8th Mar 2021
In February 2021, the African Centre for Gene Technologies (ACGT) and INSERM Toulouse (France) organized a virtual Lipidomics workshop. Lipidomics is a newly emerged discipline that studies cellular lipids on a large scale, based on analytical chemistry principles and technological tools, particularly mass spectrometry.
Following from rapid advances in genomics, transcriptomics and proteomics, Lipidomics similarly seeks to elucidate the role of fats and lipids, especially in the context of a range of human diseases, at a high coverage and throughput rate. Due to the range of fatty acid length, conjugation and saturation status, it has been challenging to study all lipids in a single experiment. The event outlined different approaches to analysing different classes of lipids in targeted and untargeted approaches.
The workshop consisted of online lectures, a seminar and interactive discussions. The event was intended to ignite a deeper interest in Lipidomics and add more interesting research avenues to those who are already working on Lipidomics and related disciplines. The workshop covered topics that included: Introduction to Lipidomics, how Lipidomics converges with and complements other “-omics” technologies, analytical flow in global and targeted quantitative Lipidomics, as well as applications of Lipidomics. The latter had a specific focus on inflammation; as highlighted in a research case study, with high development potential, in treating inflammation.
The seminar highlighted that lipids play many essential roles in cellular functions, including cellular barriers, membrane matrices, signalling, and energy depots. As a result, the ACGT is reassured that Lipidomics is a fast-growing field not only in the world, but also in South Africa. The participants of the workshop were from various research institutions spread across South Africa and also included a few delegates from the rest of Africa. Potential international and local collaborative efforts were also evaluated. Plans are being put into place to have similar workshops in future and complementary Lipidomics-related capacity building efforts.
The ACGT would like to thank the INSERM Toulouse team of Dr Justine Bertrand-Michel, Dr Pauline Le Faouder and Dr Cénac Nicolas for facilitating this event. The ACGT and the 35 participants of the workshop thank the delegates for generously donating their time in preparing and in facilitating the talks.
For further information about developments in this field, contact Mr Molati Nonyane, ACGT Liaison Scientist, and visit the MSA website.
26th Oct 2020
The African Centre for Gene Technologies (ACGT) and Metabolomics South Africa (MSA) hosted another successful metabolomics webinar on the 14th of October 2020. This Metabolomics webinar series serves as a platform for discussions on key technologies, techniques or new data analyses that could be of relevance to the rest of the South African metabolomics community.
Professor Justin J.J. van der Hooft, an Assistant Professor at Wageningen University, facilitated a webinar on the challenges of metabolite annotation and identification in untargeted metabolomics experiments of complex mixtures, typically encountered in natural products and food research. Untargeted metabolomics approaches are now widely used, spanning various disciplines including natural products discovery and “foodomics”. This webinar focused on how recently developed tools inspired by natural language processing, facilitate metabolomics analyses.
Prof van der Hooft is currently developing computational metabolomics methodologies to decompose complex metabolite mixtures aided by natural language processing and genomic tools. His interests are in plant- and microbiome-associated metabolites and the food metabolome as prime examples; where expanded knowledge on the specialized metabolome will assist in understanding key metabolic drivers of growth and health.
Similar to previous events, this webinar proved very popular to a diverse audience. It was attended by 102 participants from across South Africa, as well as from some international research institutions. There was a great Q&A session that followed and this highlighted the need for more of these sorts of meetings. The resources for those who wish to enter the field or perform a specific metabolomics application was also highlighted.The ACGT and MSA wishes to thank Prof van der Hooft for his superb webinar and look forward to collaborative opportunities in the field.
For a recording of this webinar, or for more information and suggestions about potential advanced biotechnology-related events, please contact Mr Molati Nonyane at .
16th Jul 2020
The African Centre for Gene Technologies (ACGT) and Metabolomics South Africa (MSA) are always looking for ways to create more Metabolomics platforms for discussions and training. One such initiative was to start up a Metabolomics Webinar Series that will run throughout 2020. The idea is to have a webinar hosted by a local expert once a month or so to discuss a key technique or new data that could be of relevance to the rest of the South African metabolomics community.
