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2023 June UCSD Carpentries Bootcamp - Python, Unix Shell, & Git

Workshop Details
Dates: June 26th - 29th, 2023
Days: Mon-Thurs
Time: 1-4pm
Location: Virtual via Zoom

Workshop Agenda:
https://ucsdlib.github.io/2023-06-26-UCSD/

Workshop Lessons Reviewed
Plotting and Programming in Python - http://swcarpentry.github.io/python-novice-gapminder/
Library Carpentries: The Unix Shell - https://librarycarpentry.org/lc-shell/index.html
Library Carpentries: Introduction to Git - https://librarycarpentry.org/lc-git/
Version Control with Git: Conflicts - https://swcarpentry.github.io/git-novice/09-conflict/index.html

Software Installation:
software downloads

Lesson Data (download)
Gapminder data
Shell lesson data

NOTES:

A copy of the instructor live session notes will be made available to participants upon request at the end of the workshop.

Jupyterlab will be used for the lessons
[m] Markdown cell = notes
[#]also works in code cell for notes
[b] = add cell below [a] is above
[r]Raw cells cannot have text edits

(for Python lessons)
https://www.markdownguide.org/getting-started/
https://www.markdownguide.org/basic-syntax/

Workshop Day 1

First name and Last Name/Organization/Dept./Email

Name (first & last) Organization Dept. Email
(example) Kimberly Thomas UCSD IT kkt008@ucsd.edu
Hoang Nguyen UCSD Chemistry and Biochemistry hon005@ucsd.edu
Cindy Zhong UCSD Biology l3zhong@ucsd.edu
Yipeng Li UCSD Bioeng y9li@ucsd.edu
Jessica Fong UCSD Bioengineering j6fong@ucsd.edu
Alexis Morales Flores UCSD CSE amoralesflores@ucsd.edu
Yevgeniy Yakusevich UCSD MAE yyakusevich@ucsd.edu
Daiwei Wang UCSD Biology daw008@ucsd.edu
Hamed Mojtahed UCSD ECE hmojtahed(at)ucsd.edu
Saurabh Parab UCSD MATS saparab@ucsd.edu
Samantha Kruse UCSD Chem smkruse@ucsd.edu
Celeste Kanne UCSD BMS ckanne@ucsd.edu
Tony Guan UCSD ECE jug054@ucsd.edu
Maya Morris UCSD chem mnmorris@ucsd.edu
Kanuri Roundtree UCSD Chemistry kroundtree@ucsd.edu
Gerald Henderson UCSD RMAS
Eranda Somathilake UCSD MAE esomathilake@ucsd.edu
Emily Zhu UCSD Math e9zhu@ucsd.edu
Melina Basilio Flores UCSD Chemistry mbasilio@ucsd.ed
Lisa Rhodes UCSD HTTC lmrhodes@ucsd.edu
Jose Sandoval Ortega UCSD Math CS jsandovalortega@ucsd.edu
Syeda Ullah UCSD Rady School of Management sullah@ucsd.edu
Daniel Mansour UCSD MAE dmansour@ucsd.edu
Paulina De la Garza UCSD Biological Sciences pdelagarza@ucsd.edu
Isaac Kreitzer UCSD Structural Engineering ikreitzer@ucsd.edu
Heidy Vega UCSD Biochemistry and Chemistry hvega@ucsd.edu
Chang Han UCSD Bioengineering c4han@ucsd.edu
Andrew Keller UCSD MAE akeller@ucsd.edu
Yifan Xiao UCSD Math yix001@ucsd.edu
Chuqing Shi UCSD Math chs139@ucsd.edu
James Findley de Regt UCSD Nanoengineering jfindleyderegt@ucsd.edu
Nurikemu Gulinihali UCSD Electrical Engineering ngulinihali@ucsd.edu
Nuri Chung UCSD BE nuchung@ucsd.edu
Shreesamarth Srivatsa UCSD Bioengineering ssrivatsa@ucsd.edu
Anugrah Jo Joshy UCSD MAE ajoshy@eng.ucsd.edu
Sai Jannamaraju UC San Diego Health HTTC scjannamaraju@health.ucsd.edu
Mingyue Zhang UCSD Structural Engineering miz005@eng.ucsd.edu
Anthony Cai UCSD Chemistry and Biochemistry aycai@ucsd.edu
Christopher Frobenius UCSD Chemistry & Biochemistry cfrobeni@ucsd.edu
Justin Hamlin UCSD Chemistry and Biochemistry jdhamlin@ucsd.edu
Tiffany Chu UCSD Biomedical Sciences t2chu@ucsd.edu
Leesa Anzaldo UCSD Math lbanzaldo@ucsd.edu
Quincy Lyons UCSD BENG qulyons@ucsd.edu
Rana Hegazy UCSD ECE rhegazy@ucsd.edu
Ari Lin UCSD ECE chl177@ucsd.edu
Asuka Zumi Alvarado SBP Snyder Lab aalvarado@sbpdiscovery.org
Tung Vu UCSD ECE tmv001@ucsd.edu
Luciann Valencia UCSD math-cs l2valencia@ucsd.edu
Maya Vasishth UCSD SBP Biomedical Sciences Snyder Lab mvasishth@heakth.UCSD.edu
Kassra Eshragh UCSD MATS keshragh@eng.ucsd.edu
Leila El Masri UCSD chem lelmasri@ucsd.edu
Jeremy Shek UCSD Biomedical Sciences jshek@ucsd.edu
Paul Bastaki UCSD ECE pbastaki@ucsd.edu
Diana Tran UCSD Chemistry dit002@ucsd.edu
Heng Zhu UCSD ECE hez007@ucsd.edu
Runqiu Xu UCSD Math r4xu@ucsd.edu
Yuanshan Wu UCSD Bioengineering yuw100@ucsd.edu
Michelle Truong UCSD Medicine mitruong@health.ucsd.edu
Jenny Nicolas UCSD MATS jnicolas@ucsd.edu
chengchangfeng lu UCSD ECE c9lu@ucsd.edu

