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Browsing All Posts filed under »Bioinformatics«
Uh-oh, Biostar: Three Years of User Metrics Analysis
It is March again and that calls for another annual follow-up of my investigations (1st year, 2nd year and bonus blog posts) into Biostar’s forum quality. Biostar is a public internet forum for the bioinformatics community where registered users can get help on a wide range of topics. Over the years I became convinced that […]
opacmo: Release 4 adds support for Amazon’s Elastic Compute Cloud
December 17, 2012
Open Access Mortar (opacmo) is a rich text-mining resource that is powered by opacmo’s unique generic text-mining pipeline implementation. Earlier releases of opacmo supported text-mining on single machines, such as laptops, as well as Oracle Grid Engine high-performance computing clusters. With the newest release of opacmo 4, it is also possible to run the text-mining […]
opacmo: Third Prize Winner in the Springer API Challenge 2.0
August 15, 2012
At the end of May I submitted Open Access Mortar (opacmo) as an entry to the Springer API Challenge 2.0 competition. The extensions that I made to opacmo’s web interface for the competition have been described in an earlier blog post, which essentially integrate search results of Springer’s Metadata API and provide a comparative analysis […]
BioMart: Automating Mart Updates
July 18, 2012
BioMart is a federated database system that provides web interfaces and web services for relational database management systems and offers tools for configuring and deploying optimised database schemas as marts. A mart is an instance of a data warehouse, which is a collection of schemas that are optimised for a given purpose. In BioMart’s case, the schemas are […]
opacmo: Release 3 is a contribution in the Springer API Challenge 2.0
June 21, 2012
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 […]
BioStar: Activity of its BioStars
March 20, 2012
This mini-series post visualises member activity within the BioStar forum. I provide stream graphs that show the total number of forum interactions, number of questions asked, number of answers provided and number of forum edits for each BioStar member since the BioStar’s inauguration in September 2009 on a monthly basis. The graphs reveal some true stars of […]
BioStar: Is the BioStar fading? An Annual Follow-Up.
March 11, 2012
One year has passed since I asked the provocative question: “Is the BioStar fading?“. At the time I concluded that the BioStar was not fading, even though the data suggested that it was not flourishing either. I have now crawled the BioStar web-sites again and updated the statistical plots from last year with up-to-date data […]
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, […]
opacmo: Release 2 of the Open Access Mortar
January 4, 2012
In July 2011 I introduced the Open Access Mortar — www.opacmo.org — that supports biologists, physicists and life science researchers to search for publications linked to biological entities as well as to provide an entity-centred fingerprints of publications in the broader research context. The latest release 2 of opacmo links publications to genes, species, diseases, […]
pubmed2ensembl: Query Improvements
October 8, 2011
Following my first post of the relatively new “mini” series, I have made some further improvements to the pubmed2ensembl query wrapper. Two new features are now implemented in bioknack‘s bk_pubmed2ensembl.rb script: retrieval of PubMed Central IDs besides the already retrievable PubMed IDs, and querying of Ensembl gene IDs by PubMed Central/PubMed ID Brief Recap www.pubmed2ensembl.org is a […]
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March 15, 2013
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