General Course Prep - bcb420-2025/Clare_Gillis GitHub Wiki
Notes about Unit 1 - Bioinfo Prep
(Did not know before going through this unit to predict it will take to complete a task or track the time it took me. Will do so in all other journal entries)
Chapter 2 Wiki - Editing
- Task 1 - Done!
- Note: I will mainly use markdown not wikitext
- See [here](https://bcb420-2025.github.io/General_course_prep/wiki.html#editing-basics) for basic WikiText formatting info
- 3-5 tildes for signature (doesn't work in GitHub)
- Can use HTML tags
- Templates don't work in GitHub
- The namespace stuff is confusing - is that only for general Wiki and not the GitHub MediaWiki? Seems like some stuff has changes since this was written in 2013...
- Task 2 - Done!
- This will be graded - make sure to reference any sources!
- This is meant to be like a lab notebook - record notes here as you work
- Add notes with headers like 1.1, 1.2... so I can reference them later and cluster by section of the project
- State objective
- Estimate duration to do activity, and record how long it actually took (work-hours)
- Document procedure and results (especially of analyses)
- Record conclusions
- Note the next step
- ADD CROSS REFERENCES WHILE WORKING (need to work on that...)
- See here for info on what file formats to use for images
- Write code using GeSHi
- Wiki Template
- Collect concise insights on tasks
- Task 3 - Done!
- Insights Template
- Full disclosure policy (like in BCB410)
- Cite things by adding statements like "inspired by..." "based on..."
- In Wiki use text tag to cite
- In R, cite in comments
- Use APA
- Task 4: Done! Citation exmples
- Task 5 - Ordering drive
- Task 6 - Since I have a Mac, I'll use TimeMachine
- Essentially just use clear, organized communication, and don't be rude (ex. singling people out)
- For further info see here
- Use good form when asking technical questions (as we went over in BCB410)
- Use these resources for specific info: R Help Mailing list posting guide, How to create a Minimal, Complete, and Verifiable example, How to Ask Questions the Smart Way for the technical minded
- Task 7 - Done!
- Task 8 - Done!
- Task 9 - NAR is on their 53rd Database volume and the 2024 Web service issue (22nd release) (Nucleic Acids Research, https://academic.oup.com/nar). Database I chose: SabDab (we love SabDab) structural antibody database by Charlotte Deane's lab at Oxford
- Task 10 - Forums: BioStars, Reddit, R-help, StackOverflow, BioConductorSupport, Cross Validated. I liked this post on BioStars by Nafi asking about inconsistency in residue numbering in PDBs since this is a question I recently had too.