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The Elvira project is a suite of tools to perform high-throughput genomic assemblies of repetitive, structured samples such as viruses or targeted regions of larger genomes.
Accent interfaces and controls systems through goals and policies
Accent (Advanced Component Control Enhancing Network Technologies) is a comprehensive tool suite that interfaces a variety of communications systems and allows these systems to be controlled through goals (high-level user aims) and policies (lower-level system rules). Accent has been applied to the domains of:
o Call Control: for telecommunications, particularly call control in Internet telephony
o Home Care: for home automation and telecare, particularly for domestic appliances...
GMOD is a set of interoperable open source software components for visualizing, annotating, and managing biological data. See http://gmod.org for more.
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MARF is a general cross-platform framework with a collection of algorithms for audio (voice, speech, and sound) and natural language text analysis and recognition along with sample applications (identification, NLP, etc.) of its use, implemented in Java.
TreeBASE is a database and web front end that stores phylogenetic trees and the data matrices used to generate them. The current iteration comprises a complete rewrite of the schema and web layer, and will include a web services layer.
Open-source weather database system for storage of weather/water observations, forecasts, analysis fields, and hindcasts. includes loading program for GRIB files. Visit project website (http://wdb.met.no) for further information.
Please note: this project has now moved to http://wdb.met.no
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This is a Java-based project for complex event extraction from text and co-reference resolution. Currently the code can read BioNLP shared task format (http://2011.bionlp-st.org/) and i2b2 Natural Language Processing for Clinical Data shared task format (https://www.i2b2.org/NLP/DataSets/Main.php). Event extraction includes finding events and the parameters for an event in a text.
The method is based on SVM but other ML algorithms can be adopted. The method details are explained in the...
GPL-licensed Electronic Medical Record and Practice Management system for medical providers that runs in any web browser in multiple languages. It provides an XML-RPC backend and multiple import and export formats, as well as reporting and other features
Parsers for biological data based on scanner generators like Flex (C), Re2c(C), Jflex (Java) and Ifickle (Tcl). This scanner generators are providing easier maintainance, development and higher speed than hand written scanners. Scanner output is SQL.
CNV Workshop is a web-enabled platform for analyzing genome variation such as copy number variation (CNV). Learn about CNV Workshop in our associated BMC Bioinformatics manuscript: http://www.biomedcentral.com/1471-2105/11/74
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.
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.
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.
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
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.
@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.
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.
Design and develop Recommendation and Adaptive Prediction Engines to address eCommerce opportunities. Build a portfolio of engines by creating and porting algorithms from multiple disciplines to a usable form. Try to solve NetFlix and other challenges.
RandService is a Web Service which supplies pseudo- or true- random numbers through JAX-RPC API. Any random number generators can be used behind this Web Service.