The first webinar of the series was hosted by Dr Shayne Mason on the 9th July 2020 at 14:00. Dr Shayne Mason is from the Laboratory for Infectious Diseases in Human Metabolomics at the North-West University (NWU) Potchefstroom campus. Dr Mason is a research leader at NWU specializing in TB meningitis and biofluid analysis. Dr Mason completed not one, but two BSc degrees; one in Biochemistry and Microbiology and the other in Statistics and Applied Mathematics. He completed his PhD in 2016 as a joint degree between NWU and VU in Amsterdam in the field of nuclear magnetic resonance (NMR) metabolomics. Dr Mason has published over 20 publications in the field and assisted and/or supervised numerous postgraduate students.
Then idea for this webinar was birthed from a question. One of the issues that stood out at a previous ACGT/MSA workshop was “how does one interpret the NMR spectra to determine the metabolites?” This webinar is aimed at answering that question and more.
And Answer it did.
The webinar addressed one of the major challenges in metabolomics which is the identification of metabolites in a highly complex mixture of compounds that produce a forest of peaks in a NMR spectrum. Dr Mason gave a practical stepwise guide description of how to perform 1H-NMR metabolite profiling on multiple complex biological samples. This metabolite identification process, called metabolite profiling, involves fitting the mixture spectrum to a set of individual pure reference spectra obtained from known pure compounds. The fitting process yields not only the identity of the metabolites, but also the accurate concentration of those metabolites. The participants were given a path to successful metabolite profiling that would provide them with a table of metabolite names and their absolute or relative concentrations.
This webinar was attended by 128 participants from all over South Africa. There was a great Q&A session that followed and this highlighted the need for more of these sorts of meetings. Please look out for future communication about the next webinar and other ACGT events.
8th Jun 2020
The African Centre for Gene Technologies (ACGT) together with the University of Pretoria’s Centre for Bioinformatics and Computational Biology (CBCB) and the CISCO Networking Academy, have been hosting the annual Linux for Life Scientists Workshops for three straight years now. This year’s course was facilitated fully online; a completely different format from that of previous years due to the current COVID-19 situation.
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. Researchers use open-source Linux to analyse the huge amounts of data they generate on multiple platforms. Linux is an alternative to expensive vendor-specific software that require periodic license renewals.
The workshop was facilitated by Mr Shaheem Sadien (CISCO Networking Academy) and Professor Fourie Joubert (University of Pretoria). The Linux course facilitated over five webinars spread out over 2 weeks in May 2020. The first webinar served as an introduction to Linux and the rest of the webinars that followed covered navigation, essential commands, resources, clusters and queuing. The workshop participants were representative of all ACGT partner institutions (ARC, CSIR, UJ, UP and Wits), as well as the National Institute for Communicable Diseases (NICD), Tshwane University of Technology (TUT), University of Cape Town (UCT) and University of the Western Cape (UWC).
The ACGT wishes to thank Mr Molati Nonyane, Ms Itseng Malao, Mr Shaheem Sadien and Prof Fourie Joubert for course content and organization. The ACGT is looking to host another iteration of this course in 2020. Kindly contact our Liaison Scientist, Mr Molati Nonyane () in this regard. The ACGT plans to continue with these kinds capacity building efforts to improve the skills level of South African scientists, especially in the field of bioinformatics and data analysis.
14th Aug 2019
The 2019 Introductory Metabolomics Workshop was held at the National Metabolomics Platform, based at North-West University’s (NWU) Potchefstroom Campus from 05-07th August 2019. This workshop was a collaborative effort between the African Centre for Gene Technologies (ACGT), NWU and the recently established Metabolomics South Africa (MSA). The workshop provided a capacity building opportunity to help delegates that are in the earlier stages of the research to build a foundation with sound metabolomics techniques and tools.
