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.