Tag: Platform

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

ELL 3.2.4 – Platform for Generic Algorithms

ELL 3.2.4

:: DESCRIPTION

The ELL (Energy Landscape Library ) provides a platform for generic algorithms to study kinetics and structure of energy landscapes with discrete states. These algorithms need an abstract representation of these states to be applied to a multitude of state instances and their corresponding energy or fitness landscapes.

::DEVELOPER

Chair for Bioinformatics Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ELL

:: MORE INFORMATION

Citation

Martin Mann, Sebastian Will and Rolf Backofen.
The energy landscape library – a platform for generic algorithms.
In Proceedings of 1st BIRD’07, OCG, 217, 83-86, 2007.

GenePattern 3.9.11 – Genomic Analysis Platform

GenePattern 3.9.11

:: DESCRIPTION

GenePattern is a powerful genomic analysis platform that provides access to more than 125 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.

GenePattern provides access to a broad array of computational methods used to analyze genomic data. Its extendable architecture makes it easy for computational biologists to add analysis and visualization modules, which ensures that GenePattern users have access to new computational methods on a regular basis.

::DEVELOPER

The GenePattern team

:: SCREENSHOTS

:: REQUIREMENTS

  • Java VM
  • MacOSX/Windows/Linux
  • Other Java-enabled Platforms

:: DOWNLOAD

GenePattern

:: MORE INFORMATION

Citation

ATARiS: computational quantification of gene suppression phenotypes from multisample RNAi screens.
Shao DD, Tsherniak A, Gopal S, Weir BA, Tamayo P, Stransky N, Schumacher SE, Zack TI, Beroukhim R, Garraway LA, Margolin AA, Root DE, Hahn WC, Mesirov JP.
Genome Res. 2013 Apr;23(4):665-78. doi: 10.1101/gr.143586.112.

Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP
GenePattern 2.0
Nature Genetics 38 no. 5 (2006): pp500-501

Viroverse – Platform for Storage, Analysis of Experimental data for Laboratory Workflows

Viroverse

:: DESCRIPTION

Viroverse is a platform for the collection, storage, retrieval, and analysis of experimental data for laboratory workflows.

::DEVELOPER

Mullins Molecular Retrovirology Lab, University of Washington.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser/ Linux ,VirtualBox

:: DOWNLOAD

Viroverse

:: MORE INFORMATION

expVIP 20180914 – RNA-seq Data Analysis and Visualization Platform

expVIP 20180914

:: DESCRIPTION

ExpVIP (expression visualization and integration platfor) is a tool that enables the integration of different RNA-Seq studies by analysing the data uniformly across experiments and provides a web interface to query the data.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

expVIP

:: MORE INFORMATION

Citation

expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform.
Borrill P, Ramirez-Gonzalez R, Uauy C.
Plant Physiol. 2016 Apr;170(4):2172-86. doi: 10.1104/pp.15.01667.

Probemapper 2.1.0 – Connect to QBRC’s ProbeMapper platform

Probemapper 2.1.0

:: DESCRIPTION

The ProbeMapper project aims to correlate microarray probes with Entrez IDs according to various sources including Vendor’s annotations, Bioconductor’s Annotate package, and a manual BLAST alignment of the probe sequences.

::DEVELOPER

The Quantitative Biomedical Research Center (QBRC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R package

:: DOWNLOAD

 Probemapper

:: MORE INFORMATION

Citation

Brief Bioinform. 2012 Sep;13(5):547-54. doi: 10.1093/bib/bbr076. Epub 2011 Dec 23.
Probe mapping across multiple microarray platforms.
Allen JD, Wang S, Chen M, Girard L, Minna JD, Xie Y, Xiao G.

ALEXA 1.1 – Microarray Design platform for ‘Alternative Expression Analysis’

ALEXA 1.1

:: DESCRIPTION

ALEXA is a microarray design platform for ‘alternative expression analysis’. This platform facilitates the design of gene expression arrays for analysis of mRNA isoforms generated from a single locus by the use of alternative transcription initiation, splicing and polyadenylation sites.

::DEVELOPER

ALEXA-Seq Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Virtual Machines

:: DOWNLOAD

  ALEXA

:: MORE INFORMATION

Citation:

Malachi Griffith,et al.
ALEXA – A microarray design platform for alternative expression analysis.
Nature Methods. Feb 2008. 5(2):118.

Proteomatic 1.2.1 – Platform for creating MS/MS data Analysis Workflows using Scripts

Proteomatic 1.2.1

:: DESCRIPTION

Proteomatic is a free data processing pipeline created for the purpose of evaluating mass spectrometric proteomics experiments. Functionality is provided via scripts, and these scripts can be chained together into a high-throughput data processing pipeline.

::DEVELOPER

Proteomatic team

:: SCREENSHOTS

Proteomatic

:: REQUIREMENTS

  • Windows/ MacOsX / Linux

:: DOWNLOAD

 Proteomatic

:: MORE INFORMATION

Citation

Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows
Specht M., Kuhlgert S., Fufezan C., Hippler M.
Bioinformatics (2011) 27(8): 1183-1184, doi: 10.1093/bioinformatics/btr081

RNAspace 1.2 – Platform for Non-protein-coding RNA Annotation

RNAspace 1.2

:: DESCRIPTION

RNAspace is a platform which aims at providing an integrated environment for non-coding RNA annotation. The platform allows running in an integrated environment a variety of ncRNA gene finders, to explore results with dedicated tools for comparison, visualization and edition of putative ncRNAs and to export them in various formats

::DEVELOPER

RNAspace Team

:: SCREENSHOTS

Document3

:: REQUIREMENTS

  • Linux
  • Python
  • cherrypy
  • cheetah
  • blastall, bl2seq
  • clustalw
  • Vienna RNA package
  • Perl

:: DOWNLOAD

 RNAspace

:: MORE INFORMATION

Citation

RNA. 2011 Nov;17(11):1947-56. doi: 10.1261/rna.2844911. Epub 2011 Sep 23.
RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA.
Cros MJ, de Monte A, Mariette J, Bardou P, Grenier-Boley B, Gautheret D, Touzet H, Gaspin C.

CloudBioLinux – Genome Analysis for Cloud Computing platforms

CloudBioLinux

:: DESCRIPTION

CloudBioLinux offers genome analysis resources for cloud computing platforms such as Amazon EC2. The software is a build and deployment system which installs a large selection of Bioinformatics and machine learning libraries on a bare virtual machine (VM) image, freshly installed PC, or in the Cloud.

::DEVELOPER

CloudBioLinux Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CloudBioLinux

:: MORE INFORMATION

Citation

Curr Protoc Bioinformatics. 2012 Jun;Chapter 11:Unit11.9.
Using cloud computing infrastructure with CloudBioLinux, CloudMan, and Galaxy.
Afgan E, Chapman B, Jadan M, Franke V, Taylor J.