20th Mar 2019
The African Centre for Gene Technologies (ACGT), the University of Johannesburg and the University of Pretoria organized the 2019 Advanced Metabolomics Workshop that was held at the University of Pretoria from 13-15th March 2019. The workshop provided a capacity building platform to address key issues and challenges in the field of metabolomics.
The workshop was facilitated by this panel of elite metabolomics experts. The facilitators were Dr Reza Salek (International Agency for Research on Cancer, Lyon, France), Dr Karl Burgess (University of Edinburgh, Scotland, UK), Dr Fabien Jourdan (INRA Toulouse, France), Dr Justine Bertrand-Michel (INSERM Toulouse, France), Dr Naomi Rankin (University Hospital Wishaw, Scotland, UK), Dr Jasper Engel (Wageningen University & Research, The Netherlands) and Dr Fidele Tugizmana (University of Johannesburg, RSA).
This workshop covered advanced metabolomics topics using a combination of lectures, interactive round table discussions and computer-based practical sessions. The topics covered in the workshop included applications of metabolomics (clinical, plant/agricultural, industrial), LC-MS/MS/NMR metabolite identification, simple and multivariate statistics, data standards and metabolomics resource, network-oriented metabolomics data mapping, advanced data analysis, lipidomics, metabolomics networks and using fragmentation to enhance metabolite IDs. Throughout the three days, the delegates also had a chance to ask project-specific questions and advice from the with facilitators.
The participants were from the ACGT partner institutions, as well as outside institutions including previously disadvantaged research institutions. There were participants from University of Pret
oria, University of Johannesburg, University of the Witwatersrand, Agricultural Research Council, Council for Scientific and Industrial Research, North-West University, University of South Africa, Tshwane University of Technology, University of the Free State, Walter Sisulu University, University of Cape Town and the University of Venda. Delegates exhibited different scientific backgrounds and had the chance to get to know each other through two-minute elevator-type flash presentations on the first day of each workshop.
The ACGT would also like to wish all the participants of the workshops all the luck with their work and future in metabolomics. Furthermore, the ACGT sends much deserved gratitude to all the members of the organizing committee; Mr Molati Nonyane, Mrs Itseng Malao, Dr John Becker, Dr Fidele Tugizimana, and the European visitors for all of their efforts in making this event a success. The ACGT would also like to extend their gratitude to the sponsors of this event in Thermo Fisher Scientific and the Embassy of France in South Africa.
If you would like to view most of the pictures from this event, please visit our facebook page:
For any metabolomics-related capacity building and networking queries, kindly contact Mr Molati Nonyane, ACGT Liaison Scientist (, 0124206139).
20th Mar 2019
The 2019 Metabolomics symposium was held at the Innovation Hub from 11-12th March 2019. This symposium was aimed at principal investigators, postgraduate and PhD students currently performing or planning to work in the metabolomics field. This event was an opportunity for both local and international metabolomics researchers to share their findings, to network and identify synergies so as to foster further collaboration amongst metabolomics researchers within SA and across Europe. This symposium was mainly a platform to officially launch Metabolomics South Africa (MSA). MSA is a non-profit organization seen as an opportunity to promote and improve the profile of metabolomics research and technology in South Africa, foster networking, training, capacity building, information sharing, mentoring, career opportunities, leadership training and professional development. The symposium was a first official event hosted by MSA with the assistance of its partner, the ACGT.
The first day of the symposium was themed “Metabolomics, where are we?”. Topics discussed throughout the day included the overview of metabolomics in South Africa, good metabolomics data, role of metabolomics in health sciences, lipidomics and plant metabolomics. The discussions on the second day of the symposium were under the theme “Metabolomics, informatics, statistics and applications” and covered topics such as metabolomics networks, statistical models, NMR metabolomics and lipidomic profiling. At the end of each day, attempts were made to finish off with round table discussions to address burning issues or questions on the day’s talks as well as other issues regarding to metabolomics or MSA.
