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HATS (Haplotype Amplification in Tumor Sequences) is a tool that calls the amplified alleles, and thus amplified haplotype, in copy number aberration regions in next generation sequencing tumor data. The amplified haplotype may reveal gene variants.
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An online database project with database and web interface to archive, manage, search and download individual-based life history data that have been collected from wild primate populations.
IDEA (Interactive Display for Evolutionary Analyses) augments PAML with a graphical interface, phylogeny reconstruction using PhyML or PHYLIP, convenient and efficient parallel processing and visualizations.
Auth0 Token Vault handles secure token storage, exchange, and refresh for external providers so you don't have to build it yourself.
Rolling your own OAuth token storage can be a security liability. Token Vault securely stores access and refresh tokens from federated providers and handles exchange and renewal automatically. Connected accounts, refresh exchange, and privileged worker flows included.
A comparative map and trait visualization framework enabling visual integration of genomic data from disparate data sources and allowing rich client-side interactivity and manipulation. Extensible through plugins for new datasources and algorithms.
JFlux is a java library and graphical user interface to work with flow cytometry data. In particular, it is adapted to the COPAS biosorter and can analyze expression profiles.
Protein Data Bank transformed into an SQL database with a very powerful search engine and a rich web interface. The engine combines chemical, sequence and 3D structure searches. The interface provides statistics, sequence and 3D structure alignments.
An open source MAGE-TAB database and import/export tools to read and write MAGE-TAB formatted data. MOLGENIS is being used to autogenerate it. Import/export tools creation is in progress.
Basic Electronical Medical Management (BEMM) is an application to control medical data of a set of patients. It is built on top of open source technologies, to provide an integration skeleton of mvn, Datanucleus, Spring, Vaadin, Acceleo technologies.
DIVAT (Diagnostic Immunohistochemistry Visualization and Analysis Tool) is designed to graphically analyse comprehensive data sets of immunohistochemical results as those used in clinical diagnostic pathology.
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
This is a java open source package for analyzing bio-data. We build this project as an inititive for people interested in bio-informatic to share new ideas and publish their innovative methods.
Contextor is a light-weight simple-to-use Java based library to help developers and researchers working with the general concept of a resource; as examples, resources can be text resources, web resources, images and videos.
Trial Criteria Online Data Entry (trialCODE): a Java-based user interface that codifies eligibility requirements used to automate the screening of potential subjects to clinical trials. Used for caMATCH screening engine on BreastCancerTrials.org site.
A Java application used in whole genome analysis to display SNPs in a genomic context. Supplementary data is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks.
A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.
The development and curation of a range of XML-based tools
for using Chemical Markup Language (CML), including
XSD XML Schemas for validation, datatyping and constraining CML
documents and XSLT Stylesheets for transforming, filtering and rendering.
Memomics Forge is a meta-project for software that utilizes the Memomics Semantic Service.
Memomics Semantic Service provides semantic data which can be embedded in applications via webservices.
Anna is lightweight Java framework to build pipeline systems of any kind.
It will take care of recurrent needs such as dependency management, data serialisation and synchronization as well as parallelization of execution.