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Oct 4, 2013 (3 years and 8 months ago)

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Overview of the

Pathway Tools Software

and

Pathway/Genome Databases



SRI International

Bioinformatics

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 International

Bioinformatics

SRI Organization

Information and

Computing Sciences

Engineering Systems

And Sciences

Physical

Sciences

Biosciences

Education

and

Policy

Bioinformatics Research Group

SRI International

Bioinformatics

Introductions



BRG Staff



Attendees


Where are you from?


What genome?


What do you hope to get out of the tutorial?

SRI International

Bioinformatics

Administrative Details


Please wear badges at all times


Escort required outside this room/hallway


Let us know when you are leaving



Use E
-
Bldg Entrance


Phone numbers to call from entrance


x1980



Meals



Restrooms

SRI International

Bioinformatics

Tutorial Format



Mixture of lectures and lab sessions


Questions welcome



Computer logins



Internet connectivity


SRI International

Bioinformatics

Terminology


“Database” = “DB” = “Knowledge Base” = “KB” =
“Pathway/Genome Database” = “PGDB”

SRI International

Bioinformatics

Why 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



Create a steady
-
state metabolic flux model that makes
phenotypic predictions



Generate a genome poster and metabolic wall chart


SRI International

Bioinformatics

Installing Pathway
Tools


Download directory offers several configurations



Choose platform and database configuration


Many combinations of databases available


All databases requires a lot of memory


Use registry to add PGDBs to configuration you downloaded


SRI International

Bioinformatics

Information 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.shtml


SRI International

Bioinformatics

Reporting Pathway Tools Problems


ptools
-
support@ai.sri.com



Comprehensive bug reports are required for us to
fix the problem you reported


What
platform you are running on


What version of Pathway Tools you are running


The error message


Result of [1] EC(2)
:zoom :count :all


What operation were you performing when the error
occurred?



New patches automatically downloaded and
loaded with PTools starts up


SRI International

Bioinformatics

Surveys / Feedback



Please complete survey at end of each day



Your feedback and suggestions on the software
are important to us!

SRI International

Bioinformatics

PGDB(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 International

Bioinformatics

Summary



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


Develop a metabolic flux model



SRI International

Bioinformatics



Go to file intro
-
to
-
ptools
-
and
-
biocyc.ppt