Open Source Java Scientific/Engineering Software - Page 41

A tool to construct the metabolic networks from KEGG, and compare the constructed metabolic networks. Phylogenetic trees can be constructed along the case.

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.

Now in Github: https://github.com/dnaase/Bis-tools/tree/master/Bis-SNP BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq and RRBS) on Illumina platform. It uses bayesian inference with either manually specified or automatically estimated methylation probabilities of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other bisulfite treated sequencing) to determine genotypes and methylation levels simultaneously. It works for both of single-end and paired-end reads.Specificity and sensitivity has been validate by Illumina IM SNP array. In default threshold 30X data (Phred scale score > 20), it could detect 92.21% heterozygous SNPs with 0.14% false positive rate Cytosine calling is not only based on reference context, so it could detect non-reference cytosine context. Google group for help: http://goo.gl/zL7Nj

Bitnets instantiates and operates on graphs and subgraphs of large complex networks, such as kinship networks. Bitnets consists mainly of a java library, a number of use examples and an interactive interpreted language interface.

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.

Near the surface (even horizon) of a black hole, there is maximum information density in units of squared plancks (and some translation to qubits). Similarly, our imagination is the set of all possible things we can draw onto our most dense layer of visual cortex in electricity patterns. Bigger layers have more neurons to handle those possibilities. A Black Hole Cortex is a kind of visual cortex that has density of neuron layers similar to density at various radius from a black hole. What we think our eyes see, the imagination, is the densest and smallest layer. SphereSurfaces outside it recursively have more neurons, more surface area, but less density since it has to eventually dimension-reduce to high level ideas, like there are 10000 Wikipedia page names that cover most parts of the world. We can think of Wikipedia as a layer above our brains, a global SphereSurface of large surface area (a cortex layered on billions of minds) and small (10000 most important pages) density.

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

Blackjack Analyst is a program allowing evaluation of blackjack playing strategies through simulation.

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.

Bloft (BLObby and sOFT) is a real-time soft-body physics simulator optimized for real-world mobile phones. It is written in Java and uses fixed-point math only. Memory allocations are minimized to suite the needs of JVMs in older mobile phones.

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.

Crossplatform menstruation calender with dynamic pdf-report-generation via server-script. The calender is intended for the CLDC profile and MIDP1.0 - like mobile phones, PDA and is written in J2ME. The server allows dynamic upload and pdf-generation and

The purpose of the project is to develop a quantitative medical imaging & visualization program for use on brain MR, DTI and MRS data. It is a joint project of the Kennedy Krieger Institute & the Johns Hopkins University, Psychiatric Neuroimaging Lab

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.

The BlueDecode frame work is an Open Source Third Party Java Library used for developing more interactive and customized 2D graphical user interfaces in Java using a MVC and object oriented programming approach.

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.