Presentations 2019: Day one

Wednesday, 17 April 2019

Cape Digital Foundation: Smart Townships and Digital Innovation

Emma Kaye

Cape Digital Foundation

Presentation overview

The Cape Digital Foundation (CDF) is passionate about initiating and driving a movement of Smart city thinkers who live in Smart townships and reap the benefits of financial inclusion through digital inclusion.

As our cities grow into being African megacities they increasingly serve as our nation’s vital economic hub. CDF assists in building Smart, digitally savvy business communities by providing digital training to township SME owners, resulting in Smart citizens who are able to use their newfound digital skills to better administer and grow their businesses. In this way Smart township entrepreneurs are enabled to contribute to building township economies – particularly through being able to both create income and spend it within the township thereby boosting the township economy.

The Cape Digital Foundation is a not-for-profit agency with an overriding passion to make an impact in seeing South Africans’ lives improved as people are enabled to take up and use technology and digital tools. The Foundation is mandated to initiate and coordinate initiatives that promote the financial and social inclusion of all people through the uptake of citizen-lead technology. By enabling active citizens who have a voice, future technology and innovations can be shaped around bringing a solution to real-world problems rather than technology prescribing a presumptuous solution from the top down. We believe that valuable innovation will be born of the Internet-enabled informal sector, it gives people agency and purpose and has the capacity to build our nation and contribute to unity.

Presenter

Emma has been named as one of the top 10 women in Science & Technology in Africa, has twice been voted as one of the top 50 women globally in mobile entertainment, elected as one of South Africa’s top businesswomen and one of the 20 most powerful women in technology in Africa. Emma is a board member for Wiki in Africa and for the last four years has been one of the Judges for the Digital Emmys.

As an entrepreneur Emma founded and ran two successful companies, is the CEO of another and Executive Director of a Foundation:

1. Executive Director of the Cape Digital Foundation, ensuring that there is a digitally connected society through Smart Townships

2. Founder and CEO of Bozza, a global marketplace for African musicians, poets and filmmakers. For this platform, she raised significant funding from Silicon Valley

3. CEO of Breakdesign which became the top 5 developers globally for Nokia

4. Founder and CEO of Triggerfish Animation - the largest and most successful animation company in Africa

CODATA/RDA Schools in research data science: teaching responsible and open data science practices

Dr Louise Bezuidenhout

Institute for Science, Innovation and Society (InSIS), University of Oxford

Presentation overview

Contemporary research – particularly when addressing the most significant, transdisciplinary research challenges – cannot effectively be done without a range of skills relating to data. This includes the principles and practice of Open Science and research data management and curation, the use of a range of data platforms and infrastructures, large scale analysis, statistics, visualisation and modelling techniques, software development and data annotation. These skills can be collectively termed ‘Research Data Science’. These skills are common to all disciplines and training in ‘Research Data Science’ needs to take this into account. For example, all disciplines need to ensure that research is reproducible and that provenance is documented reliably and this requires a transformation in practice and the promotion of the necessary culture, practice and skills.

A strategic priority shared by CODATA and the Research Data Alliance is to build capacity and to develop skills, training young researchers in the principles of Research Data Science. It is also important that Open Data and Open Science benefit research in Low and Middle Income Countries (LMICs) and do not result in even greater inequalities in research and scientific output. On the contrary, it has been argued that the ‘Data Revolution’ provides a notable opportunity for reducing research inequality in a number of respects. For this reason, particular attention is paid to the needs of young researchers in LMICs.

This talk will cover the development of the CODATA/RDA Schools in Research Data Science that have been run since 2016. These schools are aimed at postgraduate and early career researchers from LMICs. Over a two week period students are introduced to introductory material for data science competency. The student body is highly interdisciplinary, yet these tools are common to all research disciplines. The school covers the following topics: Introduction to the Command Line Programming (specifically R), Information Security, Version Control (in particular Git), Computational Infrastructures, Analysis and Data Visualisation. In addition to these technical skills, the researchers are introduced to key topics, such as Open Science, Research Data Management and Open Authorship. These topics contribute towards teaching responsible and open science citizenship.

