Data Carpentry for Biologists

Course Structure

Custom Information

  • _config.yml: Customize set up information for use as site.variables
  • index.html: Course description and site navigation
  • about/: acknowledgements.md, audience.md, and why-. files

Initialization Materials

Self-Guided

  • START-for-self-guided-students.md: Anyone should be able to start from here

Course / Workshop

  • computer-setup.md: List preparations for prerequisite knowledge & technology
  • syllabus.md: Course details and policy.

Layout and Linkages

     START-for-self-guided-students.md      syllabus.md 
                   \____________________________/
                                  |  
                             schedule.md
                                  |
           _______________________|_____________________
          /                       |                     \
      readings/               lectures/            assignments/
  • schedule.md generates links for a list of assignments: for each of the major course element: reading, lecture, assignments
  • These element: must share a title: that is inserted into the assignments: list and language:
  • element: may share a common file name, language-short-description.md.
  • assignments/ MUST have a lower case file name.
  • readings/ and lectures/ have an UPPER first letter of the file name, for proper inclusion in assignments/.
    readings/            lectures/             assignments/
---                  ---                  ---
layout: page         layout: page         layout: page
element: reading     element: lecture     element: assignment
title: Hello World   title: Hello World   title: Hello World 
language: Foo        language: Foo        language: Foo
---                  ---                  exercises: ['Ba Ram', 'Ewe']
                                          ---

    lectures/     -->     materials/
                     ---
                     layout: page
                     element: notes
                     title: Hello Foos
                     language: Foo
                     ---
  • lectures/ use links to organize materials/.
    • [link text](/semester-biology/materials/file-name)
    • NB: no .MD after file-name
                             assignments/
                    ______________|_____________
                   /              |             \
               readings/      lectures/      exercises/
                                            _____|_____  
                                           /     |     \
                                     solutions/ code/ data/
  • assignments/ organize exercises/ with the exercise: list of exercises/ title:
---
layout: exercise
topic: Practice
title: Ba Ram
language: Foo
---
  • exercises/ file names share similar values to exercises/ YAML in the form: Topic-title-Language.md.
    • From the above YAML: Practice-ba-ram-Foo.md
  • exercises/ file names MUST start with an UPPER first letter.
  • solutions/ file names MUST match the exercises/ file name and can use any extension. For example: Practice-ba-ram-Foo.txt
  • Multiple solutions/ files can be numbered following the exercises/ file name and before the file extension with a -.
    • Practice-ba-ram-Foo-1.txt,
    • Practice-ba-ram-Foo-2.jpg, …
  • code/ and data/ files can be linked to exercises
    • [Code file](/semester-biology/code/code-file.foo)
    • [Data file](/semester-biology/data/data-file.csv)