Open Source Java Bio-Informatics Software - Page 19

We present an alternative library for development of bioinformatics Java applications. a Java implementation of JGBParser was built. It consists in a library, able to analyze text files in the GenBank Flatfile (GBF) format.

JHeatChart is a simple Java library for generating heat map charts.

JMGF is a lightweight framework for handling MGF files. It supports reading, writing and parsing of MGF files. Files may be read/ written at once, or stream-based (memory efficient). It's stable, very intuitive and good integrated with Java 1.5 SDK and later.

2-D chemical structure drawing program

The JPAT API is a Java API designed to provide developers with tools for calculating the results of protease digestion of proteins and ms/ms fragmentation of peptides. JPAT also contains GUI components for displaying the results. JPAT is a nice way to get

From a pdb file, the java program calculates the van der Walls surface of the protein in the file.

JPhylo is a Java based visualization program used to display sequences of phylogenetic trees.

JPhysChem - a mathematical modeling toolbox designed to provide an abstract layer and a comprehensive graphical front-end for general model building and specific modeling and data processing in the field of mass spectrometry and physical chemistry.

Java port of primer3

JRasterCreator allows you to easily & visually build a raster file for the mass spectrometry instrument Bruker Daltonics MS ultraflex II by clicking on various spots/locations.

A set of java programs that extract coordinate and chemical information from PDB files. The binding site regions are extracted using grid based scheme. For binding site, spatio-chemical descriptor is generated based on PocketMatch algorithm of Dr. Kalidas (author of this project too).

Set of Java packages to apply Genetic Algorithms to any kind of problem. Various genetic operators are implemented and an example shows of how the system could be applied to digital circuit evolution.

The JAQPOT3 web services are OpenTox API-1.2 compliant web services. JAQPOT3 is a web application that supports model training and data preprocessing algorithms such as MLR, SVM, ANN and more.

This is an independent fork of the ensj-core Ensembl Java API. This version of the API does not receive support from Ensembl. The project is still available under the original LGPL license.

The Java Batch System (JBS) is a batch queueing system in the tradition of NQS and PBS for internal (Java-based) and system batch jobs. Stand-alone operation and integration with existing batch queueing systems, initially OpenPBS, is supported.

JGAL is a Java Genetic Algorithms Library.

The JPL project is no longer updated and maintained. It has evolved after being completely reengineered and upgraded. The new project is available at http://mzjava.expasy.org.

jrgp is a strong-typed Genetic Programming system, which features a graphical interface (gool) to setup and run GP-problems and a tool (fs-d) that greatly simplifies the definition of a GP-problem.

Based on the not-so-successful Pysimony (https://sourceforge.net/projects/pysimony/), the same determined student takes another go at the phylogenetic problem. Javamony is invoked as follows: java -jar Javamony.jar [input.fasta] [random / stepwise (starting tree)] [# of bootstraps] [outgroup taxon #1] [outgroup taxon #2] ... Not meant as a competitive phylogenetic inference program, Javamony is an opportunity for me to acquire the Java language while learning to address and solve fundamental problems in phylogenetics. Therefore, for my own educational benefit, all code is original. Of course, there are probably a good deal of mistakes as well. I distribute Javamony, as I did Pysimony, hoping that it will be of educational value to someone else or at least vaguely amusing. Upcoming features will be: - Support for Amino Acid sequences - Support for additional file formats (e.g. Nexus) - Multithreading - Additional scoring methods (e.g. maximum likelihood)

Jaybird is java-language based, source & xml & codebyte class inter-converting tool. You can write your Envolvable Code with it; You can make your computer write program itself; You can run program without compiling time; You can manage source as data

Jeep is a modular, abstract and distributed evolutionnary programming core written in Java, allowing to grow autonomous agents as well a gene pool (as in genetic algorithms).

a Java library designed to manage genotype and clinical data underlying complex diseases

Java bio-informatics library to analyze and convert genomic sequence and assembly data. This library was created and used by the J. Craig Venter Institute (JCVI)

Jyrax is a Java-based, embeddable DAS/2 client designed to work with the 'assay' portion of the evolving DAS/2 specification. Jyrax can query a DAS/2 server and select microarray or other experimental data for retrieval.

KAnalyze is a Java toolkit designed to convert DNA and RNA sequences into k-mers. It is both a command line application and an API.