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2018-12-16 03:08:03 -0500 asked a question Publish PGDB on GitHub?

Publish PGDB on GitHub? Dear, Is it possible to publish a PGDB of a microorganism on a GitHub project account as part o

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2018-09-24 03:03:33 -0500 asked a question checkpoint file error

checkpoint file error Hi all, I'm experiencing an error when I want to add an enzyme to a reaction. In Pathway Tools I

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2016-02-15 07:45:59 -0500 commented answer How to propagate MetaCyc data updates in Patway Tools 19.5

Would it be possible to install MetaCyc version 19.5 in Pathway Tools 19.0? So as to only propagate MetaCyc changes to current PGDB's in ptools-local/pgdbs but keep the current 19.0 tools, while waiting for a fix.

2016-02-15 07:20:47 -0500 commented answer How to propagate MetaCyc data updates in Patway Tools 19.5

Any work around for this problem on the 19.5 version for Mac? Possibly running the tool on the command line?

2016-02-15 07:19:25 -0500 commented answer How to propagate MetaCyc data updates in Patway Tools 19.5

I installed Pathway Tools 19.5 on a Ubuntu VM and the 'Propagate MetaCyc Data Updates' is also not available in the Linux distribution. However, installing the 19.0 version on Ubuntu did lead to a Tools menu where I could find this option and succesfully propagate MetaCyc updates to a PGDB.

2016-02-12 04:53:24 -0500 answered a question How to propagate MetaCyc data updates in Patway Tools 19.5

This is actually what I do, when I open Pathway Tools I select my PGDB in the Organism Summary Page. This opens me the Single Database Page of the PGDB I selected. Then I invoke the Tools menu in the Navigator and I don't see the 'Propagate MetaCyc Data Updates' in the menu. It doesn't seem disabled, it's just not there.

I'm on Pathway Tools version 19.5 on Mac OSX 10.9.5

Any ideas? Is there a way to run this tool on the command-line?

2016-02-12 04:48:08 -0500 answered a question How to propagate MetaCyc data updates in Patway Tools 19.5

Dear,

Thanks for the answer.

This is actually what I do, when I open Pathway Tools I select my PGDB in the Organism Summary Page. This opens me the Single Database Page of the PGDB I selected. Then I invoke the Tools menu in the Navigator and I don't see the 'Propagate MetaCyc Data Updates' in the menu. It doesn't seem disabled, it's just not there.

I'm on Pathway Tools version 19.5 on Mac OSX 10.9.5

Any ideas? Is there a way to run this tool on the command-line?

2016-02-12 04:45:10 -0500 answered a question How to propagate MetaCyc data updates in Patway Tools 19.5

Dear,

Thanks for the answer.

This is actually what I do, when I open Pathway Tools I select my PGDB in the Organism Summary Page. This opens me the Single Database Page of the PGDB I selected. Then I invoke the Tools menu in the Navigator and I don't see the 'Propagate MetaCyc Data Updates' in the menu. It doesn't seem disabled, it's just not there.

I'm on Pathway Tools version 19.5 on Mac OSX 10.9.5

Any ideas? Is there a way to run this tool on the command-line?

2016-02-11 08:13:05 -0500 asked a question How to propagate MetaCyc data updates in Patway Tools 19.5

Dear,

I include the link (ask.pathwaytools.com/question/17857/where-is-the-tools-propagate-metacyc-data-updates/?answer=17860#post-id-17860) to the previous question/answer which was made with an anonymous account.

I have downloaded a BioCyc Tier 3 PGDB in Pathway Tools from the PGDB Registry. This PGDB was originally made with Pathologic using Pathway Tools 18.5 and MetaCyc 18.5.

I would like to use this PGDB for metabolic modeling purposes using MetaFlux, however to allow proper manual curation and according to this blog (pathwaytools.blogspot.be/2014/12/propagating-updates-from-metacyc-why.html) I'd need to propagate updates in MetaCyc to my PGDB. I have already upgraded the PGDB schema to the new Pathway Tools 19.5, however according to the manual this does not include the propagation of MetaCyc updates.

I have already done some manual curation (e.g. pruning false-positive pathways, ...) which I would like to keep, but no major Reaction or Pathway edits (although I may want to do this in the future).

How could I make the 'Propagate MetaCyc Data Updates' available in my version of Pathway Tools?

2016-02-10 02:28:29 -0500 commented question Where is the Tools: Propagate Metacyc Data Updates

Any answer on this? It's quite urgent for me. Thanks in advance