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Showing 139 open source projects for "java open source projects"
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DEPRECATED PROJECT! SolexaTools is becoming the SeqWare project (http://seqware.sourceforge.net) to better reflect its expanded sequencer support. Please go to this project page for code and documentation.
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This is a project regarding parsing data from different(general) sources and representing it in form of graphs.
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Everyday Software for the Researcher of Restricted Means: This project is intended to offer scientists and students with small budgets advanced versions of aqua-built desktop-editing, graphics and statistical applications for MacOSX.
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TraceTuner
DNA sequencing quality values, base calling and trace processing
Tracetuner is a tool for base and quality calling of trace files from DNA sequencing instruments. Originally developed by Paracel, a Celera Business, this code base was released as open source in 2006. TraceTuner was used by Celera to call 30+ million reads from both Drosophila and human genome sequencing projects. In 2000, Applied Biosystems bundled TraceTuner with ABI3700 Genome Analyzers and shipped it to the customers of these capillary electrophoresis sequencers. Later versions of TraceTuner, which support mixed base calling, have been used by the research community, the private biotech sector, and the U.S. government as components of different variant detection, genotyping and forensic software applications (e.g. ... -
The AI workplace management platformBy combining AI workflows, predictive intelligence, and automated insights, OfficeSpace gives leaders a complete view of how their spaces are used and how people work. Facilities, IT, HR, and Real Estate teams use OfficeSpace to optimize space utilization, enhance employee experience, and reduce portfolio costs with precision.
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The system is designed for the automated analysis of high throughput sequencing data. At present Aped is focused on the analysis of data derived from Sanger and 454 sequencing. Additional functionality exists for SAGE and taxonomic profiling.
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The Flow Cytometry Laboratory Information Management System (FlowLIMS) is a web-based software system that gives users the ability to create and manage experiment protocols for the DiVa and FACScan flow cytometers
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Turn traffic into pipeline and prospects into customersDocket is an AI-powered sales enablement platform designed to unify go-to-market (GTM) data through its proprietary Sales Knowledge Lake™ and activate it with intelligent AI agents. The platform helps marketing teams increase pipeline generation by 15% by engaging website visitors in human-like conversations and qualifying leads. For sales teams, Docket improves seller efficiency by 33% by providing instant product knowledge, retrieving collateral, and creating personalized documents. Built for GTM teams, Docket integrates with over 100 tools across the revenue tech stack and offers enterprise-grade security with SOC 2 Type II, GDPR, and ISO 27001 compliance. Customers report improved win rates, shorter sales cycles, and dramatically reduced response times. Docket’s scalable, accurate, and fast AI agents deliver reliable answers with confidence scores, empowering teams to close deals faster.
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DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV
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Data and animal management software for large-scale phenotype screening Used by GNF for mouse ENU mutagenesis project. Data visualization & analysis, animal husbandry management, & automated QTL mapping. Usable as stand alone animal husbandry system.
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epiPATH is a platform to store and analyze evolutionary, population and epidemiological data from infectious diseases. It is designed to aid users in daily work with data generated in sequencing projects as well as clinical and epidemiological data.
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LT4eL (Language Technology for e-Learning) develops a framework of multilingual language technology tools and semantic web techniques for improving the retrieval and the metadata annotation of learning material.
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@Note2 is now available in www.anote-project.org @Note is a Biomedical Text Mining workbench that integrates current Biomedical Text Mining (BioTM) methods and provides biologists with intuitive tools capable of supporting their bibliographic searches and further literature curation.
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The goal of the GeneText project is the development of a software package that will enable users to dynamically generate an information summary page from multiple sources given a search term. Fields of interest are biology, genetics and bioinformatics.
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GTdb - Modular genotype database for all markers. The database has core which captures information common to different variation measurements and extensions to method and instrument specific data.
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MutationFinder is a biomedical natural language processing (NLP) system for extracting mentions of point mutations from free text. MutationFinder achieves high performance (99% precision, 81% recall on blind test data) as an information extraction system
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The BioArray Software Environment (BASE) v1.2 is a comprehensive free web-based database solution for the massive amounts of data generated by microarray analysis. PrognoChip-BASE extends BASE v1.2.16, providing more functionalities.
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Howe is a spoken dialogue system project designed for browsing instructions. The project serves as a base for research on new dialogue system capabilities.
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hypKNOWsys aims at developing a Java-based workbench for knowledge discovery and knowledge management. Currently, hypKNOWsys has released two intermediate tools: DIAsDEM Workbench (text mining for semantic tagging) and WUMprep (Web mining pre-processing)
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The Genomic Diversity and Phenotype Data Model (GDPDM) captures molecular and phenotypic diversity data. MySQL databases are used to implement the schema. This project develops software tools (written in Java, Perl, etc.) associated with this model.
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LabJ-ng is a laboratory notebook for organic chemists. It has a client-server architecture with a web browsers interface. Data is stored on MySQL database. Chemical reactions are drawned in java applet window. See projct website for example.
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CosmicOS is a framework for creating stand-alone messages suitable for sending to ourselves in the distant future, or to use in SETI research. It is inspired by Hans Freudenthal's language, Lincos, and Carl Sagan's book, Contact.
