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2018-11-08 18:00:39 -0500 commented answer Running the www server with SSL?

It should also be noted that the contents of this file should be properly secured as it essentially contains your websit

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2017-08-18 13:06:28 -0500 edited answer Configuration for multiple curators

If you plan to have multiple curators update a PGDB, there are several possible ways to configure their usage of Pathway

2017-08-18 12:56:19 -0500 answered a question installation

This particular error is a result of missing X libraries. Did you review the installation guide and system requirements?

2017-07-31 17:01:20 -0500 asked a question asking a test question for email notifications

asking a test question for email notifications test, please ignore

2017-07-31 16:16:06 -0500 edited answer Help with fatal error: The slot PROCESS is unbound...

Two things: 1) Your version of Mac OSX is quite old. It's possible there could be some issue with the libraries not bei

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2017-07-31 16:13:49 -0500 answered a question Help with fatal error: The slot PROCESS is unbound...

Two things: 1) Your version of Mac OSX is quite old. It's possible there could be some issue with the libraries not bein

2017-07-17 15:44:05 -0500 answered a question Metabolic Pathway

Have you checked the SBML importer tool in Section 5.2 of the User Guide (under Help > User Guide)? Could you elabor

2017-07-17 15:37:54 -0500 answered a question Interproscan results parsed into a PGDB

Pathway Tools provides a number of different import/export tools (see Chapter 5 of the User Guide under Help > User G

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2017-03-31 16:45:20 -0500 answered a question How to convert gff3 files to Genbank files for input into Pathway Tools?

Pathway Tools currently doesn't support the GFF3 format. We do intend to add that at some point in the future, but we don't have a schedule of when that feature will be available.

Doing a quick search on those two formats, there appears to be quite a number of conversion tools from genbank to gff3. However, I'm not sure if those tools will convert in the other direction.

2017-03-27 13:18:26 -0500 answered a question growth media

What kind of metadata are you trying to import for growth medium?

2017-02-27 15:31:42 -0500 answered a question Anyone got an error "Duplicate genetic element ID NIL"

The underlying engine of Pathway Tools is built upon lisp. NIL is a default value of variables etc, analogous to NULL in C or undefined in other languages. It's probably failing to parse some of our input data and thus defaults to a NIL value. However to get a better idea, you'll need to submit more information such as a back trace or a log file for further investigation.

2017-02-27 15:26:57 -0500 answered a question How to publish my PGDB

I apologize for the late response, we've been having some email filtering issues from our cloud provider of this service.

Short answer is, yes, you can do this via our PGDB Registry service. Please refer to Chapter 6 (Database Sharing Via the PGDB Registry). When your PGDB is ready for submission, you can also send an email to biocyc-support about adding it to BioCyc. We typically only host bacterial organisms but that policy may evolve. The PGDBs in the registry are a snapshot of a PGDB. It is not intended to be a way of collaborating (editing). If you do that, it's best to set up your own curation database server for collaborating curation.

2017-02-01 19:45:19 -0500 answered a question is pathway tools downloadable in pakistan?

On the academic license request page, if you don't see your organization in an "Request Use Under Existing License", you can scroll down to the bottom section of the page with the button "Request NEW License" and request a license for your organization, if you are an authorized agent of your organization (see section "Signer of License", in RED).

2017-01-03 15:19:45 -0500 answered a question Pathway Tools won't start after upgrading XQuartz

We've recently discovered that new versions of XQuartz (v2.7.10+) will break Pathway Tools. If you're prompted to upgrade to a new version of XQuartz, please do NOT update. Choose "Skip" when prompted to upgrade XQuartz. Upgrading XQuartz will render Pathway Tools completely inoperable.

If you've already upgraded to XQuarz 2.7.10+, you can "revert" by following these instructions:

1) Exit out of the XQuartz application (its icon is a big "X").

2) Drag your XQuartz folder into the trash

3) Download the last known working version with Pathway Tools, version 2.7.9:

NOTE: This step will require you to log out in order for changes to XQuartz to take affect.

4) Reinstall Pathway Tools

When XQuartz prompts to update, choose "skip"

Pathway Tools Support.

