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

FFTbor / FFTbor2D 2.0.2 – 2D Energy Landscape of / RNA Secondary Structures

FFTbor / FFTbor2D 2.0.2

:: DESCRIPTION

FFTbor computes Boltzmann probability for RNA structural neighbors using the fast Fourier transform.

Given an RNA sequence having metastable secondary structures A,B, the program FFTbor2D computes the ensemble free energy E(x,y)=-RT log Z(x,y), taken over all secondary structures having base pair distance x from A,and base pair distance y from B.

::DEVELOPER

Clote Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

FFTbor2D , FFTbor

:: MORE INFORMATION

Citation:

PLoS One. 2012;7(12):e50506. doi: 10.1371/journal.pone.0050506. Epub 2012 Dec 19.
Using the fast fourier transform to accelerate the computational search for RNA conformational switches.
Senter E1, Sheikh S, Dotu I, Ponty Y, Clote P.

J Math Biol. 2015 Jan;70(1-2):173-96. doi: 10.1007/s00285-014-0760-4. Epub 2014 Feb 12.
RNA folding pathways and kinetics using 2D energy landscapes.
Senter E1, Dotu I, Clote P.

Zem 0.3 – 2D Molecular Editor

Zem 0.3

:: DESCRIPTION

Zem is a  molecular editor. Built using openbabel and Qt Zem reads and writes more than 80 chemical formats and several graphic formats including .bmp .jpg .svg and .png.

::DEVELOPER

Nicola Zonta (nicola.zonta*gmail.com)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX

:: DOWNLOAD

 Zem

:: MORE INFORMATION

JVirGel 2.2.3 – Create Virtual 2D Pretein Gel

JVirGel 2.2.3

:: DESCRIPTION

JVirGel is a software for the simulation and analysis of proteomics data. The software determines the theoretical isoelectric points (pI) and the calculated molecular weights (MW) of proteins and visualizes these as a virtual two-dimensional (2D) protein map. The user is able to control the presentation of the calculated 2D gel interactively by selecting a pI/MW range and an electrophoretic timescale of interest.

::DEVELOPER

Karsten Hiller (k.hiller@tu-bs.de) @ Institute for Microbiology, Technical University of Braunschweig

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

 JVirGel

:: MORE INFORMATION

Citation:

Hiller, K.; Grote, A.; Maneck, M.; Münch, R.; Jahn, D.
JVirGel 2.0: computational prediction of proteomes separated via two-dimensional gel electrophoresis under consideration of membrane and secreted proteins.
Bioinformatics, 2006, 22, 2441-2443

GSA Image Analyser 4.0.3 – 2D Images Analysis

GSA Image Analyser 4.0.3

:: DESCRIPTION

GSA Image Analyser is a program for the scientific evaluation of 2D images (image analysis). The possibilities of the program are varied and can be divided in three main groups:Object surface calculationObject length calculationObject counting.

::DEVELOPER

GSA

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

GSA Image Analyser

:: MORE INFORMATION

BPDA2d 1.0 – A 2D Global Optimization based Bayesian Peptide Detection algorithm for LC-MS

BPDA2d 1.0

:: DESCRIPTION

The BPDA2d software package can be used for peptide detection in LC-MS data with resolution high enough to baseline-resolve isotopic peaks. BPDA2d achieves peptide deisotoping and charge state deconvolution simultaneously. It systematically evaluates all possible combinations of possible peptide candidates for spectra interpretation, and optimizes peptide signals in order to minimize the mean squared error between inferred and observed spectra.

::DEVELOPER

BPDA2d team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • MatLab

:: DOWNLOAD

 BPDA2d

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Feb 15;28(4):564-72. doi: 10.1093/bioinformatics/btr675. Epub 2011 Dec 6.
BPDA2d–a 2D global optimization-based Bayesian peptide detection algorithm for liquid chromatograph-mass spectrometry.
Sun Y1, Zhang J, Braga-Neto U, Dougherty ER.

JChemPaint 3.3-1210 – Editor for 2D Molecular Structures

JChemPaint 3.3-1210

:: DESCRIPTION

JChemPaint (or JCP ) is the editor and viewer for 2D chemical structures developed using CDK. It is implemented in several forms: a Java application and two varieties of Java applet.

::DEVELOPER

Steinbeck group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

JChemPaint

:: MORE INFORMATION

Citation:

JChemPaint – Using the Collaborative Forces of the Internet to Develop a Free Editor for 2D Chemical Structures
Stefan Krause, Egon Willighagen and Christoph Steinbeck.
Molecules 5, 93-98 (2000).

Seg2Dgel 0.5.12 – 2D Electrophoresis Gel Spot Segmenter

Seg2Dgel 0.5.12

:: DESCRIPTION

Seg2Dgel is a Java 2D-electrophoretic gel segmentation program for finding and measuring the integrated density and position of spots in a gel or image with similar types of data. We are enhancing it to segment spots in 2D LC-MS images.

::DEVELOPER

Biomedical Image Processing and Database Analysis Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

 Seg2Dgel

:: MORE INFORMATION

 

Flicker 0.87.2 – Compare 2D Gel Images

Flicker 0.87.2

:: DESCRIPTION

Flicker is an open source Java application for comparing 2D gel (or similar) images across the Internet or locally. It is possible to visually compare a user gel image with a SWISS-2DPAGE image and then select spots for identification with the Expasy SWISS-PROT protein ID database. It also has rudimentary manual quantification of spot data.

::DEVELOPER

Flicker Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

 Flicker

:: MORE INFORMATION

Citation:

Comparing 2-D Electrophoretic Gels Across Internet Databases,
PF Lemkin, GC Thornwall, J Evans (2005)
“The Proteomics Handbook”, JM Walker (Ed), Humana Press Inc, Totowa, NJ, pp 279-305.