Introduction to Cytoscape and Network Biology for Computer Scientists
The course will introduce the basic concepts of biological network analysis and provide practical instruction on programmatic access and control of Cytoscape to analyze and visualize biological networks. The course will comprise theoretical and practical sessions where course participants will learn about underlying network analysis and visualization algorithms, database designs and APIs, including how to build tools and services within the Cytoscape Ecosystem with mulitple programming languages and for diverse environments.
By the end of this course you will be able to:
- Understand the major applications of network biology
- Import network and table data into Cytosacpe
- Understand network analysis and visualization algorithms
- Navigate the Cytosape Ecosystem
- Programmatically control and access Cytoscape services
- Integrate Cytoscape into your bioinformatics pipelines
- Know where to find Cytoscape repos and developer materials
Expertise in one or more programming languages, web development or software architecture is expected. No prior experience with Cytoscape or Network Biology is required.
Target audience is computer scientistst, software engineers and advanced bioinformaticians.
Bring your laptop. Instructions on installing Cytoscape will be provided prior to the course.
This is an introductory workshop in the Network Analysis and Visualization series. Directed specifically to bioinformaticians, programmers and software engineers, you should already be familiar with software architecture, software development, APIs or pipelines. No additional prerequisites.
Please go through this pre-workshop checklist before the class:
- Install the pre-release version of Cytoscape 3.8, available for:
- That’s it! You’re ready for 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.
- Access the Online Slides. (link)
- Go through the slides at your own pace. Speaker notes are available for non-obvious slides. Press 's' to pop-up the speaker view. Navigate the slides by 'spacebar' or 'down arrow' to go through each module.
- Hands-on exercises are recommended at the end of the presentation (here).
- Contact bioinformatics@gladstone.ucsf.edu with any questions you have and we will reply promptly. For Cytoscape-specific questions, you can access a larger community of help here.