News/Pathway Tools 17.0 Released
Version 17.0 is a major release that includes updates to the BioCyc Web site, downloadable data files, and downloadable Pathway Tools software/database bundle. Version 17.0 of BioCyc contains 2,920 Pathway/Genome Databases.
- Groups Enhancements
- A number of enhancements have been made to both Web Groups and Desktop Groups including re-organization of Web Groups menus and addition of new transformations.
- Rate-Limiting Reactions
- A reaction can now be designated as rate limiting with respect to a given metabolic pathway, using the pathway editor. Rate-limiting reactions are identified as such in pathway diagrams using an hourglass icon.
- Web Omics Pop-ups
- When using the Cellular Omics Viewer you can view a graph of omics data (e.g., plotting gene-expression data over time for a given gene). To do so, paint expression data on the Cellular Overview. Then mouse over a reaction (or metabolite) of interest. Click "Omics" in the menu of the resulting pop-up window, which will graph the omics data for that reaction.
- PGDB Registry Speedups
- The PGDB registry is a facility whereby Pathway Tools users can share and download PGDBs via the Internet. As the number of PGDBs in the registry grew, the speed of the registry became far too slow; the registry interface has been re-designed so that finding PGDBs within the registry is much faster.
RouteSearch -- Metabolic Route Search
The new Web-based RouteSearch tool, accessible from command Tools -> Metabolic Route Search, supports two types of searches in metabolic networks. For both types of search, the user specifies a starting and ending metabolite of interest, and the software generates alternative reaction pathways connecting those metabolites.
- Mode 1 -- Within Organism Searches
- In this mode the search makes use of reactions within the selected PGDB only.
- Mode 2 -- Synthetic Pathway Searches
- In this mode the search makes use of reactions within the selected PGDB plus reactions within the MetaCyc DB. The user may specify a higher penalty for introducing reactions from MetaCyc. This mode is not available within public Pathway Tools web servers but may be accessed by installing Pathway Tools locally and running a web server accessible on an intranet.
- Pathway Abundance Scores for Metagenome Data
- PathoLogic can now compute abundance scores for pathways based on gene abundance values provided in a .PF input file. Gene entries in a .PF file may contain ABUNDANCE fields that specify the number of times that gene was observed in a metagenomics dataset. The abundance scores are present in file pathways-report.txt in the PGDB reports directory. More information on calculation of abundance scores will be provided in a future blog post.
Full details in the Pathway Tools release notes.