Day 1 Lessons Reviewed

*Running and Quitting
*Variables and assignments
*Data Types and Type Conversion
*Built-in Functions and Help

Day 1 Questions:

Please enter any questions not answered during live session here:

End Day 1

Workshop Day 2

First name and Last Name/Organization/Dept./Email

Name (first & last) Organization Dept. Email
Celeste Allaband UCSD Pediatrics callaban@health.ucsd.edu
Eranda Somathilake UCSD MAE esomathilake@ucsd.edu
Gerald Henderson UCSD RMAS gehenderson@health.ucsd.edu
Maya Morris UCSD Chem mnmorris@ucsd.edu
––––––––––- –– ––––––––––––– ––––––––––––
Anugrah Jo Joshy UCSD MAE ajoshy@eng.ucsd.edu
Yipeng Li UCSD Bioeng y9li@ucsd.edu
Heidy Vega UCSD Biochemistry and Chemistry hvega@ucsd.edu
Jessica Fong UCSD Bioengineeering j6fong@ucsd.edu
Nuri Chung UCSD BE nuchung@ucsd.edu
Nurikemu Gulinihali UCSD Electrical Engineering ngulinihali@ucsd.edu
Michelle Truong UCSD Medicine mitruong@health.ucsd.edu
Daniel Mansour UCSD MAE dmansour@ucsd.edu
Tony Guan UCSD ECE jug054@ucsd.edu
Daiwei Wang UCSD Biology daw008@ucsd.edu
Leila EL Masri UCSD CHem lelmasri@ucsd.edu
Leesa Anzaldo UCSD Math lbanzaldo@ucsd.edu
Justin Hamlin UCSD Chemistry jdhamlin@ucsd.edu
Hamed Mojtahed UCSD ECE hmojtahed(at)ucsd.edu
Jenny Nicolas UCSD MATS jnicolas@ucsd.edu
Jeremy Shek UCSD Biomedical Sciences jshek@ucsd.edu
Hoang Nguyen UCSD Chemistry and Biochemistry hon005@ucsd.edu
Andrew Keller UCSD MAE akeller@ucsd.edu
Kanuri Roundtree UCSD Chemistry Kroundtree@ucsd.edu
Runqiu Xu UCSD MATH r4xu@ucsd.edu
Yevgeniy Yakusevich UCSD MAE yyakusevich@ucsd.edu
Chang Han UCSD Bioengineering c4han@ucsd.edu
Anthony Cai UCSD Chemistry and Biochemistry aycai@ucsd.edu
Jose Sandoval Ortega UCSD Math CS jsandovalortega@ucsd.edu
James Findley de Regt UCSD Nanoengineering jfindleyderegt@ucsd.edu
Luciann Valencia UCSD math-cs l2valencia@ucsd.edu
Yifan Xiao UCSD Math yix001@ucsd.edu
Paul Bastaki UCSD ECE pbastaki@ucsd.edu
Quincy Lyons UCSD BENG qulyons@ucsd.edu
Diana Tran UCSD Chemistry dit002@ucsd.edu
Mingyue Zhang UCSD Structural Engineering miz005@eng.ucsd.edu
Ari Lin UCSD ECE chl177@ucsd.edu
Tiffany Chu UCSD Biomedical Sciences t2chu@ucsd.edu
Yuanshan Wu UCSD Bioengineering yuw100@ucsd.edu
Syeda Ullah UCSD Rady School of Management sullah@ucsd.edu
chengchangfeng lu UCSD ECE c9lu@ucsd.edu