It is worth mentioning several key speakers that participated and contributed to the symposium. The speakers mentioned below are all key contributors to the field of Metabolomics and we are thankful that they shared their work and experiences. These were the presenters at the event in no specific order:
- Dr Reza Salek is currently with the International Agency for Research on Cancer, Lyon, France. Dr Salek has extensive experience in metabolomics research in academia, industry and research institutes with extensive metabolomics knowledge, both analytical and data handling. Dr Salek has worked in clinical trial settings and is interested in setting up workflow infrastructures for metabolomics data handling and analysis using cloud computing.
- Dr Karl Burgess is from the University of Edinburgh, Scotland, UK. Most of Dr Burgess’s workfocuses on the use of mass spectrometry in biomedical research, particularly in the understanding of infectious disease. This multidisciplinary research area builds on his fruitful collaborations with cell biologists, engineers, bioinformaticians, instrumentation developers and clinicians.
- Dr Fabien Jourdan is a research scientist at the French National Research Institute for Agricultural Research (INRA). Dr Jourdan develops computational methods to study human genome-scale metabolic network aimed at retrieving parts of the metabolism affected by genetic or environmental perturbations. These methods are mainly applied to toxicology and human health.
- Dr Naomi Rankin is from the University Hospital Wishaw, Scotland, UK. Dr Rankin’s research interests focus on the use of NMR for metabolite profiling and advanced lipoprotein profiling of serum and plasma samples. She is particularly interested in the use of these methods in epidemiology/clinical trials, especially with a view towards translation of NMR molecular profiling approaches into the clinic.
- Dr Jasper Engel is a researcher at Biometris at Wageningen University & Research. Dr Engel’s primary research interests are in applied statistics. He is interested in the development and careful evaluation of statistical approaches for processing and analysis of complex high-dimensional data sets, and their application in high-dimensional chemical, biological or medical problems. Over the last several years his research has mainly focused on method development for analysis of metabolomics experiments.
- Dr Justine Bertrand-Michel is the co-director of the MetaToul Lipidomic facility at INSERM in Toulouse, France. Dr Bertrand-Michel is a lipidomics expert and she was invited to this symposium because of her work in lipidomics a field that most people in metabolomics have shown a keen interest in.
- Dr Fidele Tugizimana is the chairman of MSA, a research scientist at the University of Johannesburg, a specialist scientist in the international R&D management of the Omnia (Pty) Ltd company (SA) and a scientific consultant in the L.E.A.F. Pharmaceuticals LLC (USA & Rwanda). Dr Tugizimana applies metabolomics approaches in plant-environment interactions (involving abiotic/biotic stresses, beneficial microorganisms, etc.).
- Prof Du Toit Loots is the secretary of MSA and a key member of the national metabolomics platform based at the North-West University in Potchefstroom. Prof Loots has made a substantial contribution to the advancement of metabolomics, by means of developing much of the published methodology and applications in terms of identifying new markers for better disease characterization, diagnostics and treatment since 2002.
- Dr Aurelia A. Williams is the deputy secretary of MSA and a senior lecturer at the biochemistry department of the North-West University. Her research interests include characterizing the impact of molecular traits, metabolism and the immune response on disease pathogenesis. She believes metabolomics will serve as a tool in better characterizing infectious diseases such as HIV/AIDS, HIV-associated comorbidities, virus-host interactions, treatment response mechanisms and pathogenesis-associated phenotypes.
- Dr Zandile C. Mlamla is a committee member of MSA and a post-doctoral research fellow at the Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town (UCT). Her research is currently aimed towards the validation of urinary biomarkers of Tuberculosis Disease. She continues to gain experience and expertise in the cutting-edge field of MS-based lipidomics.
