Cytoscape Automation: APIs and Scripting

[AlexanderPico]

Background

Cytoscape is a desktop application with a user friendly interface, but it also can be controlled programmatically through a few different means. The control or automation of Cytoscape by scripts and other programs is an essential capability and is gaining rapidly in terms of adoption. How documentation for automation could use some work, including high-level desciptions of what it is and how to interface with it, as well as detailed and consistent descriptions of functions and parameters. One of the key challenges is that there are many ways to do the same thing, given the incremental implemenation over time. This is source of confusion for developers and users.

Goals

• A high-level description of what automation is, when to use it and how to use it; in particular, where to start.
• Updated content descriptions and terminology used across all API docs
• A process for adding new features to maintain consistency

Technical Skills

• Experience with API documentation (must have)
• GitHub wiki markdown syntax (nice to have)
• Experience with web service and scripting documentation (nice to have)

Links

• Current Automation Site: http://automation.cytoscape.org
• Curated articles on Cytoscape apps with automation: https://f1000research.com/gateways/cytoscapeapps/automation
• Current depiction of automation: https://github.com/cytoscape/cytoscape-automation/blob/master/for-scripters/README.md

Potential Mentors

Alex Pico

Contact

Alex Pico

[vivekrj0]

Hey @AlexanderPico ,
I am Vivek Raj, a 3rd-year undergraduate student from IIT Kharagpur India. Recently I have set the environment of Cytoscape on my PC. I found this project seeks my attention and also would like to contribute during GSoD '19. I am having an experience of Java, Python, RESTful API and a little bit of Swagger documentation. I am enthusiastic to contribute to NRNB upon this project for my upcoming semester.
Thanks.

[AlexanderPico]

Great. Looking forward to seeing you application. Be sure to include samples of technical writing. Thanks!

[vivekrj0]

Thanks for the response @AlexanderPico
I wanna know what are the specific assessment criteria or the issues/microtasks related to project should I start with?