Since the first school in 2016 that ran in Trieste, versions of the school have also run in Sao Paulo, Brazil, Brisbane, Australia and most recently Kigali, Rwanda. Around 180 students have been taught from over 30 countries. In 2019 this network of schools will expand further in Africa, South America and Asia. This talk will discuss how the curriculum has evolved since 2016 to match the needs of the students. It will discuss the key challenges of running such an event, namely organising and financing such an operation and how the delivery of their materials can, for the most part, be delivered by locally-based instructors. It will also point to the difficulties of implementing the school in different locations and the typical infrastructure required (either using a cluster of PC's or having students bring their own laptops).

Presenter

Louise Bezuidenhout is a research fellow at the Institute for Science, Innovation and Society (InSIS) at the University of Oxford. Her work focuses on the challenges that LMIC scientists experience in relation to data sharing, Open Data and access to information. Her work is highly empirical, and she has conducted embedded research in Kenya, Uganda, South Africa, Zimbabwe and Sudan. In addition to her research, Louise is a co-chair of the CODATA-RDA Schools in Research Data Science.

The role of national infrastructures in promoting the re-use of data and scientific software and empowering the next generation of researchers

Attie de Lange, Juan Steyn

South African Centre for Digital Language Resources (SADILAR)

Presentation overview

The South African Centre for Digital Language Resources (SADiLaR) (www.sadilar.org) is a new research infrastructure (RI) set up by the Department of Science and Technology (DST) as part the new South African Research Infrastructure Roadmap (SARIR).

SADiLaR’s mandate is firstly to expand the digitisation of language resources, and produce enabling technologies and tools to exploit these resources. SADiLaR further ensures that the data and software adhere to international protocols, and are available to scholars nationally and internationally. As a data repository SADiLaR endorses Force113 and in particular, aims to provide re-usable scientific resources. SADiLaR also provides a dedicated space for the research community to deposit and publish enriched scientific datasets in line with its mandate. This is primarily done through specialisation projects conducted by SADiLaR's nodes as well as through open call funding provided to the South African research community.

This contribution will reflect specifically on the following:

How does a RI practically support the re-use and publication of scientific resources within the Humanities and Social Sciences?
How can a RI support and train the next generation of researchers and/or support staff to function within the "new" Digital Scholarship/RDM context?
What were the lessons learned by SADiLaR since its inception as part of the South African Research Infrastructure Roadmap?

Presenters

Attie de Lange is the Director of the South African Centre for Digital Humanities (SADiLaR). He is a Professor of English and former Director of the Research Unit Languages and Literature in the SA Context at the NWU. He has worked in the field of Modernism, with a focus on the work of Joseph Conrad.

Juan Steyn is the Project Manager at SADiLaR. He has been involved in multiple Digital Humanities and Educational technology related projects. He also has a special interest in training and capacity building through his involvement within the Software and Data carpentry community as well as the Digital Humanities Association of Southern Africa.

Astronomy as a platform for data skills development

Vanessa Mc Bride, Kevin Govender, Ramasamy Venugopal

Office of Astronomy for Development

Presentation overview

Skills like statistics, programming and mathematics are foundational for entry into data science careers and are core skills for building knowledge economies. While these subjects can be notoriously ‘dry’ and difficult to teach, astronomy’s inspirational qualities make it a potential gateway into these subjects. In this presentation we will examine methods for teaching and learning of data science and statistics skills, focussing on initiatives that have been supported by the Office of Astronomy for Development. These include both summer schools, which aim to provide data skills training, and an online toolkit (https://datascience.astro4dev.org) to host astronomy and data science related teaching materials. We present these interventions and discuss their relevance in a rapidly evolving landscape.

Presenters

Vanessa McBride is an astronomer at the Office of Astronomy for Development. She has a PhD in Astrophysics from the University of Southampton and her research centres around populations of evolved, massive stars in binaries. Her experience comprises teaching at an undergraduate level and supervising postgraduate research. Dr McBride works towards bridging the gap between the community of professional astronomers and the development world with a view to helping astronomers apply their skills to problems related to socioeconomic development.

Kevin Govender is the director of the Office of Astronomy for Development (OAD), an organisation jointly supported by the National Research Foundation and the International Astronomical Union. The OAD aims to use the cultural, technological and scientific aspects of astronomy to effect socioeconomic development. A nuclear physicist by training, Mr Govender led the SALT collateral benefits team for 5 years before being appointed as the founding director of the OAD. His leadership in the field has been recognised internationally through the award of the 2016 Edinburgh medal for Science and Society.

