cut down.
Layout pictures can be saved in various formats.
| PMID:
22446067
|
MetVis-extension tool
(url is not available)
|
This visualization approach is suitable for an intuitive interpretation of simulation
data of metabolic networks under dynamic as well as steady-state conditions.
| PMID:
17939866
|
Edinburgh Pathway Editor
(Homepage)
|
It is a visual editor for Systems Biology. It allows you to draw Graphical Notations
commonly used in Systems Biology. In particular it supports Systems Biology
Graphical Notations (SBGN) and supports Windows, Mac and Linux
| Ref:
Paper
|
Cytoscape
(Homepage)
|
It is an open source software platform for visualizing complex networks and integrating
these with any type of attribute data. A lot of Apps are available for various
kinds of problem domains, including bioinformatics, social network analysis, and semantic web.
| PMID:
14597658
|
BioUML
(Homepage)
|
It is an open source integrated Java platform for building virtual cell and virtual
physiological human. It spans a comprehensive range of capabilities, including
access to databases with experimental data, tools for formalized description
of biological systems structure and functioning, as well as tools for their
visualization, simulation, parameters fitting and analyses.
| Ref:
Paper
|
BioTapestry
(Homepage)
|
It is designed around the concept of a developmental network model,
and is intended to deal with large scale models with consistency and clarity.
It is capable of representing systems that exhibit increasing complexity over time.
| PMID:
21938637
|
JDesigner
(Homepage)
|
It is a Win32 application which allows to draw a biochemical network and export the
network in the form of SBML. The Designer has an Systems Biology Workbench (SBW)
interface that allows it to be called from other SBW compliant modules.
In addition, it has the ability to use Jarnac as a simulation server (via SBW)
thus allowing models to be run from within JDesigner.
| Ref:
Paper
|
SimWiz
(Homepage)
|
Simulation Wizard (SimWiz) is a computer program for defining, validating,
analyzing, communicating and running a discrete event simulation model.
| PMID:
17052128
|
CADLIVE
(Homepage)
|
Computer-Aided Design of LIVing systEms (CADLIVE) is a comprehensive computational
tool for constructing large-scale biological network maps, analyzing the
topological features of them, and simulating their dynamics.
| PMID:
15805500
|
Cellware
(Homepage)
|
It has been designed to conduct modeling and simulation of gene regulatory and
metabolic pathways and also offers an integrated environment for diverse
mathematical representations, parameter estimation and optimization.
In addition, a user-friendly graphical display and capability to run large and
complex models would be provided by default.
| PMID:
14871872
|
ProMoT
(Homepage)
|
It is the Process Modeling Tool, a software for the construction and manipulation
of complex technical and biological systems. Together with the simulation
environment Diana, it provides capabilities for the development of dynamic
models based on differential-algebraic equations, and their simulation and
further analysis. It has being used as a modeling tool not only for the setup
of dynamic models, but also for the visual construction of Boolean models
that can be analyzed with CellNetAnalyzer.
| PMID:
12801880
|
CellDesigner
(Homepage)
|
It is a structured diagram editor for drawing gene-regulatory and biochemical networks.
Networks are drawn based on the process diagram, with graphical notation system and are
stored using the Systems Biology Markup Language (SBML). Networks are able to link
with simulation and other analysis packages through Systems Biology Workbench (SBW).
It supports simulation and parameter scan by an integration with SBML ODE Solver, SBML
Simulation Core and Copasi. You can browse and modify existing SBML models with
references to existing databases, simulate and view the dynamics through an
intuitive graphical interface.
| PMID:
24927840
|
Cell Illustrator
(Homepage)
|
It is a software tool that enables biologists to draw, model, elucidate and simulate
complex biological processes and systems. It has outstanding drawing capabilities,
moreover it allows researchers to model metabolic pathways, signal transduction cascades,
gene regulatory pathways as well as dynamic interactions of various biological
entities such as genomic DNA, mRNA and proteins. In addition, it provides
researchers with model diagrams of publication quality and simulation result charts.
| PMID:
21685571
|
SimBiology
(Homepage)
|
It provides an application and programmatic tools to model, simulate, and analyze dynamic
systems, focusing on pharmacokinetic/pharmacodynamic (PK/PD) and systems biology
applications. It provides a block diagram editor for building models, or you can
create models programmatically using the MATLAB language. It includes a library of
common PK models, which you can customize and integrate with mechanistic systems biology
models. A variety of model exploration techniques let you identify optimal
dosing schedules and putative drug targets in cellular pathways. It uses ordinary
differential equations (ODEs) and stochastic solvers to simulate the time course
profile of drug exposure, drug efficacy, and enzyme and metabolite levels.
