Open Source Java Bio-Informatics Software - Page 10

Bioinformatics as an emerging research area spreads out many challenges to both the Bioinformaticists and the Bioinformaticians. BioGenie is presented as a complete package for tackling these challenges. Accommodating all three platforms, that is, a desktop application, a web application and a mobile (android-based) application, BioGenie outperforms all existing softwares engineered to assist heavy and complex computations. The GUI is very well-designed guiding the user technically with ease.

BioGeoTools is a Java based package that is aimed at providing a program and libraries for biogeorgaphy analyses.

BioMa is a specimen based Biodiversity database Manager. It is designed to store, organize, and manipulate biodiversity-related scientific data, either for the purposes of museums, scientific collections, or research projects.

BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. Models presented are annotated and linked to relevant data resources and are available in various format

The BioNLP UIMA Component Repository provides UIMA wrappers for novel and well-known 3rd-party NLP tools used in biomedical text prosessing, such as tokenizers, parsers, named entity taggers, and tools for evaluation.

BioNote is a knowledge base that combines unstructured wiki technology with structured annotation to form a collaborative environment. BioNote adds the concepts of page types and semi-structured annotation to extend the unstructured nature of wiki pages

BioPro project has been moved to http://www.bioera.net/

BioQuery is a bioinformatics tool that acts as a query builder for genetic, protein, publication, and other biomedical databases. BioQuery is also an update service that periodically resubmits saved searches and sends you new data as it is found.

BioSap-Blast Integrated Oligonucleotide Selection Accelerator Package. BioSap selects unique oligos for microarrays by detecting user-defined parameters and running parallel instances of Featurama and Blast on compute engines, producing xml output files.

The BioSimz project aims to deliver a library (as well as the interface) to conduct large-scale biomolecular simulations at their atomic scales of detail. The initiative idea is to observe the protein crowding in vivo; it now can do much more than that!

BioStream enables bioinformatics researchers to create, query and apply tools to their own databases. It supports sequence files and other data types by allowing the creation of metadata definition files.

A Collection of classes related to biological and bioinformatical topics.

The BioUtils - Proteomics package is a lightweight Java framework for handling commonly used data produced and needed in the field of Mass spectrometry in general and especially in the field of Proteomics. It's stable, intuitive to use and good integrated with Java 6 SDK and later.

The aim of the BioWeka project is to add bioinformatics functionalities such as e.g. alignments to the popular machine learning framework Weka.

BioX (pronounce as bio cross) is a system for the management of local and remote (currently supporting RMI, CORBA and SOAP Web Services) components such as files and services (e.g. BLAST). Additionally, the components can be composed to workflows.

It moves by itself inside networks like virus infection & plagues, it is being written to solve computer virus problem drastically and responsibly. It is legal, free and open for public domain to improve W3 ICT Security.

Biodiversity Information Group develops software tools and data standards that enable herbaria and museums to create dynamic distributed queries of their online databases. See http://bit.ly/bfirSh and http://bit.ly/bwpnSY for latest developments.

Biogranat (Molecular Biology Graph Visualisation and Analysis Tool) is a new tool for the analysis and visualisation of large datasets.

Workbench for visualizing biological networks (regulatory, interaction, and metabolic). Can be used as a front-end for BNDB datawarehouses, but also as stand-alone tool.

BIRBU (BIological Relationship BUilder) is a Java tool for microarray gene expression data analysis. BIRBU identifies biologically significant relationship between genes using microarray data and prior knowledge on relationships between genes.

The Biomolecule Naming Service (BNS) is loosely inspired by DNS servers used to resolve host names and IP addresses. BNS uses the Lightweight Directory Access Protocol (LDAP) to resolve gene/protein names and identifiers.

The Blast2SNP is able to pick out synonymous, non-synonymous mutations and indels from draft assembly sequences by performing BLAST search against the reference ORF sequences.

A biobank registry system for handling data regarding human biological samples.

BorderFlow implements a general-purpose graph clustering algorithm. It maximizes the inner to outer flow ratio from the border of each cluster to the rest of the graph.

Decision support tool that assesses breast cancer risk and identifies risk-reducing interventions. Includes web service implementations of established models -- BRCAPRO, Gail, Claus, BCSC Density -- for calculating breast cancer risk.