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# UCSD Spring 2025 Carpentries Workshop https://swcarpentry.github.io/shell-novice/aio.html **Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.** ### Where: Online. ### When: May 6-9, 2025; 8:30 am - 12:30 pm PDT ## **Code of Conduct** Use welcoming and inclusive language Be respectful of different viewpoints and experiences Gracefully accept constructive criticism Focus on what is best for the community Show courtesy and respect towards other community members More details at https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html **Guidelines** Zoom chat can be used to ask questions or provide comments or express difficulties during the lesson. To request assistance, message helper or indicate the red x "no" in the participants chat. Helpers may continue to reply there or via zoom private chat as needed. If necessary, helpers may temporarily move to a zoom breakout room with you to discuss in details using audio/screen sharing. You can return to the main session by leaving the breakout room. You can participate in the polls during the lesson by clicking Zoom Participants Panel and clicking on yes/no. For a single screen, it can be split to have the zoom window and the window where we'll be working, both open side by side. Please rename yourself to add the Operating System (OS) after your name in zoom. e.g. Annajiat (Linux) Having a Great Online Learning Experience: A Guide for Students, https://carpentries.org/blog/2020/04/great-online-learning-student # **Day 1 Unix Shell** ## **Teaching team:** **Name / Affiliation / email** Reid Otsuji/UCSD/rotsuji@ucsd.edu **Helpers:** **Name / Affiliation / email** Renee Hui Xin Ng/UCSD/hxng@ucsd.edu Kira Dunn/UCSD/kcdunn@ucsd.edu --- ## Sign In (Put your OS next to your name in Zoom): ### Name (OS) / Affiliation / email / Favorite animals Reid Otsuji (MacOS/Windows) / UCSD/ rotsuji@ucsd.edu/ cat, fish, dog, snake Abhi Dalal (MacOs) / OUTbio SD / abhi@outbiosandiego.org / dolphin Meredith Rutledge (MacOS) / UCSD / marutledge@ucsd.edu / gelada baboons Lucia Ageitos (windows)/UCSD/lageitoscastineiras@ucsd.edu/quokka Eric Leslie (MacOs) / UCSD / e2leslie@ucsd.edu/ dog Alex Foote (MacOs) / UCSD / agfoote@ucsd.edu / dog Ewa Merz (MacOS) /UCSD/e2merz@ucsd.edu / cat Mallory Evanoff (Windows)/UCSD/mevanoff@ucsd.edu/rabbit Renee (Hui Xin) Ng (Windows) /UCSD/ hxng@ucsd.edu/ dog, red panda Kira Dunn (Windows)/ UCSD / kcdunn@ucsd.edu/ chicken Gabriela Navas (MacOS) / UCSD / mnavaszuloaga@ucsd.edu / Chris Hill (MacOS)/ CSUSB/ christopher.hill@csusb.edu / Shark Sara Dochnal (MacOS)/UCSD/sdochnal@health.ucsd.edu/elephant Sakshi Mohta (Windows) / UCSD / smohta@ucsd.edu / dog, cat, rabbit Leah Bushin (Windows) / UCSD / lbushin@ucsd.edu / cat Marie Duong (Windows) / UCSD / mpduong@health.ucsd.edu / rabbit, cat Tian Lan (Windows)/ UCSD / t5lan@ucsd.edu / dog Alex Babczyk (MacOS)/UCSD/ababczyk@ucsd.edu/ cat Andres Garzon-Oechsle/SIO/agarzonoechsle@ucsd.edu/ chameleon Yvonne Hu (windows)/UCSD/yyhu@ucsd.edu/dog Sanzida Akhter Anee (MacOS) / IUB/ sanzidaanee987@gmail.com/ dog Edward Nguyen (MacOS) / UCSD / edn005@ucsd.edu / dog Sungsik Kim (MacOS) / UCSD / suk073@health.ucsd.edu / dog ### Shared Notes: ## Type shared notes here: www.explainshell.com --- # Challenges ### Challenge 1 ```bash= Challenge 1 Starting from /Users/nelle/data, which of the following commands could Nelle use to navigate to her home directory, which is /Users/nelle? 