An extraordinary journey in three universities

Last November, I received some very welcome news.  The Deputy Vice-Chancellor for Academics at the University of the Western Cape informed me that I had been named an Extraordinary Professor in the Department of Biotechnology!  My work within that department had been going well, when persistent student protests closed the university through the end of 2016.  This letter reflected the ongoing hope of Biotechnology that our collaboration would continue when the students returned to their studies.  Today I received my official badge, so I would like to write about the work that is developing at each of the three local universities at which I have an appointment.

I have written about my travels among the campuses in and around Cape Town.  I would stress that I spend most of my time at my home institution, the Tygerberg campus for Stellenbosch University.  Bioinformatics has seen considerable investment by the university.  The South African Tuberculosis Bioinformatics Initiative represents the concentration of bioinformatics investigators for our campus: Gerard C. Tromp, Gian van der Spuy, and me.  There are other data scientists, though!  The Centre for Evidence-based Healthcare, led by Taryn Young, offers statistical expertise.  Tonya Esterhuizen specializes in biostatistics.  As I will explain in a moment, I hope to work with them more in the days to come.  This year, my formal teaching duties at my home campus will double.  Don’t worry for me, though, since I will host the Honours students for the Division of Molecular Biology and Human Genetics for only eight days!  I am glad that bioinformatics will have the “standard” module length for our Honours program, equal to Immunology and several other subjects.  I have been supplementing my teaching through an informal “course,” called the “Useful Hour.”  I have begun teaching all comers about a range of subjects, from computers to programming and statistics.  I hope to pull in some philosophy of science soon, as well.  I have been filming these subjects as a bit of an experiment, and it has been handy for those who cannot attend.img_20170126_152122

Hugh Patterton, Gerard Tromp, and I coordinate our efforts near Simonsberg.

The Stellenbosch campus of Stellenbosch University has made strides in bioinformatics, as well.  Hugh Patterton, a professor in the Department of Biochemistry, has been named to lead bioinformatics efforts at this campus.  Naturally, our group (SATBBI) has been talking with Hugh about ways we can reinforce each other’s efforts.  Some of our consultations on the Stellenbosch campus have pointed in the direction of microbiome research, an area that is replete with bioinformatics challenges.  I look forward to seeing what emerges!

I am highlighting the University of the Western Cape in this post, of course!  In describing bioinformatics at the campus, I should start by mentioning the South African National Bioinformatics Institute (SANBI).  Alan Christoffels leads this group of investigators.  They’re an interesting group, with considerable success in capacity development within South Africa and across the continent.  My home on the campus, however, has been with the Department of Biotechnology.  In many respects, this reflects how I have spent my career.  I set the mold in graduate school, when I was a bioinformaticist surrounded by analytical chemists.  I like being close to the people who generate the data I work with!  In the Department of Biotechnology, I work most closely with the group of Ashwil Klein, the lecturer who heads the Proteomics Research and Service Unit.  They have primarily emphasized a gel-based workflow, meaning that they partially isolate proteins on a 2D gel before identifying the spot based on the peptide masses they observe on the Bruker Ultraflex TOF/TOF.  The group is actively moving toward additional instruments, though, and the acquisitions should greatly broaden their capabilities.  I enjoy the intellectual challenges their group produces, since the rules of the road are somewhat less established for agricultural proteomics.

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The new UWC Chemical Sciences and Biological Sciences Buildings rise above the Cape Flats Nature Reserve.

In attending the department’s recent strategic retreat, I was introduced among the researchers of UWC Biotechnology more broadly.  I was particularly glad to meet with Dr. Bronwyn Kirby, who heads the Next Generation Sequencing Facility.  We discussed the Honours course offered for the department (I taught bioinformatics for the proteomics module last year), and I believe I’ll get to add some bioinformatics for the sequencing module in 2017!  I was also delighted to meet the SARChI chair who heads the Institute for Microbial Biotechnology and Metagenomics (IMBM), Marla Trindade.  We spoke about what the students of the institute most needed, and establishing a structured curriculum for biostatistics seemed very high on the list.  I mentioned the biostatistics researchers at Stellenbosch above.  My hope is to be able to use much of the structure Stellenbosch has already built in its Biostatistics I and II classes as a model for teaching biostatistics at UWC Biotechnology.  It would be my first effort at teaching biostatistics formally; I hope that I have absorbed enough to be a good teacher for this subject!

I continue to spend my Tuesdays with the University of Cape Town medical school and to visit the Centre for Proteomics and Genomics, as well.  UCT named me an Honorary Professor in the Department of Integrative Biomedical Sciences halfway through 2016.  My interactions there have principally taken place within the Institute of Infectious Disease and Molecular Medicine (IDM), borrowing from the network of relationships that Jonathan Blackburn has established there.  I have worked with Nelson Soares, his Junior Research Fellow, to create monthly programs for the Cape Town community invested in proteomics.  This Tuesday, we started this series for 2017 with an introduction to the methods we use for identifying and quantifying proteins.  I was really pleased that Brandon Murugan, a senior graduate student in the Blackburn Lab, felt comfortable enough to present this material!

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I enjoyed my sundown cruise with the SATVI team in May of last year!

From the very beginning of my time in South Africa, I have been working with the South African Tuberculosis Vaccine Initiative (SATVI).  Recently they began having their research in progress meetings on Tuesday morning, allowing me to take part.  I really like the interaction.  They take my questions seriously, and I think we all learn from working together.  Certainly I would find great meaning in being part of a successful vaccine trial for this disease!

I have another group I must mention in describing bioinformatics across these three universities.  Nicola Mulder’s “CBIO” team has been an opening wedge in bioinformatics education for South Africa.  Their H3Africa BioNet courses have been used to supplement the content of B.Sc. education in places like the University of Limpopo.  It should be no surprise that many of the people I have mentioned in today’s post have collaborated in a manuscript describing the growth of bioinformatics in South Africa.  Our field is key to the future of public health and to the advances in biotechnology yet to come!

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One thought on “An extraordinary journey in three universities

  1. Pingback: Enjoy 28 landscapes in South Africa on your desktop! | Picking Up The Tabb

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