Ramasamy Venugopal is the operations manager at the Office of Astronomy for Development (OAD). He is in charge of managing the OAD Call for Proposals and the projects funded by the office. He spent time as a Visiting Fellow at the OAD following his MSc in space studies at the International Space University. An engineer by training, he has worked in software development at Verizon and telecom services configuration at Ericsson in India. He is also an active member of the Space Generation Advisory Council.

Steps towards harmonising data from multiple health and demographic surveillance systems in South Africa: creating a national research infrastructure

Taurayi Mudzana, Kobus Herbst

South African Research Medical Council

Presentation overview

SAPRIN (South African Population Research Infrastructure Network) is a long term investment into a national research infrastructure funded by the Department of Science and Technology (DST).The project will harmonise data from three of South Africa’s existing rural health and demographic surveillance systems (HDSS) namely; 1) Agincourt HDSS in Bushbuckridge District, Mpumalanga 2) Dimamo HDSS in Dikgale District, Limpopo 3) Africa Health Research Institute HDSS in uMkhanyakude District, KwaZulu-Natal. The project will then harmonize data from a further four HDSS nodes that will be created in urban areas. This will result in a national network of seven surveillance population sites.

A HDSS is a standardised, field-based information system engaged in the prospective and longitudinal collection of population, health and socio-economic data for geographically-defined sections of impoverished and developmentally-constrained communities, both rural and urban. Individual and household indicators are routinely collected and assessed. The indicators that are collected include vital events such as births, deaths residence and migration, socio-economic status, disease monitoring, and measures of wellbeing represented by labor status, education and social protection. The HDSS systems will be complemented by linking to public sector records of health system utilization, school performance and access to social grants, to enable research on the factors associated with access to services or lack thereof.

Through this network of HDSS field sites, SAPRIN is capable of producing reliable data that will help strengthen policy and better inform decision-making on health and socio-economic matters. Furthermore harmonized data can provide an opportunity to answer novel research questions that could not be addressed using a single HDSS.

Presenters

Taurayi Mudzana is a Data Scientist at the South African Medical Research Council.

Kobus Herbst is the Deputy Director at the South African Medical Research Council and the Chief Information Officer at Africa Health Research Institute.

Put the researcher first: reporting on an enabling journey

Martin Dreyer, Zine Sapula

North-West University

Presentation overview

Within the ever changing world of research we find ourselves always scrambling to develop and support research. This includes best practices in research and skills development within the research environment. Within this falls not only the academic staff but also the support or enabling staff.

The relationship between researcher and researcher enabler is not a new concept, however it is an often vastly overlooked relationship. All research focus areas believe their research will change the world and their research is the top priority. Within the academic environment it is often taken for granted that all personnel under research and researchers. However, it is often clear that it is not the case within the researcher enabler's environment. The vernacular differs to an extent that it will often see as if the two parties are communicating in different languages and planets.

To put the research first at the NWU a couple of steps had to be taken. These included a few different schools of thought. The first being to better understand the research environment and to better the relationship between researcher and researcher enabler. This was done in the form of the "NWU Enablers: meetings that we do every quarter. These meetings focus specifically on the people that enable research such as the libraries, IT, The Research Office, and all the personnel that work with the researchers. It gives the platform to communicate and ask questions so that everyone can better understand each others environment and focus within the research life-cycle.

This, however, did not solve the fact that we need to prepare our researchers for the 21st century research. The average researcher of today needs to be able to do a lot more than their counterparts of 20 years ago. Researchers need to understand High Performance Computing, Computer programming, scripting, etc. The list is endless. Thus, we run data and software carpentry workshops throughout the year. These workshops focus on bettering the skills of the current as well as aspiring researchers in the way that they work with their data and to better understand the tools needed to refine and analyse said data.

The presentation will go into detail about the steps taken by the NWU to put the research first and to build a capacity to do better research at the NWU. Most activities have focussed on awareness among researchers and research enablers, information session about existing best practices and training opportunities.

Presenters

Martin Dreyer is an IT systems analyst at the the North-West University. Martin completed a Masters Degree (Cum Laude) in Computer Information Systems at Stellenbosch University and is currently working towards a PhD at NWU. His work focusses on eResearch, which includes the Open Acces drive at NWU, research data management, research support and many more.

Zine Sapula is a Research Support Librarian at North West University, Potchefstroom campus. Her work focuses on training, bibliometrics, researcher profiles, eResearch this includes Open Access, Research Data Management, and many more. She has a vast experience acquired from special, public and national library which enables her to understand different user groups and their behaviors.

