• Constructive stakeholder discussions facilitated on South African Bioprospecting Regulations at the University of Pretoria

    Constructive stakeholder discussions facilitated on South African Bioprospecting Regulations at the University of Pretoria
    5th Nov 2019

    Life Science researchers from different background

    Life science researchers from and around Gauteng, gathered at the University of Pretoria for a Bioprospecting Regulations Forum on the 23rd of October 2019. This information sharing day was intended give the life science community an overview of the national legislative provisions on bioprospecting and biodiversity in South Africa and to address the concerns of the researchers on how these relate to their work. For context, “Bioprospecting economy is based on searching for, collecting, harvesting and extracting living or dead indigenous species or derivatives and genetic material thereof for commercial or industrial purposes.”

    Information sharing
    Healthy discussions and debates

    There was a clear need for these discussions between the Department of Environment, Forestry and Fisheries (DEFF) personnel and Life Science researchers on the bioprospecting regulations. The meeting consisted of presentations that provided definitions and clarifications on different aspects of bioprospecting and biodiversity regulations in South Africa. The attendees were guided through key regulatory frameworks for bioprospecting, the Nagoya protocol, permits, compliance and benefits sharing. Healthy discussions and debates occurred throughout and after the presentations. Some of the discussion points were on how long the permit applications take, differences between bioprospecting vs scientific/basic research permits, amendments to the Biodiversity Act, the importance of the Nagoya Protocol and provincial level capacity and limitations.

    The African Centre for Gene Technologies (ACGT) believes that the forum will improve the communication between the DEFF and the researchers applying for permits and also believes that interests are now more aligned. This event raised significant awareness on national bioprospecting regulations and addressed the concerns of the researchers in attendance. The ACGT is looking forward to working with the DEFF on other future initiatives such as this one. We would like to thank Ms Natalie Feltman and Mrs Lactitia Tshitwamulomoni from the DEFF and the delegates that were in attendance, for their contributions to the success of this event.

    For more info on the event; visit our Facebook page: link or contact Mr Molati Nonyane for further information at

  • National symposium confirms that South Africa is a major player in Cell and Gene Therapy research

    National symposium confirms that South Africa is a major player in Cell and Gene Therapy research
    29th Oct 2019

    Calendar events are a great motivator and serve as a milestone to plan for and to work towards. Researchers from academia and science councils, clinicians, industry representatives and scientific vendors came together for one such networking event- the 5th National Cell and Gene Therapy Meeting, on the 26th and 27th of September 2019 at the Innovation Hub in Pretoria. The purpose of the meeting was for stakeholders active in the field to showcase their research. The two-day event attracted close to 70 delegates from across South Africa.

    The stakeholders presented their efforts to find therapies for different diseases and ailments. The work presented touched on a range of applications and possibilities; from the different uses of multiple cell types and genes to different ways to administer said cells in therapeutic treatments. Lively discussions followed almost every talk that due to the high quality and relevance of the work being presented. Symposium panel discussion sessions focused on relevant issues around cell and gene therapy such as CAR-T cells, genome editing, technology exploitation and possible harms.

    The meeting was also used to launch the special edition of the South African Medical Journal on Cell & Gene Therapy. The attendees were fortunate to receive a free copy of the journal to take home. The issue presented another opportunity and platform to showcase the great work that is being done by the different SA groups and researchers.

    At the end of the two days, Professor Michael Pepper from the University of Pretoria made a strong plea for stakeholders to contribute to ongoing development and drafting of specific policies and legislation governing Cell and Gene Therapy in South Africa. It is critical to have appropriate regulatory frameworks to allow patients to benefit from advances in the field, while at the same time protecting them from exploitation and harm.

    The organizers (Prof Michael Pepper, Dr Janine Scholefield and the ACGT Team) would like to thank Haemotec, Separations Scientific, the Scientific Group, inqaba biotec, Beckman Coulter, Whitehead Scientific and ACGT for the financial support. Without their contribution the travel and accommodation arrangements for some of the delegates would not have been possible. The organizers would also like to extend their sincere gratitude to the speakers and panellists for their participation in the meeting. The speakers represented the Universities of Pretoria, Cape Town, the Witwatersrand, Stellenbosch as well as the South African Medical Research Council, Royal Holloway University of London, Council for Scientific and Industrial Research, Biolawgic (Pty) Ltd, University College Cork, Ireland and the Albert’s Cellular Therapy centre (ACT). Without their involvement this event would not have been possible. We hope to see the delegates again at the next meeting. The date for the next meeting will be communicated soon. For more images use this link.

