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

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Week 1:  
 
Week 1:  
  
Attended all sessions of Data Science Boot Camp  
+
-Attended all sessions of Data Science Boot Camp  
  
Attended good research practices talk  
+
-Attended good research practices talk  
  
Attended lab meeting  
+
-Attended lab meeting  
  
Discussed project with advisor and made milestones and goals for the summer  
+
-Discussed project with advisor and made milestones and goals for the summer  
  
Learned about biological processes related to my project  
+
-Learned about biological processes related to my project  
  
 
Week 2:  
 
Week 2:  
  
Attended scientific writing seminar  
+
-Attended scientific writing seminar  
  
Emailed citi certificates to Dr. Brylow  
+
-Emailed citi certificates to Dr. Brylow  
  
Reviewed R preprocessing functions and technique  
+
-Reviewed R preprocessing functions and technique  
  
Learned about website building and learned about programming language options  
+
-Learned about website building and learned about programming language options  
  
Downloaded eclipse for PHP and eclipse for Jave EE  
+
-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  
+
-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  
+
-Learned about and utilized tomcat servlet for making web apps  
  
 
Week 3:  
 
Week 3:  
  
Went to research talk with Dr. Praveen.  
+
-Went to research talk with Dr. Praveen.  
  
Met with Bithi on Monday and Friday  
+
-Met with Bithi on Monday and Friday  
  
Attended lab meeting  
+
-Attended lab meeting  
  
Learned more about web development and how all aspects of the code interact.  
+
-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 syntax and format for front-end code(html, and java review)  
  
Learned about folder structure for web code  
+
-Learned about folder structure for web code  
  
Week 4:  
+
-Week 4:  
  
Read Bithi’s paper for CTDPathSim to gain a better understanding of what the original scripts were accomplishing.  
+
-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.  
+
-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  
+
-Meet with Bithi on Monday, Tuesday, and Friday  
  
Attended lab meeting on Thursday  
+
-Attended lab meeting on Thursday  
  
Atteneded the research talk on Wensday  
+
-Atteneded the research talk on Wensday  
  
Updated the wiki with my Project description  
+
-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.  
+
-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:  
 
Week 5:  
  
Met with Bithi on Monday and Tuesday; Monday to disucss we app, and tuesday to change to R package  
+
-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.  
+
-Made halfway point presentation, and presented presetnation on wensday.  
  
Listened to all presenters on Wensday  
+
-Listened to all presenters on Wensday  
  
Attended lab meeting on Thursday  
+
-Attended lab meeting on Thursday  
  
Researched contents of packages, and stipulations specific to bioconductor  
+
-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  
+
-Spent time looking at the code and matching it up to the different parts of the paper  
  
Attended the good presentations talk on Monday  
+
-Attended the good presentations talk on Monday  
  
 
Week 6:  
 
Week 6:  
  
Met with Bithi on Monday and Friday to discuss package progress  
+
-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  
+
-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.  
+
-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  
+
-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.  
+
-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  
+
-Attended the talk on Monday about data ethics  
  
 
Week 7:  
 
Week 7:  
  
Met with Bithi on Monday, and Friday to discuss progress and talk about project  
+
-Met with Bithi on Monday, and Friday to discuss progress and talk about project  
  
Met with Reu group on wensday to discuss our projects  
+
-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  
+
-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  
+
-Met with Jake Petrie to talk about package vignettes/documentation  
  
Learned about/how to use github and how that relates to package submission process  
+
-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  
+
-Downloaded gitbash to make ssh key and then made ssh key for github  
  
Worked on package contents like the description, namespace and news files  
+
-Worked on package contents like the description, namespace and news files  
  
 
Week 8:  
 
Week 8:  
  
Met with Bithi on Monday to talk about the project.  
+
-Met with Bithi on Monday to talk about the project.  
  
Attended the talk on Wednseday about grad school.  
+
-Attended the talk on Wednseday about grad school.  
  
Attended lab meeting on Thursday  
+
-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  
+
-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  
+
-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:
 
Week 9:
Start work on paper, poster and presentation.
 
  
Attend Reu meeting
+
-Start work on paper, poster and presentation.
  
Attend Lab meeting
+
-Attend Reu meeting
  
Meet with Bithi
+
-Attend Lab meeting
 +
 
 +
-Meet with Bithi
  
 
Week 10:
 
Week 10:
  
Finish work on paper, poster and presentation.
+
-Finish work on paper, poster and presentation.
  
Give presentation
+
-Give presentation
  
Attend virtual poster session
+
-Attend virtual poster session
  
Watched other REU members presentations
+
-Watched other REU members presentations

Latest revision as of 20:49, 7 August 2020

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