Catalysing African research: the strategic imperative to optimise shared facilities

Renate Meyer

University of Cape Town

Presentation overview

Universities are home to a myriad of research facilities and resources. These facilities and the specialised skills required to run them are a pivotal part of the research ecosystem and academic institutions are recognising that they are also key components of the university’s strategic vision.

Both globally and locally, the higher education sector is looking for ways to improve graduate education, develop sustainable career paths for emerging researchers and encourage collaboration through research and innovation. Driven by research needs of the faculties and the institution’s strategic vision, these facilities play a large part in enabling cutting-edge research, developing and retaining leading scholars and they serve as a nexus for inter-disciplinary collaboration. It is clear then, that these institutional facilities are part of a growing trend that emphasizes a team-based approach to research. They facilitate collaborations and advance the research mission of universities. As such they have joined libraries, laboratories and computing centres as the physical embodiments of shared resources on campus.

Within the African context there is a further drive to accelerate African scholarship and enable the use of emerging technologies to support scientific research on the continent. While a number of national and regional collaborations are building the framework for such research, there is further potential for universities to optimise research innovation through the effective usage of the myriad of research facilities based within their institutions.

Presenter

Renate Meyer is currently employed as an eResearch Analyst at the University of Cape Town’ eResearch Centre. She joined the university in 2001 as an archivist, and later, Director at the Centre for Popular Memory in the Humanities faculty. Prior to her current position she headed up Special Collections and archives within the Libraries. During her time at UCT, Renate has been at the forefront of developing and managing transdisciplinary Digital Humanities and Scholarship projects and advocating for the preservation, curation and visualisation of UCT primary research outputs. She has a Fine Arts Degree, a Master’s in History and is currently completing a Master’s in Public Health.

Strategic positioning of a multidisciplinary data science curriculum for graduate employment prospects

Carolina Ödman

Inter-University Institute for Data Intensive Astronomy, University of the Western Cape

Presentation overview

Data science is fundamentally multi-disciplinary and the education of data scientists must reflect this. Being rooted in technology however, and ever hungry for new algorithms and approaches, data science as applied in industry also evolves faster than the kind of knowledge imparted during studies for more traditional university degrees. This presents a challenge of agility and responsiveness for tertiary education institutions.

We describe an analysis of data science through the lens of skills and market demands. This analysis is intended as a methodology to develop data science curricula that are strategically positioned to match a fast fluctuating but high-demand employment market. The purpose of the analysis and its application is to ensure that publicly funded institutions are able to respond to market demands by producing graduates that quickly reach high levels of productivity in an industry environment, and have the ability to think critically in the bigger context of data science and society.

Finally, we highlight the role of data literacy in other disciplines. We describe how teaching basic data science thinking can improve the ability of other professionals, especially in non-scientific and non-technical disciplines, to understand and exploit data for the betterment of their practice.

Presenter

Dr. Carolina Odman holds a masters in Physics Engineering from EPFL in Switzerland and a PhD in cosmology from Cambridge University. She has worked in research, education, development and in the private sector. Odman is currently Associate Director of the Inter-University institute for Data Intensive Astronomy, Development and Outreach, and Associate Professor at UWC.

mGenAfrica, an online tool for genomics education: tackling the STEM shortage in our youth

Verena Ras

University of Cape Town

Presentation overview

mGenAfrica is an e-learning platform and soon to be mobile application that promotes engagement between high school learners and research staff working in genomics and other health sciences fields. Although the key aim of the project centers around research careers, there are three main themes around which the site was developed. These themes are: 1) the ability to develop a career plan in genomics/genetics, 2) the ability to make informed decisions about participating in research studies and, 3) the uptake of healthcare services based on increased awareness of genetics. These themes are embedded in all the content available on the site. The content for the site was co-developed after a needs assessment with several groups which included teachers, learners and researchers. Some of the interesting features on the site include: a career corner where learners can read about potential career paths and the experience of current professionals within those positions. Learners are also able to schedule live chat session and interact with genomics and health science professionals from throughout Africa. A unique feature of mGenAfrica is the “translation corner”, where learners can simplify biomedical terms and even translate them into their mother tongues, so others may understand and learn better but also to ensure there is an opportunity for users to contribute to the site so that the interactions are two-way in nature. Formative evaluation, alongside summative, will also be undertaken throughout the project to continually develop content in line with need.

