Melanie 8.0 – 2D Gel Analysis Platform

Melanie 8.0

:: DESCRIPTION

Melanie provides powerful and innovative solutions to shorten the path from data acquisition to protein information, both for conventional 2-DE and DIGE gels. The superior spot detection and matching algorithms facilitate the extraction of statistically valid differences between groups of 2-D gels, while requiring minimal user intervention and therefore speeding up analysis time.

::DEVELOPER

Geneva Bioinformatics (GeneBio) SA

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Melanie

:: MORE INFORMATION

PhyDesign – Phylogenetic Informativeness Analysis

PhyDesign

:: DESCRIPTION

PhyDesign is a platform-independent online application that implements the Townsend phylogenetic informativeness analysis, providing a quantitative prediction of the utility of loci to solve specific phylogenetic questions. An easy-to-use interface facilitates uploading of alignments and ultrametric trees to calculate and depict profiles of informativeness over specified time ranges, and provides rankings of locus prioritization for epochs of interest.

::DEVELOPER

the Townsend Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No

:: MORE INFORMATION

Citation

Lopez-Giraldez F., and J.P. Townsend, 2011.
PhyDesign: an online application for profiling phylogenetic informativeness.
BMC Evol. Biol., 11: 152.

ASTRO – Analysis of Short Time-series using Rank Order preservation

ASTRO

:: DESCRIPTION

ASTRO is a web server for analyzing and visualizing short time-series gene expression data

::DEVELOPER

Benos Lab

 SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Aug 20;10:255. doi: 10.1186/1471-2105-10-255.
Extracting biologically significant patterns from short time series gene expression data.
Tchagang AB, Bui KV, McGinnis T, Benos PV.

mirConnX – Analysis of mRNA and microRNA (miRNA) Gene Regulatory Networks

mirConnX

:: DESCRIPTION

mirConnX is a user-friendly web interface for inferring, displaying and parsing mRNA and microRNA (miRNA) gene regulatory networks. mirConnX combines sequence information, and computational predictions with gene expression data analysis to create a disease-specific, genome-wide regulatory network.

::DEVELOPER

Benos Lab

 SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W416-23. doi: 10.1093/nar/gkr276. Epub 2011 May 10.
mirConnX: condition-specific mRNA-microRNA network integrator.
Huang GT, Athanassiou C, Benos PV.

sLDA – Sparse Linear Discriminant Analysis

sLDA

:: DESCRIPTION

sLDA (Sparse Linear Discriminant Analysis) is a software for testing the significance of Gene Pathways when signal is relatively weak. Also included is general code for running two-group L1 penalized linear discriminant analysis.

::DEVELOPER

Michael Wu’s Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • R
:: DOWNLOAD

 sLDA

:: MORE INFORMATION

Citation

Wu, M.C., Zhang, L., Wang, Z., Christiani, D.C., Lin, X. (2009).
Sparse linear discriminant analysis for simultaneous gene set/pathway significance test and gene selection“.
Bioinformatics, 25,1145-1151.

fRMA 1.39.0 / frmaTools 1.39.0 – Single Microarray Preprocessing and Analysis

fRMA 1.39.0 / frmaTools 1.39.0

:: DESCRIPTION

fRMA (Frozen robust multiarray analysis) is a single-array preprocessing algorithm that retains the advantages of multiarray algorithms and removes certain batch effects by downweighting probes that have high between-batch residual variance.

frmaTools: Extension and customization of the frma package.

::DEVELOPER

Matthew N. McCall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • R package
  • Bioconductor

:: DOWNLOAD

 fRMA / frmaTools

:: MORE INFORMATION

Citation

Thawing Frozen Robust Multi-array Analysis (fRMA).
McCall MN, Irizarry RA.
BMC Bioinformatics. 2011 Sep 16;12:369. doi: 10.1186/1471-2105-12-369.

BioAnalyzer 2100 – Analysis of BioAnalyzer data

BioAnalyzer 2100

:: DESCRIPTION

The Agilent 2100 BioAnalyzer is a nanofluidics device that preforms size fractionation and quantification of small samples of DNA, RNA, or Protein. In addition, the BioAnalyzer is able to preform flow cytometry on small numbers of cells.

::DEVELOPER

the MIT BioMicro Center

:: SCREENSHOTS

BioAnalyzer

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 BioAnalyzer

:: MORE INFORMATION

GenSSI 2.0 – Structural Identifiability Analysis of Biological Models

GenSSI 2.0

:: DESCRIPTION

GenSSI (Generating Series for testing Structural Identifiability) is a software which enables non-expert users to carry out  structural identifiability analysis of biological models analysis.

::DEVELOPER

(Bio)Process Engineering group, IIM-CSIC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux /MacOsX
  • Matlab

:: DOWNLOAD

 GenSSI

:: MORE INFORMATION

Citation:

Chis, O., Banga, J.R., Balsa-Canto, E. (2011).
GenSSI: a software toolbox for structural identifiability analysis of biological models,
Bioinformatics, doi: 10.1093/bioinformatics/btr431.

SAM 4.01 – Significance Analysis of Microarrays

SAM 4.01

:: DESCRIPTION

SAM (Significance Analysis of Microarrays) is a statistical technique for finding significant genes in a set of microarray experiments, a supervised learning software for genomic expression data mining.

The input to SAM is gene expression measurements from a set of microarray experiments, as well as a response variable from each experiment. The response variable may be a grouping like untreated, treated [either unpaired or paired], a multiclass grouping (like breast cancer, lymphoma, colon cancer, . . . ), a quantitative variable (like blood pressure) or a possibly censored survival time.

::DEVELOPER

Stanford University Statistics and Biochemistry Labs

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 SAM

:: MORE INFORMATION

Citation

Jun Li and Robert Tibshirani (2011)
Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data.
Stat Methods Med Res. 2011 Nov 28.

MetaGeneAlyse – Analysis of Gene Expression and Metabolite data

MetaGeneAlyse

:: DESCRIPTION

MetaGeneAlyse is a web-based tool for the visualization and analysis of large-scale transcript and metabolite profile datasets. Standard methods (PCA, clustering) are provided as well as state-of-the-art methods such as independent component analysis (ICA).

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2003 Nov 22;19(17):2332-3.
MetaGeneAlyse: analysis of integrated transcriptional and metabolite data.
Daub CO, Kloska S, Selbig J.