Skyline 21.1 – Targeted Proteomics Environment

Skyline 21.1

:: 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.

systemPipeR 1.27.27 – NGS Workflow and report Generation Environment

systemPipeR 1.27.27

:: DESCRIPTION

systemPipeR is an R package for building and running automated end-to-end analysis workflows for a wide range of next generation sequence (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.

::DEVELOPER

Girke Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • R package
  • BioConductor

:: DOWNLOAD

systemPipeR

:: MORE INFORMATION

Citation

H Backman TW, Girke T.
systemPipeR: NGS workflow and report generation environment.
BMC Bioinformatics. 2016 Sep 20;17:388. doi: 10.1186/s12859-016-1241-0. PMID: 27650223; PMCID: PMC5029110.

Chaste 2021.1 – Cancer, Heart and Soft Tissue Environment

Chaste 2021.1

:: 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.

EMIRGE v0.61.1 – Expectation-Maximization Iterative Reconstruction of Genes from the Environment

EMIRGE v0.61.1

:: DESCRIPTION

EMIRGE reconstructs full length ribosomal genes from short read sequencing data.

::DEVELOPER

Banfield Lab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux/windows /MacOsX
  • Python

:: DOWNLOAD

EMIRGE

:: MORE INFORMATION

Citation

Miller CS, Baker BJ, Thomas BC, Singer SW, Banfield JF.
EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data.
Genome Biol. 2011;12(5):R44. doi: 10.1186/gb-2011-12-5-r44. Epub 2011 May 19. PMID: 21595876; PMCID: PMC3219967.

OpenCMISS 1.3.0 – Mathematical Modelling Environment for Complex Bioengineering Problems

OpenCMISS 1.3.0

:: DESCRIPTION

OpenCMISS is a mathematical modelling environment that enables the application of finite element analysis techniques to a variety of complex bioengineering problems

::DEVELOPER

OpenCMISS Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 OpenCMISS

:: MORE INFORMATION

Citation

Prog Biophys Mol Biol. 2011 Oct;107(1):32-47. doi: 10.1016/j.pbiomolbio.2011.06.015. Epub 2011 Jul 7.
OpenCMISS: a multi-physics & multi-scale computational infrastructure for the VPH/Physiome project.
Bradley C, et al.

R/maanova 1.60.0 – Environment for Microarray Analysis

R/maanova 1.60.0

:: DESCRIPTION

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

::DEVELOPER

The Churchill Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  •  / Java / MatLab

:: DOWNLOAD

 R/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

:: 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.

 

HLP – Predicting Half-life of Peptides in Intestine like Environment

HLP

:: DESCRIPTION

HLP is a server developed for predicting half-life of peptides in intestine like environment. It generates all possible mutants (single mutation at each position per cycle) for a peptide and predict/calculate half-life and physicochemical properties (e.g. charge, polarity, hydrophobicity, volume, pK) of mutant peptides.

::DEVELOPER

HLP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Designing of peptides with desired half-life in intestine-like environment.
Sharma A, Singla D, Rashid M, Raghava GP.
BMC Bioinformatics. 2014 Aug 20;15:282. doi: 10.1186/1471-2105-15-282.

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.

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