Presenter and authors

Verena Ras is a training and outreach coordinator within H3ABioNet, a Pan African Bioinformatics Network and holds an MSc in Biodiversity and Conservation Biology from the University of the Western Cape (UWC). Her expertise lies in the fields of taxonomy and conservation genetics. Her previous work focused on resolving the taxonomic status of Scyphozoans along the southern African coast line and in the process discovered a new species Chrysaora agulhensis sp. nov. (Ras et al. in submission) and assisted in the discovery of another Catostylus sp. nov (Moodaley et al. in submission). She is currently enrolled as a PhD student at UWC and hopes to provide valuable information on the population biology and genetic connectivity of scyphozoan jellyfish along the West and East African coast line, with the aim of barcoding these species and building a complete reference genome for the problematic Chrysaora fulgida which wreaks havoc along the west African coastline on an annual basis. She hopes to further refine and develop her skills in these areas while at H3ABioNet. Verena is also passionate about student development and science education and regularly engages with community projects that addresses the development of science in schools and beyond.

Vicky Nembaware is the training coordinator and a bioinformatician for the H3Africa and H3ABioNet consortiums. She is involved in several H3Africa working groups and is Chair of the Ontology Task Force. Vicky earned her PhD in Bioinformatics in 2008 from the University of Cape Town under the Supervision of Prof. Cathal Seoighe. In addition, she was also awarded an MPhil in Monitoring and Evaluation in 2012. She has experience in Bioinformatics and in the Public Health field in designing, monitoring and evaluating of programs/research studies particularly in the Information Communication Technologies field. Her broadbase of training and experience is reflected in a her research interests which include creating standards in the genomics and bioinformatics field and in using next generation sequencing technologies to advance translational research in Africa. She is passionate about training and mentoring the next generation of African scientists.

Professor Nicola Mulder heads the Computational Biology division and leads H3ABioNet, a Pan African Bioinformatics Network of ~30 institutions in 17 African countries. Prior to her position at UCT, she worked for 9 years at the European Bioinformatics Institute (EBI) in Cambridge, as a Team Leader for bioinformatics resources. At UCT, her research focuses on genetic determinants of susceptibility to disease, African genome variation, microbiomes, microbial genomics and infectious diseases from both the host and pathogen perspectives. Prof Mulder is actively involved in training and education as well as curriculum development in bioinformatics and genomic medicine.

Kagisho Montjane is a postgraduate student in the Division of Human Genetics, Pharmacogenetics and Drug metabolism group under the stewardship of Professor Dandara. Born and bred in the rural villages of Limpopo where career exhibitions were almost nonexistent and the gap between high schools and tertiary education was vividly wide. In response to address such, he started a school engagement program and he has since been in that space and continues to engage schools till today.

Jean-Michel Safari Serufuri is a Software Developer Consultant for the H3ABioNet consortiums. Jean-Michel earned a Masters in Bioinformatics and a Postgraduate Diploma in Mathematical Sciences from the University of Cape Town. Besides this, Jean-Michel has worked in the telecommunication industry and has an extensive experience in developing information systems. Using technology of information to ease management and learning processes is Jean-Michel’s passion and current interest.

Using a knowledge management tool to facilitate engaged scholarship for societal impact: the case of Stellenbosch University

Joanne Williams

Stellenbosch University

Presentation overview

This presentation sets out how the Division for Social Impact (DSI) at Stellenbosch University (SU) facilitates and enables engaged scholarship for social impact via an online electronic platform.

SU’s vision is to be a leading African university which is globally recognised and which advances knowledge in service of society. It aims to serve South Africa and the continent by contributing to its knowledge base, showing relevance, serving various stakeholders and contributing to the realisation of global development goals.

Research which is relevant and beneficial to society has become an imperative and a 21st century university needs to engage in transdisciplinary collaboration to address the complex challenges of society in new, holistic and sustainable ways.

SU’s Social Impact Platform (http://www.sun.ac.za/si) is a knowledge management system and a socio-technical solution. It is a tool for bringing stakeholders, technology and processes together to enable and enhance societal impact.

The purpose of the platform is to document social impact initiatives and align SU’s expertise and interests with the needs and collaboration opportunities with civil society, government and business. In addition, the platform enables institutional coordination of activities, collaboration, monitoring and evaluation (both formative and summative) and reporting for information and decision-making.

