Difference between revisions of "CTDPathSim: Cell line-tumor deconvoluted pathway-based similarity in the context of precision medicine in cancer"
| Line 5: | Line 5: | ||
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 | + | -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
