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Timeline

Eight vignettes are planned and include, but are not limited to:

  1. social networks and interactions,
  2. species co-occurrence networks,
  3. metabolic interactions,
  4. protein-protein interactions,
  5. customer interaction and analysis,
  6. functional association networks,
  7. cell signaling networks, and
  8. gene regulatory networks

Deliverables and Timeline:

Community Bonding Period

I would use this time to:

  • get to know the mentors
  • understand the direction of Cytoscape and cyREST development
  • familiarise myself with the code base for RCy3
  • investigate the availability of APIs accessible by REST in Cytoscape plugins
  • investigate what RCy3 plugins and vignettes would be most useful for Cytoscape users with the help of Paul Shannon and Tanja Muetze
  • work through Advanced R - http://adv-r.had.co.nz/ (19 sections) -R package development - http://r-pkgs.had.co.nz/ (15 sections)
  • write an introductory blog post

May 23rd - June 7th

organization of the project:

  • decide on scope and detail of the vignettes
  • investigate and decide on the best approach for querying plugin APIs
  • find datasets for use with different vignettes

June 8th - June 21th

MILESTONE 2: First blog post

  • Develop first vignette on microbial co-occurrence networks
  • Write a blog post highlighting this vignettes.
  • Build function to query plugin APIs via REST in R

June 22nd - July 5th

  • Incorporate feedback from blog post into vignette
  • Complete vignettes two on enrichment map
  • Vignette three on X.
  • Test querying function on various plugins to find a general solution

July 6th - July 19th

MILESTONE 3: R function for querying Cytoscape plugins and Second blog post

  • Write documentation on using R function(s) to programmatically use Cytoscape plugins
  • Write tests for the above function(s)
  • Write a blog post highlighting a vignette.
  • Complete vignettes four and five
  • Create and present poster highlighting use of RCy3 for scientists at the EMBO Viruses of Microbes meeting.

July 20th - August 2nd

  • Incorporate R function for using plugins into RCy3
  • Incorporate feedback from blog post into vignette
  • Complete vignettes six and seven highlighting the use of plugins via R

August 3rd - August 15th

MILESTONE 4: Third Blog post

  • Write a blog post highlighting a vignette.
  • Complete vignette eight
  • Incorporate vignettes into RCy3 package
  • Submit pull requests for RCy3 code improvements

August 15th - August 23rd

  • post updated package to Bioconductor and CRAN
  • write final blog post
  • promote project within the Cytoscape and R communities.
  • plan with developers/mentors on how to keep vignettes up to date