The platform creates an enabling environment for SU’s Social Impact mandate and is a means to support and enhance the work of the institution in a meaningful way. It provides the institution with qualitative and quantitative data and aligns social impact initiatives with the Sustainable Development Goals, SA’s National Development Plan and the Western Cape’s Provincial Strategic Goals. The platform supports knowledge sharing and new knowledge creation.

Implementation and evaluation of a blended learning training model for African bioinformatics education

Paballo Chauke, Verena Ras, Shaun Aron

University of Cape Town

Presentation overview

Most African countries lack the expertise, resources and skills in a myriad of areas within science and education, including, but not limited to: medicine, design and bioinformatics, to name just a few. The Introduction to Bioinformatics Training (IBT) course’s main aim is to address the scarcity of bioinformatics skills and expertise on the African continent, which are an obstacle towards experiential learning, overcoming the main challenges of internet instability and lack of funds. H3ABioNet (https://www.h3abionet.org/) developed the IBT course as a pro-active and reactive response to these impediments. The course has multiple objectives, but in essence focuses on explaining the use of bioinformatics and providing guidance on the key bioinformatics techniques and tools. Introduction to Bioinformatics Training is the flagship multi-approach and blended learning model course spearheaded by H3ABioNet (www.h3abionet.org) a Pan-African Bioinformatics Network for H3Africa (https://h3africa.org/). IBT is a free-of-charge course delivered through distance, face to face and online methodology over a period of 3-months. The course has recently just completed its third iteration in 2018, with further plans to offer the fourth iteration in 2019 (Graph 1 and Table 1). The course is geared towards African individuals with a molecular biology background who are interested in learning about the basic and/or fundamental bioinformatics tools and analyses. Several bioinformatics module topics are covered, which emanated from iterative consultations about bioinformatics competencies and appropriate curriculum. Topics such as databases and resources; genomics; Linux; sequence alignment; and phylogenetics are taught. Over the past three years, the number of participating African countries and trainees as well as support staff has grown significantly. In 2016 the course had 364 participants in 10 African countries, which has increased to over 700 pupils in 13 African countries last year, demonstrating that the numbers as well as impact have more than doubled (Graph 1 and Table 1).
Different institutions host local classrooms across different African countries. In these classrooms, locally based, trained volunteer teaching assistants and system administrators act as additional support to the videos available on YouTube and Vula (an online course management platform) presented by high caliber expert trainers. Monitoring, Evaluation and Learning (MEL) are iteratively used to improve the course, hence the move from our WordPress site to YouTube, making the videos more widely accessible and easy to verify impact. Over a period of 3 months of intensive biweekly contact sessions, the course combines theoretical and practical sessions to allow participants to gain practical experience in using various tools and resources. During contact sessions, classrooms meet virtually to discuss the session’s content with each other and the trainer. This blended-learning, largely virtual/long distance educational model has proved successful and we plan on using the model to create other courses to complement the introductory courses in future.

Presenter

Paballo Chauke has an MSc in Biodiversity, Conservation and Management (BCM) from the School of Geography and Environment (SoGE) at the University of Oxford (Oriel College) in the United Kingdom. His MSc research was titled “Fighting the “Good” Fight: Green Violence and Anti-Poaching of Rhino in the Kruger National Park, South Africa”. Mr Chauke also has two degrees from the University of Cape Town, an undergraduate degree (cum laude) with a triple major in Sociology, Environmental Geographical Sciences and Xhosa Communication. He also holds an honours degree in Environmental Geographical Sciences from the same institution. He has a multi-trans and cross disciplinary background and has a vast experience in research, coordination, facilitation, teaching, translation, supervision, mentoring and volunteering. He has a myriad of overlapping interests and skills/experience ranging from climate change, (sexual) health, bioinformatics training, land restitution, genomics medicine, nature conservation and social justice just to name a few.

Verena Ras is a training and outreach coordinator within H3AbioNet. A Pan African Bioinformatics Network and holds an MSc in Biodiversity and Conservation Biology from the University of the Western Cape (UWC). Her expertise lies in the fields of taxonomy and conservation genetics. Her previous work focused on resolving the taxonomic status of Scyphozoans along the southern African coast line and in the process discovered a new species Chrysaora agulhensis sp. nov. (Ras et al. in submission) and assisted in the discovery of another Catostylus sp. nov (Moodaley et al. in submission). She is currently enrolled as a PhD student at UWC and hopes to provide valuable information on the population biology and genetic connectivity of scyphozoan jellyfish along the West and East African coast line, with the aim of barcoding these species and building a complete reference genome for the problematic Chrysaora fulgida which wreaks havoc along the west African coastline on an annual basis. She hopes to further refine and develop her skills in these areas while at H3ABioNet. Verena is also passionate about student development and regularly engages with community projects that addresses the development of science in schools and beyond.

