The following changes to the PeptideAtlas database should be made when
upgrading SBEAMS

from version 0.21

to 0.22 or later or to the latest code in the SVN repository

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Create new table "search_key" as generated by generate_schema.pl

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Add new PeptideAtlas settings from $SBEAMS/lib/conf/SBEAMS.conf.template
to your local $SBEAMS/lib/conf/SBEAMS.conf

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2006-01-12

Schema changes:

- Added to table 'atlas_build' column 'probability_threshold' after
  column 'biosequence_set_id'

- Added to table 'sample' column 'original_experiment_tag' after
  column 'sample_tag'

- Added to table 'sample' column 'instrument_model_id' after
  column 'sample_description'

- Also in table 'sample', some columns were re-ordered, but this should
  not affect existing systems

There were many other changes to the tables in the driver table files, but
these have not yet been created in our production database.  But they
will be soon.

2006-01-25

- Removed Glycopeptide tables from PeptideAtlas schema, moved to Glycopeptide module.
  GP_ipi_version
  GP_ipi_data
  GP_cellular_location
  GP_glyco_site
  GP_identified_peptide
  GP_predicted_peptide
  GP_peptide_to_tissue
  GP_tissue_type
  GP_identified_to_ipi
  GP_glyco_sample
  GP_synthesized_peptide

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