228 projects tagged "Bioinformatics"

No download Website Updated 28 Jan 2009 Electronic Support for Public Health

Pop 12.53
Vit 44.11

ESP is a secure, automated system that analyzes electronic medical record (EMR) data to identify and report patients with notifiable diseases to the Massachusetts Department of Public Health. The growing use of electronic medical record systems (EMRs) permits efficient re-use of data already being collected by clinicians during routine private practice, offering an unparalleled opportunity to improve public health practice. Information held in EMR systems includes diagnoses, procedures, laboratory test, and treatment information, as well as patient demographic data. This software permits secure, simple, and robust messaging from electronic medical record systems to public health authorities.

Download Website Updated 20 Dec 2008 Plasmidb

Pop 28.62
Vit 4.80

Plasmidb is a database management system for manipulating, viewing, and storing molecular biology information rapidly and easily. It is capable of handling constructed plasmids, clones, standard vectors, primers, antibiotics, enzymes, and more.

Download Website Updated 19 Nov 2008 Java Machine Learning Library

Pop 39.42
Vit 1.91

The Java Machine Learning Library is a set of reference implementations of machine learning algorithms. These algorithms are well documented, both in the source code as on the documentation site. Along with real machine learning algorithms, many supporting algorithms are provided: distance measures, evaluation criteria, data sets for validation purposes, and some sample code.

Download Website Updated 12 Sep 2008 Redet

Pop 219.08
Vit 10.98

Redet is a tool for developing and executing regular expressions using any of more than 50 search programs, editors, and programming languages, intended both for developing regular expressions for use elsewhere and as a search tool in its own right. For each program in each locale, a palette showing the available constructs is provided. The properties of each program are determined by runtime tests, which guarantees that they will be correct for the program version and locale. Additional features include persistent history, extensive help, a variety of character entry tools, and the ability to change locale while running. Redet is highly configurable and fully supports Unicode.

Download Website Updated 04 Aug 2008 EPoS

Pop 11.66
Vit 1.42

EPoS is a modular software framework for phylogenetic analysis and visualization. EPoS combines a powerful graphical user interface with a plugin system that allows simple integration of new algorithms, visualizations, and data structures. EPoS currently supports distance based tree construction from multiple sequence alignments and distance matrices as well as different algorithms to create consensus trees and supertrees. EPoS also integrates a tree visualization module that can be used to compare two trees and export visualizations.

No download Website Updated 17 Jun 2008 Indiana University CLSD Parser Scripts

Pop 8.37
Vit 46.59

The Indiana University CLSD Parser Scripts are data ingest parsers for the Centralized Life Science Data service for use with IBM DiscoveryLink/DB2.

Download Website Updated 17 Jun 2008 IU Parallel FastDNAML

Pop 8.00
Vit 46.59

IU parallel fastDNAml is a program that infers evolutionary histories from genetic sequences, modified and extended from the serial version of fastDNAml to run in parallel on heterogeneous and widely distributed systems.

No download Website Updated 03 Jun 2008 Fura

Pop 21.79
Vit 1.43

Fura is a self-contained grid middleware that allows enablement and distribution of applications on heterogeneous computational platforms. It features a Web-based GUI, wizard-guided installation and configuration, and Web Service compliance.

Download Website Updated 20 May 2008 ParseGenBank

Pop 9.59
Vit 1.00

ParseGenBank is a minimalistic, incremental, event-driven GenBank Flat File Format parser. It aims to efficiently produce events for keywords, features, qualifiers, and coding data. It does not attempt to parse the contents of feature or qualifier data, but provides a framework on which such a system can be built.

No download Website Updated 15 Apr 2008 ThermonucleotideBLAST

Pop 12.96
Vit 1.46

ThermonucleotideBLAST is a software program for searching a target database of nucleic acid sequences using an assay specific query that is based on biochemical assays (i.e. a pair of oligonucleotide sequences representing PCR primers or Padlock probes, a triplet of oligos representing PCR primers and a TaqMan probe, or a single oligo representing a hybridization probe). Unlike existing programs (i.e. BLAST) which use heuristic measures of sequence similarity for identifying matches between a query and target sequence, ThermonucleotideBLAST uses free energy and melting temperature.


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A command-line network analysis workbench.