BioPerl 1.7.2 – Perl Code in Biology

BioPerl 1.7.2

:: DESCRIPTION

Bioperl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. As such, it does not include ready to use programs in the sense that many commercial packages and free web-based interfaces do (e.g. Entrez, SRS). On the other hand, Bioperl does provide reusable Perl modules that facilitate writing Perl scripts for sequence manipulation, accessing of databases using a range of data formats and execution and parsing of the results of various molecular biology programs including Blast, clustalw, TCoffee, genscan, ESTscan and HMMER. Consequently, bioperl enables developing scripts that can analyze large quantities of sequence data in ways that are typically difficult or impossible with web based systems.

::DEVELOPER

BioPerl History

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Perl

:: DOWNLOAD

BioPerl

:: MORE INFORMATION

Citation

An Introduction to BioPerl.
Stajich JE.
Methods Mol Biol. 2007;406:535-48.

Biology Flashcards for Life 1.0.2 – Study Aid for Learning Biology

Biology Flashcards for Life 1.0.2

:: DESCRIPTION

Biology Flashcards for Life (iPad app) is a great study aid for anyone learning biology. Designed by Thundercloud Consulting to accompany the textbook Life: The Science of Biology, published by Sinauer Associates and W.H. Freeman, these flashcards cover all the terminology introduced in the typical introductory or AP biology course.

::DEVELOPER

Thundercloud Consulting, LLC

:: SCREENSHOTS

flashcards

:: REQUIREMENTS

  • iPad

:: DOWNLOAD

 Biology Flashcards for Life

:: MORE INFORMATION

BRISK – Biology-Related Information Storage Kit

BRISK

:: DESCRIPTION

BRISK is a package of several web-based data management tools that provide a cohesive data integration and management platform. It was specifically designed to provide the architecture necessary to promote collaboration and expedite data sharing between scientists.

::DEVELOPER

Genapha

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Apache
  • MySQL

:: DOWNLOAD

   BRISK

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Sep 1;27(17):2422-5. doi: 10.1093/bioinformatics/btr389. Epub 2011 Jun 27.
BRISK–research-oriented storage kit for biology-related data.
Tan A, Tripp B, Daley D.

MyMiner – Text Mining tools for Biology

MyMiner

:: DESCRIPTION

MyMiner is a free and user-friendly text annotation tool aimed to assist in carrying out the main biocuration tasks and to provide labelled data for the development of text mining systems.

::DEVELOPER

MyMiner team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Sep 1;28(17):2285-7. Epub 2012 Jul 12.
MyMiner: a web application for computer-assisted biocuration and text annotation.
Salgado D, Krallinger M, Depaule M, Drula E, Tendulkar AV, Leitner F, Valencia A, Marcelle C.

AMEN 1.5.4 – Molecular Systems Biology Data Analysis

AMEN 1.5.4

:: DESCRIPTION

AMEN (Annotation, Mapping, Expression and Network) is a stand-alone, unified suite of tools to manage, explore and combine biological multifaceted high-throughput data such as annotation, chromosomal location, expression and interaction data.

::DEVELOPER

Frédéric Chalmel and Michael Primig

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

  AMEN

:: MORE INFORMATION

Citation:

Frédéric Chalmel and Michael Primig
The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology
BMC Bioinformatics 2008, 9:86doi:10.1186/1471-2105-9-86

simbTUM 3.0a – Simulation of Stochastic processes and ODE models in Biology

simbTUM 3.0a

:: DESCRIPTION

simbTUM allows to define ODE-models or stochastic compartemental models of biological processes, to simulate, to fit data and to do some statistics (fitting and statistics for deterministic models only).

::DEVELOPER

Institute of Computational Biology, German Research Center for Environmental Health (GmbH)

:: SCREENSHOTS

simbTUM

:: REQUIREMENTS

  • Windows 

:: DOWNLOAD

 simbTUM

:: MORE INFORMATION

Biochemistry Lab Suite 3.0.1 – Tools Covering different fields of Biochemistry, Biology and Chemistry

Biochemistry Lab Suite 3.0.1

:: DESCRIPTION

Biochemistry Lab Suite app aims in helping scientists and students working in the field of mass spectrometry based proteomics, metabolomics, biochemistry, biology and chemistry but also aids in general lab work.

::DEVELOPER

rpor

:: SCREENSHOTS

BiochemistryLS

:: REQUIREMENTS

  • Android

:: DOWNLOAD

 Biochemistry Lab Suite 

:: MORE INFORMATION

bioECS 1.0 – Biology Easy Cluster Search

bioECS 1.0

:: DESCRIPTION

BioECS is an ad hoc search engine to help biologists to isolate EST clusters corresponding to their research target, based on cross references between TIGR and Unigene. It allows to filter out EST clusters by combining several criteria based on information about tissues, species, and development stages associated to the EST sequences that form the clusters. The user interface allows to easily access all EST sequences forming the clusters and to browse known GO (Gene Ontology) functions associated to them. The client/server software architecture is based on JAVA and MySQL. It comprises a ‘server’ program responsible for the web-based transactions and local caching of information from the public database servers. A ‘client’ program allows biologists to execute researches.

::DEVELOPER

the Systems and Modeling research unit at the University of Liège (Belgium).

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

  BioECS

:: MORE INFORMATION

Judi 1.0 – Data and Model Integration for Biology

Judi 1.0

:: DESCRIPTION

Judi ( Java platform for unsupervised data and model integration ) is a software written in Java, with an aim to provide a user-friendly tool for general unsupervised data and model integration. For many problems in biology, such as gene function prediction and differentially expressed gene identification, and general feature selection problems, there are often multiple data sources available and/or multiple models/tools have been developed to solve the problem. The combination of evidences from multiple data sources and the integration of the output from different models will probably enhance our ability to solve the problem. Judi implements several algorithms and also provides a user-friendly interface to facilitate this process.

::DEVELOPER

Xuebing Wu

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

  Judi

:: MORE INFORMATION

Citation

Xuebing Wu, Feng Zeng, Rui Jiang (2008)
Integrative inference of gene networks from expression data.
Poster at RECOMB Regulatory Genomics/Systems Biology/DREAM3, Oct 29-Nov 2, 2008. MA, USA

bioNMF 2.0 – Non-negative Matrix Factorization in biology

bioNMF 2.0

:: DESCRIPTION

bioNMF is a web-based tool designed to provide a set of analysis methods using the Non-negative Matrix Factorization (NMF) model, widely used in the last few years by the biomedical community due to its intuitive nature, since it has the ability to extract highly-interpretable additive parts from datasets, reducing therefore its dimensionality.

::DEVELOPER

bioNMF team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 bioNMF

:: MORE INFORMATION

Citation

Pascual-Montano A, Carmona-Saez P, Chagoyen M, Tirado F, Carazo JM, Pascual-Marqui RD .
bioNMF: A versatile tool for non-negative matrix factorization in biology
BMC Bioinformatics. 2006, 7:366

E. Mejía-Roa, P. Carmona-Saez, R. Nogales, C. Vicente, M. Vázquez, X. Y. Yang, C. García, F. Tirado and A. Pascual-Montano.
bioNMF: a web-based tool for nonnegative matrix factorization in biology.
Nucl. Acids Res. 2008, 36 (suppl 2, Web Server issue), W523-W528.