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