QIMR Berghofer: Oct 3-4, 2018

QIMR Berghofer

Oct 3-4, 2018

9:00 am - 4:30 pm

Instructors: Conrad Leonard, Scott Wood

Helpers: Xiaping Lin

General Information

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Room 311 ITS training, Education Level 3 Central, 300 Herston Rd Herston QLD. Get directions with OpenStreetMap or Google Maps.

When: Oct 3-4, 2018. Add to your Google Calendar.

Requirements:

Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) They are also required to abide by Software Carpentry's Code of Conduct.
An account on the Institute's HPC environment.
If using the QIMR-Guest or eduroam wireless networks, users must contact ITS to ensure they have working access to the QIMR VPN.
An ssh client to connect to the HPC. On Linux and Mac, this is likely in the base install. Windows users may need to submit a ticket to ITS requesting a copy of PuTTY be installed.
A X-Server on their laptop. For Linux laptops, this will likely already be installed. Windows users may need to submit a ticket to ITS requesting a copy of XMing be installed. Mac users may need to submit a ticket to ITS requesting a copy of XQuartz be installed.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

The room is wheelchair / scooter accessible.
Accessible restrooms are available.

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email conrad.leonard@qimrberghofer.edu.au for more information.

Collaboration: We will be using an interactive etherpad for discussion and examples at http://bionode06.adqimr.ad.lan:9001/p/SWC_2018_Q3

Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

Setup

Day 1

Download the shell-novice-data.zip file and extract it to your /working/[lab_head]/[user] directory on the HPC.

Day 2

Download the gapminder dataset and extract it to your /working/[lab_head]/[user] directory on the HPC.

Schedule

		Pre-workshop setup	Download files required for the lesson
Day 1	09:00	1. Introducing the Shell	What is a command shell and why would I use one?
	09:05	2. Navigating Files and Directories	How can I move around on my computer? How can I see what files and directories I have? How can I specify the location of a file or directory on my computer?
	09:45	3. Working With Files and Directories	How can I create, copy, and delete files and directories? How can I edit files?
	10:15	4. Pipes and Filters	How can I combine existing commands to do new things?
	10:45	5. Morning Coffee	Break
	11:00	6. Loops	How can I perform the same actions on many different files?
	11:30	7. Shell Scripts	How can I save and re-use commands?
	12:00	8. Finding Things	How can I find files? How can I find things in files?
	12:30	Finish
Day 2	09:00	9. Running and Quitting	How can I run Python programs?
	09:15	10. Variables and Assignment	How can I store data in programs?
	09:35	11. Data Types and Type Conversion	What kinds of data do programs store? How can I convert one type to another?
	09:55	12. Built-in Functions and Help	How can I use built-in functions? How can I find out what they do? What kind of errors can occur in programs?
	10:20	13. Morning Coffee	Break
	10:35	14. Libraries	How can I use software that other people have written? How can I find out what that software does?
	10:55	15. Reading Tabular Data into DataFrames	How can I read tabular data?
	11:15	16. Pandas DataFrames	How can I do statistical analysis of tabular data?
	11:45	17. Plotting	How can I plot my data?
	12:15	18. Lunch	Break
	13:00	19. Lists	How can I store multiple values?
	13:20	20. For Loops	How can I make a program do many things?
	13:45	21. Looping Over Data Sets	How can I process many data sets with a single command?
	14:00	22. Writing Functions	How can I create my own functions?
	14:25	23. Variable Scope	How do function calls actually work? How can I determine where errors occurred?
	14:45	24. Afternoon Coffee	Break
	15:00	25. Conditionals	How can programs do different things for different data?
	15:25	26. Programming Style	How can I make my programs more readable? How do most programmers format their code? How can programs check their own operation?
	15:55	27. Wrap-Up	What have we learned? What else is out there and where do I find it?
	16:15	28. Feedback	How did the class go?
	16:30	Finish

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