Most researchers venturing into the daunting world of genomics research these days find themselves overwhelmed by new terminology, computational skills required for data analysis, and complex study design considerations.
It is not uncommon nowadays for researchers from diverse study areas such as microbiology, biochemistry, nutrition, zoology, pharmacy, and psychology, to apply high level genomics technologies in their research projects. It is also not an unfamiliar phenomenon to see research institutions invest large sums of money into purchasing technology platforms supporting this research without considering and supporting the lifecycle of data - from generation to analysis and ultimately publication.
The North-West University proudly boasts two next generation sequencing platforms (Illumina MiSeq and Ion Torrent PGM) along with several other types of research equipment used in genomics, proteomics, and metabolomics studies. These research platforms generate large volumes of data that often needs to be transferred to where it can be analysed since specialised software and computational power are required. The data also needs to be stored and shared to support publications - in the case of human data as anonymised data sets. For more info about other *omics platforms available at NWU please see the Centre for Human Metabolomics and the Analytical Platforms.
eResearch Supporting Our Researchers
In 2015 the North-West University’s IT department, under the leadership of Boeta Pretorius, embarked on a journey to learn how IT@NWU can better support researchers. The eResearch Initiative (eRIn), a partnership between researchers, IT, the libraries, and the Research Support Office, and supported by the Deputy Vice Chancellor for Research, Innovation and Technology was established based on similar visions by the various partners.
The NWU Genomics Hacky Hour Study Group
During various engagements with researchers working on genomics projects, it was very quickly established that an intervention was needed to provide support not only for postgraduate students applying state-of-the-art technologies, but also for study leaders. The Genomics Hacky Hour (GHH) was born in September 2015. The GHH is modelled on user group meetings where students and researchers meet informally on a regular basis to discuss challenges experienced or creative solutions found in their current stage of research. Skill sharing occurs between various “levels” of researchers and not only in a top-down manner as would happen in a more formal environment.
The GHH started off by meeting biweekly on a Friday from 10:00 - 12:00. Anyone working specifically on next generation sequencing (NGS) projects were welcome to join. A website, based on the Mozilla Science Study Group Handbook template, was created and is available at http://anelda.github.io/GenomicsHackyHour/. A Google Group to facilitate centralised communication between group members was also created and can be joined through a request.
Online and Offline Courses to Expand Our Knowledge
Although the original intention of the study group was to bring researchers together to work on their current projects, it was very soon realised that constructive communication between participants were greatly hampered by their diverse backgrounds and lack of exposure to NGS vocabulary. Therefore the first few sessions took on a more formal flavour where specific topics were discussed and the session was lead by the study group leader. In November 2015 several of the GHH folks participated in a locally ran Software Carpentry workshop. Software Carpentry teaches the basics of reproducible research using various tools, in this case the Shell, git and GitHub, Python, and R.
After discussion amongst the participants it was decided that members of the study group would enroll for the Johns Hopkins/Coursera Genomics Data Science MOOC starting in January 2016. Participation in the MOOC would provide for a more formal opportunity to learn about genomics technologies, data analysis, and tools, and could be complemented by a biweekly informal hacky hour meeting where co-working on projects could occur. Joining the MOOC was an attractive option, as the study group leader wouldn’t have to invest time in the development of lesson material and participants had an opportunity to register for an internationally recognised certificate.
In January 2016 more than 10 study group participants enrolled for the first module of the MOOC - Introduction to Genomic Technologies. The study group has been meeting weekly to ensure participants follow along and have an opportunity to discuss challenges experienced, questions about the material, and other topics related to the study group. The first module had 622 participants from 27 countries according to the course website. Although learners can enrol at no cost for the various modules, a registration fee of US$ 49 can be paid per module (or US$ 392 for the specialisation) in order to receive a Coursera/Johns Hopkins certificate upon completion.
We are grateful for support from Prof Frikkie van Niekerk (our DVC Research Innovation and Technology), Boeta Pretorius (IT Director), the Mozilla Science Lab (specifically Bill Mills who was previously affiliated with them, and Aurelia Moser who invited us to participate in the WOW workshop in Berlin and is providing ongoing support) as well as Maia Lesosky from the Cape R User Group who initially showed us the value of user groups. Finally we want to thank Coursera and the instructors who put together the Genomics Data Science course for making their materials available online.
(written by Anelda van der Walt, Bianca Peterson, Henriette van der Zwan)