SVGMap 1.5.1 – Image Browser for Experimental data

SVGMap 1.5.1

:: DESCRIPTION

The aim of SVGMap is helping in the visualisation of experimental data which are associated with some graphical representation. Thus SVGMap browser allows to generate images with colored areas corresponding to the chosen data and color scale.

::DEVELOPER

Biomedical Genomics Group at the Biomedical Research Park in Barcelona (PRBB)

:: SCREENSHOTS

:: REQUIREMENTS

Windows/Linux / MacOsX
Java

:: DOWNLOAD

SVGMap

:: MORE INFORMATION

Citation

Rafael-Palou X, Schroeder MP and Lopez-Bigas N.
SVGMap: configurable image browser for experimental data
Bioinformatics (2012) 28(1):119-20.

GNomEx – Genomic Experimental Data Repository and Core LIMS

GNomEx

:: DESCRIPTION

GNomEx provides a web accessible database and LIMS to organize and track the generation of raw genomic data, its associated downstream analysis, and to programmatically distribute the data to client applications such as IGB and the UCSC Genome Browser.

::DEVELOPER

The Bioinformatics Shared Resource

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / MacOsX
Java

:: DOWNLOAD

GNomEx

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Sep 9;11:455. doi: 10.1186/1471-2105-11-455.
Next generation tools for genomic data generation, distribution, and visualization.
Nix DA1, Di Sera TL, Dalley BK, Milash BA, Cundick RM, Quinn KS, Courdy SJ.

VANTED 2.6.5 – Visualization and Analysis of Networks containing Experimental Data

VANTED 2.6.5

:: DESCRIPTION

VANTED (Visualisation and Analysis of Networks containing Experimental Data) is an open source software that offers the possibility to load and edit graphs, which may represent biological pathways or functional hierarchies. It allows to integrate different *omics data into the functional context and provides a variety of functions for data mapping and processing, statistical analysis, and visualisation. With the VANTED Add-on interface it is easily possible to extend the functionality of the software.

::DEVELOPER

Life Science Informatics – Prof. Dr. Falk Schreiber

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux/ MacOSX
Java

:: DOWNLOAD

VANTED

:: MORE INFORMATION

Citation

Klukas and Schreiber (2010)
Integration of -omics data and networks for biomedical research with VANTED.
Journal of Integrative Biology, 7(2)

Björn H. Junker, Christian Klukas and Falk Schreiber (2006)
VANTED: A system for advanced data analysis and visualization in the context of biological networks.
BMC Bioinformatics, 7:109

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

BCL 3.6.1 – Protein Structure Determination from sparse Experimental data

BCL 3.6.1

:: DESCRIPTION

The BCL (Bio Chemical Library) is a software package that provides unique tools for biological research, such as protein structure determination from sparse experimental data.The BCL contains the widely used secondary structure prediction program JUFO, a folding algorithm that assembles secondary structure elements, and loop construction tools that complete protein backbones. With this series of protocols the BCL allows construction of backbone models for large and membrane proteins from the primary sequence. Among its unique strengths are the incorporation of sparse and low resolution data into folding simulations.Additionally, the BCL contains a suite of cheminformatics tools that allow construction of quantitative structure-activity-relation (QSAR) models for virtual screening, pharmacophore mapping, and drug design.

::DEVELOPER

Jens Meiler

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX

:: DOWNLOAD

BCL

:: MORE INFORMATION

Citation

BCL::Fold – De Novo Prediction of Complex and Large Protein Topologies by Assembly of Secondary Structure Elements.
Karakaş M, Woetzel N, Staritzbichler R, Alexander N, Weiner BE, Meiler J.
PLoS One. 2012;7(11):e49240. doi: 10.1371/journal.pone.0049240. Epub 2012 Nov 16.