Foundational Open Science Skills (FOSS) Lesson 4: How to Talk to Computers

Table of Contents

• Foundational Open Science Skills (FOSS) Lesson 4: How to Talk to Computers
  • Table of Contents
  • Agenda Image Not Showing Possible Reasons The image file may be corruptedThe server hosting the image is unavailableThe image path is incorrectThe image format is not supported Learn More →
  • Open Questions Set 1
  • Open Questions Set 2

Agenda

Image Not Showing Possible Reasons

• The image file may be corrupted
• The server hosting the image is unavailable
• The image path is incorrect
• The image format is not supported

Learn More →

• Welcome and week 3 review (10 minutes)
• The Unix Shell (5 minutes)
  • Introductory Shell Commands (30 minutes)
• Break?
• LLM Chatbots for Open Science (15 minutes)
  • Prompt Writing (30 minutes)

Open Questions Set 1

1
2
10
8
8
1
1
4
4
5, Google is my bestie
1
2 (I am happy to open it up and copy and paste whatever Stack Exchange tells me to, on the rare occasion needed for my work)
3
8

grep ">"
Ctrl + R
rm -r * (real answer awk)
pwd
in R, glimpse, constantly
cd
cd
vim
tmux

In more detail, here's a little more information on the terminology used

    hostname/machine           command        input file      argument/value----------------┐  
            ↓                     ↓                ↓            ↓          ↓                ↓
jovyan@aaf56ff92:~/data-store$ blastn -query <input.fasta> -db nt -out output.txt -evalue 1e-5
  ↑                    ↑                ↑                   ↑       ↑               ↑
user           current location     flag/option            flags/options------------┘

\---------------------------/  \--------------------------------------------------------------/
        shell prompt                                command

Open Questions Set 2

Text editor - redline for mistakes/revisions
Finding sources of obscure things that I vaguely remember
Turning funny texts into memes
Quickly drafting emails
Preliminary code writing
general questions as a starting point for problem solving
I use chaGPT to help with my data analysis, both for qualitative and quantitative data, and to improve my writing
Diagnosing problems with my truck
Getting plain-language, entry-level summaries of fields with which I'm unfamiliar
Improve and correct my grammar
Writing code and improving writing
Ancillary tasks (text edition, pretty basic code generation).

Nah++
No, but I'd like to know when to use different ones!
JetBrains AI Assistant to help with C++ code
Yes, besides chatGPT, I also use Claude AI, Perplexity AI and Gemini