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To provide a bunch of useful applications for daily use. The first of those applications was donated by NIH\'s DECA, it\'s called REX and is a Request/Bug tracker. All applications will be Struts 1.1 and greater based.
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idyuts is \"I Dare You to Use This Shell\"; a pre-hibernate approach to replacing an ORM written with jython functors into a pure-Java language command pattern. The \"pipeline codegen artifacts\" are simple IoC templates, and trivial to adapt
This tool integrates and enhances publicly available genome data from different sources into a local database. Using a web browser, scientists may view and query the data, keep persistent notes, and schedule batch services (such as BLAST) from NIH.
Talisman is an interpreter for a logical markup language. This language contains the content and logic of a web (or, in the future, Java Swing) based user interface, including arbitrary datatypes and processing actions.
OmniGene is a set of reausable components that have been packaged into frameworks. These frameworks are used to produce domain specific services for common bioinformatics tasks including: visualization, database access, and pipeline building.
Pattern recognition software package. It includes several classification and clustering algorithms. It can read data from a
set of images, an ASCII file or a JDBC connection. A small TCP data server with its corresponding JDBC driver is included.
JReferences is a tool to store and retrieve bibliographic references from a file or MySQL database.
It reads BibTeXML, DocBook XML and RIS type references, and can output these and BibTex.
A bibtex like alternative is also provided for DocBook XML docu
MAGMA: Multiobjective Analyzer for Genetic Marker Acquisition
A genetic algorithm for generating SNP tiling paths from a large SNP database
based on the competing objectives of cost (number of SNPs) and coverage (haplotype blocks):
Hubley R., Zitzler
A Java application and a website for those in the domain of ecological modelling. Will feature a database with the models which have already been made by someone, so that you don't have to start everything from zero!
SPedit is a new curation environment for the Swiss-Prot and TrEMBL databases. For more information about these databases see http://www.expasy.ch/sprot/ and http://www.ebi.ac.uk/swissprot/
A modular, database-backed system for 5 dimensional (5D) analytical biological microscopy and cell-based screening. Please note - we have moved. Please come visit us and download from our new site at http://cvs.openmicroscopy.org.uk
Simply put it is an Open Source Periodic Table of Elements in Java. The aim is create an open source periodic table of elements along with a database of elements data that can be extended and accessed by anyone.
CAVOR is an engine for building apps that involve both graphic and text/numeric data. Primarily GIS is the initial focus, but consider also CAD, CASE, project management (eg PERT charts), and others. Built-in scripting, C API, also supports Tcl and Java.
It is a servlet/JSP based web application to manage your research references and notes. There is also a public server for those who do not have their own servlet engines. The public server can be customized so that it act like your private one.
To log/share/analyze/optimize/simulate garden activity
An online database and cross-platform, game-like client where gardeners/farmers (small or large scale) can log their actions and measurements (such as weather, yield, current plant size).
Any user can then play it back visually, or play with the data and see a simulation inferred from the knowledge database, or calculate an optimal design within given constraints, inferred from the knowledge available at that time.
A biological data warehouse that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies.
Website:
http://bioinformatics.ubc.ca/atlas
ArrayCGH DataBase is an effort to distribute Array CGH data between clinical and research groups. It will be platform independent, and will utilize MySQL as it's persistent storage mechanism. A web client may be implemented at some point.
prOOst is a provenance storing system, which allows users to store their provenance information in OPM notation. It is based on a graph database and can be accessed for querying and adding of information through a REST interface.
Cinefile is a prototype of a category-based method of database exploration. It allows the user to identify abstract categories of films by providing examples of category members, learns to classify films as belonging or not belonging to those categories, and provides a graphical interface for exploring and comparing categories.
Cinefile is designed to work with data retrieved from the Internet Movie Database (imdb.com).