  • The CRISPR Plant Genome Editing KIT

    9th Oct 2019

    The African Centre for Gene Technologies (ACGT) and the Agricultural Research Council (ARC) hosted a plant genome editing workshop between the 3rd and the 5th of September 2019 at the ARC’s Biotechnology Platform situated on the Onderstepoort Campus.

    Scientists from the Karlsrühe Institute of Technology, Germany (KIT) presented a “starter kit” for model plant CRISPR-related work in South Africa. The relationship with KIT began in 2017 with Professor Holger Puchta visiting South Africa on an ACGT invitation, to present a keynote address at one of the annual ACGT Regional Plant Biotechnology Forum series meetings. When the ACGT approached Prof Puchta to facilitate a three-day beginner’s workshop on plant genome editing with the CRISPR/Cas technology utilized in his laboratory, he recommended his trusted colleagues, Patrick Schindele and Angelina Schindele, to facilitate the workshop, who graciously accepted the invitation.

    The three-day workshop included both theory and practical sessions during which the participants were introduced to gene targeting in plants by using the CRISPR/Cas9-system.

    Topics covered in the sessions included:

    • Classification of the CRISPR/Cas-systems currently in use
    • Designing guide RNAs manually and with online tools
    • CRISPR construction and guide RNA cloning into the KIT group’s vectors using various cloning strategies, such as Gateway cloning
    • Current applications of CRISPR/Cas technologies looking beyond gene editing
    • Approaches to Agrobacterium transformation of model plants.

    Prof Puchta’s lab generously provided constructs for the participants to work on during the practical sessions. The relationship established with KIT will be an ongoing one. Prof Puchta’s lab has offered to assist participants who attended the workshop with their published constructs and other plant genome editing related queries. Queries must be directed to the ACGT. Inqaba Biotec partnered with ACGT and ARC as the major sponsor and generously provided the majority of reagents used in the workshop.

    The plant genome editing community in South Africa is a small but growing one. The workshop provided an opportunity for scientists in the field to be aware what other institutions in the region are doing in the plant genome editing space. Indeed, collaborative discussions have already been established between the ARC and the Council for Scientific and Industrial Research (CSIR) on a possible project as a direct result of this workshop. The participants were all enthusiastic about having a more cohesive community and the ACGT will facilitate the process by creating a CRISPR list server (contact ACGT’s Liaison Scientist, Mr Thabo Khoza, to gain access) and subsequently a Genome Editing Interest Group. The participant feedback indicated that both the extensive theoretical overview of the different technologies, combined with the KIT CRISPR experts’ practical experience, provided key insights into the technology during the practical sessions, with details often not provided in laboratory protocols or papers.

    Contact Thabo Khoza:

    For more workshop images, visit our ACGT Facebook page: Click here

    Story by: ACGT, October 2019

  • ACGT and FABI jointly hosts a Plant Phenotyping and Precision Agriculture workshop at Future Africa

    ACGT and FABI jointly hosts a Plant Phenotyping and Precision Agriculture workshop at Future Africa
    8th Oct 2019

    On Tuesday, September 17, the African Centre for Gene Technologies (ACGT), Forestry and Agricultural Biotechnology Institute (FABI) and Future Africa co-hosted a Plant Phenotyping and Precision Agriculture workshop at Future Africa on the University of Pretoria’s Hillcrest Campus. The event, which was themed “Opportunities and Needs in Research and Infrastructure” was attended by 66 delegates from a variety of national research, governmental and industry institutions.

    The workshop was opened by Dr Marinda Visser (Manager: Grain Research and Policy Centre at Grain SA) who emphasised the importance of research and development in the agricultural sector, as well as the need for better coordination and collaboration.

