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Administrator's corner

Multi-Conditional Hybridization Intensity Processing System

Microarray Data Warehousing and Analysis

wherefore ?wherefore ?

This is a collection of tips and tricks for the M-CHiPS administrator (to be), ordered by when you may need them:

  • First and foremost: Don't do it! While both using and developing a system for microarray data interpretation is good fun, the administrator will be confronted with all sorts of catastrophes. Ranging from accidentally deleted experiments to scanning 70 slides upside-down (no, I'm not joking and yes, imaging software affiliated wrong IDs to each single gene). Users will drive you mad. Ok, assuming that you already know your lads and that you are at home with Unix and scripting (or maybe you just need the money):
  • The calculation server will come to you as a ready-to-use virtual machine. I strongly recommend to use it instead of installing everything yourself. The difference in performance is neglectable on reasonably new machines. In general, all it takes for the analysis of average-sized microarray data sets are 4 Gb of memory. Computing time is not an issue.
  • For the database server use a transaction-based DBMS such as Oracle or Postgres. If you're not an Oracle wizard, use Postgres! It will be fine for any number of hybridizations, also for large facilities.
  • Let it have raid5.
  • Tape-backup nightly (raid systems can burn).
  • SQL-dump each database nightly (you can't put the whole system to yesterday's version just because someone accidentally deleted an experiment).
  • See to it that above two cronjobs don't run simultaneously, if possible. Start the postgres sever with .. (in case they do).