GAL File Generator 1.2 – Well Plates Files Conversion

GAL File Generator 1.2

:: DESCRIPTION

GAL File Generator . Conversion of a file of 96 well plates into a file of 384 well plates, and conversion of a file of 384 well plates into an Axon GenePix Gene Array List file (.gal file). Several options are available for this latter function, including spot size, spacing, and orientation of plate in the arrayer with respect to the slides

::DEVELOPER

Derisi Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

GAL File Generator 1.2

:: MORE INFORMATION

GAL File Generator also named for Gal File Maker.

AMIADA 2.0.7 – Analysis of Microarray Data

AMIADA 2.0.7

:: DESCRIPTION

AMIADA is an integrated computer program for organizing, exploring, visualizing, and analyzing microarray data. It features an EXCEL-like user interface and performs data transformation, principal component analysis, a variety of cluster analysis and extensive graphic functions for visualizing expression profiles.

::DEVELOPER

Dr. Xuhua Xia

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

AMIADA

:: MORE INFORMATION

Citation : Xia, X., and Xie. Z., 2001 AMADA: Analysis of microarray data. Bioinformatics 17:569-570.

MAExplorer 0.96.34.01 – MicroArray Explorer Tool

MAExplorer 0.96.34.01

:: DESCRIPTION

The MAExplorer is a Java-based bioinformatics exploratory data-analysis and data-mining program for analyzing sets of quantitative spotted cDNA or oligonucleotide microarray data . It includes data management, graphics, statistics, clustering, reports, gene data-filtering, user written MAEPlugins, documentation, tutorials, demo data. The exploratory data analysis environment provides tools for the data-mining of quantitative expression profiles across multiple microarrays.

With MAExplorer, it is possible to: 1) analyze the expression of individual genes; 2) analyze the expression of gene families and clusters; 3) compare expression patterns and outliers; 4) directly access other genomic databases for genes of interest. Previously quantified array data is copied to your local computer where it is read by MAExplorer and intermediate results as well as the data mining session state may be saved between data mining sessions.

::DEVELOPER

Dr. Peter Lemkin (LECB/NCI-Frederick) with help from Gregory Thornwall (SAIC) and Jai Evans (DECA/CIT, NIH)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Linux
  • MacOsX
  • Java

:: DOWNLOAD

MAExplorer 0.96.34.01 , Manual

:: MORE INFORMATION

MAExplorer is available as Open Source at the SourceForge at http://maexplorer.sourceforge.net/ under the Mozilla Public License 1.1 (MPL 1.1) with an acompanying LEGAL document required by the U.S. Government.

ANTHEPROT 3D 1.0.162- Molecule Viewer to look at PDB files

ANTHEPROT 3D 1.0.162

:: DESCRIPTION

Antheprot 3D is a molecular graphics program intended for the visualisation of proteins, nucleic acids from RCSB archive. The program is aimed at display, teaching and generation of publication quality images.

The program reads in a molecule coordinate file (PDB format) and interactively displays the molecule on the screen in a variety of color schemes and molecule representations. Currently available representations include wireframes, sticks, spheres, ball and stick, atom labels and distances. PDB files that are available either locally (Ctrl+O or File=>Open) or distantly at “POLE Bioinformatique Lyonnais” (Ctrl+I) or File=> PBIL URL can be loaded directly into AntheProt3D.

The program is made of 3 different windows:

  • A 3D view window which allows the user to interactively move the molecule
  • A group selection panel for group selection
  • A text window for provinding the user the list of clicked atoms, information (F2) and PHI, PSI values

A Ramachandran interactive plot is also available

Features

  • Alpha trace, wireframe, space filled,Balla nd Sticks, Sticks and surface mode.
  • Full support of clipping (“molecule slicing”)
  • Full support of stereo (side by side, anaglyph or quad buffer stereo)
  • Interactive Ramachandran plot
  • Hydrogen addition or removal by reduce
  • Selection of amino acids by group, chain or within a sphere
  • Surface viewer for MSMS files (Sanner, M.F., Spehner, J.-C., and Olson, A.J. (1996).Biopolymers, 38 (3), 305-320.
  • Ribbon or cylinder mode from Molscript program (P. J. Kraulis, (1991) Journal of Applied Crystallography 24, pp 946-950.)
  • Support for Delphi electrostatic potential Rocchia, W.; Alexov, E.; Honig, B. (2001) J Phys. Chem. 105, 6507-6514

::DEVELOPER

Pr Gilbert Deléage at France Institute of Biology and Chemistry of Proteins

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

ANTHEPROT 3D 1.0.162

:: MORE INFORMATION

ANTHEPROT3D album

If you use ANTHEPROT on PC, please cite one of the following references :

Deleage G, Combet C, Blanchet C, Geourjon, C
ANTHEPROT: An integrated protein sequence analysis software with client/server capabilities?
(2001) COMPUTERS IN BIOLOGY AND MEDICINE 31 (4): 259-267

Chemis3D 2.89b – Java 3D Molecular Viewer Applet

Chemis3D 2.89b

:: DESCRIPTION

Chemis3D is a Java Applet which renders virtual 3D molecular models within a Web document. It is specially designed for open interactive molecular visualization on the Internet or via an intranet. Molecular structures can be manipulated in real-time and rendered in various styles and appearances.