    The morning session was dedicated to introducing various aspects of phenotyping and precision agriculture to the delegates. This involved phenotyping at several different scales and applied to a variety of plant species. The programme and the national and international speakers who delivered the presentations are listed below:

    Morning presentations:

    Prof Carlos Poblete-Echeverria, Stellenbosch University Precision viticulture: digital technologies for monitoring and management of the vineyards
    Prof Dave Berger, FABI, University of Pretoria Deep learning for automated classification of maize diseases
    Dr Abraham Singels and Natalie Hoffman, SASRI, KZN Remote sensing of canopy cover and crop water status with drones to assist sugarcane breeding: Preliminary results
    Dr Nicky Taylor, University of Pretoria

     

    Assessing relatively simple tools for estimating canopy size in orchards
    Dr Moses Cho, CSIR Evolution in remote sensing of foliar nutrient and chlorophyll content as indicators of vegetation health
    Dr Nadia Shakoor, Donald Danforth Plant Science Centre, Missouri, USA

     

    Phenomics at scale: Driving advances in crop breeding with insights from diverse sensor platform technologies
    Dr Rosita Yocgo, African Institute of Mathematical Sciences, Rwanda

     

    A phenomics approach to the analysis of the influence of glutathione on leaf area and abiotic stress tolerance in Arabidopsis thaliana
    Dr Dirk Swanevelder, ARC Biotechnology Platform

     

    Plant phenotyping and remote sensing at the ARC
    Mr Maurits Voogt, eLEAF, Wageningen, Netherlands Making research work: how FruitLook evolved to generate impact at scale

     

    Adding to the diversity of speakers, delegates also represented institutions and initiatives that included: the University of Johannesburg, Tshwane University of Technology, the Royal Science and Technology Park: eSwatini, the Department of Science and Innovation, Corteva Agrisciences, Sensako Seed Company and Link Seed. ACGT and FABI post-graduates and researchers were very well represented.

    In the afternoon session, facilitated by Prof Bernard Slippers (Director: FABI, UP), delegates were tasked to discuss issues around opportunities to meet needs for infrastructure and facilities, academic – government – industry alignment, and opportunities for South Africa, Africa and international communities. These crowd-sourced inputs will now provide a foundation for developing a network of interested parties and contain numerous ideas for projects and further development.

    A more formal report on the feedback emanating from the groupwork is in preparation. There was strong agreement that a follow-up event is required and planning will commence shortly.

    In closure, Prof Bernard Slippers thanked all the speakers and delegates, as well as the organizing committee.

    For more photos, please visit out Facebook page: click here

  • UK-South African consortium is awarded an Agri-Tech Catalyst grant by Innovate UK for African crop improvement

    UK-South African consortium is awarded an Agri-Tech Catalyst grant by Innovate UK for African crop improvement
    18th Sep 2019

    A team of academics from the Universities of Edinburgh, Pretoria and Johannesburg, in conjunction with the South Africa-based multinational fertilizer company, Omnia Group, Ltd, was recently awarded the Agri-Tech Catalyst grant by Innovate UK, the UK’s innovation agency.

    The consortium submitted a proposal for improved cultivation and nutrition of the African staple, maize, to the Agricultural and Food Systems Innovation competition. Novel biostimulants will be screened and applied in greenhouse and field scale, and the effects on cultivation, as well as nutritional value of the crop, will be determined. The project will rely heavily on cooperation between industry and the academic partners.

    The analyses will be conducted in appropriately equipped laboratories at the University of Edinburgh (EdinOmics platform, Dr Karl Burgess) as well as at the University of Johannesburg (Plant Metabolomics, Dr Fidele Tugizimana). The research component will be heavily metabolomics-based, relying on the latest high-throughput methods developed at UoE and UJ. Hence, technology and expertise transfer between the UK and SA will be a strong project outcome. In addition, stronger academic-industry partnerships will also be forged during the implementation of the programme. The African Centre for Gene Technologies (Mr Molati Nonyane and Dr John Becker) will provide coordination and oversight and exploit opportunities for further programme growth and development utilising this investment.

    The project is envisaged to kick off in November 2019.

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  • SA researchers introduced to the field at the National Metabolomics Platform

    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.

     

     

     

     

  • I attended the 2019 International Metabolomics Conference held in The Hague …and I loved it!

    I attended the 2019 International Metabolomics Conference held in The Hague  …and I loved it!
    14th Aug 2019

    My involvement with the field of Metabolomics is in my capacity as Liaison Scientist for the African Centre for Gene Technologies (ACGT) and as a committee member of Metabolomics South Africa (MSA). The ACGT represents the interests of three universities and two research councils in the Gauteng region (Wits, UJ, UP, CSIR and ARC. I coordinate ACGT’s Metabolomics capacity building activities which include, but are not limited to: meetings, workshops and symposiums; finding synergies between researchers and subsequently building linkages amongst ACGT partner institutions and relevant outside institutions. 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.

