JAMSS – A GUI Java Mass Spectrometry Simulation Suite

JAMSS

:: DESCRIPTION

JAMSS is a fast, self-contained in silico simulator capable of generating simulated MS and LC- MS runs while providing meta information on the provenance of each generated signal.

::DEVELOPER

Rob Smith

:: SCREENSHOTS

JAMSS

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • Java

:: DOWNLOAD

 JAMSS

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Nov 3. pii: btu729.
JAMSS: Proteomics Mass Spectrometry Simulation in Java.
Smith R1, Prince JT

CompNet – A GUI based tool to Compare Multiple Biological Interaction Networks

CompNet

:: DESCRIPTION

CompNet, a GUI based network comparison tool , allows to visually compare multiple networks based on node and edge similarities.

::DEVELOPER

CompNet team

:: SCREENSHOTS

CompNet

:: REQUIREMENTS

  • Linux / Windows
  • R package

:: DOWNLOAD

 CompNet

:: MORE INFORMATION

Citation:

CompNet: a GUI based tool for comparison of multiple biological interaction networks.
Kuntal BK, Dutta A, Mande SS.
BMC Bioinformatics. 2016 Apr 26;17(1):185. doi: 10.1186/s12859-016-1013-x

InteractiveROSETTA 2.1 – GUI for PyRosetta Protein Modeling Suite

InteractiveROSETTA 2.1

:: DESCRIPTION

InteractiveROSETTA is a wxPython graphical interface for the PyRosetta and Rosetta protein modeling suites

::DEVELOPER

Chris Bystroff

:: SCREENSHOTS

InteractiveROSETTA

:: REQUIREMENTS

:: DOWNLOAD

 InteractiveROSETTA

:: MORE INFORMATION

Citation

InteractiveROSETTA: a graphical user interface for the PyRosetta protein modeling suite.
Schenkelberg CD, Bystroff C.
Bioinformatics. 2015 Aug 26. pii: btv492

RNASeqGUI 1.0.0 – GUI for the Identification of Differentially Expressed Genes

RNASeqGUI 1.0.0

:: DESCRIPTION

RNASeqGUI R package is a graphical user interface for the identification of differentially expressed genes from RNA-Seq experiments.

::DEVELOPER

Computational & Biology Open laboratory

:: SCREENSHOTS

RNASeqGUI

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package

:: DOWNLOAD

  RNASeqGUI

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 May 7. [Epub ahead of print]
RNASeqGUI: A GUI for analysing RNA-Seq data.
Russo F1, Angelini C.

SearchGUI 2.0.5 – GUI for Proteomics Identification Search Engines

SearchGUI 2.0.5

:: DESCRIPTION

SearchGUI is a user-friendly, lightweight and open-source graphical user interface for configuring and running two proteomics identification search engines simultaneously, namely the Open Mass Spectrometry Search Algorithm (OMSSA) and X!Tandem.

::DEVELOPER

The Proteomics Unit at the University of Bergen (PROBE)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux
  • Java

:: DOWNLOAD

SearchGUI

:: MORE INFORMATION

Citation

Vaudel et al:
SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches.
Proteomics 2011;11(5):996-9.

Gromita 3.01 – GUI for GROMACS

Gromita 3.01

:: DESCRIPTION

Gromita is a Graphical User Interface (GUI) for GROMACS (v.3 and 4). It is writen in perl making extensive use of perl/tk achieving portability in a wide variety of operating systems and architectures. Gromita provides friendly to use buttons in a windows-based environment while maintaining a terminal mode for the experienced user.

::DEVELOPER

Gromita Team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 Gromita

:: MORE INFORMATION

Citation

Sellis D, Vlachakis D, Vlassi M. (2009)
Gromita: A Fully Integrated Graphical User Interface to Gromacs 4.
Bioinform Biol Insights 2009:3 99-102

siMBa 1.0 – A simple GUI for MrBayes.

siMBa 1.0

:: DESCRIPTION

siMBa (simple MrBayes) is a graphical user interface for the phylogenetic analysis software, MrBayes.

::DEVELOPER

Thines Lab.

:: SCREENSHOTS

siMBa

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

 siMBa

:: MORE INFORMATION

Citation:

Mishra B, Thines M (2014)
siMBa — a simple graphical user interface for the Bayesian phylogenetic inference program MrBayes.
Mycological Progress 13:1255–1258

J/qtl 1.3.4 – Java GUI for R/qtl

J/qtl 1.3.4

:: DESCRIPTION

J/qtl is a Java graphical user interface (GUI) for the popular QTL data analysis software R/qtl.

::DEVELOPER

 Hao Wu, Lei Wu and Keith Sheppard.

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 J/qtl 

:: MORE INFORMATION

Citation

Methods Mol Biol. 2009;573:175-88.
Quantitative trait locus analysis using J/qtl.
Smith R, Sheppard K, DiPetrillo K, Churchill G.

AUDocker 1.1.2 – GUI for AutoDock Vina

AUDocker 1.1.2

:: DESCRIPTION

AUDocker is a GUI for AutoDock Vina. helps in virtual screening of huge number of ligands continuously. Helps in resumption of work in accidental shutdowns. This program can help you in docking several ligands automatically in to a prescribed protein receptor site.

::DEVELOPER

Dr M Murali Krishna Kumar

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 AUDocker 

:: MORE INFORMATION

Citation

BMC Res Notes. 2011 Oct 25;4:445. doi: 10.1186/1756-0500-4-445.
AUDocker LE: A GUI for virtual screening with AUTODOCK Vina.
Sandeep G, Nagasree KP, Hanisha M, Kumar MM.

PrimerPy 0.97a – GUI tool for QPCR Primer Design

PrimerPy 0.97a

:: DESCRIPTION

PrimerPy is a GUI tool for optimal SG QPCR primer design. This branch, Huckleberry, uses “Primer3” as backend engine. The design’s been validated by laboratory experiences; also applicable to conventional PCR.

::DEVELOPER

Suzhao Li

:: SCREENSHOTS

PrimerPy

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

 PrimerPy

:: MORE INFORMATION