Summary and Schedule

This is a new lesson built with The Carpentries Workbench.

	Setup Instructions	Download files required for the lesson
Duration: 00h 00m	1. Using Markdown	How do you write a lesson using Markdown and sandpaper?
Duration: 00h 12m	2. Computer setting – UNIX, R, and Python Fundamentals	How do you setup your computer for bioinformatic analysis?
Duration: 00h 24m	3. Sequence alignment fundamentals, algorithms and applications (Database Searching & Alignments, Consensus Sequence)	How do you write a lesson using Markdown and sandpaper?
Duration: 00h 36m	4. Structural Bioinformatics (Molecular Docking)	How do you write a lesson using Markdown and sandpaper?
Duration: 00h 48m	5. Biological Network Analysis (Metabolomics)	How do you write a lesson using Markdown and sandpaper?
Duration: 01h 00m	6. Primer Design & in silico Molecular Cloning (Benchling, Plasmid Design)	How do you write a lesson using Markdown and sandpaper?
Duration: 01h 12m	7. Next-Generation Sequencing Analysis (Variant Calling / Metagenomics)	How do you write a lesson using Markdown and sandpaper?
Duration: 01h 24m	Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.

Overview

Questions

• How do you setup your computer for bioinformatic analysis?

Objectives

• Explain how to use markdown with The Carpentries Workbench
• Demonstrate how to include pieces of code, figures, and nested challenge blocks

Introduction

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This is a lesson created via The Carpentries Workbench. It is written in Pandoc-flavored Markdown for static files and R Markdown for dynamic files that can render code into output. Please refer to the Introduction to The Carpentries Workbench for full documentation.

What you need to know is that there are three sections required for a valid Carpentries lesson:

1. questions are displayed at the beginning of the episode to prime the learner for the content.
2. objectives are the learning objectives for an episode displayed with the questions.
3. keypoints are displayed at the end of the episode to reinforce the objectives.

Instructor Note

Inline instructor notes can help inform instructors of timing challenges associated with the lessons. They appear in the “Instructor View”

Challenge 1: Can you do it?

What is the output of this command?

R

paste("This", "new", "lesson", "looks", "good")

Output

OUTPUT

[1] "This new lesson looks good"

Challenge 2: how do you nest solutions within challenge blocks?

Show me the solution

You can add a line with at least three colons and a solution tag.

Figures

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You can use standard markdown for static figures with the following syntax:

![optional caption that appears below the figure](figure url){alt='alt text for accessibility purposes'}

You belong in The Carpentries!

Callout

Callout sections can highlight information.

They are sometimes used to emphasise particularly important points but are also used in some lessons to present “asides”: content that is not central to the narrative of the lesson, e.g. by providing the answer to a commonly-asked question.

Math

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One of our episodes contains \(\LaTeX\) equations when describing how to create dynamic reports with {knitr}, so we now use mathjax to describe this:

$\alpha = \dfrac{1}{(1 - \beta)^2}$ becomes: \(\alpha = \dfrac{1}{(1 - \beta)^2}\)

Cool, right?

Key Points

• Use .md files for episodes when you want static content
• Use .Rmd files for episodes when you need to generate output
• Run sandpaper::check_lesson() to identify any issues with your lesson
• Run sandpaper::build_lesson() to preview your lesson locally