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Tuesday
Sep242013

Software Carpentry Bootcamps (Adelaide and Melbourne)

Application Deadline Extended to Sat 31st August 2013

 

Adelaide

Melbourne

Date:

24th-26th September 2013

1st -3rd October 2013

Location:

Room 218 Collaborative Teaching Suite
Ingkarni Wardli (Map ref F12),
North Terrace

Engineering PC Labs  G18 & G19
Building 60 (Map ref C3)
Monash University Clayton Campus

Bootcamp Aims

To improve the productivity of researchers through teaching good programming/software skills/practices.

Target Audience

This bootcamp is not the standard SWC bootcamp which is usually aimed at novices. Instead it is aimed at an intermediary skill level. As such the target audience will be wanting to improve their productivity by enhancing their skills and knowledge of good programming/software practices.

We will accept non-bioinformaticians onto the bootcamp if space permits, so please submit an application by the deadline if you are interested.

Expected Skills/Experience

You will be expected to have working knowledge of a UNIX/Linux operating system and at least one programming/scripting language in which you would consider yourself competent. You should be interested in learning more about the core content covered in the bootcamp, which includes: Python, version control, testing, classes and objects, program design, documentation, shell scripting and Makefiles.

Since funding for running the bootcamps has come via the Australian Bioinformatics Network (ABN), preference will be given to applicants who identify as bioinformaticians.

Application Procedure and Registration Fee

Attendance at the bootcamp is via a selection process and so you must complete and return a short application form indicating which venue you would like to attend. You will then be notified if your application has been successful or not. Applications have now closed.

If your application is successful you will be provided with details on how to pay the registration fee. The bootcamps will be fully catered (lunch + morning and afternoon tea).

Normal Registration: $200       Student/Technician: $100

Until we receive payment, your position on the bootcamp is not finalized. To be fair to those whose applications were declined or are on the waiting list, your seat at the bootcamp is non-transferable.

Program Details

The bootcamp will run over three full days and consist of a series of short informal “lectures” and longer hands-on sessions with opportunities for building networks and collaborations. The bootcamp will cover topics around the theme of “good programming practices”. Many of the concepts covered are exemplified using Python. As such, the first part of day 1 teaches/orientates the trainees in Python programming concepts. The second day teaches concepts of writing tests to demonstrate the behaviour of the code is as designed/expected as well as the use of version control. The final day is about putting your newfound skills into practice!


Day 1

Day 2

Day 3

08:15 – 09:00

Setup



09:00 – 10:30

Python: Basics

Testing

Program Design, shell scripting, Makefiles

10:30 – 11:00

Break

Break

Break

11:00 – 12:30

Python: Data Structures

Testing

Collaborative Group Exercises

12:30 – 13:00

Lunch

Lunch

Lunch

13:00 – 14:00

Python: Control Flow

Version Control

Collaborative Group Exercises

14:00 – 15:00

Python: Functions and Modules

Version Control

Collaborative Group Exercises

15:00 – 15:30

Break

Break

Break

15:30 – 16:30

Classes and Objects

Documentation

Collaborative Group Exercises: Assessment

16:30 – 17:00

Daily Wrap-up

Daily Wrap-up

Daily Wrap-up

19:00 – Late

Instructor Dinner/Drinks



 

Collaborative Group Exercises

These will provide an opportunity to put into practice what you have learned at the bootcamp. The current plan is to run these on the 3rd day of the bootcamp, but we may instead decide to sprinkle them throughout the three days.

Ben Morris - Principle Instructor

Website: http://www.bendmorris.com/

Ben is a Ph.D. student in the Department of Biology at the University of North Carolina. He is a macroecologist who uses informatics, historical biogeography and large heterogeneous datasets to answer questions about global patterns of biodiversity. He also develops open source software to make ecological and biodiversity data more accessible. 

Ben is a qualified Software Carpentry instructor and has taught alongside the likes of Prof. Ethan White.

What to Bring on the Day(s)

  • No need to bring food - morning and afternoon tea/coffee/food will be provided, as too will lunch!

  • No need to bring a laptop, we’ll provide computers and a Virtual Machine (VM) on which you will be working.

Social Media

You are free, actually encouraged, to use any social media streams available to you during the workshop. Please use the following hashtag in your Tweets:

Adelaide bootcamp:    

Melbourne bootcamp:  

Or mention:                 

Also recommended:    

                                   

                                   

Acknowledgements

Financial Support

Australian Bioinformatics Network (ABN), Bioplatforms Australia (BPA), Bioinformatics Interest Group of South Australia (BIG SA), CSIRO Bioinformatics Core

           

Other sponsors