BCB420 Journal - bcb420-2022/Inika_Prasad Wiki

2. Bioinfo Prep

Objective: make notes for the Bioinfo Prep Bookdown to refer to later, and thus prep for the upcoming quiz. Sections to work through: Course Journal, Insights, Plagiarism & Academic Integrity, Data Backup, Network Etiquette, Technical Questions, Info Sources

Time estimated: 2 h, 2022-01-23 Time taken:

Tasks Remaining:


1. Course Journal

2. Insights

3. Plagiarism & Academic Integrity

Time estimated: 20 minutes, started on 21:10, 2022-01-23 Time elapsed: 40 min (20 minutes extra to read linked sources), ended on 22:40, 2022-01-23

  • a procedure in the methods section of a journal article, as you would cite it in a technical report;
  • a piece of code you found in a StackOverflow article, as you would put it as a comment into computer code;
  • some contents from a classmate’s journal that you incoporate into your own journal.

4. Data Backup Best Practice

5. Netiquette

Time estimated: 20 min Time taken: 5 min

6. Technical Questions

Time estimated: 20 min Time taken: 45 min

6.1 How To Ask Questions The Smart Way By Eric Steven Raymond Time expected: 15 minutes, 23:18 on Jan 23, 2022 Time taken: 30 minutes, 23:48 on Jan 23, 2022

6.2 How to Create a Minimal Reproducible Example

Time expected: 10 min, 23:10 on Jan 23,2022 Time taken: 5 minutes

6.3 How to ask good questions that prompt useful answers

Time expected: 10 min, 22:56 on Jan 23, 2022 Time taken = 10 min, completed 23:07 on Jan 23, 2022

1. Setup and Installing Docker

Objective: Complete task 1 for BCB420 due 2022/01/14.

Estimated duration: 3 hours Taken: 4 hours


This includes

  1. Start course journal on your repo wiki. Done
  2. Add links to your wiki and repo to the main Student Wiki page (Links to an external site.) Done
  3. download and install docker (Links to an external site.) Done
  4. create a new image and container from the bcb420 Dockerfile Done, just the notebook has been a problem
  5. Document your progress as a new entry in your journal Done


docker run -e PASSWORD=changeit --rm \ -v "$(pwd)":/home/rstudio/projects -p 8787:8787 \ risserlin/bcb420-base-image:winter2022

I just tried restarting Docker and there are far more containers there than originally. Possible that it just takes a little longer than I expected. There are 4 containers running, amongst which this seems to be the right one: intelligent roentgen risserlin/bcb420-base-image:winter2022 Port 8787

Comes with the warning Image may have poor performance, or fail, if run via emulation

Clicking opening in browser gives same error message. Port is correct (8787) and container is running.

Next steps:

Try making a notebook. Perhaps restarting the computer will help with performance.

0. Journal Template



Task 1:

Task 2:

Conclusion & Outlook

Next steps:

Footnotes & References

Material adapted from