2017-01-03 15:19:06 -0500 asked a question Pathway Tools won't start after upgrading XQuartz

I recently upgraded XQuartz and now Pathway Tools doesn't work. How can I fix it?

2016-11-04 18:52:27 -0500 answered a question Which Blast database is needed with hole filler?

Joe, under the Tools menu, there's an option "Prepare BLAST Reference Data" (See UserGuide section It uses the PGDB and the provided sequence data to create the BlastDB for you. The resulting blastDB files are in the xxxcyc/VERSION/data directory. The Hole Filler then uses this BlastDB as the reference. You can look at the protseq.fsa and dnaseq.fsa for your genome. It's possible, the source sequence you used with Pathologic has problems. You can inspect these files for errors.

2016-11-03 16:37:38 -0500 answered a question Pathway tools web server behind nginx

Madison, we don't have any direct experience with Nginx, but we do run our software behind an Apache reverse proxy without the problem you're seeing. I think it's a configuration issue with your proxy settings. Doing a quick search of what works for us on Apache, I think you need to look into the proxy_pass directives:

On our Apache reverse proxy, we have to use both the ProxyPass AND the ProxyPassReverse directives. One possible difference, is that we also use a named based vhost set up, so "/" always translates to "/". Hope this helps.

2016-10-07 16:06:03 -0500 commented answer How do I perform a silent installation?

Example on Linux: ./pathway-tools-20.0-linux-64-tier1-install --InstallDir /home/smith/pathway-tools/v200 --PTOOLS_LOCAL_PATH /home/smith/pathway-tools --InstallDesktopShortcuts 0 --mode unattended

2016-10-07 15:46:56 -0500 answered a question how can I install pathway tool on HPC without root

While Pathway Tools itself does not need to be installed as root, it depends upon libraries and packages that MUST be installed PRIOR to installing Pathway Tools. If you can request the system administrators of your cluster install the pre-requisite packages first, you don't need root to finish the Pathway Tools install.

2016-09-19 11:50:14 -0500 answered a question How do I perform a silent installation?

Most of the the installer variables can be supplied via the command line. You find find all the command line options by calling the installer with the "--help" option. The 4 Pathway Tools specific variables are:

  • InstallDir (destination directory, defaults to $HOME/pathway-tools)
  • PTOOLSLOCALPATH (data/configuration directory, defaults to $HOME as the prefix. So the final location of the directory is $HOME/ptools-local, but you only specify $HOME prefix). There are "underscores" between each word, but it doesn't appear to be showing up on the posting.
  • InstallDesktopShortCuts (0 or 1, default=1 meaning, yes, install desktop shortcuts. For Unix and Mac, basically creates a symlink)
  • UninstallPrevious (Uninstall older versions before installing new version, default=1)

For "silent installation", you also need to specify -mode unattended option.

2016-09-01 17:25:26 -0500 commented answer How do you start web mode on port 80?

In addition, you'll want to read the FAQ on running in headless mode for setting up Xvfb:

2016-09-01 13:16:15 -0500 marked best answer Graphics do not get generated

My Ptools website doesn’t display graphics.

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2016-09-01 13:14:53 -0500 answered a question How do I import a draft genome?

As long as these draft genomes are available in genbank format, you an use them to build a PGDB using Pathologic. Please refer to Chapter 7 on how to run Pathologic using genbank formatted files.

2016-09-01 13:11:24 -0500 answered a question How to save pathway images with omics data overlaid?

Although you're using Pathway Tools in desktop mode, you can also run your version of Pathway Tools in "web mode". Have you tried doing that? Most images in desktop mode are not in a form that can be saved. However, you can save the images generated in web mode. Here's a brief summary of the differences in desktop vs web mode:

Please refer to Chapter 10 about web mode of the UserGuide under the Help menu of the desktop mode.

2016-09-01 13:04:54 -0500 answered a question Can I improve pathway calculation by adding Tier3 relatives?

