LLDA – Latent Variable Model for Chemogenomic Profiling

LLDA

:: DESCRIPTION

The LLDA (Labelled Latent Dirichlet Allocation) model is an instance of a general family of probabilistic models, known as probabilistic graphical models. Probabilistic graphical models provide a general Bayesian framework for representing joint probability distributions over collections of variables, and for computing posterior distributions on subsets of those variables.The algorithm clusters genes and experiments without requiring that a given gene or drug only appear in one cluster. The model also incorporates the functional annotation of known genes to guide the clustering procedure. The procedure is optimized to work with so-called “fitness” data where in the gene information is encoded in the growth defect of a strain deleted for that gene over a set of conditions.

::DEVELOPER

The Arkin laboratory 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows/ MacOsX
  • MatLab

:: DOWNLOAD

 LLDA

:: MORE INFORMATION

Citation

Bioinformatics. 2005 Aug 1;21(15):3286-93. Epub 2005 May 26.
A latent variable model for chemogenomic profiling.
Flaherty P, Giaever G, Kumm J, Jordan MI, Arkin AP.

Deduce – Deduction of Molecular Reaction Network Structure from Measured Time-series

Deduce

:: DESCRIPTION

Deduce is a now very old but still surprisingly effective correlation-based method of reconstructing molecular reaction networks from time-series data.

::DEVELOPER

The Arkin laboratory 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows/ MacOsX
  • C Compiler

:: DOWNLOAD

 Deduce

:: MORE INFORMATION

Simulac – Simulator for Complex Gene Expression Circuits

Simulac

:: DESCRIPTION

Simulac is an old but flexible simulator for complex gene expression circuits. Used initially to model complex promoter, elongation, and expression dynamics of the bacteriophage lambda lysis/lysogeny switch.

::DEVELOPER

The Arkin laboratory 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows/ MacOsX
  • C Compiler

:: DOWNLOAD

 Simulac

:: MORE INFORMATION

MamPhEA – Mammalian Phenotype Enrichment Analysis

MamPhEA

:: DESCRIPTION

MamPhEA is a web application dedicated to understanding functional properties of mammalian gene sets based on mouse-mutant phenotypes.

::DEVELOPER

MamPhEA team

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Sep 1;26(17):2212-3. doi: 10.1093/bioinformatics/btq359. Epub 2010 Jul 6.
MamPhEA: a web tool for mammalian phenotype enrichment analysis.
Weng MP1, Liao BY.

M-pick – Modularity-based Clustering method for OTU picking

M-pick

:: DESCRIPTION

M-pick is a modularity-based clustering method for OTU picking

::DEVELOPER

Xiaoyu Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 M-pick

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Feb 7;14:43. doi: 10.1186/1471-2105-14-43.
M-pick, a modularity-based method for OTU picking of 16S rRNA sequences.
Wang X1, Yao J, Sun Y, Mai V.

GEMSiRV 20130911 – GEnome-scale Metabolic Model Simulation, Reconstruction and Visualization

GEMSiRV 20130911

:: DESCRIPTION

GEMSiRV is a software platform to provide functionalities of easy metabolic network drafting and editing, amenable network visualization for experimental data integration and flux balance analysis tools for simulation studies.

::DEVELOPER

GEMSiRV team

:: SCREENSHOTS

GEMSiRV

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 GEMSiRV

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jul 1;28(13):1752-8. doi: 10.1093/bioinformatics/bts267. Epub 2012 May 4.
GEMSiRV: a software platform for GEnome-scale metabolic model simulation, reconstruction and visualization.
Liao YC1, Tsai MH, Chen FC, Hsiung CA.

D-Tailor 20130924 – Automated Analysis and Design of DNA Sequences

D-Tailor 20130924

:: DESCRIPTION

D-Tailor (DNA-Tailor) is a fully extendable software framework for biological sequence analysis and multi-objective sequence design. D-Tailor permits the seamless integration of an arbitrary number of sequence analysis tools into a Monte-Carlo algorithm that evolves synthetic sequences towards user-defined goals.

::DEVELOPER

The Arkin laboratory 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows/ MacOsX
  • Python

:: DOWNLOAD

 D-Tailor

:: MORE INFORMATION

Bioinformatics. 2014 Jan 13.
D-Tailor: automated analysis and design of DNA sequences.
Guimaraes JC1, Rocha M, Arkin AP, Cambray G.

QCGWAS 1.0-8 – Quality Control of Genome Wide Association Study results

QCGWAS 1.0-8

:: DESCRIPTION

QCGWAS is an R package that automates the quality control of genome-wide association result files.

::DEVELOPER

Peter J. van der Most <p.j.van.der.most at umcg.nl> and Ilja M. Nolte

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows/ MacOsX
  • R

:: DOWNLOAD

 QCGWAS

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jan 13.
QCGWAS: A flexible R package for automated quality control of genome-wide association results.
van der Most PJ1, Vaez A, Prins BP, Munoz ML, Snieder H, Alizadeh BZ, Nolte IM.

SigHunt – Horizontal Gene Transfer Finder optimized for Eukaryotic Genomes

SigHunt

:: DESCRIPTION

SigHunt analyses genomic signature of a DNA sequence and outputs the score DIAS.

::DEVELOPER

Institute of Biostatistics and Analyses, Masaryk University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R

:: DOWNLOAD

 SigHunt

:: MORE INFORMATION

Citation

SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes.
Jaron KS, Moravec JC, Martínková N.
Bioinformatics. 2014 Feb 6.