Enhance Cytoscape command-line scripting

scootermorris commented 8 years ago

Background

Cytoscape 3 includes the capability to read and execute command scripts, including commands exposed by Apps. Users can also enter commands via a command line dialog that provides very rudimentary help and command input.

Goal

There are two, features that have often been requested that we do not currently support. First, it would be extremely useful to support some kind of variable substitution. This could be as simple as "special" strings (e.g. %SELECTED_NODES% or something) or more elaborate for untyped variables. Second, some simple loop constructs would really be useful. Together these two features would allow users to create very useful extensions to Cytoscape without having to be able to program in Java or Python.

Once these two features are implemented, there are a number of useful changes to the CommandLineDialog that would significantly improve it's usability as a tool to create and debug scripts.

Difficulty level: 2

Prior experience with Cytoscape, network semantics, and scripting language specification is recommended.

Technology and Skills

Java, Cytoscape

Possible Mentors

Scooter Morris

Contact

scooter@cgl.ucsf.edu

gvaibhavraj2 commented 8 years ago

@scootermorris Hi! I am Vaibhav Raj Gupta, third year undergrad from IIT Roorkee,India. I am highly interested in this project.

jooolia commented 8 years ago

Hi,

I've been working with CyREST API using R (and sometimes Python). I know this is quite different from what is proposed here, but would there be any interest in developing a package during GSOC that would facilitate the use of this API in R?

khanspers commented 8 years ago

@jooolia and @gvaibhavraj2 : Please contact the mentor directly at scooter@cgl.ucsf.edu. Messages github may go unnoticed.

jooolia commented 8 years ago

Thanks @khanspers! Will do.

khanspers commented 8 years ago

Chosen as GSoC 2016 project.

nrnb / GoogleSummerOfCode