The future of South African metabolomics will be in great hands if the student sessions over the two days are anything to go by. On day one, the student presenters were Mr Efficient Ncube from the University of Johannesburg, Mr Emile Jansen van Rensburg and Ms Monique Combrink both from the North-West University. The student session on day two was by three students from the North-West University in Ms Karin Terburgh, Mrs Zinandre´ Stander and Christiaan van Zyl. The students presented their ongoing work and they received great contributions from the people that attended the symposium in the form of question and suggestions.
Well over 140 delegates from over 25 institutions attended this symposium. They consisted of principal investigators, post-doctorates, researchers, post graduate students and several industry players. The hope is that most of them will register as member of MSA and take an active role in the growth of MSA and metabolomics in general. The ACGT and MSA would like to thank all the delegates who registered to attend this event as well as all the members of the organizing committee; Mr Molati Nonyane, Mrs Itseng Malao, Dr John Becker, Dr Fidele Tugizimana, MSA Committee and the European visitors for all of their efforts in putting together this event. The ACGT and MSA would also like to extend their gratitude to the sponsors of this event in Shimadzu, Thermo Fisher Scientific, Microsep/Waters and the Embassy of France in South Africa. Please look out for more MSA and/or ACGT events similar to this symposium in the future.
If you would like to view more of the pictures from this event, please visit our facebook page:
26th Feb 2019
The Africa Centre for Gene Technologies (ACGT), in conjunction with the University of Zurich, University of Pretoria and the Agricultural Research Council, hosted a successful whole transcriptome sequencing (RNA sequencing or RNASeq) data analysis workshop for researchers from the 1st to the 8th of February 2019. The workshop was held at the Hatfield campus of the University of Pretoria.
RNA sequencing aims to unravel the sum of all transcripts in an organism at any given moment in time and can give important clues to changes occurring in an organism following a variety of environmental cues or life stage transitions. The workshop started with two days of introductory courses in Linux and R. The introductory courses were facilitated by Professor Fourie Joubert from the University of Pretoria and Dr Rian Pierneef from the Agricultural Research Council. These courses offered the delegates basic command line skills needed to manipulate RNA sequencing data.
The two days of introductory courses were followed by a four-day interactive and hands-on RNA Sequencing workshop. The workshop was facilitated by renowned experts and academics from the Institute of Molecular Life Sciences at the University of Zurich in Switzerland: Professor Mark Robinson and Dr Simone Tiberi. Professor Mark Robinson is involved in research that applies statistical methods and data science to experimental data with biological applications within the context of genomics data types. Dr Simone Tiberi is a post-doctoral research fellow who is working on the development of cutting-edge statistical methods in bioinformatics, mostly for bulk and single-cell RNASeq data.
The workshop covered theoretical aspects of RNA sequencing such as new technologies, applications, experimental design, batch effects, dimension reduction, clustering, quality control, limma, normalization quantification and differential expression, among other things. There were also one-on-one sessions with delegates to address their specific queries or to clarify any issues that may have arisen. The delegates hailed mostly from the ACGT partner institutions; University of Pretoria, University of Johannesburg, University of the Witwatersrand and the Agricultural Research Council. The feedback from the delegates was very positive in how the course was designed, organized and conducted. The ACGT is hopeful that the course will be beneficial to all the researchers that came to the workshop and to those that work close with them.
The ACGT and all of its partners would like to extend enormous gratitude to Professor Mark Robinson, Dr Simone Tiberi, Dr Rian Pierneef and Professor Fourie Joubert for sharing their time and expertise with the attendees. The ACGT would also like to thank Professor Fourie Joubert and Mrs Itseng Malao for all of their assistance in organizing this event. The Centre wishes all the participants the best of luck with applying their newly learned skill to their work.
To view some additional pictures from the event please visit our facebook page.
29th Jan 2019
Wageningen University and Research (WUR) is a higher institute of learning based in the Netherlands that specialises in the areas of food and food production, living environment, and health, lifestyle and livelihood. WUR opens its doors to the international community and offers short courses in the areas that the institution specialises in. One such course came to ACGT’s attention as it related closely to what the ACGT as an organization is mandated to achieve and the projects that the ACGT is involved in.
