Search Results for "java open source" - Page 75
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Showing 2101 open source projects for "java open source"
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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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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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BioNote is a knowledge base that combines unstructured wiki technology with structured annotation to form a collaborative environment. BioNote adds the concepts of page types and semi-structured annotation to extend the unstructured nature of wiki pages
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Atera all-in-one platform IT management software with AI agentsAtera’s AI agents don’t just assist, they act. From detection to resolution, they handle incidents and requests instantly, taking your IT management from automated to autonomous.
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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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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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TaxonGrab is an NLP (Natural Language Processing) solution written in PHP, which leverages systematic nomenclature rules that are used for taxonomic nomenclature in scientific publications.
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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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BioGeoTools is a Java based package that is aimed at providing a program and libraries for biogeorgaphy analyses.
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Desktop and Mobile Device Management SoftwareDesktop Central is a unified endpoint management (UEM) solution that helps in managing servers, laptops, desktops, smartphones, and tablets from a central location.
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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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TAS (Transcription Analysis System) is a multi-tier framework for running parameterized SQL queries. Users can analyze new data or new combinations of data with a few clicks in a GUI. Potentially complex/repetitive database interaction is all automated
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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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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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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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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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GEOSS: Gene Expression Open Source System (used to be called Genex Va) GEOSS is a secure, multiuser, gene expression database and analysis package. GEOSS is distinguished by a well developed web based user interface, and analysis/reporting.
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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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CompLearn is a general-purpose compression-based machine learning system that uses data compression to learn or data mine patterns in arbitrary data.
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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.