    I discovered through one of our colleagues from the University of Edinburgh that a Metabolomics Conference was to be held at the World Forum in The Hague, Netherlands from 23-27 June 2019. Attending relevant information dissemination events like the 2019 International Metabolomics Conference, helps me perform my roles well for the ACGT and its partners and also enables me to keep up with the trends in metabolomics research. A decision was then made that I would be attending the conference. I therefore registered to attend the conference and began with the travel arrangements. The visa came out in the nick of time, they do say better late than never. I managed to conquer the usual worries of travelling: Did I pack enough clothes? Did I forget something? Constant reminder that whatever I do, I better not miss the flight. Thankfully, there were no glitches in my travel and all went well. As a bonus, the city of The Hague in itself is amazing with efficient public transport and some great sites.

    There was a great South African presence at the workshop with delegates from University of Johannesburg, University of South Africa and North-West University. The conference provided an opportunity to listen to international metabolomics researchers from all over the world sharing their findings, an opportunity to network and identify relevant synergies so as to foster further collaboration amongst metabolomics researchers within SA and across the world. The ACGT already has relationships with some key international metabolomics players who have been assisting with capacity building activities over the past several years. This event provided an opportunity for some stakeholder management to continue to strengthen these relationships. This conference was also an opportunity to expand our contact list and open up new opportunities for collaborations and relationships with South Africans researchers.

    My takeaway from this conference is simply that there is a significant and continuing growth of metabolomics all over the world. The discipline has diverse applications in health, agriculture and industry. The ACGT and MSA will do all in its power to assist in pushing African Metabolomics in the right direction and keeping it globally competitive. I would like to encourage anyone who is involved in metabolomics or metabolomics related work to attend future International Metabolomics Conference as this was a worthwhile experience.

    My interests and professional involvements are not only limited to the field of metabolomics, I also continue to be involved in genomics and in life science research in aspects that include capacity building, fundraising and research coordination, nationally and internationally. For queries relating to any of the above fields, feel free to contact me at and we can discuss how I and/or the ACGT can be of assistance.

    Story by: Molati Nonyane

  • Much needed Linux training held at the University of Pretoria for Life Scientists

    Much needed Linux training  held at the University of Pretoria for Life Scientists
    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.

    The Africa Centre for Gene Technologies always looking to contribute to Africa’s capacity building

    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.

  • Stem cell treatment – excitement is understandable but let’s tread carefully

    20th Jun 2019

     

    Stem cells not a panacea.

    There is no doubt that the stem cell field is generating a great deal of excitement and hope. Efforts are underway across the globe to find cures for incurable diseases. Yet despite these exciting developments, only a limited number of procedures are approved for routine therapy.

    A spinal cord injury

    Bone marrow transplantation, which has been performed for cancers and blood disorders for several decades, is one for the few universally approved and routinely practiced forms of stem cells therapy.

    On 31 May 2019, Health24 published an article stating that stem cell treatment had improved the quality of life of a rugby player who sustained a spinal cord injury. Rugby injuries are often low velocity injuries and in many cases, the injuries that are sustained are incomplete.

    The implication is that recovery is possible, to a greater or lesser degree, with follow up rehabilitation. To date, despite numerous research efforts and clinical trials, there is virtually no evidence that stem cells can cure spinal cord injury. Several factors are critical when assessing a case such as the one mentioned above. What was the origin of the cells used? How were they administered? Was the patient walking before the stem cells were administered?

    Equally important, did the administration of the stem cells comply with the laws of the country, and since this is an unproven therapy, should it have been considered as a clinical trial? In the case of the latter, a number of critical steps would have needed to be followed.

    No guarantee

    While not wanting to detract from the great joy of seeing someone recover from a debilitating injury, accurate reporting is important if one is to ensure that vulnerable patients are not emotionally and financially exploited. There is regrettably a global trend involving “stem cell clinics” that seeks to treat a range of diseases using unproven stem cell therapies. Propagating the idea that there is a direct causal relationship between the administration of stem cells and a positive outcome, without considering all of the facts, may be misleading and may prompt other vulnerable patients to undertake similar unproven therapies.

    It is therefore the responsibility of the person reporting the story to do so in a manner that is objective, and to avoid implicating direct causality unless this can be proven. Evidence-based and ethical marketing is also important in order to avoid misleading vulnerable patients and their families. An advertisement, currently running on one of the local radio stations, indicates that the future use of stored stem cells will “overcome my diabetes” and “treat my autism”.

