Search Results for "java open source" - Page 58

BACContigEditor is a simple sequence alignment editing tool, written in Java. It is originally developed for finishing BAC shotgun sequencing projects, but the program could be easily extended to the whole genome project.

A fast parallel error correction tool for short reads. This software have been added to the NVIDIA Tesla Bio Workbench (http://www.nvidia.com/object/ec_on_tesla.html)

Open Source Clinical Information Management System. From research to laboratory. Gathering / storing of analytical data within an SQL database.

The Hanalyzer is a tool designed to help biologists explain results observed in genome-scale experiments and to generate new hypotheses. It combines information extraction, semantic data integration, reasoning, and visualization.

ReAlignerV is an alignment tool focusing on genomic nucleotide sequences upstream of genes. ReAlignerV integrates TRANSFAC(R) Match(TM) results to detect the conserved TFBSs. ReAlignerV is robust against transposable element insertions.

Genome Properties is a system for asserting specific structures, pathways or systems are present in a genome to provide high-level conceptual descriptions of genomic content.

"Plasmidb" is a database management system (RDMS) used to manipulate, view and store molecular biology information rapidly and easily. Editable information includes: constructed plasmids, clones, standard vectors, primers, antibiotics, enzymes and more

Implematation of robust depth-based inference tools for microarray data (a scale curve, to measure the dispersion of a set of curves, a rank test to decide if two groups of curves come from the same population, and classification techniques).

An open source implementation of a protein threading program based on the energy functions and techniques originally introduced by Prospect.

GPSR is a resource for genomics, proteomics and systems biology. The aim of this project is to build comprehensive resources in the field of bioinformatics.

sd_clust is Expressed Sequence Tag (EST) clustering software. It produces clusters very similar to those produced by d2_cluster. The project is now being hosted on google and can be found here - http://code.google.com/p/sdclust/

TreeSoft is a collection of softwares that build or manipulate phylogenetic trees.

Our software can test for HLA allele and amino-acid differences between two populations. It examines zygosity, tests for strongest association, interaction & linkage disequilibrium among amino acid epitopes.

Java port of primer3

A Perl client library to access Sequence Retrieval System (SRS) servers using the REST/CGI API provided by SRS.

Integration of results from multiple homology searches

Mathematics, Chemistry and Bio-informatics semantic knowledge editor and simulation environment. It should serve as interactive science learning program or science classroom notebook and workshop.

User friendly PDB (Protein Data Bank) file editor with graphic user interface for protein crystallographers to expedite selective parallel edit / data extraction / analysis of their PDB files

Given a reference sequence, simhtsd will create a large set of short nucleotide reads, simulating the output from today's high-throughput DNA sequencers, such as the Illumina Genome Analyzer II.

http://ewi.utwente.nl/~biorange/rshell - The RShell project is a plugin for the Taverna workflow system. It enables one to execute R scripts within the Taverna workflow system. The RShell processor is built on the RServe project. For more info:

FreeLIMS is a Laboratory Information Management System ( LIMS ). Manage samples; create sample types from methods & parameters; easily generate reports & certificates; fine tune user rights. FreeLIMS is Open Source and Free.

EXPR is a software package for the recording and analysis of animal behaviour. Recording is done by pressing particular keyboard keys on the computer. The software then saves the sequence and timing of behaviours. Note that the DOS (1995: https://sourceforge.net/projects/expr/files/expr/fb-port-expr-00-1995/EXPR-binary-DOS-0.0.1995.tar.gz/download) version is currently the only fully functional and is recommended for use. On modern computers, DOS software can run in DOSBOX (https://www.dosbox.com/).

A lightweight, browsing-based, 100% Python, federated data integration framework. Users may create custom schemas for disparate sources, query and expand results across sources to find related data; for use in fields such as bioinformatics and datamining

A polynomial-time algorithm for constructing level-2 phylogenetic networks from dense sets of rooted triplets.

This is a web based disease monitoring for monitoring diseases like chikungunya, malaria - reported by hospitals in a district, county, state or country. There is a reporting & analysis module and a GIS module which displays the data using google maps.