Computing resources

Hardware

If you are thinking about buying a new machine, we strongly recommend a macOS or Linux-based system, especially if you’ll be working with climate models. Suggest 16 GB RAM minimum (the more, the better), and as much storage as you’d like. Feel free to ask Kylie or Dave for more info. Note that Apple offer Education discounts for students purchasing a new Mac or iPad.

If you require an external hard-drive for your work, we recommend to buy an SSD (as opposed to a HDD), and look into setting up a RAID configuration. Ask Kylie or Dave for recommendations. External storage options that lab members have bought in the past include:

Useful software

  • R
  • RStudio: The best IDE for R (whilst we almost exclusively use RStudio in our lab, VSCode is another good and free IDE if you use multiple languages)
  • Endnote: You may wish to use EndNote for reference management. Endnote is for researchers and HDR and Honours students and students whose final year course involves a major research project. UniSC researchers get a free licence.
  • GitHub Desktop: A simple Github manager, and our main method of interacting with git/Github.
  • FileZilla: A great SFTP client for MacOS/Windows/Linux for moving files around.
  • Adobe Creative Cloud: HDR students can request an Adobe Creative Cloud licence from IT services for access to Adobe Illustrator, Photoshop etc on their personal machines. Email IT to set that up. SRP and Honours students can access these programs on campus through any UniSC computer, or, through USC Anywhere.
  • Microsoft Office Suite: Again, USC students get a free licence.
  • Panoply: a quick and easy way to visualise netCDFs
  • Zoom: Used for lab meetings and attending UniSC seminars
  • Quarto: Used with R and RStudio for generating beautiful and reproducible documents, websites and books (such as this lab manual!)

Common R packages that we use are listed below. Run the following R code to ensure these are installed on your machine.

 # List of packages 
    list.of.packages <- c("terra", "sf", "tidyverse", "raster", "stars", 
                          "tmap", "maps", "ncdf4")
  # If not installed already, install the package
    new.packages <- list.of.packages[!(list.of.packages %in% 
                                         installed.packages()[,"Package"])]
    if(length(new.packages)) install.packages(new.packages)

If you wish to access the UniSC network on a personal device, use UniSC Anywhere. USC Anywhere is a service offered by the IT department that lets all current USC staff and students access files and (licensed) applications anywhere, anytime and from (almost) any internet-capable device. USC Anywhere is the only way that you can connect to USC networks on a personally owned device.

R Drive

All research projects, whether you require R: Drive storage or not, require you to complete a Research Data Management Plan via the online form: RDM Plan.

Please note: At the beginning of the project you may not know all the details, so fill it out as best as you can. You will get opportunities to update it throughout your project.If you require any assistance, please email research-respository@usc.edu.au

More information can be found via Research Data Management page.

You can access R Drive from home via files.usc.edu.au.

Data confidentiality

We often have projects in our lab that are subject to legally-binding data confidentiality restrictions (e.g., because of fishing logbook data or electronic monitoring footage). We value our collaborations with industry partners and government agencies, and as such, it is of the utmost importance that we all adhere to and respect all signed agreements. This may include, but is not limited to: (i) only saving copies of confidential datasets on a secure, encrypted folder on your R Drive, (ii) restrictions on outreach activities/media opportunities, and (iii) spatially aggregating maps/risk surfaces to a predetermined spatial resolution before sharing at conferences or in publications. If you are unsure of the restrictions surrounding your project (if any), talk to Kylie.

Research integrity training is available in the Research Ethics and Integrity module on Canvas and takes approximately one hour to complete.

Tip

On note-taking - some of us use Notion, others Microsoft OneNote, others Obsidian… the list goes on. Experiment and choose what’s best for your workflow. However, if your note-taking system is cloud based and/or through a third party (i.e., Notion, OneNote), do not include or save any information that could be interpreted as sensitive, or subject to the above confidentiality requirements. And of course, don’t save or publish any confidential data/outputs on Github.

QCIF

UniSC is a member of QCIF, who offer a range of courses, e-research help and access to HPC (high-performance computing) facilities.

Courses

QCIF offers a wide range of short format training in programming, data science, bioinformatics, data management, and other research computing applications. Most of their courses are delivered as live, online workshops via Zoom, with a small number of face to face sessions. Course catalogue here.

Face-to-face e-research help and HPC

UniSC researchers who would like advice about QCIF’s services, accessing HPC resources, or help with anything eResearch-related, may contact Danny Meloncelli, UniSC’s e-research analyst: eResearch@usc.edu.au.

UniSC also run weekly ‘Hacky Hours’ at Sippy Downs. Hacky Hour occurs regularly and its aim is to help researchers (staff and students) with research computing related problems. Hacky Hour is free, informal and all researchers are welcome to drop in for advice, or offer their IT expertise to help others.
Time: Wednesdays, 12-1pm.
Location: In person – The CAVE (H2 G.15), Sunshine Coast campus. Online – https://usc-au.zoom.us/j/89182014305

Printing

  • As part of the Student Services and Amenities Fee (SSAF), all enrolled students are issued a $20 credit on their MyPrint account each year. The $20 SSAF credit is issued at the start of the year and will expire at the end of the year.
  • If you need to print from your own device, you can do so via WebPrint. Then, access any of the printers on campus and follow the prompts. List of printer locations here.
  • UniSC Print Services is a good option if you need to print a conference poster. A0 posters are ~$40, you can use your SSAF funds to pay for it, and are usually ready for collection within 2 business days.