The institution offers a short course (three weeks) called “Facilitating Multi-Stakeholder Partnerships to Foster Sustainable Food Systems”. This course was deemed quite applicable for ACGT staff as the Centre is itself a multiple stakeholder partnership mandated to build capacity in the area of advanced biotechnology for five institutions (three universities and two science councils).
The ACGT found it necessary to send one of its staff members, Mr Thabo Khoza – Liaison Scientist at ACGT, to the Netherlands to attend this three-week course in order to enable ACGT staff to be better multi-stakeholder facilitators. The course ran from the 22nd of October 2018 till the 9th of November 2018.
The course took the participants on a journey of (1) establishing what sort of a multiple stakeholder partnerships (MSPs) are required for different projects and needs, (2) who to involve in such MSPs, (3) how to design the required MSP, and (4) how to facilitate the MSP to yield desired outcomes. While all four mentioned steps are crucial in ending up with an MSP that works, step 4 would require the most effort and resources from the MSP facilitator. This effort is especially highlighted when dealing with different stakeholders who have different interests and varying levels of influence. The course gave the participants a number of tools to use in the facilitation process to make sure that the MSP is a success. Each tool would be chosen based on the stakeholders involved as well as on the type of MSP that has been created.
The course had theory and practical components to it. The participants were divided into groups at the beginning of the course and they were tasked to come up with a problem (project) that would require an intervention of an MSP. Throughout the course, the participants would then have to apply what they were learning in their project. At different levels of formulating their MSPs, the participants would give presentations on how they applied what they have learned during their projects.
The participants were also given a real life problem to design an MSP on. This scenario took the participants to Friesland where they had to design a pathway of creating a cooperative that would address the biodiversity problems that are faced in the Friesland region. The participants had to interview farmers, government officials, business owners, nature reserve experts, activists and civil society. The participants then, based on the interviews and what they had been learning at Wageningen, created a roadmap for establishing this cooperative. This roadmap was presented to the community of Friesland where all the stakeholders were invited. The presentation took about two hours with Mr Khoza being the master of ceremonies, together with a fellow participant from Indonesia. The MSP design suggested by the course participants was well received with the project lead promising to use the suggested roadmap.
The course came to an end with participants giving presentations based on their individual MSP that they want to set up when returning to their home countries. The course facilitators as well as the course participants gave suggestions at the end of each presentation.
The course was also a great platform for networking as it was attended by individuals from 14 different countries representing different sectors and expertise such as government and policy makers, scientists and NGOs. The participants have an active network and are actively looking for opportunities for collaboration.
The ACGT hopes that Mr Khoza will put into practice the knowledge he acquired at Wageningen University and Research especially in creating new initiatives for the ACGT community, such as the Proteomics Society for South Africa.
Story by: ACGT Team, January 2018
21st Jan 2019
RNA Seq aims to unravel the sum of all transcripts in an organism at any given moment in time and can give important clues to changes occurring in an organism following a variety of environmental cues or life stage transitions. The ACGT, in conjunction with the Universities of Zurich, Pretoria and the Agricultural Research Council, will host a whole transcriptome sequencing (RNA sequencing or RNA Seq) data analysis workshop for researchers in Pretoria during the first week of February 2019. In preparation for the workshop, there will also be introductory sessions to Linux and R for those accepted to attend the workshop.
Important dates:· 01 February 2019 (Friday) – Introduction to Linux
· 04 February 2019 (Monday) – Introduction to R
· 05-08 February 2019 (Tuesday to Friday) – RNA Seq WorkshopTopics:
· Theoretical aspects (technologies and applications, experimental design, batch effects, dimension reduction, clustering, QC, limma, normalization)
· Environment setup (Organizing files, running QC on datasets)
· Differential expression
· Advanced topics (Geneset testing, single cell pre-processing, workflow)
· One-on-one sessions with delegates to address their specific queries or to clarify any issues that may have arisen.