You can investigate system dynamics and guide experimentation using parameter
sweeps and sensitivity analysis. You can also use single subject or population
data to estimate model parameters.
| NA
|
SBMLToolbox
(Homepage)
|
It is built on top of libSBML and provides a set of basic functions allowing SBML
models to be used in both MATLAB and Octave. It provides functions for creating
and validating models; and manipulating and simulating these models using
ordinary differential equation solvers.
| PMID:
16574696
|
NetworkX
(Homepage)
|
It is a Python language software package for the creation, manipulation,
and study of the structure, dynamics, and functions of complex networks.
| NA
|
Pathway Studio
(Homepage)
|
Pathway Studio (formerly PathwayAssist) is a Microsoft Windows application that
combines an extensive set of features with a polished graphic user interface.
It includes, most notably, customizable network display styles for assigning visual
attributes such as node color, size and shape, multi-user support, subcellular
localization visualization and tight integration with several databases.
| PMID:
14594725
|
Osprey
(Homepage)
|
It was one of the first tools specifically designed to visualize and analyze large
networks. All but one network layout in Osprey are elaborations of the circular
layout because they can be quickly computed.
| PMID:
12620107
|
PATIKA
(Homepage)
|
The PATIKA Project provides a WWW-based visual editor, PATIKAweb, for accessing a
central database containing pathway data from several sources including Reactome.
| PMID:
16287939
|
VisANT
(Homepage)
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It provides network drawing capabilities, including support for very large networks.
It is also one of the first such packages to support creation, visualization,
and analysis of mixed networks, i.e. networks containing both directed and undirected links.
| PMID:
23716640
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ProViz
(url is not available)
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It leverages the power of the graph drawing package Tulip for handling graphs containing
millions of nodes and edges, while maintaining a guaranteed response time
(i.e. it will never make the user wait longer that predefined length of time).
| PMID:
15347570
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PathSys
(Homepage)
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It is a part of BiologicalNetworks project and extends Cytoscape and includes
much of the functionality of Pathway Studio.
| PMID:
16464251
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GenMAPP
(Homepage)
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It is a computer application designed to visualize gene expression and other
genomic data on maps representing biological pathways and groupings of genes.
| PMID:
11984561
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MSMB
(Homepage)
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Multistate Model Builder (MSMB) is a flexible editor for compact biochemical models.
It provides two separate advances on existing network model editors: 1)A simple
but powerful syntax is used to describe multistate species. This reduces the number
of reactions needed to represent certain molecular systems, thereby reducing the
complexity of model creation. 2)Extensive feedback is given during all stages of
the model creation process on the existing state of the model.
Users may activate error notifications of varying stringency on the fly,
and use these messages as a guide toward a consistent, syntactically correct model.
| PMID:
24708852
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FluxMap
(Homepage)
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It is a tool for the advanced visualization and exploration of flux data in the
context of metabolic networks. The template-based flux data import assigns
flux values and optional quality parameters (e. g. the confidence interval)
to biochemical reactions. It supports the discrimination between mass and
substance fluxes, such as C- or N-fluxes. After import, flux data mapping
and network-based visualization allow the interactive exploration of the dataset.
Various visualization options enable the user to adapt layout and network
representation according to individual purposes.
| PMID:
22548786
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Escher
(Homepage)
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A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of
Biological Pathways
| PMID:
26313928
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Mimoza
(Homepage)
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Web-based semantic zooming and navigation in metabolic networks
| PMID:
25889977
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