Today is the day! The first day of coding for the 2015 Google Summer of code program begins today. I didn’t write an announcement piece in April, but I’m onboard now and will write a new blog post here every week for the duration of the summer. April 27th to May 25th was considered the Community bonding period. I had a whole host of tasks I set for my self and a few from my mentor that I needed to complete in order to bring myself up to speed with the GEO-AWS project. I really wanted to set-up my new laptop with updated packages and the latest version of R, [R version 3.2.0 (Full of Ingredients)] and get a good understanding of the biological background for microarray analysis, gene expression and bioinformatics and I was able to do all of that.
Last Fall when I was beginning to work on the project, it was easy for me to complete my coding tasks without knowing the biological context but that won’t cut it for the summer program. I’m grateful that I took the time during the Community bonding session to learn more and also draw the connection to the aspirational goals behind Bioinformatics, which is personalized therapy and precision medicine. I also made a dent in my first week’s tasks so that free’s up this week to investigate other features that need to be worked on for the coming weeks. I was able to integrate an extra line of JQuery in the callback function of the datatables to allow the application user to select their choices in a “easy” and intuitive manor by just clicking on the row, which fills in the the sidebar panel with that selection (that is actually similar to the GEO2R tool but without the bad UX). For right now the differential expression analysis only needed to be edited and the full data table to be used with the survival analysis will need multi-selection, which I will also clean up this week.
Our intention is to submit this shiny project as a full-fledge package to Bioconductor and host the live application via a RStudio/Shiny option. I’m beyond excited and generally geeking-out about being a student developer for the R Project this summer and hope to learn a lot about open-source software development.
Oh and of course Google sent some fun welcome swag:
if you are interested here is my repository of code: https://github.com/jasdumas/GEO-AWS
R Project for Statistical Computing 2015 wiki: https://github.com/rstats-gsoc/gsoc2015/wiki