CTDPathSim: Cell line-tumor deconvoluted pathway-based similarity in the context of precision medicine in cancer
Description: Build a web app to make use of R scripts for the CTDPathSim easier to use. The CTDPathSim scripts are used to find correlation between cell lines and the actual tumor.
Project goal: To build a web app that runs CTDPathSim in a user friendly way, so biologists, doctors and anybody needing to utilze the scripts that are not fluent in R programming are able to do so.
Week 1:
-Attended all sessions of Data Science Boot Camp
-Attended good research practices talk
-Attended lab meeting
-Discussed project with advisor and made milestones and goals for the summer
-Learned about biological processes related to my project
Week 2:
-Attended scientific writing seminar
-Emailed citi certificates to Dr. Brylow
-Reviewed R preprocessing functions and technique
-Learned about website building and learned about programming language options
-Downloaded eclipse for PHP and eclipse for Jave EE
-Worked on hello world applications to give introduction to syntax and see which one I think will work best for our project
-Learned about and utilized tomcat servlet for making web apps
Week 3:
-Went to research talk with Dr. Praveen.
-Met with Bithi on Monday and Friday
-Attended lab meeting
-Learned more about web development and how all aspects of the code interact.
-Learned syntax and format for front-end code(html, and java review)
-Learned about folder structure for web code
-Week 4:
-Read Bithi’s paper for CTDPathSim to gain a better understanding of what the original scripts were accomplishing.
-Learned about the biological processes and terminiology that are used with/in CTDPathSim and the corresponding paper through googles searches and such.
-Meet with Bithi on Monday, Tuesday, and Friday
-Attended lab meeting on Thursday
-Atteneded the research talk on Wensday
-Updated the wiki with my Project description
-Looked at R code for CTDPathSim to see how it will interact with the web app/front-end and to gain a better understanding of how the pipeline for CTDPathSim works.
Week 5:
-Met with Bithi on Monday and Tuesday; Monday to disucss we app, and tuesday to change to R package
-Made halfway point presentation, and presented presetnation on wensday.
-Listened to all presenters on Wensday
-Attended lab meeting on Thursday
-Researched contents of packages, and stipulations specific to bioconductor
-Spent time looking at the code and matching it up to the different parts of the paper
-Attended the good presentations talk on Monday
Week 6:
-Met with Bithi on Monday and Friday to discuss package progress
-Met with Karl Stamm, a colleague of Dr. Bozdag’s who recently published a package, to discuss Bioconductor package submission
-Installed developer version of R on my local machine and the developer version of all packages needed to test on the developer version.
-Learned about some different code to be used in vignettes that allow to the package to be self encapsulated
-Had some errors involving package development and worked to solve them, specifically I spent a time trying to fix an warning/error saying that the directory inst/doc needed to be included, however, this was only there because I was trying to fix an error saying qpdf needed to be installed.
-Attended the talk on Monday about data ethics
Week 7:
-Met with Bithi on Monday, and Friday to discuss progress and talk about project
-Met with Reu group on wensday to discuss our projects
-Spent time learning about how to resolve certain errors/warnings/notes related to R CMD check and R CMD BiocCheck
-Met with Jake Petrie to talk about package vignettes/documentation
-Learned about/how to use github and how that relates to package submission process
-Downloaded gitbash to make ssh key and then made ssh key for github
-Worked on package contents like the description, namespace and news files
Week 8:
-Met with Bithi on Monday to talk about the project.
-Attended the talk on Wednseday about grad school.
-Attended lab meeting on Thursday
-Worked out a Github problem where a large file was accidentally added to the repository and I needed to edit the pack file so it would not create a problem for the BiocCheck
-Continued to work on package contents and sort out any errors/warnings/notes that came up during the CMD check and the CMD BiocCheck
Week 9:
-Start work on paper, poster and presentation.
-Attend Reu meeting
-Attend Lab meeting
-Meet with Bithi
Week 10:
-Finish work on paper, poster and presentation.
-Give presentation
-Attend virtual poster session
-Watched other REU members presentations