Shaun Aron is currently a bioinformatics consultant and lecturer at the Sydney Brenner Institute for Molecular Bioscience (SBIMB) at the University of the Witwatersrand in Johannesburg, South Africa. After pursuing an undergraduate degree in Genetics and Microbiology followed by an Honours degree in Human Genetics, he handed over the pipettes to the experts and entered the then still developing field of bioinformatics pursing an MSc degree. Currently he is a member of the H3Africa Pan African Bioinformatics Network (H3ABioNet), which is a network consisting of 28 research institutes in 18 countries, tasked with developing and supporting informatics and genomics research in Africa. His research interests include GWAS of complex diseases in African populations, exploring population diversity, structure and admixture in Africa and bioinformatics education and training.

Sumir Panji obtained his PhD in Bioinformatics from the University of the Western Cape as part of the Stanford South Africa Biomedical Informatics (SSABMI) programme where he developed computational and analyses pipelines to determine the intersection between bacterial virulence and positive selection in Professor Winston Hide's laboratory. He completed his postdoctoral studies in Professor Alan Christoffels' laboratory at the South African National Bioinformatics Institute (SANBI) where his focus was on genome assembly, annotation, data mining, large scale statistical analysis of genomics data and development of various computational pipelines and analyses workflows for a myriad of genomics' data types. Dr Panji's main interests are in creating and implementing computational and analyses workflows, statistical analysis of biomedical data, biological algorithms, high performance computing and the overall application of bioinformatics and genomics methods to better understand complex biological systems. Sumir is currently a bioinformatician within the H3ABioNet consortium who is interested in genome science, data analysis workflows, statistical analyses of large 'omics datasets, implementation and interpretation of bioinformatics solutions to diverse biological problems and providing bioinformatics support to the H3Africa projects.

Suresh Maslamoney is a techie at heart and has experience in system and network administration as well as in designing and developing ICT infrastructure. Suresh joined CBIO in February 2013 as a systems administrator and is tasked with developing and providing support on the core computational infrastructure for the CBIO and the H3ABioNet consortium. Prior to joining CBIO, Suresh spent 3 years in the UK working in various ICT posts before returning to RSA where he joined the South African Tuberculosis Vaccine Initiative (SATVI). At SATVI Suresh was responsible for managing the IT section and all ICT related technical matters.

Prof Nicola Mulder heads the Computational Biology division and leads H3ABioNet, a Pan African Bioinformatics Network of ~30 institutions in 17 African countries. Prior to her position at UCT, she worked for 9 years at the European Bioinformatics Institute (EBI) in Cambridge, as a Team Leader for bioinformatics resources. At UCT, her research focuses on genetic determinants of susceptibility to disease, African genome variation, microbiomes, microbial genomics and infectious diseases from both the host and pathogen perspectives. Prof Mulder is actively involved in training and education as well as curriculum development in bioinformatics and genomic medicine.

Towards an educational model for data scientists in higher education institutions (HEIs) in South Africa

