Search Results for "gnu linux" - Page 55
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Showing 1554 open source projects for "gnu linux"
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Plotamber is a Perl script for an easy and automated plotting of properties derived from molecular dynamics or minimization calculations done with Amber, NAMD or Charmm.
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Winnow is a graphical application for importing and organising articles from PubMed. It gives access to abstracts, full text and allows references to be saved. It can also predict what a user will find interesting through adaptive filtering.
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Disease Gene Profiler (DGP) comprises of a set of (bioinformatics) tools that can be used to identify the genes underlying susceptibility to common multifactorial diseases (such as diabetes, asthma and cancer) using freely available datasources.
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Find restriction enzymes that help differ known homologe DNA sequences (RFLP). Simulate electrophoresis gels. Usefull to investigate the diversity of a population by one of their common genes. Written in perl, uses bioperl modules and the GD library.
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Thea, Tools for High-throughput Experiment Analysis, is an integrated information processing system dedicated to the annotation of data issued from classification systems with biological information coming from a knowledge base.
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ESTminer is a Web application and database schema for interactive mining of expressed sequence tag (EST) contig and cluster data sets.
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LineageEvolver is a simulation system for molecular evolution. Sequence evolution is simulated using modular processes such as substitutions, gene duplication/death, horizontal gene transfer, and more.
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The Gene Ontology Annotative Listing (GOAL) is an open-source PHP application for assembling and visualizing Biological Sequences based on their corresponding hierarchal Gene Ontology structure, described by the gene ontology consortium.
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neochip is a collection of algorithms for high-density oligonucleotide microarrays. The current version contains heuristic algorithms that attempt to improve the quality of arrays by re-designing their layout (the location of the probes on the chip).
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MicroArray Genome Imaging and Clustering Tool (MAGIC tool) is a platform-independant java program for analyzing MicroArray data (.tiff scans & .txt godlists) via graphs and clustering operations (including QT-clustering). http://www.bio.davidson.edu/magic
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DNAGalaxy is an attempt to produce an open-source bioinformatics software alternative to the expensive DNAStar Lasergene software. Its features currently include Blast and Entrez searching, a frontend to clustal and a sequence editor. It requires java1.5
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CodonW is a programme designed to simplify the Multivariate analysis (correspondence analysis) of codon and amino acid usage. It was written in ANSI compliant C. See the README file for more information.
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runsbml - Pathway Simulation Tool emulates the dynamics of biological pathways by calculating concentrations of biochemical compounds at different times and conditions.
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BioGeoTools is a Java based package that is aimed at providing a program and libraries for biogeorgaphy analyses.
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IBD on the Web is a statistical resource for analyzing the relationship between genetic and geographic distance using mantel testing, bootstrapping, and reduced major axis regression.
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BioCSharp is an open-source project designed to provide a bioinformatics .NET framework for processing biological data. It will include objects for manipulating sequences, file parsers, DAS, database access and analysis and statistical routines.
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IndelExtractor is a GUI and command-line application written in Perl that generates various molecular sequence alignment masks, including one to make identification and removal of Indels and their surrounding ambiguous alignment quick and simple.
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JAligner is an open source Java implementation of the dynamic programming algorithm Smith-Waterman with Gotoh's improvement for biological local pairwise sequence alignment with the affine gap penalty model.
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TSE is a test bed for a web service approach to federating taxonomic name databases. Put in English, it takes your query and talks to a number of different databases, asking each one whether they contain that name.
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Perl Entrez Gene Parser project provides Perl parsers for NCBI's Entrez Gene based on regular expression, Parse::RecDescent, Parse::Yapp and Perl-byacc. Some can parse human genome annotations in minutes. Documentation and user guides are provided.
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A command-line program to manipulate annotated genetic sequences (initially in EMBL format). The user supplies a pattern to identify which features or qualifiers to process. These can then be deleted, renamed etc
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Multilayered feed-forward neural network software written in C++. Backpropagation and RPROP are available as training algorithms. Design goals: speed of execution when calculating the output to new data, and quality of training (preprocessing: PCA).
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ArrayOligoSelector (AOS) systematically designs gene specific long oligo probes for entire genomes. The program optimizes the oligo selections for several parameters, including uniqueness in the genome, internal repeats, self-binding, and GC content.
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DNA, Amino Acid And RNA Tests: free software for probabilistic measurement and annotation of biological sequences, using phylogenetic Markov chains and stochastic grammars.