No, the Pathway prediction is only affected by the "reference" PGDB and the genome annotation itself. Besides the default reference PGDB of MetaCyc, it does not take into consideration other PGDBs that is accessible from Pathway Tools. Please refer to Chapter 7 of the UserGuide under the Help menu for details on how Pathologic works. There's also a paper that describes how the Pathway Prediction works:

The main way to improve Pathway Prediction is to improve the underlying genome annotation.

2016-08-30 17:48:53 -0500 answered a question How do you enable SmartTables?

SmartTables builds on top of the Pathway Tools web accounting system, as such, it requires a mysql database to be set up to store the account and SmartTables data. To do this:

  1. Review Chapter 10.8 of the UserGuide under the Help menu.
  2. Create a mysql database with appropriate database permissions that allows the account to create tables
  3. Edit the User-Account-RDBMS-* parameters in the ptools-init.dat file to correspond to the account created in step #1.
  4. Set the WWW-Enable-Groups Y in ptools-init.dat config file.
  5. Start Pathway Tools in lisp mode and evaluate (init-st-db) at the EC prompt.
  6. Restart in web mode
  7. Create a web account and log in
  8. SmartTable enabled features of the website should not be active.
2016-08-30 17:29:26 -0500 asked a question How do you enable SmartTables?

I would like to make use of the SmartTables feature of the Pathway Tools web server. How do you enable it?

2016-08-29 15:08:05 -0500 answered a question Where is my flagellum?

Dear Clarissa,

The pathways in BioCyc are in general small molecule pathways (although there are some exceptions). The software does not permit using an image, as in the KEGG Flagellar Assembly "pathway", and we are limited to showing pathways that consist of chemical reactions. Thus there is no flagellar biosynthesis pathway in MetaCyc, and no such pathway can be predicted in any database. This explains why you couldn't find the pathway.

What can be done is to specify the flagellum as a giant protein complex. This has been done in EcoCyc (, but this operation is not performed automatically and is thus missing from all of the tier 3 PGDBs. You could generate it yourself using EcoCyc as a guide.

Regarding the missing genes, this is a different issue, and I do not have an explanation. The Pathway Tools software uses the annotation found in the genome, so if a gene has been annotated with a particular name such as "flagellar motor switching and energizing component", the name should appear in the database. Are you sure the genes are missing? if this is indeed the case, you will probably need to contact ptools-support, and they may ask you to send them your PGDB so they could troubleshoot the issue.

I hope this helps, Ron

2016-08-12 12:32:38 -0500 answered a question Pathway Tools install seems to hang

Pathway Tools requires the X11 environment installed AND working before launching Pathway Tools. If you've recently upgraded your Mac to a new version of the OS, it may remove the XQuartz system from your Mac. The Pathway Tools installer will prompt you to install XQuartz if it is not installed.

However, at the end of the XQuartz install, it's best to restart or log out of your Mac BEFORE finishing the Pathway Tools install. If you do proceed to the end of the Pathway Tools installer and it prompted to install XQuartz, you MUST log out or reboot your Mac before Pathway Tools will work correctly even though the installer may finish without any errors.

2016-07-05 12:15:27 -0500 marked best answer Does Pathway Tools work on Yosemite?

I just upgraded to Yosemite and now Pathway Tools doesn't work, what's wrong?

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2016-07-05 12:10:26 -0500 marked best answer How do you start web mode on port 80?

Is it possible to start the Pathway Tools web server on the default web port of 80?

2016-07-05 12:08:09 -0500 marked best answer Importing a Flat-File PGDB into Pathway Tools

How do you take a PGDB downloaded from the BioCyc website, and import it into Pathway Tools?

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2016-07-05 12:07:48 -0500 marked best answer MySQL PGDBs: Creating & querying them

How can I convert my locally created file PGDB to a MySQL PGDB? If I do this, will I be able to query my PGDB using SQL?

2016-07-05 12:07:28 -0500 marked best answer User-generated ortholog data & Pathway Tools

I have ortholog data. How do I get it into Pathway Tools?

2016-07-05 12:07:11 -0500 marked best answer Configuring Proxy Server Access to Circumvent a Firewall for Patch Downloading

I’m running Pathway Tools behind a firewall. How do I ensure that we are getting software patches?