The Facilitators:The workshop will include a mix of lectures and hands-on practical sessions facilitated by renowned and expert academics. The facilitators will include:
· Professor Mark Robinson: Professor of Statistical Genomics at the Institute of Molecular Life Sciences at the University of Zurich in Switzerland – Research interests are in the application of statistical methods and data science to experimental data with biological applications within the context of genomics data types.
· Doctor Simone Tiberi: Post-Doctoral Research Fellow, also from the University of Zurich, who works on on the development of cutting-edge statistical methods in bioinformatics, mostly for bulk and single-cell RNA-seq data.
· Professor Fourie Joubert: Bioinformaticist and Director of the Centre for Bioinformatics and Computational Biology at the University of Pretoria.
· Doctor Rian Pierneef: Bioinformatics Research Scientist at the Biotechnology Platform of the Agricultural Research Council.Application Process:
Should you be interested in attending this course, please provide your details and your reasons for attending the course before noon on Wednesday, 23 January 2019.
Please use this link to apply:
Kindly be as descriptive as possible in answering questions as selections will be based on the answers you provided. If you know someone else who stands to benefit from this course, kindly forward this email to the relevant party. Please note that incomplete applications will not be considered. We look forward to receiving your applications.
On behalf of the organising committee
African Center for Gene Technologies
Experimental Farm, South Street
University of Pretoria
Tel: +27 12 420 6139/ +27 71 887 0438
20th Dec 2018
The second Regional Plant Biotechnology Forum for 2018, co-hosted by the ACGT and the University of Johannesburg, centered around plant-pathogen interactions; a particular area of interest for numerous researchers in the partnership and beyond. As is appropriate in the “-omics” and systems biology era, the theme for the forum was “Advances in Plant Defense Responses: Towards Plant-Pathogen System Perspectives”. The topic was deliberately chosen to provide a platform for those who aim to unravel such responses from a wider systems perspective.
The wide variety of presentations, most with a focus on genome-wide approaches to deciphering plant defence systems, managed to attract in excess of 60 delegates from a range of universities, science councils (the majority being from ACGT partner institutions) as well as funders. The keynote speaker for the event was Dr Naadirah Moola, a researcher associated with both the University of Cape Town and the University of Ghent, Belgium. The title of her address was “A cereal killer’s killer: chitosan and plant defence”. Her address was followed by ten additional presentations, mostly from researchers associated with the Universities of Johannesburg and Pretoria. The presentations included studies utilizing technologies including transcriptomics, proteomics, multi-platform metabolomics, as well as combinations of the above. In addition, classical biochemical approaches were also utilised in addressing the research questions at hand.
The forum provided an excellent networking opportunity for researchers active in this field and exposed them to different approaches to elucidating plant-pathogen interactions in different systems.
The ACGT would like to sincerely thank the organizing team at ACGT (Thabo Khoza, Molati Nonyane and Itseng Malao), as well as UJ (Dr Farhahna Allie, Dr Ian Dubery and Dr Fidele Tugizimana).
18th Dec 2018
Two University of Pretoria (UP) academics have received prestigious A1 ratings by the National Research Foundation (NRF) for 2018, bringing the number of UP scientists rated in the A category to 14.
Prof. Don Cowan, Director of the Centre for Microbial Ecology and Genomics, has received an A1 rating, up from his previous A2 rating, while Prof. Mike Wingfield, founding director of UP’s Forestry And Biotechnology Institute (FABI), had his A1 rating renewed.
An NRF rating is a measure of the quality of a researcher, based on peer reviews of their publication performance and impact, including international recognition. A researcher in the A-rated category is recognised by all reviewers as a leading scholar in his/her field internationally for the high quality and wide impact – beyond a narrow field of specialisation – of his/her recent research outputs.
