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This is a MATLAB toolbox for the quality control and scoring of EMAP and SGA genetic interaction data. It includes a graphical user interface and some automatic plot-generating tools.
Executable program that measures sizes and other properties of colonies arrayed in a grid format (intended for 768, 384, or 96 colonies on agar plates) from jpeg images
The Xholon project explores: software as systems of linked nodes, organized hierarchically. The Xholon toolkit supports this back-to-basics approach, and demonstrates practical benefits through examples from numerous domains.
Automatically produce functional annotations for prokaryotic genomes, consisting of protein name, EC number, GO terms, & TIGR role. Initial version developed by JCVI; uses BLAST hits from Panda sequence database, and HMM hits from TIGRFAMs and Pfams.
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These classes are useful for signal processing in Matlab or C++. They bring together tools and methods which may be used interchangeably for Matlab and C++. Their initial use is in conjunction with work towards my degree at UC Berkeley.
Ordered Bijective Interpolated Warping (OBI-Warp) aligns matrices using Dynamic Time Warping with a one-to-one (bijective) smooth warp-function. It is ideal for the chromatographic alignment of complex mass spectrometry proteomics data.
Open Source project for visualizing protein structure. Written in C++ with Qt and OpenGL the software is designed to be multi-platform (Linux, FreeBSD and Windows). On web: www.msprot.com Copyright 2008 Federal University of Sao Paulo - UNIFESP
SARSE is a scientific data editor that uses the extendable column format, allows interactive overview, tracks editing history, and has a user extendable tool box.
A comparative map and trait visualization framework enabling visual integration of genomic data from disparate data sources and allowing rich client-side interactivity and manipulation. Extensible through plugins for new datasources and algorithms.
Suite of software tools for transcription factor binding site search, gene annotation, and orthology filtering. Some tools in the CisOrtho package are required along with MAQ for use in MAQGene.
JFlux is a java library and graphical user interface to work with flow cytometry data. In particular, it is adapted to the COPAS biosorter and can analyze expression profiles.
BigRedBin is a web-based tool designed to pre-process metabolomics data generated by a mass spectrometer in an attempt to increase the signal-to-noise ratio. This is accomplished by using information from multiple technical replicates.
Free software tools released by the Virtual Institute for Microbial Stress and Survival, including WIST (a toolkit for LIMS development) and PCAPStore (a file repository for LIMS).
Basic Electronical Medical Management (BEMM) is an application to control medical data of a set of patients. It is built on top of open source technologies, to provide an integration skeleton of mvn, Datanucleus, Spring, Vaadin, Acceleo technologies.
This library is a lightweight implementation of genetic algorithm, contains the most popular types of chromosomes and the basic algorithms for selection, elitism, crossing and mutation.
CNV Workshop is a web-enabled platform for analyzing genome variation such as copy number variation (CNV). Learn about CNV Workshop in our associated BMC Bioinformatics manuscript: http://www.biomedcentral.com/1471-2105/11/74
Molecular Graphics and Dynamics. Molecular model builder. Part of the Ascalaph Designer http://sourceforge.net/projects/asc-designer/ project. Windows & Linux.
RAPD Primer Design from Metagenomes (RPD-M) scans metagenome sequences identifying and determining relative frequency of candidate primers for Random Amplification of Polymorphic DNA (RAPD) assays.
ChiBE (Chisio BioPAX Editor) is an open source pathway editor for biological pathways in BioPAX format. ChiBE converts BioPAX graphs into process diagrams where complexes and compartments are represented with compound nodes.
!!! For latest version, please see !!!
http://code.google.com/p/chibe