This Saturday I attended the first workshop run by Open Science Workshops at the Inspire9 collaborative workspace. Open Source Workshops is a new initiative aiming to promote open source tools and techniques to the scientific community.

The workshop consisted of two main parts: an introduction to the basics of Github (creating repositories, commiting, forking, merging…) and the SageMathCloud; and a serious of talks:

  • General discussion of how and why you should take an open approach to scientific research (Alex Ghitza, Pure Maths Lecturer, University of Melbourne).
  • Authorea - An online platform for collaborative manuscript editing designed for digital publishing that can combines Latex, Markdown etc. with interactive visualisations, embedded IPython notebooks and built in citation management (Andrea Bedini, Maths and Stats, University of Melbourne).
  • SciRate - A social media approach to rating and sharing the papers available in at arXiv.org (Jaiden Mispy).
  • SageMathCloud - Collaborative cloud platform set up with particular support for IPython and Latex as well as a terminal. Kind of like Google docs meets a VM.
  • NeCTAR - Cloud facility available to Australian researchers. Also the Genomics Virtual Laboratory set up that allows quick launching of a VM with Galaxy and other bioinformatics tools as well as IPython and RStudio (Clare Sloggett, VLSCI).
  • Software Capentry - Bootcamps for training in scientific computing includiang Git (work tracking), UNIX (automation), Programming (modularisation) and SQL (structured data) (Scott Ritchie).
  • eLIFE - A new open access life sciences journal in the UK that uses a consulative peer review process as well as their eLIFE Lens and oline system for viewing their papers or anything in PubMed via the OA Sandbox (Ian Mulvany).

A common theme running through the talks (apart from open access) was the need to move towards 21st century tools and processes, both for collaboration and publishing.

Overall it was a worthwhile experience and hopefully there will be more in the future, if you are interested in the details the talks and agenda are available here on Github.