Chemis3D is a small applet running well on any Java-enabled browser and requiring no specialized plug-in nor professional applications.

Features

  • Real-time manipulation and fast 3D rendering.
  • Wide variety of molecular representations including special styles and color coding schemes for proteins and nucleic acids .
  • Enhanced interface using popumenu and key shortcuts .
  • Multi-models display and molecular animation capabilities.
  • Measuring and analysing tools.
  • Support of the most popular molecular data formats :Brookhaven Protein DataBank (*.pdb).MSC XMol files (*.xyz).MDL molfiles (*.mol).

::DEVELOPER

Didier COLLOMB

:: SCREENSHOTS

:: REQUIREMENTS

  • Java-enabled browser

:: DOWNLOAD

Chemis3D 2.89b

:: MORE INFORMATION

Chemis3D MAY BE FREELY USED FOR PERSONNAL, ACADEMIC AND NON-COMMERCIAL PURPOSES, IN AGREEMENT WITH THE FOLLOWING RESTRICTIONS.

RasTop 2.2 – Molecular Visualization Software Adapted for Rasmol

RasTop 2.2

:: DESCRIPTION

RasTop is a molecular visualization software adapted from the program RasMol, which was initially developed by Roger Sayle. RasTop is particularly adapted for educational purposes and for the rapid analysis of macromolecules at the bench.  RasTop wraps a user-friendly graphical interface around the “RasMol molecular engine”. There is no need to type on the command line; each command in the menu generates its own script. Through an extended menu and a command panel, users can manipulate numerous molecules rapidly and learn about them. Work sessions are saved in script format and are fully regenerated with a simple mouse click.

::DEVELOPER

Philippe Valadon

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Linux with Wine
  • Mac with Virtual PC

:: DOWNLOAD

RasTop 2.2 , Version Francaise

:: MORE INFORMATION

RasTop 2.2 is distributed both under the GPL license ad the Rasmol license.  Certain conditions apply to users and to developers to ensure that RasTop remain open source. Please, consult the license.txt and raslic.txt file in the package.

ArrayMaker 2.6 – Provides Robotic Control of Microarrayer Robots

ArrayMaker 2.6

:: DESCRIPTION

ArrayMaker provides high performance robotic control of microarrayer robots with an incredibly intuitive, easy to use interface. ArrayMaker is optimized for use with the new generation of ultra fast linear servo driven arrayers, yet it is backwards compatible with the original MGuide style of ball-screw driven arrayers.

Features highly flexible configuration options, orange packing, replicate spots, replicate arrays, multiple slide and plate orientations.

::DEVELOPER

Derisi Lab

:: SCREENSHOTS

:: REQUIREMENTS

Windows 98/2000/NT/XP, Galil DMC-1832 Series PCI Bus Controller Card

:: DOWNLOAD

ArrayMaker 2.6, File Size:2,494K

:: MORE INFORMATION

This version has a new parameter in the “motor.cfg” file for a separate acceleration value for the x-stage during test prints. This value should be entered on the 19th line of your “motor.cfg” file, inserted between the “HPrintZ” line and the “SpeedX” line.

SilVA 1.1.1 – Silent Variant Analysis using random Forests

SilVA 1.1.1

:: DESCRIPTION

SilVA (Latin for “forest”) is a tool for the automated harmfulness prediction of synonymous (silent) mutations within the human genome. SilVA bases its predictions on a number of features, including conservation, codon usage, splice sites, splicing enhancers and suppressors, and mRNA folding free energy. Given variants in a VCF file, SilVA will rank the rare synonymous variants according to their predicted harmfulness.

::DEVELOPER

Orion Buske and Michael Brudno

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Perl
  • Python
  • R package

:: DOWNLOAD

 SilVA

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Aug 1;29(15):1843-50. doi: 10.1093/bioinformatics/btt308.
Identification of deleterious synonymous variants in human genomes.
Buske OJ, Manickaraj A, Mital S, Ray PN, Brudno M.

sampletrees 20151127 / Rsampletrees 1.0.3 – Sampling Gene Genealogies Conditional on SNP Genotype data

sampletrees 20151127 / Rsampletrees 1.0.3

:: DESCRIPTION

The program sampletrees is a Markov chain Monte Carlo sampler of gene genealogies conditional on either phased or unphased SNP genotype data. The companion program Rsampletrees is for pre- and post-processing of sampletrees files, including setting up the files for sampletrees and storing and plotting the output of a sampletrees run.

::DEVELOPER

Graham & McNeney Labs

:: REQUIREMENTS

:: DOWNLOAD

 sampletrees / Rsampletrees 

:: MORE INFORMATION

Citation

sampletrees and Rsampletrees: Sampling gene genealogies conditional on SNP genotype data.
Burkett KM, McNeney B, Graham J.
Bioinformatics. 2016 Jan 18. pii: btv763.