VLDP – Analysing Protein Structures in their Environment

VLDP

:: DESCRIPTION

VLDP ( Voronoi Laguerre Delaunay Protein) webserver is designed to determine protein contacts, accessibility and residue volume using Laguerre diagram.

::DEVELOPER

the DSIMB bioinformatic group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

VLDP web server: a powerful geometric tool for analysing protein structures in their environment.
Esque J, Léonard S, de Brevern AG, Oguey C.
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W373-8. doi: 10.1093/nar/gkt509.

CartograTree 2.0 – Connecting Tree Genomes, Phenotypes and Environment

CartograTree 2.0

:: DESCRIPTION

CartograTree is a web-based application that allows researchers to identify, filter, compare, and visualize geo-referenced biotic and abiotic data. Its goal is to support numerous multi-disciplinary research endeavors including: phylogenetics, population structure, and association studies

::DEVELOPER

CartograTree team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Mol Ecol Resour. 2013 May;13(3):528-37. doi: 10.1111/1755-0998.12067. Epub 2013 Feb 25.
CartograTree: connecting tree genomes, phenotypes and environment.
Vasquez-Gross HA1, Yu JJ, Figueroa B, Gessler DD, Neale DB, Wegrzyn JL.

Chaste 3.3 – Cancer, Heart and Soft Tissue Environment

Chaste 3.3

:: DESCRIPTION

Chaste is a general purpose simulation package aimed at multi-scale, computationally demanding problems arising in biology and physiology. Current functionality includes tissue and cell level electrophysiology, discrete tissue modelling, and soft tissue modelling.

::DEVELOPER

Chaste Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux

:: DOWNLOAD

 Chaste

:: MORE INFORMATION

Citation

G.R. Mirams,et al.
Chaste: An Open Source C++ Library for Computational Physiology and Biology.
PLoS Comput Biol 9(3):e1002970, 2013. doi: 10.1371/journal.pcbi.1002970.

HXE 1.0 – Haplotype Environment Interaction Analysis software

HXE 1.0

:: DESCRIPTION

HXE is a haplotype environment interaction analysis software

::DEVELOPER

Epstein software

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 HXE

:: MORE INFORMATION

Citation

Kwee LC, Epstein MP, Manatunga AK, Duncan R, Allen AS, Satten GA. (2007)
Simple methods for assessing haplotype-environment interactions in case-only and case-control studies.
Genet Epidemiol. 31(1):75-90.

Skyline 3.1 – Targeted Proteomics Environment

Skyline 3.1

:: DESCRIPTION

Skyline is a freely-available, open-source Windows client application for building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM), Parallel Reaction Monitoring (PRM – Targeted MS/MS and DIA/SWATH) and targeted DDA with MS1 quantitative methods and analyzing the resulting mass spectrometer data. It aims to employ cutting-edge technologies for creating and iteratively refining targeted methods for large-scale proteomics studies.

::DEVELOPER

MacCoss Lab

:: SCREENSHOTS

Skyline

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Skyline

 :: MORE INFORMATION

Citation

Bioinformatics. 2014 May 9. [Epub ahead of print]
A framework for installable external tools in Skyline.
Broudy D1, Killeen T, Choi M, Shulman N, Mani DR, Abbatiello SE, Mani D, Ahmad R, Sahu AK, Schilling B, Tamura K, Boss Y, Sharma V, Gibson BW, Carr SA, Vitek O, Maccoss MJ, Maclean B.

R/maanova 1.36.0 & J/maanova 1.1.1 & MAANOVA 2.0 – Environment for Microarray Analysis

R/maanova 1.36.0 & J/maanova 1.1.1 & MAANOVA 2.0

:: DESCRIPTION

R/maanova (MicroArray ANalysis Of VAriance) is an extensible, interactive environment for Microarray analysis.

J/maanova is an open sourced desktop application with the aim of simplifying the analysis of microarray experiments. J/maanova allows researchers to access a subset of the functionality available in the R/maanova package through a graphical user interface.

MAANOVA is the Matlab version of R/maanova.

::DEVELOPER

The Churchill Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  •  / Java / MatLab

:: DOWNLOAD

 R/maanova , J/maanova , MAANOVA

:: MORE INFORMATION

Citation

J Comput Biol. 2000;7(6):819-37.
Analysis of variance for gene expression microarray data.
Kerr MK1, Martin M, Churchill GA.

Badger 1.1 – An Accessible Genome Exploration Environment

Badger 1.1

:: DESCRIPTION

Badger provides an easy to use and intuitive way to explore and store genome data and gene predictions. It can be used as a central hub for genome projects allowing project members to search and access data as and when it is available. The database can hold multiple species, each with multiple genome versions and each genome with multiple gene prediction sets.

::DEVELOPER

The Blaxter Lab at The Institute of Evolutionary Biology University of Edinburgh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  Badger

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Nov 1;29(21):2788-9. doi: 10.1093/bioinformatics/btt466. Epub 2013 Aug 11.
Badger–an accessible genome exploration environment.
Elsworth B1, Jones M, Blaxter M.

SPACE – Tools for Structure Prediction and Analysis based on Complementarity with Environment

SPACE

:: DESCRIPTION

SPACE is a suite of SPACE tools for analysis and prediction of structures of biomolecules and their complexes.

::DEVELOPER

Edelman-Sobolev Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SPACE

:: MORE INFORMATION

Citation:

SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment.
Sobolev V, Eyal E, Gerzon S, Potapov V, Babor M, Prilusky J, Edelman M.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W39-43.

ProteoSAFe 1.2.6 – Proteomics Environment

ProteoSAFe 1.2.6

:: DESCRIPTION

ProteoSAFe is a Proteomics Environment which is Scalable in utilizing distributed computing, Accessible via reconfigurable, easy-to-learn user interfaces, and Flexible in tool chaining.

::DEVELOPER

To-ju Huang (t3huang@ucsd.edu)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ProteoSAFe

:: MORE INFORMATION

GEB – Genome Environment Browser

GEB

:: DESCRIPTION

GEB is a Java application developed to provide a dynamic graphical interface to visualise the distribution of genome features and chromosome-wide experimental data in high resolution.

::DEVELOPER

the Bioinformatics Support Service, Centre for BioinformaticsImperial College London, UK and the MRC Clinical Sciences Centre, London, UK

:: SCREENSHOTS

GEB

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Java
  • MySQL 

:: DOWNLOAD

 GEB

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2008 Nov 27;9:501. doi: 10.1186/1471-2105-9-501.
Genome Environment Browser (GEB): a dynamic browser for visualising high-throughput experimental data in the context of genome features.
Huntley D, Tang YA, Nesterova TB, Butcher S, Brockdorff N.