Day 2: Software Carpentry

SCHEDULE

• 8:45 - 9:00 - Coffee and light breakfast
• 9:00 - 10:30 - Workshop by Dr. Istvan Albert, Professor of Bioinformatics
• 10:30 - 11:00 - Coffee break
• 11:00 - 11:45 - Workshop (continued)
• 12:00 - 1:30 - Lunch
• 1:30 - 3:00 - Workshop (continued)
• 3:00 - 3:30 - Coffee break
• 3:30 - 5:00 - Workshop (continued)

MATERIALS

Presentation

• Version Control, Documentation, Automation by Istvan Albert

Lessons on Software Carpentry

• Software Carpentry website
• Version control with git
• Automation with make
• Best Practices in Scientific Research

Other links

• Original Markdown and CommonMark

Off the beaten path

• Bitbucket: a different type of "GitHub"
• Fossil: a different type of source code managment
• Snakemake: a different kind of automation
• Asciidoc and Asciidoctor: a different type of text markup

PRACTICE

Install software

Has git installation and git survival guide:

1. Install Git
2. Lessons on Software Carpentry

Learn Markdown

1. Perform the 15 minute markdown tutorial

Learn Git

1. Perform the 15 minute git tutorial

Leave your Mark(down)

1. Create a GitHub account
2. Fork the bootcamp repository into your own account.
3. Find the markdown document that lists participants: web/2016/share/participants.md.
4. Add your name and affiliation to it.
5. Create a pull request back to master.
6. Watch us suffer merging changes from 30 people.
7. Enjoy the new site (once it is merged).

How good are these "best practices"

Look at Best Practices as published in Best Practices for Scientific Computing" , PLOS Biology, Jan. 2014.

Frankly there just seem to be too many of them... Imagine that you need to simplify this list:

1. Suppose that must reduce to just three. Which one will these be and why?
   Basically: What are the most important best practices?
2. Suppose that want to remove three. Which one will these be an why?
   Basically: What are the least useful best practices?

Add your own and see the results at Best Practices: Keep or Toss

Advanced topics

The following are optional:

1. Install and run fossil
2. Install and run asciidoctor
3. Install and run snakemake

Create a markdown page in the web/2016/share folder that summarizes your expreiences. fossil vs git, asciidoc vs markdown, make vs snakemake