validate – Omics Validation Calculator

validate

:: DESCRIPTION

validate is a key component of performing any genomics experiment for validation of significant features (genes, proteins, etc.). This software can be used to assess the statistical evidence for validation of a particular analysis/technology on the basis of a random sample of significant results.

::DEVELOPER

Jeffrey Leek

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • R package

:: DOWNLOAD

 validate

:: MORE INFORMATION

Citation

Leek JT, Rasgon JL, and Taub MA (2011)
A statistical approach to selecting and confirming validation targets in -omics experiments
BMC Bioinformatics 2012, 13:150

LACS – Validate Protein NMR Chemical Shifts

LACS

:: DESCRIPTION

LACS ( linear analysis of chemical shifts) is a validation tool for protein backbone NMR chemical shift data. Based on the observation that secondary chemical shift (difference between the chemical shift of an amino acid and its random coil chemical shift) well indicate the local backbone geometry, LACS correlates the secondary chemical shifts of a nucleus to that of Ca-Cb of itself (referencing independent), thus avoiding any geometry or structure assumptions, to estimate referencing offsets and identify possible miss-assignments.

::DEVELOPER

Liya Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Matlab

:: DOWNLOAD

 LACS

:: MORE INFORMATION

Citation

Wang, L.; Eghbalnia, H. R.; Bahrami, A.; Markley, J. L.,
Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications,
J. Biomol. NMR 25, 32, 13-22.

MMCIF Dictionary Suite 2.250 – Parse, Validate, Manage data dictionaries used by the PDB

MMCIF Dictionary Suite 2.250

:: DESCRIPTION

MMCIF Dictionary Suite is a collection of tools to parse, validate, manage data dictionaries used by the PDB. Applications are also included, which convert data dictionaries to XML schema, provide HTML browsing, produce mapping information for relational database loaders (Db Loader) and convert data files between related CIF dialects

::DEVELOPER

RCSB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

   MMCIF Dictionary Suite

:: MORE INFORMATION

MFPaQ 4.0.0 – Parse, Validate, and Quantify MS Proteomics Data

MFPaQ 4.0.0

:: DESCRIPTION

MFPaQ (Mascot File Parsing and Quantification ) is a new web application dedicated to parse, validate, and quantify proteomics data. It allows fast and user-friendly verification of Mascot result files, as well as data quantification using isotopic labeling methods (SILAC/ICAT) or label free approaches (spectral counting, MS signal comparison).

::DEVELOPER

the MFPaQ developper

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsx
  • Firefox 2 or higher
  • Mascot server 2.1 or higher
  • Apache
  • Perl

:: DOWNLOAD

 MFPaQ

:: MORE INFORMATION

Citation

Bouyssié D, Gonzalez de Peredo A, Mouton E, Albigot R, Roussel L, Ortega N, Cayrol C, Burlet-Schiltz O, Girard J-P, and Monsarrat B.
MFPaQ, a new software to parse, validate, and quantify proteomic data generated by ICAT and SILAC mass spectrometric analyses: application to the proteomic study of membrane proteins from primary human endothelial cells
Molecular & Cellular Proteomics, 6, 1621-1637