Pathway Tools Tutorial on Metabolic Modeling using Flux Balance Analysis:
SRI's Bioinformatics Research Group will be holding a Pathway Tools Flux Balance Analysis Tutorial
Oct 15th - Oct 16th, 2014, at SRI International in Menlo Park, California.
The goal of the tutorial is to teach scientists how to use the Pathway Tools software to to create quantitative metabolic models for an organism of interest. These steady-state models can predict cellular growth rates under different nutrient conditions, and can predict the lethality of gene knock-outs.
It is recommended that you have a significant familiarity with Pathway Tools prior to arrival at the tutorial, since we will not have time for going over basic functionality.
The Pathway Tools MetaFlux modeling tool can reduce the time required for metabolic model construction by months.
Topics for the Tutorial
Generating a metabolic model; the Cellular Overview Omics Viewer; a closer look at the LP file; instantiation of reactions; balanced and unbalanced reactions; fine control over metabolic model generation; reaction gap filling. Topics and scheduling is subject to change.
Each day's tutorial will last from 9:00 AM to 5:30 PM. Each day will combine lectures with lab sessions in which students apply the software to a PGDB. No programming experience is required.
Four example PGDBs are:
- EcoCyc http://EcoCyc.org/
- HumanCyc http://www.HumanCyc.org/
- Yeast pathway database: http://pathway.yeastgenome.org/biocyc/
- Arabidopsis pathway database: http://www.arabidopsis.org/biocyc/index.jsp
Please see above for the registration types and fees. This registration fee is non-refundable.
Early registration rates are available for those who register before Sep 19th.
Online registration means one or more attendees will participate in the tutorial remotely. Attendees will be able to see the presentations via WebEx and will hear the presenter via a call-in number. The call-in number will not be toll-free. Questions may be asked via the WebEx chat interface or via the teleconference, but the ability of SRI staff to answer complex questions during the lab sessions for online attendees will be very limited. Online registration attendees will be sent the login information in advance of the tutorial.
Computers and Software
We recommend that you execute a Pathway Tools license agreement before you attend the tutorial, which can be done online at [Pathway Tools License].
We will provide 64-bit Linux computers for participants, but we recommend that attendees use their own 64-bit Linux/Mac/Windows computer with Pathway Tools already installed for use at the tutorial. Participants can either use a 64-bit Linux laptop, or can use one of our computers to connect to a 64-bit Linux server at the participant's home institution. This enables the user to leave with not only knowledge of how to use Pathway Tools, but with a working installation on their own computer with a PGDB-based Flux Balance Analysis model.
If you plan on working with your own computer (either in the form of a laptop or a server), it is mandatory that you install Pathway Tools and verify that the SCIP libraries are working in advance of arrival at SRI. Please see the Pathway Tools Installation Guide for more information.
Bring a PGDB
You are encouraged to bring a PGDB with you to use in learning how to perform Flux Balance Analysis using Pathway Tools. You may select a tier 3 PGDB for this purpose if you do not have a previously-built PGDB to use.
We suggest that you read the following before the tutorial:
Readings on Flux Balance Analysis:
- "What is flux balance analysis?" Orth JD, Thiele I, Palsson BØ. Nat Biotechnol. 2010 Mar;28(3):245-8. Abstract (PMID: 20212490)
- Construction and completion of flux balance models from pathway databases.
Latendresse M, Krummenacker M, Trupp M, Karp PD.
Bioinformatics. 2012 Feb 1;28(3):388-96. doi: 10.1093/bioinformatics/btr681.
- "A protocol for generating a high-quality genome-scale metabolic reconstruction". Thiele I, Palsson BØ. Nat Protoc. 2010;5(1):93-121. Epub 2010 Jan 7. PMID: 20057383
- Pathway Tools User Guide, Chapter 8: FBA: Flux Balance Analysis
General Background on Pathway Tools:
- Pathway Tools User's Guide Chapters 1-3, 6.1-6.5, 7. This document is present in the Pathway Tools software distribution in directory aic-export/pathway-tools/ptools/VERSION/doc/manuals/
- "Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology"
- "The MetaCyc Database"
We also have webinars on various aspects of using the Pathway Tools software.
For those of you travelling from out of town, please be advised that SRI is approximately 20 miles from both San Francisco International Airport (SFO) and San Jose International Airport (SJC), and is approximately 30 miles from Oakland International Airport (OAK). SRI is about 30 minutes south of SFO by car on highway 101.
We suggest you try these two hotels first so that most people end up staying at the same hotels: Menlo Park Inn, Red Cottage Inn.
The SRI web site contains directions to SRI, other nearby hotels, and driving directions to SRI. Please see [SRI Directions].
SRI International is at 333 Ravenswood Ave in Menlo Park, between Middlefield Rd and El Camino. 101 exit: Willow Road.
SRI is about 30 minutes south of SFO by car on highway 101. You can take Super Shuttle from the airport to save money over a taxi cab, but they will probably make a few stops along the way.
You can also take the Caltrain commuter train line. Take BART or a taxi from SFO or OAK airports to the Millbrae Caltrain station. Then take Caltrain south to the Menlo Park stop. There is also a free shuttle that takes passengers from SJC airport to the Santa Clara Caltrain station. Caltrain has week-day rush-hour express trains and runs every hour otherwise. Caltrain schedules are subject to change. Please see the Caltrain website for up-to-date schedules.
Arriving at SRI
Note: There are two entrances to SRI on Ravenswood Ave. Please use the western entrance, closer to Laurel Avenue than to Middlefield Road, for parking your car. The sign by this entrance says, at the bottom, "Building-E Visitors". Please take a look at the SRI campus map below, and park your cars in the parking lot next to Building E. After parking your car, you should proceed to the Building E Lobby.
When you arrive in the Building E entrance/lobby, call Wilma Lenz from the telephone in the lobby, at extension 4904. If she does not answer, ask the receptionist to reach Quang Ong and tell them you have arrived for the Pathway Tools tutorial hosted by Peter Karp's group.