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Introduction to Pathway Modeling

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Kristina Hanspers edited this page Jul 28, 2020 · 22 revisions

Description

An introduction to Pathway Modeling for Biologists. We will begin with "why" and "how" to use pathways in research and publication figures. Before the hands-on section, we will provide an overview of pathway drawing, covering tools and curation steps, including PathVisio, WikiPathways, Curation Guidelines and the WikiPathways Curation Process. The hands-on portion will get you familiar with pathway drawing tools. You will then build your own pathways model based on a figure. You can use your own pathway of interest in this exercise.

Learning Path

Intermediate   This is an intermediate workshop in the Pathway Analysis series. Prior experience with pathway analysis is optional but recommended:

Materials

Pre-workshop Instructions

  1. Install PathVisio
  • Install the binary version of PathVisio. This will download a zipped folder. Unzip it and move the folder, "pathvisio-3.3.0” to Applications.
  • On Mac: To launch PathVisio, start Terminal and navigate to the "pathvisio-3.3.0” folder under Applications. Type "sh pathvisio.sh” in the Terminal to launch PathVisio.
  • On Windows: double-click the pathvisio.bat file in the "pathvisio-3.3.0" folder. Note: If PathVisio doesn't launch, you may not have Java installed, or may have the wrong version. PathVisio requires Java 8, which is available for download here.
  • Install the WikiPathways plugin for PathVisio by going to “Plugins > Plugin manager” and selecting the “WikiPathways plugin”. If you are having problems installing the plugin, see PathVisio FAQs.
  • Download mapping databases. For this workshop, you will need two databases: the Metabolites database from the Metabolites section and the Homo sapiens from the Gene product/protein database section. In PathVisio, load the two databases under "Data>Select Gene Database" and "Data>Select Metabolite Database" respectively.

For detailed installation instructions see the PathVisio website.

  1. Create an account at WikiPathways
  • Go to WikiPathways and create an account
  • Send an email to kristina DOT hanspers AT gladstone DOT ucsf DOT edu with your WikiPathways account name. This is so that we can update permissions for your account to enable you to upload pathways to WikiPathways.
  1. Optional: Find a pathway to use for the hands-on part of the workshop. This can be any pathway figure from the scientific literature, or a manually created pathway figure relevant to your research, in any graphical format. We will also review strategies for how to find pathway figures during the workshop.

Online Learning

You can access these materials remotely at any time and go through them at your own pace. Here's how:

  1. Perform the pre-workshop instruction steps above.
  2. Go through the Presentation until hands-on session 1.
  3. For hands-on session 1, complete Drawing Challenge 1 and 2 here.
  4. Continue with the slides until hands-on session 2.
  5. For hands-on session 2, use PMC or a similar resource to search for pathway figures that you can model in PathVisio.
  6. Contact bioinformatics@gladstone.ucsf.edu with any questions you have and we will reply promptly.
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