Introduction to Pathway Modeling
Note: This workshop is currently not offered by the Bioinformatics core. Instructions for self-guided learning are available in the Online Learning section.
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.
This is an intermediate workshop in the Pathway Analysis series. Prior experience with pathway analysis is optional but recommended:
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Create a WikiPathways account: https://academy.wikipathways.org/stages/wp-account/
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Install PathVisio and setup mapping databases: https://academy.wikipathways.org/stages/walk-install-pv/
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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.
You can access these materials remotely at any time and go through them at your own pace. Here's how:
- Perform the pre-workshop instruction steps above.
- Go through the Presentation until hands-on session 1.
- For hands-on session 1, complete Drawing Challenge 1 and 2 here.
- Continue with the slides until hands-on session 2.
- For hands-on session 2, use PMC or a similar resource to search for pathway figures that you can model in PathVisio.
- Contact bioinformatics@gladstone.ucsf.edu with any questions you have and we will reply promptly.