Administering Pathway Tools Obtaining Pathway Tools SRI International

Administering Pathway Tools

Obtaining Pathway Tools SRI International Bioinformatics l Free to non-commercial organizations l To obtain license agreement go to Bio. Cyc. org and click on Software/Database Download l Follow Installation Guide l ptools-local directory l Locate in common directory l PGDBs created by all users who use this ptools installation l PGDBs downloaded via the registry l ptools-init. dat for this ptools installation

New Pathway Tools Releases l l l SRI International Bioinformatics Major releases = External software releases l Twice per year l Announced on ptools-users mailing list Minor releases twice per year affect only our Bio. Cyc. org Web site and flatfile distributions We support one prior release only Releases announced on ptools-users@ai. sri. com Read release notes at l http: //brg. ai. sri. com/ptools/release-notes. html Install process: l Upgrade schema of your DB (software assisted)

PGDB Storage: File or Relational Database l File storage: l Advantages: u l Disadvantages: u u u l No RDBMS installation and configuration Must be loaded and saved in its entirety No transaction history No concurrent access for multiple users Oracle/My. SQL storage: l Advantages: u u u l Faster read access, faster saves Concurrent update access for multiple users Stores history of all PGDB updates Disadvantages: u RDBMS must be installed and configured SRI International Bioinformatics

Multiuser Access to PGDBs l PGDB l Each SRI International Bioinformatics stored within one Oracle or My. SQL server curator installs PTools on their workstation l Different curators can use different software platforms l Workstations query RDBMS server via internet l Local disk cache speeds access l For each frame access, PTools queries l In-memory cache, disk cache, RDBMS server l After curator saves changes, all changes made by other users are loaded into curator’s session

How to Release a PGDB? l l l Decide on release frequency and schedule l Don’t wait until it’s perfect to release it! Freeze curation for 1 week Quality assurrance l Run consistency checker u u l l SRI International Bioinformatics Tools -> Consistency Checker Also updates organism-summary statistics Update publications, authors in organism frame l Update via Organism editor Create new version of PGDB l ptools-local/pgdbs/yeastcyc/1. 0/kb/yeastbase. ocelot l Edit against the new version, release the old version Author release notes Register PGDB in SRI PGDB registry l Will allow SRI to include it in Bio. Cyc