Open Source Java Bio-Informatics Software - Page 18

ISYS (Integrated SYStem) is a Java-based plugin framework for loosely-coupled integration of independently developed components. It provides both service-oriented and event-based communication whose semantics may be contributed by component developers.

Identifiers.org is a system providing resolvable and persistent identifiers, in the form of URIs, used to identify data for the scientific community, with a current focus on the Life Sciences domain. The provision of resolvable identifiers (URLs) fits well with the Semantic Web vision, and the Linked Data initiative. The resolving services of Identifiers.org rely on the information stored in the MIRIAM Registry.

This progect using for testing imagination of people with help of some math-process(in this case using method of conjugate gradient for minimisation of function)

http://www.princeton.edu:80/pr/pwb/01/0326/1b.shtml http://www.cs.princeton.edu/immsim/ Immsim is an immune system simulation used by Immunology students and researchers. Currently it is being used at Princeton University.

ImportWizard - a Java based, dialog driven user interface for importing simple data files

InUtero is a fetal genetic risk assessment calculator being developed for UCSD.

Info Sapient will be an Open Source, Common License 0.5, 100% Pure Java based program that is a mechanism for the expression and execution of business rules.

NOTE: The IntAct package is now hosted at google code: http://intact.googlecode.com IntAct is an open source package to store and manipulate molecular interaction data.

IntEnz is the name for the Integrated relational Enzyme database. IntEnz contains data curated and approved by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB).

The Integrative Biology VRE is a web-based graphical user interface and repository that provides an environment where biological simulation experiments can be constructed without the need for any knowledge of unix, cluster computing, or shell scripting.

Io (ISREC ontologizer) is a program to classify high-throughput genomics data (e.g. microarray results) in the Gene Ontology. Io includes a statistical estimation of the significance of data in the GO nodes and reannotation files for Affymetrix chips.

IslandEv distributes a Genetic Algorithm (like <a href="/projects/jaga">JaGa</a>) across a network (see <a href="/projects/distrit">DistrIT</a>) using an island based coevolutionary model in which neighbouring islands swap migrating individuals every

J2dPathway project are composed of several packages: J2dPathway(biological pathway viewer), Pyrus Pathway Editor (biological CAD), and DNASequenceViewer (platform-independent sequence viewer).

Java API for implementing any kind of Genetic Algorithm and Genetic Programming applications quickly and easily. Contains a wide range of ready-to-use GA and GP algorithms and operators to be plugged-in or extended. Includes Tutorials and Examples.

Jazoo. The Zoo of virtual evolving creatures. Mostly focused on evolving communication between intelligent agents. It's in VERY early stage. Everyone's invited to join, participate, suggest, discuss etc.

JAligner is an open source Java implementation of the dynamic programming algorithm Smith-Waterman with Gotoh's improvement for biological local pairwise sequence alignment with the affine gap penalty model.

VI Compute Server (VICS) is a collection of grid-enabled bioinformatics tools with HTTP (browser) and Web Services (scriptable) interfaces. JCVI VICS is licensed under the Perl Foundation Artistic License 2.0.

The primary goal of the JES is to develop Distributed Configuration Service for client/server,clusters,grids,agent based architectures.

JFASTA is a lightweight framework for handling FASTA files. It supports reading, writing and parsing of single- or multi-FASTA 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.

JFinisher is software for alignment, editing and manipulation of biological sequences. It aims to assist in the finishing of genome assembly. Starting from a reference sequence, the program align contigs using Smith-Waterman local alignment algoritm with auxiliary methods, allowing management of the alignments generated. It has graphical interface for manipulation and visualization of the actions, uniting features that help in editing the sequences. It has internal projects manageable and ability to export results in the standard formats of the area.

This project is a genome browser and annotation tool in java.

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