CLIME v1.1 Beta – Clustering by Inferred Models of Evolution OMIM results

CLIME v1.1 Beta

:: DESCRIPTION

CLIME is an algorithm that partitions an input gene set of interest into distinct, evolutionarily conserved modules (ECMs). It then expands each module with genes sharing an inferred evolutionary history.

::DEVELOPER

Jun Liu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOS

:: DOWNLOAD

CLIME

:: MORE INFORMATION

Citation

Li Y, Calvo SE, Gutman R, Liu JS, Mootha VK.
Expansion of biological pathways based on evolutionary inference.
Cell. 2014 Jul 3;158(1):213-25. doi: 10.1016/j.cell.2014.05.034. PMID: 24995987; PMCID: PMC4171950.

FASTCORE 1.0 – Fast Reconstruction of Compact Context-Specific Metabolic Network Models

FASTCORE 1.0

:: DESCRIPTION

FASTCORE is a generic algorithm for reconstructing context-specific metabolic network models from global genome-wide metabolic network models such as Recon X.

::DEVELOPER

Life Sciences Research Unit, University of Luxembourg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOSX
  • MatLab

:: DOWNLOAD

 FASTCORE

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2014 Jan;10(1):e1003424. doi: 10.1371/journal.pcbi.1003424. Epub 2014 Jan 16.
Fast reconstruction of compact context-specific metabolic network models.
Vlassis N, Pacheco MP, Sauter T

BLUP_GEN / BLUP_SNP – Estimate Solutions for Genomic Selection Models

BLUP_GEN / BLUP_SNP

:: DESCRIPTION

BLUP_GEN and BLUP_SNP are (Fortran90) programs to estimate solutions for genomic selection models, parameterized in terms of genomic relationship matrices or SNP effects. The programs accept heterogeneous variances as is often the case if pre-corrected phenotypes (DYD’s) are used

blup_snp computes solutions for snp effects considering them as random, with a common variance.

Blup_gen solves an equivalent system of equations based on G, the matrix of covariances among individuals.

::DEVELOPER

Andrés Legarra , andres dot legarra at toulouse point inra punto fr , Anne Ricard, Olivier Filangi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Fortran90

:: DOWNLOAD

 BLUP_GEN / BLUP_SNP

:: MORE INFORMATION

mozCellML 0.3.1 – Utility for Manipulating initial conditions and integrating CellML models

mozCellML 0.3.1

:: DESCRIPTION

mozCellML is a Mozilla based CellML tool. It can be used to edit boundary conditions, integrate models(using a Runge-Kutta method), and fit parameters to models(using Levenberg-Marquardt).

::DEVELOPER

mozCellML Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX

:: DOWNLOAD

 mozCellML 

:: MORE INFORMATION

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