General Information

Software Carpentry's mission is to help scientists and engineers get more research done in less time and with less pain by teaching them basic lab skills for scientific computing. 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.

Where: Alan Gilbert Theatre 3. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a wifi-capable laptop, from which they will logon to the Data Intensive Tools for the Cloud (DIT4C) environment on the NeCTAR Research Cloud. This environment has all the required software pre-installed, so there's nothing participants need to bring or do in preparation for the workshop. Having said that, there are software installation instructions below for participants who'd like to install the software on their own computer before or after the workshop. Also note that participants are required to abide by Software Carpentry's Code of Conduct.

Wifi: University of Melbourne staff/students can connect to the UniWireless network; instructions on how to do this and where to get assistance can be found here. Attendees from other Australian universities should find out (from the IT website of their home institution) how to connect to the Eduroam wireless network.

Contact: Please mail scottr@student.unimelb.edu.au for more information.

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Schedule

Etherpad: https://etherpad.mozilla.org/2015-06-29-qaeco-unimelb.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.

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Syllabus

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Workshop Setup

Create a GitHub account

GitHub is an online hosting service for all your code. We'll be using it in the lesson on version control, and GitHub credentials are used for login authentication on DIT4C. GitHub accounts are free, so sign up for one if you don't already have an account.

Login to DIT4C

During the first session of the workshop, the instructors will give you the compute node name and access code you'll need for the Data Intensive Tools for the Cloud (DIT4C) environment that is hosted on the NeCTAR Research Cloud. Once you've got that name and code, navigate to the DIT4C homepage (it works best in the Chrome browser) and follow these instructions:

1. Click the "login" button and proceed to login using your GitHub credentials.
2. Go to the "compute nodes" tab and click "claim compute node access".
3. From the drop down menu, select the name of the compute node that the instructor gave you and enter the corresponding access code.
4. Go to the "containers" tab and add a new container named after yourself (e.g. johnsmith). The reason for this is that container names are unique (i.e. you can't have the same container name as anyone else in the room). Select the "RStudio" image from the drop down menu, set the initial state to on and then hit the create button.
5. When the container is "on", its name should turn blue and you can click on it to launch your environment in a new tab of your browser.
6. Once you're finished for the day, simply close all the extra tabs that have opened up and turn your container "off". When you come back tomorrow, simply switch back to the 'on' position to continue using that container.

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Post-workshop software installation instructions

The DIT4C environment comes with all the required software pre-installed, however if you would like to install the software on your own computer (either before or after the workshop), here are the instructions to do so.

A list of common issues that occur during installation and their fixes can be found here. Ignore the sections on Python and SQL. Configuration Problems and Solutions wiki page.