Prof. Cowan established the Centre for Microbial Ecology and Genomics in 2013. The Centre works on various aspects of soil microbial ecology, with a particular focus on hot and cold desert ecosystems. The team uses the latest metagenomic and bioinformatics methods to investigate the structure, function, adaptation and resilience of soil microbial communities, to further understanding of their roles in soil health, plant productivity and the provision of genetic resources. “I am absolutely delighted with the NRF rating result,” Prof. Cowan says. “One of the wonderful elements of academia is that it is possible to be rewarded for working on something about which one is passionate. But this is not a solo effort: I must also gratefully acknowledge and sincerely thank all those who have played their part, whether big or small, in this wonderful result: my research collaborators, my postdocs and students, my friends and my colleagues, and my wife.”
Prof. Wingfield’s research interests are focused on the broad area of forest health, particularly those caused by insect pests and pathogens of trees, and their patterns of global movement. Together with his colleagues and collaborators, the research team applies a wide range of biotechnology tools in order to better understand the biology and epidemiology of tree pests, and reduce the dramatic impact they are having globally. Asked about once again receiving an A1 NRF rating, Prof. Wingfield said, “This award belongs as much to me as it does to the amazing FABI team, including a wonderful group of colleagues, students and collaborators globally. I hope they will enjoy the fruits of the award with me and, more importantly, continue to have fun doing impactful research in the interests of forests and forestry globally.”
Meanwhile, Dr Eshchar Mizrachi, a senior lecturer at FABI, is one of four scientists in South Africa to be awarded a highly prestigious P rating for research on understanding the molecular biology of polysaccharide metabolism, especially cellulose and xylan, during wood formation in Eucalyptus trees. This rating is assigned to researchers normally under 35 years of age who have held a doctorate or equivalent qualification for less than five years at the time of application. His research primarily focuses on constructing a model of the regulatory network (genes, proteins and pathways) that play a role in influencing the partitioning of carbon and the deposition of cellulose and xylan in wood, and identifying candidate pathways or processes for biotechnological improvement of trees (applied via breeding using molecular selection tools, or genetic modification).
Prof. Slippers, Director of FABI, said, “These recent ratings show that we do not only compete locally in terms of excellence, but also with the best in the world. It is exciting to have both established world leaders and upcoming young and leading scientists in FABI. That is good for the future of the institute and University, and shows that we have a vibrant academic environment.”
All three scientists are academically linked to the Department of Biochemistry, Genetics and Microbiology. Head of Department Prof. Paulette Bloomer said, “It is a true privilege to be the academic home of these world-leading scientists, to share their passion for discovering the fundamental basis of biology, and to do research that is locally and internationally relevant.”
In addition to these A and P ratings, so far in the current round of awards and renewals of NRF ratings, UP academics have received a total of no less than 30 new ratings, and 49 renewed ratings, of which 2 are A ratings, 20 are in the B category, with 43 C and 9 Y ratings. The University of Pretoria now hosts 507 rated researchers, representing about 12% of the total number of rated researchers in South Africa.
Prof. Stephanie Burton, UP Vice-Principal for Research and Postgraduate Education, said the University is proud of the achievements of all these academic colleagues. “We are one of the biggest producers of university research in the country and Africa, and we produce research that is relevant and which matters.”
Story by: Buyisiwe Nkonyane, University of Pretoria
28th Nov 2018
The African Centre for Gene Technologies (ACGT) reached out to numerous metagenomics researchers throughout the country and determined that most of their capacity-building needs were data orientated. A large number of metagenomics stakeholders generate huge amounts of data from samples derived from diverse environments. The stakeholders felt they were not getting maximum value out of vast amount of metagenomics data they have gathered due to limitations in skills to effectively analyse and interpret the data. The ACGT decided to assist in addressing this issue by organizing multiple training initiatives starting with a metagenomics data visualization & data interpretation workshop.
