IMP 2.0 – Integrative Multi-species Prediction

IMP 2.0

:: DESCRIPTION

IMP is an interactive web server that enables molecular biologists to interpret experimental results and to generate hypotheses in the context of a large cross-organism compendium of functional predictions and networks.

::DEVELOPER

Troyanskaya Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Wong AK*, Krishnan A*, Yao V*, Tadych A, Troyanskaya OG.
IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.
Nucleic Acids Research. July 2015;43:W128-W133.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W484-90. doi: 10.1093/nar/gks458.
IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.
Wong AK, Park CY, Greene CS, Bongo LA, Guan Y, Troyanskaya OG.

ClusterONE 1.0 – Detecting Overlapping Protein Complexes in Protein-protein Interaction Networks

ClusterONE 1.0

:: DESCRIPTION

ClusterONE (Clustering with Overlapping Neighborhood Expansion) is a graph clustering algorithm that is able to handle weighted graphs and readily generates overlapping clusters. Owing to these properties, it is especially useful for detecting protein complexes in protein-protein interaction networks with associated confidence values.

::DEVELOPER

Paccanaro Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/ Linux / MacOsX
  • Java

:: DOWNLOAD

 ClusterONE

:: MORE INFORMATION

Citation

Nat Methods. 2012 Mar 18;9(5):471-2. doi: 10.1038/nmeth.1938.
Detecting overlapping protein complexes in protein-protein interaction networks.
Nepusz T1, Yu H, Paccanaro A.

Workflow4Metabolomics 4.0 – Metabolomics data Processing, Analysis and Annotation

Workflow4Metabolomics 4.0

:: DESCRIPTION

Workflow4Metabolomics (W4M) is a first fully open-source and collaborative online platform for computational metabolomics.

::DEVELOPER

Workflow4Metabolomics team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/Oracle/virtual machines (VM)

:: DOWNLOAD

 Workflow4Metabolomics

:: MORE INFORMATION

Citation

Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics.
Giacomoni F, Le Corguillé G, Monsoor M, Landi M, Pericard P, Pétéra M, Duperier C, Tremblay-Franco M, Martin JF, Jacob D, Goulitquer S, Thévenot EA, Caron C.
Bioinformatics. 2014 Dec 19. pii: btu813.

iRegulon 1.3 – Sequence-based Discovery of Human Regulons

iRegulon 1.3

:: DESCRIPTION

iRegulon is a Cytoscape plugin that detects the TF, the targets and the motifs from a set of genes.

::DEVELOPER

Laboratory of Computational Biology @ the Center for Human Genetics (CME), at the Faculty of Medicine

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • Java
  • Cytoscape
:: DOWNLOAD

 iRegulon

:: MORE INFORMATION

Citation

Rekin’s Janky, et al.
PLoS Comput Biol. 2014 Jul 24;10(7):e1003731. doi: 10.1371/journal.pcbi.1003731. eCollection 2014.
iRegulon: from a gene list to a gene regulatory network using large motif and track collections.

PINTA – Gene Prioritization by Network Analysis

PINTA

:: DESCRIPTION

PINTA is a gene prioritization tool that identifies the most promising candidates within a region when only sparse information about the phenotype is available by replacing this knowledge by experimental data on differential gene expression between affected and healthy individuals. Considering the problem from the perspective of a gene/protein network, it assesses the relevance of a candidate gene by considering the level of differential expression in its network neighborhood under the assumption that strong candidates tend to be surrounded by differentially expressed neighbors.

::DEVELOPER

Bioinformatics Research Group, Belgium

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W334-8. doi: 10.1093/nar/gkr289. Epub 2011 May 20.
PINTA: a web server for network-based gene prioritization from expression data.
Nitsch D, Tranchevent LC, Gon?alves JP, Vogt JK, Madeira SC, Moreau Y.

FuseNet – Gene Network Inference by Fusing data from Diverse Distributions

FuseNet

:: DESCRIPTION

FuseNet is a Markov network formulation that infers networks from a collection of nonidentically distributed datasets.

::DEVELOPER

FuseNet team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 FuseNet

:: MORE INFORMATION

Citation

Gene network inference by fusing data from diverse distributions.
Žitnik M, Zupan B.
Bioinformatics. 2015 Jun 15;31(12):i230-i239. doi: 10.1093/bioinformatics/btv258.

Red – Inference of Epistatic Gene Networks

Red

:: DESCRIPTION

Red is a conceptually new probabilistic approach to gene network inference from quantitative interaction data

::DEVELOPER

BioLab , University of Ljubljana

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 Red

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jun 15;30(12):i246-i254. doi: 10.1093/bioinformatics/btu287.
Gene network inference by probabilistic scoring of relationships from a factorized model of interactions.
Zitnik M1, Župan B2.

GenePath – Analysis of Genetic Data and Discovery of Genetic Networks

GenePath

:: DESCRIPTION

GenePath is a web-enabled intelligent assistant for the analysis of genetic data and for discovery of genetic networks.

::DEVELOPER

BioLab , University of Ljubljana

:: SCREENSHOTS

:: REQUIREMENTS

  • Any Web Browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation:

GenePath: from mutations to genetic networks and back.
Juvan P, Demsar J, Shaulsky G, Zupan B.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W749-52.

BiGG Models 1.6 – A Platform for integrating, standardizing and sharing Genome-scale Models

BiGG Models 1.6

:: DESCRIPTION

BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions.

::DEVELOPER

the Systems Biology Research Group at theUniversity of California, San Diego.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web server
  • Python

:: DOWNLOAD

  BiGG Models

:: MORE INFORMATION

Citation:

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models.
King ZA, Lu J, Dräger A, Miller P, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, Lewis NE.
Nucleic Acids Res. 2015 Oct 17. pii: gkv1049.

Metabomxtr 1.25.0 – R package for Mixture-model Analysis of non-targeted Metabolomics Data

Metabomxtr 1.25.0

:: DESCRIPTION

The functions in Metabomxtr package return optimized parameter estimates and log likelihoods for mixture models of truncated data with normal or lognormal distributions.

::DEVELOPER

Metabomxtr team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R
  • BioConductor

 Metabomxtr

:: MORE INFORMATION

Citation

Metabomxtr: an R package for mixture-model analysis of non-targeted metabolomics data.
Nodzenski M, Muehlbauer MJ, Bain JR, Reisetter AC, Lowe WL Jr, Scholtens DM.
Bioinformatics. 2014 Jul 29. pii: btu509