Open Source Java Bio-Informatics Software - Page 11

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.

The BGSSJ allows for easy and interactive querying using different gene identifiers (GenBank ID, UniGene, SwissProt, gene symbol), generates a summary page with listings of the frequencies of Gene Ontology annotations for each functional category (cluste

The code here is a parser for CALBC corpus into Java object.

CAMERA is a research environment and repository for metagenomic data

CB-Commander is a plugin based tool that tries to integrate high throughput sequencing algorithms. It allows researchers to design and execute their experiments through a user friendly interface.

A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.

The Octet-CDK interoperability package.

CEGA is a highly extendable layout plugin for Cytoscape based on an Evolutionary Algorithm. In contrast to other layout algorithms, CEGA lets users decide which features are important for the visualization of their graphs.

Cell Electrophysiology Simulation Environment (CESE)

Source code for the Chemical Informatics and Cyberinfrastructure Collaboratory project.

CIG-P is a higher order visualization tool for AP-MS which generates intuitive circular diagrams for visually appealing final representation of AP-MS data. CIG-P can be used to compare a) different AP-MS datasets of various baits or b) a particular bait under various perturbations (lenticular section CIG-P). The output of CIG-P is a simple and intuitively easy to grasp visualization of a complex dataset. Publication: CIG-P: Cicular Interaction Graph for Proteomics http://www.biomedcentral.com/1471-2105/15/344/ Previously known as PIVOT (Protein Interaction Visualization and Observation Tool)

CIP-FOSS will serve as a common entry page for Free and Open Source Software developed at the International Potato Center (CIP), Lima, Peru (http://www.cipotato.org).

CLIMS is a Laboratory Information Management System for protein Crystallography that features a novel graphical interface to a relational database. CLIMS has been reviewed as one of the top two LIMS for crystallographers by CCP4.

CNV Workshop is a web-enabled platform for analyzing genome variation such as copy number variation (CNV). Learn about CNV Workshop in our associated BMC Bioinformatics manuscript: http://www.biomedcentral.com/1471-2105/11/74

COB editor is a collaborative editor for biological ontology (e.g., Gene Ontology) building. Building on the idea of modular ontology from KR research, it supports multiple people to work on the same ontology.

COHCAP (City of Hope CpG Island Analysis Pipeline, pronounced "co-cap") is an algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). Please note: 1) The SourceForge version of COHCAP is no longer being updated. Please see the GitHub version: https://github.com/cwarden45/COHCAP This was the source repository for the Bioconductor version, with some changes after the decision to only provide the code through GitHub. 2) In addition to the original NAR paper, please see the following links: Benchmarks: http://www.nature.com/protocolexchange/protocols/2965#/introduction Protocol Exchange Files: http://sourceforge.net/projects/cohcap/files/Protocol_Exchange_Example.zip 3) Custom Annotation Files (including EPIC Array): https://sourceforge.net/projects/cohcap/files/additional_Bioconductor_annotations.zip/download