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).
4th Apr 2018
One of the objectives of the African Centre for Gene Technologies (ACGT) is to improve the advanced biotechnology skills level of scientists in South Africa. The quality of the work done locally should match, or even exceed, related work from any part of the world and the best way to do that is through continuous capacity building efforts.
To this end, the ACGT recently facilitated two metabolomics workshops to provide a platform to address key issues and challenges in the field of metabolomics, including subsequent data analyses. The two workshops were meant for different audiences and were held at the University of Pretoria. The first was an Introductory Workshop that ran from the 12th to the 14th of March 2018. This event was aimed at those who have limited knowledge of metabolomics techniques and applications. The second, an Advanced Workshop, subsequently ran on the 15th and 16th of March 2018 and covered more advanced topics in the field. The latter workshop was intended for those with existing metabolomics knowledge and already working with some metabolomics techniques, or are actively engaged in data analyses emanating from metabolomics experiments.
Both workshops were designed to include a mixture of lectures, interactive round-table discussions and computer-based practical sessions. The Introductory Workshop covered topics that ranged from experimental design, introduction to techniques, applications of metabolomics, analysis of metabolomics data, metabolite identification, statistics and metabolomics data interpretation. The Advanced Metabolomics Workshop focused on advanced data analysis, quantitative metabolomics, metabolomics networks and data sharing.
The participants hailed from the ACGT partner institutions, as well as institutions outside the partnership, including previously disadvantaged research institutions (University of Pretoria, 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 and the Central University of Technology (Free State). 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 workshops were facilitated by a team of renowned metabolomics experts, both local and international. The local facilitators included Dr Fidele Tugizimana and Professors Ian Dubery and Paul Steenkamp from the University of Johannesburg. The international facilitators included Dr Reza Salek from the University of Cambridge, Dr Jos Hageman from Wageningen University, Dr Fabien Jourdan from the French National Research Institute for Agricultural Research, and Drs Naomi Rankin and Karl Burgess (both from the University of Glasgow).
Following the brief ice breaker presentations by the individual participants on their backgrounds and areas of interest, the workshops then proceeded onto a variety of subjects that influence and shape metabolomics research. Web tools and practical applications of metabolomics were demonstrated, as well as hands-on exercises that focused on data analysis and interpretation. The sessions were kept as interactive as possible to create a relaxed environment where the participants could ask questions pertaining to their own work.
The ACGT and all of its partners would like to extend enormous gratitude to all those who contributed to making these workshops a success, including the facilitators who again took a lot of time out of their busy schedules to contribute to capacity building in South Africa. The ACGT would also like to wish all the participants of the workshops all the luck with their work and future in metabolomics.
There has since been positive feedback from the participants of both workshops. There was a general sense from the workshop evaluations that the workshops were informative, practical and interesting. The participants enjoyed interacting with the expert facilitators from different parts of the globe. They felt that the facilitators were knowledgeable and showed willingness to help. Moving forward, there are plans to adjust the duration of the course to increase subject coverage, as well as to include additional practical sessions. Due to limited space, the Centre could not host everyone that applied, but the ACGT encourages those that were not placed this year to keep an eye out for future workshops.
The workshops represent one of the means towards building a sense of community- further building on a stakeholder session that was facilitated earlier in 2018 towards the establishment of a more formal grouping of metabolomics stakeholders. More news on the establishment of an association to follow soon.
For any metabolomics-related capacity building and networking queries, kindly contact Mr Molati Nonyane, ACGT Liaison Scientist ( ,
012 420 6139 )
20th Oct 2013
As part of the ACGT’s drive to build a sense of community among national proteomics stakeholders and address training needs in the field, a Proteomics Bioinformatics Workshop was recently held at the University of Pretoria’s Bioinformatics and Computational Biology Unit (BCBU).
The three-day workshop was facilitated by Prof Lennart Martens, a world-renowned bioinformatics expert, who is affiliated to the Flemish Institute for Biotechnology (VIB) and Ghent University, Belgium. The Workshop was a logical continuation of training hosted by the ACGT, and linked very well to the national workshop facilitated by Prof Kathryn Lilley, of Cambridge University, hosted in the two-week period preceding.
The workshop covered a range of topics, which included the principles of mass spectrometry and proteomics. This was an excellent introduction for those who are in the initial stages of their proteomics experiments. These principles were also important for considering different statistical approaches to data analysis; which were covered in detail later in the workshop.
The workshop included daily practical sessions following introduction of different proteomics principles and considerations in the lecture sessions. Course participants were also introduced to open source software developed by Prof Martens and his team.
Feedback from participants was extremely positive. Some of the participants had this to say about the workshop:
– “The workshop was of a very high quality and was very professionally organised and presented.”
– “Prof Lennart Martens is a true expert in Proteomics-Bioinformatics field. For someone like myself without a lot of background in the field, to be able to follow and understand his lectures says it all.”
– “It was an excellent experience to attend this workshop. I really appreciate efforts put by ACGT and CSIR to bring researchers together to attend these workshops. Thank you very much.”
The participants included students as well as principal investigators who have been active in the field for some time. With the ACGT’s efforts of trying to reach the proteomics community at a national level, the participants included delegates from the ACGT partner institutions as well as other institutes such as the University of the Western Cape and the University of Fort Hare.
The ACGT is currently planning the proteomics workshops and training events for 2014. For more information on all proteomics related events, please contact Mr Thabo Khoza at .
Please also visit (and join) the LinkedIn page: Proteomics SA.