GenomeRunner / Blog: Edit

GenomeRunner / Blog: Editing "MySQL retirement"

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GenomeRunner was initially designed and works with MySQL database containing various genome annotation elements and epigenomic features. It works locally, but often poises a problem to other users accessing MySQL database hosted by us. Network load and latency, severe weather disruptions of our servers, security considerations - many factors lead to the decision to make GenomeRunner completely stand-alone.

From July we will retire our MySQL database (no relation to Google Reader retirement). GenomeRunner will be able to use SQLite databases, downloadable from this site. Advantages are obvious - users can run analyses locally, a single file serves as a snapshot of the data being used for the analysis, no need to use login credentials for the remote database. There are disadvantages - SQLite is slower, even if used locally, database files, especially for human, are large, updates will require downloading new files. But at the end, I hope, SQLite version of GenomeRunner will be much appreciated.

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Annotation and enrichment of Next-Gen sequencing data

GenomeRunner / Blog: Editing "MySQL retirement"