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This software collection is for a DNA sequencing laboratory. It is used to design closure/finishing reactions following a shotgun sequencing experiment. It requires a draft assembly composed of contigs and scaffolds.
Simulates and visualizes swarming algorithms with limited communication. Also provides an interface to animate particle motion by playback (with pause, fastforward, and rewind) of path information from files. Can output EPS figures and avi frames.
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AutoPrime allows to rapidly design primers for real-time PCR measurement of eukaryotic expression.
By connecting to the EnsEMBL database gene structure information is used to find primers spanning exon borders. This way only expressed sequences are captured. Additionally mispriming on repetitive regions can be avoided using information from RepBase.
STOCHSIM is a stochastic simulator for biochemical reactions. The particles are represented as individual software objects which react according to probabilities derived from concentrations and rate constants. Simple spatial structures can be built.
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The Genomic Diversity and Phenotype Data Model (GDPDM) captures molecular and phenotypic diversity data. MySQL databases are used to implement the schema. This project develops software tools (written in Java, Perl, etc.) associated with this model.
Comprehensive & high performance data distribution &transformation system. Features a simple, user-friendly event driven scripting interface transparently generates & execs highly efficient Perl/C code. Uses:ETL,datawarehousing,statistics,data-cleansing.
unPIC is a Perl script that disassembles Microchip microcontroller's HEX files. This is a powerful tool for all reverse engeneers that creates a well understandable assembly source from a binary file. Creates xrefs, labels, subroutines and much more...
Biolet is project aimed to analyze genomic DNA sequences using wavelets. Of additional interest may be a batch processing tool for doing round-robin scheduling of jobs on a beowulf cluster. For that checkout the project robin from the CVS.
SaskSAGE is package designed to exploit SAGE data. Csage is employed to identify and match SAGE tags in a biologically meaningful manner. Tags are analyzed for significance using a Chi squared test for independence between TAG and treatment.
A command line script to integrate the Weatherhawk Personal Weatherstation into the Nagios NMS framework. The script can also be used from the command line to retrieve data. Values can be stored into a RRD database for future reference.
Zonal Phylogeny Software (ZPS), given a protein-coding gene, searches for any footprints of recent/short-term positive selection, based on zonal phylogeny and related zone-based statistics.
LabJ-ng is a laboratory notebook for organic chemists. It has a client-server architecture with a web browsers interface. Data is stored on MySQL database. Chemical reactions are drawned in java applet window. See projct website for example.
This project aims to develop a cross platform environment for utilisation of various open source and freely available molecular dynamics and bioinformatics tools. Some extra features are included such as protein hydrophobicity and hydrophilicity plots.
GEOSS (Gene Expression Open Source System), formerly known as GeneX Va, provides a web-based interface for the storage and analysis of Affymetrix GeneChipŽ and other microarray data. It has been developed by engineers at the GeneChip/Microarray Bioinform
COBALT (COntext-based AnaLysis of Transcription factor binding sites) is a novel package to predict DNA-binding sites based on their cis-regulatory context.
Weather station web display for the Davis Instruments Vantage pro2 and the Vantage pro2 Plus. This Perl script creates an interactive web front end like the actual Davis console but for the web, instead of the technical Davis web front end.
CosmicOS is a framework for creating stand-alone messages suitable for sending to ourselves in the distant future, or to use in SETI research. It is inspired by Hans Freudenthal's language, Lincos, and Carl Sagan's book, Contact.