Monday, May 2, 2011

FBA Tutorial Announcement

One of the exciting new features in the Pathway Tools 15.0 release is a Flux Balance Analysis (FBA) module.  FBA models are steady-state quantitative models of the metabolic network that can be used for predicting growth phenotypes under different nutrient conditions and under gene knock-outs.  An FBA model predicts the steady-state flux rates of metabolic reactions given a set of nutrients, secretions, and metabolites to produce (i.e. the biomass reaction), and the set of reactions in a PGDB.

There are two main tasks involved in flux balance analysis: developing a model, and then solving it.  Pathway Tools can aid in both of these tasks.  Developing an accurate FBA model might require the addition of new reactions to a PGDB, altering the directionality of some reactions, modifying the biomass reaction (which lists all the chemical components of the cellular biomass), and adding new nutrients and secretions. The Pathway Tools FBA module can guide the user by suggesting changes, such as possible new reactions to add to produce a needed compound.

Solving an FBA model involves determining the correct fluxes of reactions given a set of nutrients, secretions, and biomass metabolites to produce, and is performed once a feasible FBA model has been generated.  Pathway Tools uses the SCIP solver for this task.  Since the results of solving the model can point out problems in the original model, these two tasks, model-generation and solving, are often invoked in an iterative fashion. Results can also be viewed on the Cellular Overview Diagram.

We are pleased to announce that SRI will be hosting a tutorial on the new Pathway Tools module for generating and refining metabolic flux models using flux-balance analysis at SRI's main campus in Menlo Park, CA from June 21-22.  The purpose of the workshop is to describe the use of this new module in significant detail, to offer advice on strategies for refining FBA models, and to assist attendees in hands-on refinement of Pathway Tools based FBA models.

More details and registration are available at  A remote online attendance option for the tutorial is available.

If you're at all interested in these new capabilities, please join us -- we'd love to see you!

Thursday, April 28, 2011

Talkin' 'Bout My Regulation

The Regulation Summary Diagram for the bglG gene
in EcoCyc

You may have seen our new regulation summary diagrams on our EcoCyc gene pages. Or played with the regulatory overview. And you may have wished that you could get those visualizations for your own PGDBs. Unfortunately, there is as of yet no equivalent of PathoLogic for regulation -- no tool that will infer regulatory relationships, transcription factor sites, etc. from the genome annotation. Much of the regulatory data in EcoCyc was painstakingly curated from the primary literature (either by us or by the folks at RegulonDB) and entered piece by piece using our curation tools. That makes it an extremely valuable resource, but makes it difficult to replicate in other PGDBs without expending an equivalent amount of effort.
The Regulatory Overview Diagram for EcoCyc

Fortunately, there are other, faster ways to generate regulation data. High-throughput experiments and computational prediction programs can identify regulatory relationships and/or transcription factor binding sites en masse, and a number of groups have generated such data for their own organisms. The question that remains is how to bulk-load that data into a PGDB.

Thursday, March 24, 2011

Are You Being Served?

A table of pathways with omics data.
(click to enlarge)
This post will provide a brief survey of the Pathway Tools Web Services.  These services can be used to access any site running the latest version (15.0) of Pathway Tools.  Thus, you can invoke them for any of the 1000+ PGDBs served by the BioCyc website without installing the Pathway Tools software locally, or you can install and run the software yourself in order to create queries (or allow other users to create queries) that access your own PGDBs.

Thursday, March 17, 2011

Hello, world!

Welcome to the inaugural post for the Pathway Tools developers’ blog!  If you’re not already familiar with Pathway Tools, the links to the right can help you find out what Pathway Tools is, what it can do for you, how to get it, and what it looks like in action.  The purpose of this blog, on the other hand, is to alert you to newer features of which you may not be aware, to pass along tips for accomplishing various tasks, to disseminate news, and in general to create a mechanism by which the developers can communicate and interact with the user community at large.  We hope you'll find it useful and informative.  Feel free to offer suggestions for any topics you’d like to see covered!