BioContext 1.0 – System for Extraction and Contextualization of Biomedical Events

BioContext 1.0

:: DESCRIPTION

BioContext is a text mining system for extracting information about molecular processes in biomedical articles.Using the data extracted by BioContext, it is possible to get an overview of a range of biomolecular processes relating to a particular gene or anatomical location.

::DEVELOPER

the Nenadic group & the Bergman lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
UCSC tools
Python

:: DOWNLOAD

BioContext

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Aug 15;28(16):2154-61. Epub 2012 Jun 17.
BioContext: an integrated text mining system for large-scale extraction and contextualization of biomolecular events.
Gerner M, Sarafraz F, Bergman CM, Nenadic G.

GiA Roots – Analysis of Plant Root system Architecture

GiA Roots

:: DESCRIPTION

GiA Roots is a software package designed to assist in the high-throughput analysis of root system architecture.

::DEVELOPER

the Weitz group at Georgia Tech, the Harer group at Duke University and the Benfey laboratory at Duke University.

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOsX

:: DOWNLOAD

GiA Roots

:: MORE INFORMATION

Citation:

Galkovskyi, T, Mileyko, Y., Bucksch, A., Moore, B., Symonova, O., Price, C.A., Topp, C.N., Iyer-Pascuzzi, A.S., Zurek, P.R., Fang, S., Harer, J., Benfey, P.N. and Weitz, J.S. (2012)
GiA Roots: software for the high-throughput analysis of plant root system architecture.
BMC Plant Biology. 12:116.

MARS 1.2.0 – Microarray Analysis and Retrieval System

MARS 1.2.0

:: DESCRIPTION

MARS (Microarray Analysis and Retrieval System) provides a comprehensive MIAME supportive suite for storing, retrieving, and analyzing multi color microarray data. The system comprises a lab notebook, a laboratory information management system (LIMS), a quality control management, as well as a sophisticated user management system. MARS is fully integrated into an analytical pipeline of microarray image analysis, normalization, gene expression clustering, and mapping of gene expression data onto biological pathways.

::DEVELOPER

Genomics & Bioinformatics Graz, Graz University of Technology

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / MacOsX
Java
Oracle / PostgreSQL / MySQL

:: DOWNLOAD

MARS

:: MORE INFORMATION

Citation

Maurer M, Molidor R, Sturn A, Hartler J, Hackl H, Stocker G, Prokesch A, Scheideler M, Trajanoski Z.
MARS: microarray analysis, retrieval, and storage system.
BMC Bioinformatics. 6: 101-101 (2005)

ISAS – Imagenix Sequence Alignment System

ISAS

:: DESCRIPTION

ISAS (Imagenix Sequence Alignment System )is a software for DNA Sequence Alignment, Array Probe Design, or Genomics Research. ISAS can be run on a single computer, and produce the same results, in less time than the standard sequence alignment software does when running on a big cluster of computers

::DEVELOPER

Imagenix Technologies

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / WIndows

:: DOWNLOAD

ISAS

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Jan 15;27(2):272-4. Epub 2010 Nov 12.
The uniqueome: a mappability resource for short-tag sequencing.
Koehler R, Issac H, Cloonan N, Grimmond SM.

MOLA – System for Virtual Screening using AutoDock4/Vina on Computer Clusters

MOLA

:: DESCRIPTION

MOLA is an easy-to-use software for Virtual Screening (VS) in a non-dedicated computer cluster using AutoDock4/Vina. Several tasks needed for AutoDock4/Vina are automated with MOLA including: ligand preparation, AutoDock4/Vina jobs distribution, result analysis and ligand ranking. A Graphical User Interface (GUI) is used for easy selection of parameters and easy handling of input/output files generated in a VS project. MOLA is integrated in a Live-CD GNU/Linux Live Distribution designed to boot from the CD on any available computer without ever using the computer hard-disk drive. When a VS project is finished the computers can be restored to the original operating system by simply removing the CD and restarting.

::DEVELOPER

Hugo Froufe and Rui Abreu

:: SCREENSHOTS

:: REQUIREMENTS

CDROM

:: DOWNLOAD

MOLA

:: MORE INFORMATION

Citation

Rui MV Abreu, Hugo JC Froufe, Maria João RP Queiroz, and Isabel CFR Ferreira
MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters
J Cheminform. 2010; 2: 10.

SloppyCell – system for Modeling Biochemical Reaction Networks

SloppyCell

:: DESCRIPTION

SloppyCell is a software environment for simulation and analysis of biomolecular networks.

::DEVELOPER

Ryan Gutenkunst while in the groups of Jim Sethna and Chris Myers at Cornell University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Mac / Linux
Python

:: DOWNLOAD

SloppyCell

:: MORE INFORMATION

Citation

Christopher R. Myers, Ryan N. Gutenkunst, James P. Sethna
“Python unleashed on systems biology”
Computing in Science and Engineering 9:34 (2007);