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Browsing All posts tagged under »Open-Source«
opacmo: Release 3 is a contribution in the Springer API Challenge 2.0
Open Access Mortar (opacmo) is a rich text-mining resource of scored/weighted links between open-access publications and named entities. Entities in the latest release 3 of opacmo describe diseases (DO), chemical entities (ChEBI), cellular components, biological processes and molecular functions (GO), as well as genes (NCBI Entrez Gene and RefSeq) and species (NCBI taxonomy). Release 3 […]
opacmo: Supporting Text-Mining on High-Performance Computing Clusters
March 6, 2012
Past releases of the Open Access Mortar (opacmo) were created on a single Amazon EC2 instance, which has become an obstacle with the increasing number of ontologies that are included in opacmo now. Currently a friend of mine is extending opacmo’s build scripts to offer a pipeline that can be executed on multiple EC2 instances, […]
Yoctogi: A FastCGI Database-Interface
September 27, 2011
Yoctogi is a tiny FastCGI server that provides a simple interface for querying denormalised databases. Its JSON/HTTP interface permits to submit queries as JSON objects, which is compatible with the Remote Procedure Calls (RPC) of libraries such as jQuery or MooTools. Query results are returned as either JSON object, as TSV file, or as Excel […]
flystockdb: An Open-Source Experience
May 9, 2011
In my previous posts I have presented flystockdb, which is a free on-line Drosophila melanogaster database that I am working on in my spare time. flystockdb‘s initial development started at the University of Manchester as part of the grant: Establishment of a Drosophila Core facility Biomedical resources grant; 087742/Z/08/Z; 2009-12, Wellcome Trust Dr R. Baines*, Dr C. […]
flystockdb is dead. Long live flystockdb
March 17, 2011
flystockdb has recently become an open-source community driven project, which is recaptured in this blog post. I also briefly address flystockdb‘s current hosting situation, i.e. where it is currently installed and accessible, and highlight some of the features that are provided. flystockdb is dead The on-line fly-stock database flystockdb has made the transition from an […]
Portfolio
June 21, 2012
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