The workshop was facilitated by a panel of local metabolomics experts from several institutions from all over the country. The facilitators from North-West University were Dr Aurelia Williams, Prof Du Toit Loots, Dr Mari van Reenen, Dr Shayne Mason, Dr Zander Lindeque, Mr Emile Jansen van Rensburg and Ms Zinandre Stander. The facilitators from the University of Johannesburg included Dr Fidele Tugizimana and Mr Msizi Mhlongo. University of Pretoria was represented by Prof Duncan Cromarty and the University of Cape Town by Dr Zandile Mlamla.
The focus on day one of the workshop was on the different metabolomics workflows, experimental design and the application of metabolomics in different disciplines and industries. On the second day of workshop the delegates were given an opportunity to participate in real wet lab experiments using NMR and Mass spectroscopy. On the final day of the workshop, the focus was mostly on data handling and interpretation. This involved normalization, quality assurance, statistics, metabolite identification and metabolomics resources.
The participants were from multiple research institutions from all over South Africa. There were participants from the Universities of Pretoria, Johannesburg, the Witwatersrand, Council for Scientific and Industrial Research, North-West University, University of South Africa, Tshwane University of Technology, University of Cape Town, University of Limpopo and the University of KwaZulu-Natal. Below is a few takes offered by the delegates about the workshop:
“The content of the course was well balanced to suite newbies and experienced researchers in metabolomics. It was a great mix of people at different levels of research and different themes which made it rich.”
“The course is very insightful to beginners, gives an idea of how to tackle metabolic profiling as well as how to analyse the data. Personally, the course has answered a lot of questions I had, and it inspired me.”
“The statistical analysis was extensively covered and will be very useful in considering the best possible statistical tool to use on one’s data.”
“ I enjoyed learning about the different applications of metabolomics and how various types of research questions can be answered through the platform.”
“The area of research is still evolving and there is the need to prepare next generation of researchers for the task ahead to apply it in various fields apart from the human area alone.”
“I found the workshop well- structured, comprehensive and rich in content.”
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, Dr Aurelia Williams, Mrs Itseng Malao, Dr John Becker and Dr Fidele Tugizimana 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: Shimadzu, Microsep, Separations and the Scientific Group. You are welcome to visit our facebook page for more visuals from the event.
19th Jul 2019
In the post-genomic era, life scientists are generating more data than ever. To enable researchers to manipulate and analyze their own data, the ACGT, together with the Centre for Bioinformatics and Computational Biology (CBCB, University of Pretoria) hosted a three-day workshop on the use of the operating system. Linux is open-source software allows researchers to analyze data generated on multiple platforms, in contrast to expensive vendor-specific software that require periodic license renewals.
The workshop was facilitated in conjunction with the CISCO Networking Academy, and a trainer from this academy, Mr Shaheem Sadien, facilitated the training sessions, with Professor Fourie Joubert providing context and practical examples on structural and next-generation sequencing data. Delegates were representative of all ACGT partner institutions (ARC, CSIR, UJ, UP and Wits), as well as the South African Medical Research Council. The delegates had wide-ranging interests, ranging from precision medicine, food technology, crop protection to animal genetics.
All delegates indicated that they would recommend the course to their colleagues, and their suggestions for future courses were noted. The trainers provided the delegates with ample online resources to work from in the future but there is a plan that in future workshops, the trainers will make time to assist each delegate with their own specific data sets. Should delegates complete the requisite online modules, they also receive a certificate of competence from CISCO.
Brief feedback from some of the delegates, on what they enjoyed most, can be found below:
“I really enjoyed the application of skills presented on the Thursday. But the rest of the course was definitely necessary to understand that section!”
“Doing the exercises in the class where you can ask questions and the lecturers were awesome.”
“Despite the fact that the course was provided in class, explaining concepts and allowing practice, a detailed online course is also provided. This repetition I think works well to allow lasting memorization of the course content – which is basically a language that needs to be remembered.“
Kindly also see the ACGT’s Facebook page for pictures of the event. The ACGT wishes to thank Mr Molati Nonyane, Ms Itseng Malao, Mr Shaheem Sadien and Prof Fourie Joubert for course content and organization. The ACGT is looking to host another iteration of this course in 2020. Kindly contact our Liaison Scientist, Mr Molati Nonyani () in this regard.
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).
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.
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).