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General Information

Researchers spend much of their time wrestling with software, but most are self-taught programmers. As a result, they spend hours doing things that should take minutes, reinvent a lot of wheels, and still don't know if their results are reliable. To tackle this problem, an international volunteer organisation known as Software Carpentry has been running workshops for a number of years now, teaching basic lab skills for computing like 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.

With support from the ITS Research Services department at The University of Melbourne, the Research Bazaar project has been running and supporting Software Carpentry bootcamps around Australia since 2013. For this particular workshop we are teaming up with COMBINE, the national student group for students and early career researchers in bioinformatics and computational biology, although there are places available for researchers who aren't members of COMBINE.

Who: This workshop is open to postgraduate students, post-docs and other researchers who have a basic familiarity with programming concepts like variables and tabular data, but want to learn how to use R, and learn the basic practices in scientific computing to help them work more productively. While the workshop is being hosted at the University of Melbourne in conjunction with COMBINE, people from other research institutions and disciplines are welcome.

Where: Theatre 2, Alan Gilbert Building, University of Melbourne.

Requirements: Participants are asked to bring their laptop. They will be given access to the Data Intensive Tools for the Cloud (DIT4C) environment on the NeCTAR Research Cloud, so it's critical that this laptop is able to connect to either the UniWireless or Eduroam wifi networks (see wifi and DIT4C login instructions below). The DIT4C environment has all the required software installed, however there are software installation instructions below for participants who would like to install the software on their own laptop. Also note that participants are required to abide by Software Carpentry's Code of Conduct.

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

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Schedule

Etherpad: https://etherpad.mozilla.org/2014-12-08-combine-r.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.

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Syllabus

Setup

Wifi

Prior to the workshop, University of Melbourne staff/students should ensure that their laptop can connect to UniWireless. 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.

Since the bootcamp will be conducted on the NeCTAR Research Cloud, participants are not required to install any software prior to the bootcamp. For those people who'd like to install the software used in the bootcamp on their own machine for use after the bootcamp, we've included the relevant installation instructions below (and we're happy to provide assistance with this during the bootcamp).

Create a DIT4C Account

During the week prior to the workshop, one of the instructors will email 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 and follow these instructions:

1. Click the "login" button and proceed to login using your GitHub credentials (a GitHub account is required during the Git lessons, so go ahead and get yourself a free GitHub account if you don't have one already).
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 emailed to 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 an "RStudio" image from the drop down menu 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.

Optional Software Installation

At the end of the bootcamp you may wish to install the software covered on your laptop or on your lab machine later. We've included an overview of the software as well as installation instructions below.

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