Administering Pathway Tools

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Administering Pathway Tools
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Obtaining Pathway Tools

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

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Reporting Pathway Tools Problems

• E-mail to ptools-support_at_ai.sri.com
• Include
• Error message
• Result of 1 EC(2) zoom count
  all
• error.tmp
• What version and platform you are running
• What operation were you performing when the error
  occurred?
• New patches automatically downloaded and loaded
  with PTools starts up
• Auto-Patch
• Tools -gt Instant Patch -gt Download and Activate
  All Patches

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New Pathway Tools Releases

• Major releases External software releases
• Twice per year
• Announced on ptools-users mailing list
• Minor releases twice per year affect only our
  BioCyc.org Web site and flatfile distributions
• We support one prior release only
• Releases announced on ptools-users_at_ai.sri.com
• Read release notes at
• http//brg.ai.sri.com/ptools/release-notes.html
• Install process
• Renames your old software directory tree out of
  the way
• Creates new directory tree for new version
• Upgrade schema of your DB (software assisted)

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PGDB StorageFile or Relational Database

• File storage
• Advantages
• No RDBMS installation and configuration
• Disadvantages
• Must be loaded and saved in its entirety
• No transaction history
• No concurrent access for multiple users
• Oracle/MySQL storage
• Advantages
• Faster read access, faster saves
• Concurrent update access for multiple users
• Stores history of all PGDB updates
• Disadvantages
• RDBMS must be installed and configured

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Multiuser Access to PGDBs

• PGDB stored within one Oracle or MySQL server
• Each curator installs PTools on their workstation
• Different curators can use different software
  platforms
• Workstations query RDBMS server via internet
• Local disk cache speeds access
• For each frame access, PTools queries
• In-memory cache, disk cache, RDBMS server
• After curator saves changes, all changes made by
  other users are loaded into curators session

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How to Release a PGDB?

• Decide on release frequency and schedule
• Dont wait until its perfect to release it!
• Freeze curation for 1 week
• Quality assurrance
• Run consistency checker
• Tools -gt Consistency Checker
• Also updates organism-summary statistics
• Update publications, authors in organism frame
• Update via Organism editor
• Create new version of PGDB
• ptools-local/pgdbs/yeastcyc/1.0/kb/yeastbase.ocelo
  t
• Edit against the new version, release the old
  version
• Author release notes
• Register PGDB in SRI PGDB registry
• Will allow SRI to include it in BioCyc

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Pathway Tools Data Import/Export

• File-gtExport
• File-gtImport
• Export/import to/from tab-delimited files
• Export to Genbank, SBML, BioPAX
• Export to attribute-value files
• Attribute-value files can be imported into
  BioWarehouse
• Relational database system for bioinformatics
  database integration

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Napster Comes to Bioinformatics

• Public sharing of Pathway/Genome Databases
• PGDB registry maintained by SRI at URL
  http//biocyc.org/registry.html
• Registry operations
• List contents of registry
• Download PGDBs listed in the registry
• Register PGDBs you have created

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Registry Details

• Why register your PGDB?
• Declare existence of your PGDB in a central
  location
• Facilitate its download by other scientists
• Facilitate its inclusion in BioCyc.org
• Why download a PGDB?
• Desktop Navigator provides more functionality
  than Web
• Comparative operations
• Programmatic querying and processing of PGDB
• Registration process
• Registered PGDBs have open availability by
  default
• Authors can provide their own license agreements
• Registered PGDBs reside in authors FTP site or
  HTTP server

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Pathway Tools Workshop

• Planned for June 12-16, 2006
• Presentations by users on results they have
  attained, suggested enhancements, software
  developments
• SRI presentations on new developments,
  programming examples

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New Pathway Tools Features Coming Soon

• Improvements to electron transport
• Include updates to genome annotation in a PGDB
• Ability to manage more types of regulation
• Better support for signaling pathways
• Find dead-end metabolites
• Improve accuracy of pathway predictor
• Web login/preferences system
• Graph tracks for displaying ChIP/Chip data
  against genome

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Why Create a PGDB?

• Perform pathway analyses as part of a genome
  project
• Analyze omics data
• Create a central information resource for the
  organism
• Lay the foundation for creating a FBA model
• Perform comparative analyses

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Model Organism Databases

• DBs that describe the genome and other
  information about an organism
• Curated by experts for that organism
• No one group can curate all the worlds genomes
• Distribute workload across a community of experts
  to create a community resource
• Every sequenced organism with an active
  experimental community requires a MOD
• Integrate genome data with information about the
  biochemical and genetic network of the organism
• Integrate literature-based information with
  computational predictions

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Rationale for MODs

• Each complete genome is incomplete in several
  respects
• 40-60 of genes have no assigned function
• Roughly 7 of those assigned functions are
  incorrect
• Many assigned functions are non-specific
• MODs are platforms for global analyses of an
  organism
• Interpret omics data in a pathway context
• In silico prediction of essential genes
• Characterize systems properties of metabolic and
  genetic networks

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What is Curation?

• Ongoing updating and refinement of a PGDB
• Correct false-positive and false-negative
  predictions
• Incorporate information from experimental
  literature
• Update genome sequence
• Update gene functions, gene positions, gene names
• Author comments and citations
• Add new pathways, modify existing pathways
• Enter information about regulatory networks

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Issues in Creating Public MODs

• Obtaining funding
• Scoping the project
• Identify user community
• Obtain buy-in and help from scientific community
• IT Set up database server, Web server
• Hire and train curators

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Questions

• Do you intend to make your PGDB public and to
  update it on an ongoing basis?
• To create a Model Organism Database?

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• Desktop vs Web functionality in Pathway Tools
• http//biocyc.org/desktop-vs-web-mode.shtml