Search Results for "java open source" - Page 74
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Showing 2101 open source projects for "java open source"
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This is a lightweight database system to support bioinformatics data mining. See BMC Bioinformatics. 2005 Mar 24; 6(1): 72 for the first publication. It supports large-scale data mining and data mining tools.
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Here we offer for download ClawHMMer, a streaming implementation of hmmsearch, running on commodity graphics. processors and parallel rendering clusters. The original HMMer version is located at http://hmmer.wustl.edu/ (also under GPL).
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ScientificIcons is a central repository of icons for scientific programs, including molecular biology, lab automation, sample tracking, chemistry, biology, physiology, etc. Looking for an icon for a flask, chemical, gene, plate, robot, atom?
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PSIMAP is the Protein Structural Interactome MAP, a map of all the domain level protein-protein interactions in the Protein Data Bank (PDB). PSIsoft is an archive of the software used to generate and analyse PSIMAP.
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SIP (Sample Inventory Program) is a web application for managing mass quantities of lab samples. It is the first out-of-the-box Zope 3 app, and is field-proven. SIP may be used as-is, or as inspiration for other Zope 3 apps. (e.g. O/R RDBMS storage)
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The GenDB system for the annotation of prokaryote genomes. The Perl/MySQL/Apache based system supports cmd-line mode annotation, integrating dozens of bioinformatics tools, but also provides a user-friendly web interface for community annotation efforts
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eQTLexplorer is a database application for the visualization and integrated mining of genetical genomics experiments.
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MethylMapper is a collection of perl scripts that allow for easy viewing of methylatable sites in stretches of DNA.
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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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CSBI is a component based framework that allows for inter-component data sharing and access. GINY is an Open Source Graph Library.
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Sampsize computes sample size and power for surveys, comparative studies including non-inferiority trials and case-control studies.
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In order to facilitate standardization and exchange of microarray layout, this project provides an ADF (Array design File))/MAGE-ML converter.
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MyGenBank is a set of OpenSource software for managing a local copy of GenBank (www.ncbi.nih.gov/Genbank). It is implemented using Perl, MySQL, and Linux so that you can manage a complete or partial copy of GenBank on a computer as small as a laptop.
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The ORIEL workbench is a data browsing interface for REST-based information retrieval services. Originally developed for Bioinformatics applications.
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A gene and protein homology database toolset that uses existing data from ensembl and entrezgene online databases.
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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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Python library to convert networks from/to many different formats, like the ones used in Pajek, Cytoscape and other popular graph formats like GML. It also includes support to integrate experimental data to the netowork.
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We use R (www.r-project.org) in order to generate a greater specificity and sensitivity of protein identification by Mass Spectrometry. These functions are implemented as add-on packages to the open source GPL software R.
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The ISOTOPIC PATTERN CALCULATOR is a small linux tool for mass spectrometry. It calculates the isotopic distribution for a given chemical formula or peptide sequence. GIPS is a GUI Version of the Isotopic Pattern Calculator.
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ISYS (Integrated SYStem) is a Java-based plugin framework for loosely-coupled integration of independently developed components. It provides both service-oriented and event-based communication whose semantics may be contributed by component developers.
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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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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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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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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.
