HTS and Message Queues

In my previous post I discussed how we’d like to automate some of our screens – starting from the primary screen, going through data processing and compound selection and completing the secondary (follow up) screen. A key feature of such a workflow is the asynchronous nature of the individual steps. Messaging and Message queues (MQ)┬áprovide […]

A GPL3 Oracle Cheminformatics Cartridge

Sometime back I had mentioned a new cheminformatics toolkit, Indigo. Recently, Dmitry from SciTouch let me know that they had also developed Bingo, an Oracle cartridge based on Indigo, to perform cheminformatics operations in the database. This expands the current ecosystem of Open Source database cartridges (PGChem, MyChem, OrChem) which pretty much covers all the […]

Oracle Notes

Some handy settings when running a query from the command line via sqlplus set echo off set heading on set linesize 1024 set pagesize 0 set tab on set trims on set wrap off — might want to set column formats here — e.g.: column foo format A10 spool stats — dump results to stats.lst […]

R and Oracle

It’s been a while since my last post, but I’m getting up to speed at work. It’s been less than a month, but there’s already a ton of cool stuff going on. One of the first things I’ve been getting to grips with is the data infrastructure at the NCGC, which is based around Oracle. […]