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Data curation tool to maintain variables for the National Survey of Health and Development managed by the Lifelong Health and Ageing Unit of the Medical Research Council.
SyMBA is a Data Archive and Integrator that is based on the Functional Genomics Object Model (http://fuge.sf.net) and which archives, stores, and retrieves raw high-throughput data. See http://symba.sf.net and http://www.cisban.ac.uk
Soaplab is a generator of Web Services providing a programmatic access to command-line (and other) applications on remote computers (an example of its usage is available at http://www.ebi.ac.uk/soaplab/)
VELMA stands for Visualization & Exploration of Large Multiple sequence Alignments. VELMA is a Java tool for visualizing alignments of large numbers of biological sequences that exceed the capabilities of existing software.
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Clinical study tracker tracks case study members through activities.
Developed at Medical Research Council UK to meet a common clinical trial need to track various types of clinical data. Users log dates of completed tasks against participant ID. Simple, useable, reduces lost data! Makes graphical progress reports.
The program versusSNP is a flexible tool for mining SNPs between two close related genomes. First, we align all the orthologous genes and select SNPs, then the SNPs are separated into categories based on their mutation types.
MSA2SNP is a tool for mining SNP sites in multiple sequence alignment (MSA). This tool inherits the easy-to-use interface from MEGA4 Explorer with advance data presentation. MSA2SNP lets you visualize alignments and import from CLUSTAL program directly.
The creation of quantitative SBML models is a time-intensive manual process. Saint, an automated SBML annotation integration tool, aids the modeller and reduces development time by providing information about a model in an easy-to-use interface.
3D Genome Tuner draws circular genome map and enables viewing multi-genomes in 3D context. It also provides genome analysis and sequence alignment, making it a powerful tool in genome studies and demonstrations.
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OpenVista(R) is the open-source version of VistA, an enterprise grade health care information system developed by the U.S. Veterans Affairs and deployed at 1,500 global facilities. OpenVista is a registered trademark of Medsphere Systems Corporation
A set of software utilities for processing and analyzing 16S rRNA genes including generating NAST alignments, chimera checking, and assembling paired 16S rRNA reads according to reference sequence homology.
CloudBurst is a parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics.
This is an independent fork of the ensj-core Ensembl Java API. This version of the API does not receive support from Ensembl. The project is still available under the original LGPL license.
A bioinformatics tool for the annotation and tag-counting of next-gen Illumina Solexa datasets. TASE works with CASAVA 1.0 builds, providing annotation, tag counts and visualization in a rapid manner.
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
The final build of this software now is distributed in R, embedded in "RedeR': an R/Bioconductor package for hierarchical and nested network analysis... more about RedeR: http://bioconductor.org/packages/2.9/bioc/html/RedeR.html
A wrapper for Apache UIMA (http://incubator.apache.org/uima/) that connects to the Open Biomedical Annotator (OBA) rest service from the National Center for Biomedical Ontology (http://www.bioontology.org/wiki/index.php/Annotator_User_Guide).
Knime (http://www.knime.org) nodes for sequence bioinformatics. Sequime is an eclipse plug-in for the KNIME data mining platform, providing additional nodes for reading, processing and visualizing sequence information.
RssGsc (Rank Sum Statistics for Gene Set Collections) is a bioinformatics tool used to find meaningful gene sets using a ranked list of genes (obtained form an experiment).
This is a pipeline that is used to store an EST or Genome assembly information including reads and their alignment in a mysql database. Further more, it provides a set of scripts to mine SNPs and other statistics from the assembly.