Entry 3: Plagiarism Module in Bioinfo Prep - bcb420-2025/Izumi_Ando GitHub Wiki

Estimated time for completion: 20 mins
Actual time taken for completion: 40 mins (finding sources for examples took way too long...)

Plagiarism Module Page

Notes

  • "Full Disclosure Policy for this course" means, all non-original ideas have a source and those sources must be referenced.
  • Do not reuse previous material from previous courses.

How to cite

  • Wiki : use text tag to organize citations
  • R code : in a comment
  • Use APA citation format for this course.

When / what to cite

  • Basically, when you learn how to do something that is not common knowledge (ex how to write a loop in X language) you should probably cite it.
  • Code that has no copyright restrictions should also be cited, citations are about authorship, copyright is a legal status.

Task 4

Smart Strategies by UofT
How Not to Plaggiarize
Using Quotations
Paraphrase and Summary
Standard Documentation Formats

a procedure in the methods section of a journal article, as you would cite it in a technical report

We used van Kempen et al.'s approach to represent amino acid residue interactions using the 3Di alphabet [1].

[1] van Kempen, M., Kim, S. S., Tumescheit, C., Mirdita, M., Lee, J., Gilchrist, C. L. M., Söding, J., & Steinegger, M. (2024). Fast and accurate protein structure search with Foldseek. Nature Biotechnology, 42(2), 243–246. https://doi.org/10.1038/s41587-023-01773-0

a piece of code you found in a StackOverflow article, as you would put it as a comment into computer code

# code below was taken from s StackOverflow article by Guibor Camargo Salamanca
# https://stackoverflow.com/collectives/r-language/articles/76047656/create-multiple-pdf-html-reports-using-r-markdown-in-a-loop

# b. Create a ggplot2 graph
p <- iris %>%
  # b1. Filter the dataset by an specific species:
  filter(Species == params$species) %>% 
  
  # b2. Create a plot
  ggplot(aes(Sepal.Length)) +
  geom_density(fill = "cyan4", alpha = .6) +
  theme_minimal() +
  theme(text = element_text(family = "serif"),
        plot.title = element_text(hjust = .5)) +
  labs(title = paste0(params$species, "'s sepal length"))

# b3. Save the plot with ggsave as a ".png" figure
ggsave("plot.png", p, height = 3, width = 4)

# b4. Import it with knitr::include_graphics()
knitr::include_graphics("plot.png")

some contents from a classmate’s journal that you incoporate into your own journal

My classmate Bob had an interesting idea logged in his journal (page linked below) ... I took inspiration from it to do ...
Bob daBuilder's Course Journal Entry (github.com/bcb420-2025/Bob_daBuilder/wiki/cool-idea)

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