    While there is ongoing research in both of these areas, and many more, there is no guarantee that stem cells will be able to be used to treat these conditions in the future. Given the extent of the emotional involvement around matters pertaining to children, potential customers might be made to believe that by banking their newborn’s stem cells, “the child you have today will be protected tomorrow”.

    Complex matter

    While there is the potential that stored stem cells might well be used in the future for bone marrow transplantation or for regenerative medicine purposes, this information should be convened objectively, which includes placing the possibility of a future cure into perspective relative to the evidence currently available. Why is it important to proceed cautiously with new treatments that have the potential to cure previously incurable diseases?

    One important reason is highlighted in a recent court decision in the US. As noted by the International Society for Cell and Gene Therapy, “this ruling an important step towards the regulation of an industry that has eluded regulatory oversight for many years, causing substantial financial, and in many cases, physical harm to patients through direct-to-consumer advertising of unproven and poorly tested “stem cell” treatments”.

    In other words, as long as a treatment that eludes regulatory oversight does no harm, financial loss will be the only issue that needs to be contended with. However, in the case mentioned above, four patients were blinded by stem cells administered directly into their eye. And there are many more examples of cases in which patients have been harmed by unproven “stem-cell” therapies. The argument is often put forward that the use of the patient’s own stem cells does not require regulatory oversight.

    Exploitation and possible harm

    This is a complex matter, particularly since the cells are often processed in one form or another before being re-administered to the patients, which would qualify them as being “minimally-manipulated”. While there is no specific legislation governing this matter in South Africa, international best practice requires regulatory oversight with the use of such a product. To conclude, evidence-based and ethical reporting and marketing are necessary if patients are to benefit from the great strides being made in the stem cell field.

    Not to do so exposes vulnerable people to exploitation and possible harm. It is critical that the South African Government provides an appropriate regulatory framework to allow patients to benefit from advances in the stem cell field while at the same time protecting them from exploitation and harm. This will also promote much needed research, investment and entrepreneurship in the stem cell field for the benefit of all of the people of our country.

     

    Story by: Prof Michael Pepper for Health24

    *Michael S. Pepper MBChB (Cape Town), PhD (Geneva), MD (Geneva), PD (Geneva)Professor, Dept. Immunology, Faculty of Health Sciences, University of PretoriaDirector, Institute for Cellular and Molecular Medicine, University of PretoriaDirector, SAMRC Extramural Unit for Stem Cell Research and Therapy

  • UCT, ACGT, SU and DIPLOMICS host the Trans-Proteomic Pipeline (TPP) Workshop

    14th May 2019

    The University of Cape Town, in partnership with the ACGT, DIPLOMICS and Stellenbosch University, hosted the Trans-Proteomic Pipeline (TPP) workshop which ran from the 21sttill the 22ndof March 2019.

    The workshop, which followed the HUPO-PSI meeting, held from the 18thtill the 20thof March 2019, was facilitated by Dr Eric Deutsch and Mr Luis Mendoza from the Institute of Systems Biology (Seattle-USA). Dr Deutsch is a lead designer for the Systems Biology Experimental Management System. He is the Chair of the HUPO-PSI and is one of the leaders of the TPP project- that aims to provide a free and open-source suite of tools for the processing and analysis of proteomic tandem mass spectrometry data.

    Mr Mendoza is a senior software engineer at the Institute for Systems Biology. He has been a main contributor to the development of the TPP for the past 14 years.

    The two-day workshop was attended by 35 delegates from Universities in the Western Cape region (University of Cape Town, Stellenbosch University, University of the Western Cape and Cape Peninsula University of Technology) as well as delegates from other provinces (Gauteng and KZN).

    The ACGT partnership was represented by four delegates at the workshop. The ACGT representatives hailed from the Council for Scientific and Industrial Research (Dr Previn Naiker and Dr Ireshyn Govender), the University of the Witwatersrand (Ms Genevieve Mezoh), and the University of Pretoria (Ms Denise Wilson). The delegates from the ACGT partnership are expected to transfer the knowledge gained from the TPP workshop by training their fellow unit/lab students/colleagues. A week after the workshop, Ms Denise Wilson reported that she was in the process of working with the Centre for Bioinformatics and Computational Biology (CBCB) at the University of Pretoria to install the TPP pipeline for command line execution on their Linux servers.

    The next proteomics training workshop will be in November 2019 and it will focus on the open-source software package Skyline, data analysis and SWATH. Information regarding this workshop will be disseminated at a later stage.

    Workshop programme: View here

    Story by: The ACGT team, 14 May 2019