PheGenEx 3.0 – Phenome-Genome Explorer

PheGenEx 3.0

:: DESCRIPTION

PheGenEx is a realtime webtool for prediction, network-based analysis and visualization of phenotype-gene associations in the context of human diseases.

::DEVELOPER

KUANG LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  rcNet

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Oct 1;27(19):2692-9. doi: 10.1093/bioinformatics/btr463. Epub 2011 Aug 8.
Inferring disease and gene set associations with rank coherence in networks.
Hwang T1, Zhang W, Xie M, Liu J, Kuang R.

BioSynther – Biosynthetic Potential Explorer

BioSynther

:: DESCRIPTION

BioSynther is a web-based tool which is developed to explore the biosynthetic potentials of precursor chemicals using BKM-react, Rhea, and more than 50,000 in-house RxnFinder reactions manually curated from about 120 thousand literature.

::DEVELOPER

HuLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BioSynther: A Customized Biosynthetic Potential Explorer.
Tu W, Zhang H, Liu J, Hu QN.
Bioinformatics. 2015 Oct 14. pii: btv599.

APE 1.0 – Allelic Path Explorer

APE 1.0

:: DESCRIPTION

APE (Allelic Path Explorer)  is a program for extending partially known genotype data on a given pedigree consistently (i.e. in accordance with the Mendelian rules) to the whole pedigree.

::DEVELOPER

Matti Pirinen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC

:: DOWNLOAD

  APE

:: MORE INFORMATION

Citation

Pirinen M and Gasbarra D (2006):
Finding Consistent Gene Transmission Patterns on Large and Complex Pedigrees.
IEEE/ACM Trans. on Computational Biology and Bioinformatics vol.3 no.3:252-262

BEReX 1.0 / iBEReX – Biomedical Entity-Relation eXplorer

BEReX 1.0 / iBEReX

:: DESCRIPTION

BEReX is a new biomedical knowledge integration, search and exploration tool. BEReX integrates eight popular databases (STRING, DrugBank, KEGG, PhamGKB, BioGRID, GO, HPRD and MSigDB) and delineates an integrated network by combining the information available from these databases.

iBEReX is a web version of BEReX.

::DEVELOPER

Data Mining & Information Systems Lab , The Tan Lab, University of Colorado Anschutz Medical Campus

:: SCREENSHOTS

BEReX

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • java

:: DOWNLOAD

 BEReX 

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jan 1;30(1):135-6. doi: 10.1093/bioinformatics/btt598. Epub 2013 Oct 21.
BEReX: Biomedical Entity-Relationship eXplorer.
Jeon M1, Lee S, Lee K, Tan AC, Kang J.

ROCCET – Receiver Operating Characteristic Curve Explorer & Tester

ROCCET

:: DESCRIPTION

ROCCET is a freely available web-based tool designed to assist clinicians and bench biologists in performing common ROC based analyses on their metabolomic data using both classical univariate and more recently developed multivariate approaches.

::DEVELOPER

the Wishart Research Group, University of Alberta

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java
  • R package
  • Apache

:: DOWNLOAD

 ROCCET

:: MORE INFORMATION

Citation

Metabolomics. 2013 Apr;9(2):280-299. Epub 2012 Dec 4.
Translational biomarker discovery in clinical metabolomics: an introductory tutorial.
Xia J, Broadhurst DI, Wilson M, Wishart DS.

GPX – Gene Phylogeny eXplorer

GPX

:: DESCRIPTION

GPX (Gene Phylogeny eXplorer) is a web-based tool that facilitates comparative genome analysis of different species. GPX displays results as an interactive map that allows users to explore and interpret genomic data representing gene evolution. It allows the visualization of consensus and conflicting evolutionary histories of genes.

::DEVELOPER

Lutz Hamel , Gogarten Lab 

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No

:: MORE INFORMATION

Citation

Nahar, Neha, Poptsova, Maria S., Hamel, Lutz, and Gogarten, J. Peter (2007)
GPX: A Tool for the Exploration and Visualization of Genome Evolution.
Proceedings of the IEEE 7th International Symposium on Bioinformatics & Bioengineering (BIBE07) Boston, pp1338 – 1342,

SME 1.8 – Sigmoid Model Explorer

SME 1.8

:: DESCRIPTION

SME (Sigmoid Model Explorer) is a Graphical User Interface of the Sigmoid Project. It is a front end that provides access to the web services of the pathway databases and Cellerator, the module responsible for simulations. Some of SME’s features are:

  • Query and retrieval of Cellerator Models in Sigmoid Database via web service
  • Graphical view of Cellerator Models with customizable icons
  • Custom selection and editing of model parameters
  • Remote simulation of customized models in Cellerator via web service

::DEVELOPER

SME Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

SME

:: MORE INFORMATION

Register to become a SIGMOID user.

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.