Saurabh Parab UCSD MATS saparab@ucsd.edu
Melina Basilio Flores UCSD Chemistry mbasilio@ucsd.edu

Day 2 Lessons Reviewed

Gapminder Dataset Needed
*1. Libraries
*2. Reading Dataframes
*3. Working with Pandas Dataframes
*4. Plotting!

Day 2 Lessons Reviewed

"*Libraries
*Reading Tabular Data into DataFrames
*Pandas DataFrames
*Plotting"

Day 2 Questions:

Please enter any questions not answered during live session here:
1.

End Day 2

Workshop Day 3

First name and Last Name/Organization/Dept./Email

Name (first & last) Organization Dept. Email
Celeste Allaband UCSD Pediatrics callaban@health.ucsd.edu
Gerald Henderson UCSD RMAS gehenderson@health.ucsd.edu
Hamed Mojtahed UCSD ECE hmojtahed(at)ucsd.edu
Jessica Fong UCSD Bioengineering j6fong@ucsd.edu
Daniel Mansour UCSD MAE dmansour@ucsd.edu
Tony Guan UCSD ECE jug054@ucsd.edu
Andrew Keller UCSD MAE akeller@ucsd.edu
Nurikemu Gulinihali UCSD Electrical Engineering ngulinihali@ucsd.edu
James Findley de Regt UCSD NanoEngineering jfindleyderegt@ucsd.edu
Kanuri Roundtree UCSD Chemistry Kroundtree@ucsd.edu
Jose Sandoval UCSD Math CS jsandovalortega@ucsd.edu
Chang Han UCSD Bioengineering c4han@ucsd.edu
Hoang Nguyen UCSD Chemistry and Biochemistry hon005@ucsd.edu
Eranda Somathilake UCSD MAE esomathilake@ucsd.edu
Syeda Ullah UCSD Rady School of Management sullah@ucsd.edu
Heidy Vega UCSD Biochemistry and Chemistry hvega@ucsd.edu
Maya Morris UCSD CHEM mnmorris@ucsd.edu
Mingyue Zhang UCSD SE miz005@eng.ucsd.edu
Yuanshan Wu UCSD Bioengineering yuw100@ucsd.edu
Yifan Xiao UCSD Math yix001@ucsd.edu
Anthony Cai UCSD Chemistry and Biochemistry aycai@ucsd.edu
Jenny Nicolas UCSD MATS jnicolas@ucsd.edu
Justin Hamlin UCSD Chemistry jdhamlin@ucsd.edu
Ari Lin UCSD ECE chl177@ucsd.edu
Anugrah Jo Joshy UCSD MAE ajoshy@eng.ucsd.edu
Tiffany Chu UCSD Biomedical Sciences t2chu@ucsd.edu
Diana Tran UCSD Chemistry dit002@ucsd.edu
Paul Bastaki UCSD ECE pbastaki@ucsd.edu
Daiwei Wang UCSD Biology daw008@ucsd.edu
Saurabh Parab UCSD MATS saparab@ucsd.edu
Leesa Anzaldo UCSD Math lbanzaldo@ucsd.edu
Runqiu Xu UCSD MATH R4XU@UCSD.EDU
Jeremy Shek UCSD Biomedical Sciences jshek@ucsd.edu
Yipeng Li UCSD Bioeng y9li@ucsd.edu
Melina Basilio Flores UCSD Chemistry mbasilio@ucsd.edu
Yevgeniy Yakusevich UCSD MAE yyakusevich@ucsd.edu

