CTDPathSim: Cell line-tumor deconvoluted pathway-based similarity in the context of precision medicine in cancer

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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