Monday, January 15, 2018

Local Downloading of BioCyc PGDBs for Pathway Tools Users

BioCyc offers thousands of PGDBS, currently 10,980 to be exact, and while subscribers can access all of these via the BioCyc web site, most desktop Pathway Tools users will want to work with a limited subset of these thousands.

Installing the desktop version of Pathway Tools provides a number of advantages:
  • Ability to create and edit PGDBs locally
  • Compare your PGDB(s) with similar organisms in BioCyc
  • Ability to query PGDB data from Python, Perl, Java, Lisp
  • Faster speed
  • Develop metabolic models 

Working with a PGDB in desktop Pathway Tools requires having a local copy. Downloading all those nearly 11,000 files would take up a lot of space and downloading time, so we provide two ways to get only the PGDBs you need.

The first download method is to download an appropriate bundle of PGDBs when you download Pathway tools. If you have a BioCyc subscription, you will have a number of options. Without a subscription (if you only have an academic download license), you will only be able to download the bundle that includes MetaCyc and EcoCyc. With a BioCyc subscription, there are seven available bundles, although a few bundle options are not available for all operating systems. Also the bundles for Windows will sometimes contain fewer PGDBs due to space constraints.

EcoCyc and MetaCyc
EcoCyc, MetaCyc

EcoCyc and MetaCyc +BsubCyc+YeastCyc
EcoCyc, MetaCyc, BsubCyc (Bacillus subtilis subtilis 168), Saccharomyces cerevisiae (YeastCyc)

EcoCyc and MetaCyc +Mammals
EcoCyc, MetaCyc, HumanCyc, Mus musculus (MouseCyc)

EcoCyc and MetaCyc  +Tier2
EcoCyc, MetaCyc, BsubCyc, HumanCyc, YeastCyc, Bacillus anthracis Ames (AnthraCyc), Arabodopsis thaliana, Agrobacterium fabrum C58, Caulbacter crescentus CB15, Helicobacter pylori 26695, Leishmania major Friedlin, Mycobacterium tuberculosis H37Rv, M. tuberculosis CDC1551, Peptoclostridium difficile 630, Plasmodium falciparum 3D7, Shigella flexneri 2a str. 2457T (ShigellaCyc), Synechococcus elongatus PC 7942, Vibrio cholera O1 biovar E1 Tor strain N16961

EcoCyc and MetaCyc + Bacilli  
EcoCyc, MetaCyc, Anthracyc, BsubCyc, Bacillus amyloliquefaciens DSM 7, B. anthracis Sterne, B. atrophaeus 1942, B. cereus ATCC 14579, B. licheniformis DSM 13, B. megaterium QM B1551, B. pseudofirmus OF4, B. pumilus SAFR-032, B. subtilis spizizenii W23

EcoCyc and MetaCyc + E. coli          
EcoCyc, MetaCyc, ShigellaCyc, E. coli 0157:H7 strain EDL933, E. coli CFT073, E. coli K-12 substr. W3110, E. coli UTI89, E. coli O157:H7 str. Sakai, E. coli B str. REL606, E. coli K-12 substr. W3110, E. coli ATCC 8739, E. coli 536, E. coli BL21(DE3), E. coli HS, Salmonella enterica enterica LT2; SGSC 1412; ATCC 700720, Shigella flexneri 301, S. flexneri 8401, S. boydii Sb227, S. sonnei Ss046

EcoCyc and MetaCyc + Mycobacteria     
EcoCyc, MetaCyc, Amycolicicoccus subflavus DQS3-9A1, M. avium 104, M. avium paratuberculosis K-10, M. bovis BCG Pasteur 1173P2, M. bovis Tokyo 172, M. gilvum PYR-GCK, M. leprae Br4923, M. marinum M, M. parascrofulaceum ATCC BAA-614, M. sp. MCS MCS, M. sp. JLS JLS, M. sp. KMS, M. gilvum Spyr1, M. sinense JDM601, Mycobacterium tuberculosis H37Rv, M. tuberculosis CDC1551, M. tuberculosis F11, M. tuberculosis KZN 1435, M. ulcerans Agy99, M. vanbaalenii PYR-1

The second download method doesn't limit you to what's available in these pre-built bundles.  SRI maintains an online repository of all SRI created PGDBs as well as dozens of PGDBs submitted by other researchers.  We call this repository the registry.  If you have a BioCyc subscription, you can use the built-in registry import command to download additional PGDBs from within Pathway Tools (Files->Import->Registry).  The importer provides a search capability so you can enter a substring and it will return a list of registry-resident PGDBs whose taxon names match the search string.  Select the taxa you want and go.  Note that after the loading is complete, you will want to close the importer window, which may be hidden by the main pathway tools window.  For more information about the registry, see chapter 6 of the Pathway Tools User's Guide.

We hope you have found this review of ways to get PGDBs helpful.  For most Pathway Tools users, the Registry is the most flexible and frequently the quickest way to set up your collection of PGDBs.

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