Overview of the Pathway Tools Software and Pathway/Genome Databases
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Overview of the Pathway Tools Software and Pathway/Genome Databases
description
Overview of the Pathway Tools Software and Pathway/Genome Databases. SRI International. Private nonprofit multidisciplinary research institute No permanent funding sources 1300 staff in Menlo Park. Founded in 1946 as Stanford Research Institute Separated from Stanford University in 1970 - PowerPoint PPT Presentation
Transcript of Overview of the Pathway Tools Software and Pathway/Genome Databases
Overview of the Pathway Tools Software
and Pathway/Genome
Databases
SRI InternationalBioinformatics
SRI International
Private nonprofit multidisciplinary research institute
No permanent funding sources
1300 staff in Menlo Park
– Founded in 1946 as Stanford Research Institute
– Separated from Stanford University in 1970
– Name changed to SRI International in 1977
SRI InternationalBioinformaticsSRI Organization
Information and Computing Sciences
Engineering SystemsAnd Sciences
PhysicalSciences
Biosciences
Education and
Policy
Bioinformatics Research Group
SRI InternationalBioinformaticsFBA Tutorial Goals
Learn basic principles of FBALearn to run existing FBA models in Pathway
Tools
Learn to develop new FBA models in Pathway Tools
Familiarity with information resources available about Pathway Tools to continue your work
SRI InternationalBioinformaticsWhy Create PGDBs?
Extract more information from your genome
Create an up-to-date computable information repository about an organism
Perform analyses on the genome and pathway complement of the organism
Analyses of omics data Analyses of cellular systems (dead-end metabolites) Reports generated by Pathway Tools
Perform comparative analyses with other organisms
Generate a genome poster and metabolic wall chart
SRI InternationalBioinformaticsInformation Sources
Pathway Tools User’s Guide /root/aic-export/pathway-tools/ptools/14.0/doc/manuals/userguide.pdf NOTE: Location of the aic-export directory can vary across different
computers Pathway Tools Web Site
http://bioinformatics.ai.sri.com/ptools/ Publications, FAQ, programming examples, etc.
Slides from this tutorial http://bioinformatics.ai.sri.com/ptools/tutorial/sessions/
BioCyc Webinars http://biocyc.org/webinar.shtm
Desktop vs Web functionality in Pathway Tools http://biocyc.org/desktop-vs-web-mode.shtml
SRI InternationalBioinformaticsInformation Sources
Publications “Pathway Tools version 13.0: Integrated Software for
Pathway/Genome Informatics and Systems Biology”, Briefings in Bioinformatics 11:40-79 2010
“A survey of metabolic databases emphasizing the MetaCyc family”, Archives of Toxicology 2011
SRI InternationalBioinformaticsInformation Sources
BioCyc Web site: Help Menu Basic Help Search Help BioCyc Glossary Publications Website User Guide PGDB Concepts Guide to EcoCyc Guide to MetaCyc
SRI InternationalBioinformaticsReporting Pathway Tools
Problems
E-mail to [email protected]
Include: What operation were you performing when the error occurred? Error message Result of [1] EC(2) :zoom :count :all error.tmp What Pathway Tools version are you are running? What platform are you running on?
New patches automatically downloaded and loaded with PTools starts up
Auto-Patch Tools -> Instant Patch -> Download and Activate All Patches
SRI InternationalBioinformaticsSRI’s Support for Pathway Tools
NIH grant finances software development and user support
Additional grants finance other software development
Email us bug reports, suggestions, questions Software: [email protected] Data: [email protected]
Comprehensive bug reports are required for us to reproduce and fix the problem you reported
Keep us posted regarding your progress
SRI InternationalBioinformaticsSurveys / Feedback
Please complete survey at end of each day
Your feedback and suggestions on the software are important to us!
SRI InternationalBioinformaticsPGDB(s) That You Build
Before you leave Tar up your PGDB directory and FTP it home, email it home,
or copy it to flash disk We will create a backup copy of your PGDB directory if the
directory is still there at the end of the tutorial Delete the PGDB directory if you don’t want us to back it up We will not give the backed up data to anyone else
SRI InternationalBioinformaticsSummary
Pathway Tools and Pathway/Genome Databases Not just for pathways! Computational inferences
Operons, metabolic pathways, pathway hole fillers Editing tools Analysis tools: Omics data on pathways Web publishing of PGDBs
Main classes of users: Develop PGDB to extract more information from genome for
genome paper Develop a model-organism DB for the organism that is updated
regularly and published on the web
SRI InternationalBioinformaticsAdministrative Details
Please wear badges at all timesEscort required outside this room/hallwayLet us know when you are leaving
Use E-Bldg EntrancePhone numbers to call from entrance
x1980
Meals
Restrooms
SRI InternationalBioinformaticsTutorial Format
Questions welcome during presentations
Lab sessions will take different amounts of time for different people
Refine your PGDB Read Pathway Tools manuals
Computer logins
Internet connectivity
SRI InternationalBioinformaticsIntroductions
BRG Staff
Attendees Where are you from? What genome? What do you hope to get out of the tutorial?
