Open Source Java Scientific/Engineering Software - Page 87

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!

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.

This project is a modification of the original evolution simulation & artificial life project by Joan Queralt Molina: https://sourceforge.net/projects/biogenesis/ In both, the original project and this modification, 2-dimensional organisms consisting of line segments interact with each other, reproduce and evolve in time. Compared to the original project, this modification explores the following features: * alternative mutation mechanisms * an alternative stress-based aging mechanism It is based on the new_design branch of Biogenesis (https://sourceforge.net/p/biogenesis/git/ci/new_design/tree/), its source code can be obatained from http://sourceforge.net/p/biogenesisxmod/code/ci/xmod/tree/ If you want to post a review, remember that this is only a modification, so comment on my changes, not on the simulation. Biogenesis discussion forum: https://sourceforge.net/p/biogenesis/discussion/

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

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.

Biomedical Information Management System (BIMS) is a modular multilayer object - oriented software architecture, which provides a flexible computational solution to capture and manage a heterogeneous biomedical data: textual and visual information.

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.

A framework built on Berkley's Ptolemy. Runs a variety of bit width optimization algorithms and suggests bit widths. Includes parsers for simulink and system generator.

The Brunswick Science Fair Project is an attempt to evolve code snippets into complex organisms. Programmed in Java

BizGEO is an open source platform developed to provide a simple interface for geographical data collection and data storage. BizGEO is integrated with a standard open source map server (GeoServer) to form an integrated GIS data collection suite. BizGEO is made up of three main components; BizGEOServer which is a facility for managing data by organising them in projects; BizGEOApp, a mobile app which is being used by the field users to collect data through set of defined forms, and GeoServer which manages and publishes the data using open standards.

A Monte Carlo Micro Black Hole event generator for Particle Physics.

A blackjack simulator

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.

BlogTEX is an ad-hoc blog posts extraction algorithm written in Java for TREC Blog08 dataset. It includes an optimized sentence model for clearly identifying sentence boundaries in each blog post. Its output can be customized using its config file.

Blogspread is an open platform for the developmend of applications that analyze data from websites like blogs and forums. Blogspread is jointly developed by the University of Mannheim, Germany, the UFPE, Recife, Brasil and the UFAL, Maceio, Brasil.

Blubber system is an Eclipse RCP application for distributed systems modeling. Designed for university researches and inlcudes: task graph editor; graph transformation tools; graph modelling on distributed system; real-time modelling on GerdaFramework.

BlueDuke is a lightweight Java Bluetooth stack. It is based on the Harald Bluetooth stack from Lund University, Sweden (http://www.control.lth.se/~johane/harald/), but will feature support for various profiles, with SDP and RFCOMM as mandatory goals

It is an application for Bluetooth-enabled mobile phones that allows you to connect to other BluetunA users in range and share music recommendations. Mobile music, metadata sharing, Bluetooth applications, proximity-based interactions, social awareness

Blunder is an automated tool for analyzing chained exceptions in Java. It's usefull for classify, generate a customized error message and a list for possible solutions.

BoPlanets is a virtual planetarium showing the planets relatively to any observing planet. The planets can be viewed in ecliptical-, equatorial- or horizontal view. The times of rise, transit and set of a planet can be determined. Click on the link below to the web site of BoPlanets to see the help file of BoPlanets.

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