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DrPangloss is a python implementation of a three operator genetic algorithm, complete with a java swing GUI for running the GA and visualising performance, generation by generation
The Canopy project is an initiative to merge and expand the functionality of Perl-speaks-NONMEM (PsN), Census, Xpose and PopED. The goal is to produce a coherent, inclusive and convenient platform for pharmacometric data analysis.
BioDOM is a JAVA library for easy creation of XML files according to simple XML schemas for describing biological data. It can also be used to convert other commonly used biological (possibly non-)XML data into these new formats.
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MASQOT-GUI is an open-source, platform-independent application for two-channel microarray spot quality control. Included is a set of tools for gridding, segmentation, quantification, multivariate spot quality assessment and data visualization.
TaxonDNA is a simple but extensible system for performing simple DNA (and other) sequence manipulations in Java. We hope to create a simple framework which can be quickly extended to create bioinformatics applications.
PROMPT is a system for retrieval, analysis, mapping and comparison of proteins. It allows easy mapping of different types of sequence IDs, data retrieval and integration, a multitude of analysis and comparison algorithms and a full-blown easy to use GUI.
DNA Replicator is a graphical tool (written in java) that compute the complementary sequence from an input DNA sequence. It's a really easy used application.
Life Science Identifier (LSID) resolution protocol, to locate biologically significant data over a network, within middle-ware providing a client A.P.I. for Life Science applications, and server software, for Industry data providers.
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GeXpert is an expert system that can be used for genetics and metabolic pathway analysis. GeXpert can help Biotechnologists do their work faster, reducing the time required for performing, analyzing and storing the results of Bioinformatics research.
This software system serves as both a DICOM image viewer as well as a diagramming tool for collaborating notes on the given image sets. This my Computer Science graduate thesis project at Loyola Marymount University.
The program siRNArules 1.0 can predict active short interfering RNA (siRNA) with a rather high efficiency (see published paper on this in RNA journal). This project aims to develop new versions, siRNArules 2.0 etc.
TRANSFOG DAS (Translational and Functional Onco-Genomics Distributed Annotation System) is an XML-based annotation system to allow the discovery and analysis of candidate genes potentially involved in cancer onset and progression.
Manuelito is a Java tool for decrypting posttranslational modification (PTM) patterns of proteins based on MALDI mass spectrometry spectra. It was built for analysing the 'histone code' but it can be applied to any other highly modified protein.
The CHIP Cluster Generator attempts to create spatio-temporal cluster data in an automated fashion to help evaluate epidemic detection software. The spatio-temporal data will then be used to determine robustness of spatial detection algorithms.
COB editor is a collaborative editor for biological ontology (e.g., Gene Ontology) building. Building on the idea of modular ontology from KR research, it supports multiple people to work on the same ontology.
BioMa is a specimen based Biodiversity database Manager. It is designed to store, organize, and manipulate biodiversity-related scientific data, either for the purposes of museums, scientific collections, or research projects.