1. cd . 2. cd / 3. cd /home/nelle 4. cd ../.. 5. cd ~ 6. cd home 7. cd ~/data/.. 8. cd xxxxx 9. cd ``` ### Challenge 2 ```bash= Challenge 2 Suppose that you created a plain-text file in your current directory to contain a list of the statistical tests you will need to do to analyze your data, and named it statstics.txt After creating and saving this file you realize you misspelled the filename! You want to correct the mistake, which of the following commands could you use to do so? 1. cp statstics.txt statistics.txt X 2. mv statstics.txt statistics.txt xxxxxxxxxxxx 3. mv statstics.txt . 4. cp statstics.txt . ``` ### Challenge 3 ```bash= Challenge 3 In our current directory, we want to find the 3 files which have the least number of lines. Which command listed below would work? wc -l * > sort -n > head -n 3 xxx wc -l * | sort -n | head -n 1-3 xx wc -l * | head -n 3 | sort -n x wc -l * | sort -n | head -n 3 x xxxxxxxx cd ``` --- # Day 2 Git Version Control https://swcarpentry.github.io/git-novice/instructor/02-setup.html setup https://swcarpentry.github.io/git-novice/instructor/index.html#setup ## Teaching team: ### Name / Affiliation / email Reid Otsuji/UCSD/rotsuji@ucsd.edu ## Helpers: ### Name / Affiliation / email Renee Hui Xin Ng/UCSD/hxng@ucsd.edu Kira Dunn/UCSD/kcdunn@ucsd.edu --- ### Sign In (Put your OS next to your name in Zoom): ### Name (OS) / Affiliation / email / Favorite drinks Reid Otsuji (MacOS/Windows) / UCSD/ rotsuji@ucsd.edu/ milk tea Kira Dunn (Windows) / UCSD / kcdunn@ucsd.edu / coffee Abhi (MacOS) / UCSD / abhi@outbiosandiego.org / matcha or chai (It is hard to choose!) Edward Nguyen (MacOS) / UCSD / edn005@ucsd.edu / coffee Leah Bushin (Windows) / UCSD / lbushin@ucsd.edu / iced tea Mallory Evanoff (Windows)/UCSD/mevanoff@ucsd.edu/jasmine milk tea with boba :) Chris Hill (MacOS) / CSUSB / christopher.hill@csusb.edu / coffee Meredith Rutledge (MacOS)/UCSD/marutledge@ucsd.edu/coffee Ewa Merz (MacOS) / UCSD / e2merz@ucsd.edu / coffee Alex Foote / UCSD / agfoote@ucsd.edu / coffee Alex Babczyk (MacOS)/ SIO / ababczyk@ucsd.edu / coke zero Andres Garzon-Oechsle (Windows) / SIO/ agarzonoechsle@ucsd.edu/ coffee Dona /Helani(windows) Tian Lan (windows) / UCSD / t5lan@ucsd.edu / coffee Lucia Ageitos (Windows) / UCSD / lageitoscastineiras@ucsd.edu / Spritz Marie Duong (Windows) / UCSD / mpduong@health.ucsd.edu / gin or plain jasmine tea Sungsik Kim (MacOS) / UCSD / suk073@health.ucsd.edu / coffee Gabriela Navas (MacOS) / UCSD / mnavaszuloaga@ucsd.edu / coffee # Day 3 Intro to Python ## Shared Notes: ## Lesson: https://swcarpentry.github.io/python-novice-gapminder/ ## Setup: https://swcarpentry.github.io/python-novice-gapminder/ Some notes about entering a git passphrase - it won't look like you're typing anything in, but its there. ## Teaching team: ### Name / Affiliation / email Celeste Allaband (MacOS/Linux) / UCSD / callaban@health.ucsd.edu ## Helpers: ### Name / Affiliation / email Renee Hui Xin Ng/UCSD/hxng@ucsd.edu Kira Dunn/UCSD/kcdunn@ucsd.edu Reid Otsuji / UCSD / rotsuji@ucsd.edu --- ### Sign In (Put your OS next to your name in Zoom): ### Name (OS) / Affiliation / email / Favorite Movie Reid Otsuji (MacOS/Windows) / UCSD/ rotsuji@ucsd.edu/ Interstellar Kira Dunn (Windows) / UCSD / kcdunn@ucsd.edu / Office Space Alexander Foote (MacOC) / UCSD / agfoote@ucsd.edu Dona Helani (windows) Chris Hill (MacOS) / CSUSB / christopher.hill@csusb.edu / Big Lebowski Patreece Suen (MacOS) / UCSD / psuen@ucsd.edu / Rush Hour Lucia Ageitos (Windows)/ UCSD / lageitoscastineiras@ucsd.edu / Les Choristes Edward Nguyen (MacOS) / UCSD / edn005@ucsd.edu / Star Wars Meredith Rutledge (MacOS) / UCSD / marutledge@ucsd.edu / Prey Mallory Evanoff (WIndows)/UCSD/mevanoff@ucsd.edu/Into the Spiderverse Alex Babczyk (Mac) / SIO / ababczyk@ucsd.edu / James Bond Leah Bushin (Windows) / UCSD / lbushin@ucsd.edu / Matchpoint Abhi Dalal (MacOs) / OUTbio San Diego / abhi@outbiosandiego.org / Mission Joy Sanzida Akhter Anee (MacOS)/ IUB/ 2521469@iub.edu.bd/ Game of thrones Marie Duong (Windows) / UCSD / mpduong@health.ucsd.edu / The Princess Diaries/Shrek 2 Renee Hui Xin Ng/UCSD/hxng@ucsd.edu/ The Lobster Gabriela Navas (MacOS) / UCSD / mnavaszuloaga@ucsd.edu / Straight Up # Day 4 Intro to Python ## Shared Notes: How to load jupyter labs From your terminal >conda env list #checks the current environment your in >conda activate carpentires #changes the environemnt >jupyter labs #launches jupyter labs Pandas resource for manipulating dataframes: Stat annotation resource: https://github.com/trevismd/statannotations?tab=readme-ov-file ## Lesson: https://swcarpentry.github.io/python-novice-gapminder/ ## Setup: https://swcarpentry.github.io/python-novice-gapminder/ Some notes about entering a git passphrase - it won't look like you're typing anything in, but its there. ## Teaching team: ### Name / Affiliation / email Celeste Allaband (MacOS/Linux) / UCSD / callaban@health.ucsd.edu ## Helpers: ### Name / Affiliation / email Reid Otsuji / UCSD / rotsuji@ucsd.edu Kira Dunn/UCSD/kcdunn@ucsd.edu ### Sign In (Put your OS next to your name in Zoom): ### Name (OS) / Affiliation / email / Favorite fruit Chris Hill (MacOS) / CSUSB / christopher.hill@csusb.edu / Strawberries Patreece Suen (MacOS) / UCSD / psuen@ucsd.edu / Cherries Dona Helani(windows) Aram Valafar (Windows) / SDSU / avalafar@sdsu.edu / Peach Mallory Evanoff (Windows)/UCSD/mevanoff@ucsd.edu / watermelon Lucia Ageitos (Windows) / UCSD / lageitoscastineiras@ucsd.edu / watermelon Kira Dunn (Windows) / UCSD / kcdunn@ucsd.edu / watermelon Sanzida Akhter Anee /IUB/2521460@iub.edu.bd/ Peach Marie Duong (Windows) / UCSD / mpduong@health.ucsd.edu / mango