The metagenomics data visualization & data interpretation workshop ran from 12-14th November 2018 at the University of Pretoria and was facilitated by a local expert, Dr Rian Pierneef. Dr Pierneef is a bioinformatics research scientist at the Biotechnology Platform of the Agricultural Research Council. Dr Pierneef specializes in biological data analysis and has conducted numerous research studies on prokaryotes in the agricultural environment. The three-day workshop focused on using R for metagenomics data visualization. R is a programming language and free software environment for statistical computing and graphics. The R language is widely used among statisticians and data miners for developing statistical software and data analysis. The workshop started with introducing R to the workshop attendees and then proceeded to direct the attendees through the use of R packages for metagenomics analysis and data visualization.
The delegates were from different research backgrounds and hailed mostly from the ACGT partner institutions; University of Pretoria, Agricultural Research Council and Council for Scientific and Industrial Research. The lectures were kept as relaxed as possible with open discussions and computer-based practical sessions. Through the interactive sessions, the attendees were able to obtain advice and assistance that was specific to their individual projects. There was a general sense from the course evaluations that the course was relevant, practical and beneficial. The ACGT and all of its partners would like to extend enormous gratitude to Dr Rian Pierneef for sharing his time and expertise with the attendees. The ACGT would also like to thank Professor Fourie Joubert and Mrs Itseng Malao for all of their assistance in organizing this event. The ACGT wishes all the participants the best of luck with applying their new earned skill to their work. Due to limited space, not all of the applicants could be hosted but the ACGT encourages those that were not placed this year to keep an eye out for future courses.
For any other capacity building and networking queries, kindly contact Mr Molati Nonyane, ACGT Liaison Scientist (, 012 420 6139).
Here is a link to some of the images taken during the event:
9th Oct 2018
Capacity building is one of the objectives of the African Centre for Gene Technologies (ACGT) as a means to improve the skills level of South African scientists, especially in the field of bioinformatics data analysis. For African scientists to continue to produce quality work that is internationally recognized and competitive, there has to be continuous efforts to equip the scientists with the most relevant and applicable skills available. Advancements in sequencing platforms and the amount of data generated require specialized skills and programs that generally require some knowledge of command-line. Linux is one such useful alternative operating system for data analysis and visualization. For this reason, the ACGT organized a Linux course to benefit life scientists and introduce them to basic Linux concepts. The Linux course ran from the 25th to 28th September 2018 at the University of Pretoria, Hatfield campus at the Centre for Bioinformatics and Computational Biology (CBCB).
The course was facilitated by Mr Shaheem Sadien from the Cisco Networking Academy from Cape Town. Mr Sadien is a renowned lecturer and skilled technician with a wealth of over 12 years of experience and knowledge on networking, operating systems and applications. The lectures were kept as relaxed as possible with open discussions and computer-based practical sessions. The topics outlined below were covered during the course:
- The shell,
- the file system,
- files and directories,
- finding files,
- basic system commands,
- redirection with command and file pipes,
- basic grep, sed and awk,
- environment variables, and
- basic shell scripts.
The sessions were kept as interactive as possible to create a relaxed environment where the participants could ask questions and get the most out of the four days. The 25 delegates were from different research backgrounds and hailed mostly from the ACGT partner institutions; the Universities of Pretoria and the Witwatersrand, the Agricultural Research Council and Council for Scientific and Industrial Research.
Following conclusion of the workshop, there has been very positive feedback from the participants of the course. There was a general sense from the course evaluations that the course was informative, practical and interesting. Moving forward, there are plans to adjust some aspects of the course such as content and more bioinformatics-specific approaches. Keep an eye on the ACGT website and e-mail alerts for news of future iterations of the Linux workshop.
The ACGT and all of its partners would like to extend enormous gratitude to Mr Shaheem Sadien and Professor Fourie Joubert for running the course smoothly and successfully. The ACGT would also like to thank all the behind-the-scenes people that had a hand in putting this course together: Itseng Malao, Johann Swart and Vaughan Beckerling. The ACGT wishes all the participants good luck with their future work. Due to limited space, not all of the applicant could be hosted but the ACGT encourages those that were not placed this year to keep an eye out for future courses.
