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OpenDMAP (Open Source Direct Memory Access Parser) is a natural language processing (text mining) application: a semantic parser for information extraction.
SLEDRIDE: Simplified Learning about Expression Data Running in a Desktop Environment. To provide a general workbench for pipe-lining microarray gene expression data from supervised learning results into unsupervised learning methods.
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AnnaF is an automatic gene annotation framework, that is used to do some automatic annotation for C. higginsianum. It was also tested on F. graminearum and should work well for fungi in general.
AnnaF was build upon the pipeline framework Anna.
Regpack is a powerful onboarding, registration, and payments platform trusted by thousands of organizations worldwide. Our mission is simple: to give you the tools to automate busywork, streamline your processes, and keep your focus where it belongs, on growing your programs and serving your clients.
A software tool enabling the user to browse through an image stack created by a confocal microscope. Points can be plotted through the stack, producing a digital 3D representation, which can be viewed in 3D and compared with other plots.
LAITOR is a text mining software developed to find co-occurrence of biological entities (gene/protein terms) together with biointeractions and concepts term from customized dictionaries.
BARNACLE is a Python library for RNA 3D structure prediction. It can be used for probabilistic sampling of RNA structures that are compatible with a given nucleotide sequence and that are RNA like on a local length scale.
SBMLforge is a tool that enables the user to convert and merge KEGG metabolic and signaling pathways (KGML format) to create a single SBML pathway model.
This is a utility to convert a set of fasta formatted sequences along with output from ELAND or SOAP (and other next generation sequence alignment in due time) to make them viewable using eagleview.
OmicBrowse, developed with Flash and Java, is a highly evaluated genome browser integrating omics knowledge ranging from genomes to phenomes and is especially appropriate for positional-cloning purposes.
A colorized interactive dotplot program designed for pair-wise comparisons of RNA & DNA. The original idea was from the mind of late Prof. William J. Dreyer of Caltech. The idea is to be able to see the "tapestry" of life, which comes alive with color.
LIGR Assembler is a sequence assembly program. It was derived from TIGR Assembler and addresses some of TIGR Assembler's shortcomings. See the CHANGES file for details.
FociCounter is a simple and user-friendly program for analysis of gamma-H2AX foci. It allows to determine the number of foci in a single cell, a foci intensity as well as a cell intensity.
An efficient implementation of the Smith-Waterman algorithm that takes advantage of SIMD instruction sets in modern CPUs. The Smith-Waterman algorithm is used for sequence alignment in bioinformatics.
JAMBLAST: Java Application Manager for the ncbi BLAST results. It is a graphic application that allow the user to display, filter, sort, import/export, store/manage BLAST results produced with the NOBLAST (https://sourceforge.net/projects/noblast).