Day 3 Lessons Reviewed

*1. Functions
*2. Lists
*3. For Loops

Day 3 Questions:

Please enter any questions not answered during live session here:

End Day 3

Workshop Day 4

First name and Last Name/Organization/Dept./Email

Name (first & last) Organization Dept.
Kanuri Roundtree UCSD Chemistry
Jessica Fong UCSD Bioengineering
Yuanshan Wu UCSD Bioengineering yuw100@ucsd.edu
Hamed Mojtahed UCSD ECE
Chang Han UCSD Bioengineering
Maya Morris UCSD Chem
Justin Hamlin UCSD Chemistry
Nurikemu Gulinihali UCSD Electrical Engineering ngulinihali@ucsd.edu
Michelle Truong UCSD Medicine
Eranda Somathilake UCSD MAE
Jenny Nicolas UCSD MATS
Syeda Ullah UCSD Rady School of Management
Jeremy Shek UCSD Biomedical Sciences jshek@ucsd.edu
Paul Bastaki UCSD ECE pbastaki@ucsd.edu
Yevgeniy Yakusevich UCSD MAE yyakusevich@ucsd.edu
Yifan Xiao UCSD Math yix001@ucsd.edu
Tiffany Chu UCSD Biomedical Sciences t2chu@ucsd.edu
Tony Guan UCSD ECE jug054@ucsd.edu
Daiwei Wang UCSD Biology daw008@ucsd.edu
Anthony Cai UCSD Chemistry and Biochemsitry aycai@ucsd.edu
Andrew Keller UCSD MAE akeller@ucsd.edu
Ari Lin UCSD ECE chl177@ucsd.edu
Mingyue Zhang UCSD SE miz005@eng.ucsd.edu
James FIndley de Regt UCSD Nanoengineering jfindleyderegt@ucsd.edu
Nuri Chung UCSD BE nuchung@ucsd.edu
Diana Tran UCSD Chemistry dit002@ucsd.edu
Saurabh Parab UCSD MATS saparab@ucsd.edu
Daibo Zhang UCSD MAE daz045@eng.ucsd.edu
Yipeng Li UCSD Bioeng y9li@ucsd.edu

Day 4 Lessons Reviewed

*1. What is the Shell?
*2. Navigating the file system
*3. Working with files and directories

*1. What is Git/Github?
*2. Getting started with G****it
*3. Sharing your work
*5. GitHub Pages

Day 4 Questions:

Please enter any questions not answered during live session here:
1.

End Day 4

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