For any other capacity building and networking queries, kindly contact Mr Molati Nonyane, ACGT Liaison Scientist (, 012 420 6139).
13th Sep 2018
The proteomics community of South African came together for a week of proteomics events in the month of August 2018. In this week, two events organised by the ACGT, CSIR, DILPOMICS and the Universities of Cape Town and the Witwatersrand took place. The Advanced Proteomics Workshop was facilitated between the 20th and 22nd of August 2018; which was followed by the South African Proteomics Symposium a day later. Both these events were hosted at the Wits Parktown Health Sciences Campus.
The proteomics week kicked off with the Advanced Proteomics Workshop, which was facilitated by three world experts in the field. Each facilitator gave a series of lectures and hands-on exercises in the field which were highly respected for. In the three days dedicated to the workshop, the delegates were taught different aspect of Spatial Proteomics, Clinical Proteomics and Quality Control. The workshop began with Prof Kathryn Lilley (Research Group Head and Director, Cambridge Centre for Proteomics, University of Cambridge) taking the delegates through a series of lectures on Quantitative Proteomics and Spatial Proteomics. Included in Prof Lilley’s sessions were tutorials on Experimental Design, which enabled the delegates work on different scenarios to design effective experiments. These tutorials allowed the delegates to think outside the box and helped them think through their own experiments and how they would design them in the future.
Prof Stephen Pennington, a professor of Proteomics and Senior Fellow at the Conway Institute of Biomolecular and Biomedical Research at the University of College Dublin, took over from Prof Lilley and facilitated the Clinical Proteomics section of the workshop.
The last section of the workshop, Quality Control, was presented by Prof David Tabb. David Tabb is a Professor in the Division of Molecular Biology and Human Genetics at the Faculty of Medicine and Health Science at Stellenbosch University. Prof Tabb combined his lectures with tutorials and assisted the delegates to work with real proteomics data.
The workshop was attended by delegates from the following national institutions:
African Health Research Institute
Cape Peninsula University of Technology
Centre for Proteomic and Genomic Research
Council for Scientific and Industrial Research
Fort Hare University
The National Health Laboratory Services
The National Institute for Communicable Diseases
University of Cape Town
University of Johannesburg
University of Pretoria
University of the Western Cape
University of the Witwatersrand
The second part of the proteomics week saw seventy-two delegates gather at the Adler Museum of Medicine (Wits Parktown Health Sciences Campus) to attend the South African Proteomics Symposium.
The symposium was opened by Dr John Becker (ACGT – Centre manager) and Prof Michele Ramsay (Champion: Molecular Biosciences Research Thrust, University of the Witwatersrand). Prof Kathryn Lilley and Prof Stephen Pennington each gave a keynote address followed by presentations from top proteomics researchers in South Africa. These South African researchers represented the following institutions: African Health Research Institute, CSIR, CPGR, Fort Hare University, North West University, Stellenbosch University, University of Cape Town, University of the Western Cape as well as the University of the Witwatersrand. The following event sponsors also gave talks at the symposium: Microsep, Anatech Instruments and Separations. Click here to view the symposium booklet that contains the full programme as well poster abstracts for posters that were displayed at the symposium.
Both the workshop and symposium gave the delegates the platform to interact with world class proteomics researchers and to explore opportunities (postdoctoral fellowships, collaborative opportunities, etc.) that may arise from the proteomics week. This week also provided the delegates with a platform to network with each other for possible future collaborative opportunities- as well as to informally have discussions around the formation of a Proteomics Society of South Africa. The ACGT has made itself available to assist in the establishment of this society. This process will be guided by the proteomics community of South Africa that the society will serve.
The ACGT would like to thank the following sponsors for financial assistance to make the workshop and symposium possible: Anatech, CPGR, DIPLOMICS, inqaba biotec, Microsep, Separations and The Scientific Group.
Story by: The ACGT team, September 2018
For more photos from these events, please visit our Facebook page: ACGT Facebook page