Patricia Chikuni

University of Cape Town

Presentation overview

Scientific research processes are accompanied by burgeoning amounts of research data that serves as findings of the research and provides a platform for the results to be verifiable. Scientific researchers are under pressure to make their data openly available to other researchers for use. Access to scientific data and its curation has become a dominant theme in scientific policy discussions (Brown, 2009). Besides the funder requirements, researchers are making their data openly available for a number of reasons that include, raising the profiles of their research outputs, to increase their citations, to validate their research outputs and for their authenticity and integrity as researchers. However, not all researchers possess the skills to curate their own data and make it openly available for use in an open environment that is FAIR (Findable, Accessible, Interoperable and Reusable). Many researchers rely on the services of their libraries to assist in curating research data. A new role is emerging in the world of data analytics, the data scientist. Data science jobs in HEIs in South Africa have been growing at a rapid rate in response to the exponential amounts of research data being generated through scientific research processes. Data science is still a new field and there are not many people who are qualified to work in this emergent career field. Choudhury (2010) described the importance of the new role of ‘data scientist’ as a person who possesses data management experience as well as domain specific knowledge, who can provide a human interface between the Library and e-Science (science that uses immense data sets).Data scientist is a buzzword that is used by people who emerged from more accomplished fields like statistics, machine learning, database operations, business intelligence etc. (Harlan, Harris, Sean Murphy and Valsman Marck,2012). There is general misunderstanding on the role of data scientists. Ambiguity reigns in describing the term and there is no shared vocabulary. There is a general misunderstanding on the different roles of data scientists (Harlan, Harris, Sean Murphy and Valsman,2012; Marc; Swan and Brown, 2008). The primary objective of this paper is to raise awareness of the strategic role of data scientists in the scientific research process. The study seeks to contribute towards a growing and emergent discourse of data science in HEIs. It also seeks to contribute towards an educational model for data scientists in HEIs in South Africa. In-order to realise these objectives the paper asks the following research questions:

How are the emergent roles of data scientists conceptualised in HEIs in South Africa?
What is the strategic role of a data scientist in the scientific research process?

This study analysed research data science and curatorship programs offered by universities in South Africa to understand how the role of data scientists is conceptualized and to delineate the scope of this emergent field. A qualitative content analysis survey method is used to analyse courses offered by HEIs in South Africa. Preliminary findings from the research revealed that data scientists are drawn from fields like mathematics, statistics, information science, and computer science. The practical jobs of data scientists as conceptualised by the majority of universities employs theories drawn from the information science, computer science and statistics. The data scientists are expected to work closely with the researchers where the research is done. Most universities are offering data science programs at post-graduate level as professional courses for learners coming in from diverse backgrounds. The study recommends that the next generation of data scientists in a South African context should possess a cocktail of skills that enable them to conduct data analysis and enquiry to enable others to work with digital data.

References

Brown, D.J. (2009), “International Council for Scientific and Technical Information (ICSTI) Annual Conference – Managing Data for Science”, Information Services & Use, Vol. 29 No. 4, pp. 103-21.
Harris-Pierce, R., Liu, Yan Quan (2012). Is data curation education at library and information science schools in North America adequate? New Library World, Volume 113 Issue: 11/12, pp. 598-613.
Aalbersberg, IJsbrand, Judson Dunham, and Hylke Koers. "Connecting Scientific Articles with Research Data: New Directions in Online Scholarly Publishing." Data Science Journal 12 (2013): WDS235-WDS242. https://doi.org/10.2481/dsj.wds-043
Harlan, Harris, Sean Murphy and Valsman Marck (2012). Analysing the analyzers: an introspective survey of data scientists and their work.O’Reilly.

Presenter

Patricia Rudo Chikuni is a Post Doctoral Research Fellow in the Centre for Innovation in Learning and Teaching (CILT) at UCT. She graduated with a PhD in Information Systems from UCT, researching on the implications of institutional e-learning policy-making processes on e-learning policy discourses in Higher Education Institutions in South Africa. She is currently conducting research on institutional Open Educational Resources (OER) policies and surveying the OER policy ecosystem in Higher Education, to understand the implications of policy on practice. Patricia has a passion for disseminating scholarly research and making it accessible for use and reuse. This passion stems from her background as a Librarian and holder of a Masters degree in Archives and Records management. Data curation, management and use are at the core of her career interests. Patricia has collaborated actively with other researchers on open learning and e-learning having worked as an intern for the Open UCT initiative, tasked with curating Open UCT data and educational records. She also worked as a research fellow for MELISSA, a joint project on e-learning between UCT, Cape Peninsula University of Technology (CPUT) and Universita della Svizzera Italiana, Switzerland and the Western Cape Education Department.

Exploring the influence of organisational, environmental, and technological factors on information security policies and compliance at South African higher educational institutions, with focus on implications for biomedical research

Oluwafemi Abiodun, Dominique Anderson, Alan Christoffels

University of the Western Cape

Presentation overview

Globally, concerns over information security vulnerabilities are growing exponentially, fuelled by several headline reports of data breach incidents, which increase in size with each occurrence. On the African continent, South Africa is ranked among the most ‘at-risk’ countries for information security vulnerabilities, having lost approximately fifty billion rand to cybercrime in 2014. South Africa is currently considered to be the most cybercrime-targeted country in Africa. Worldwide, cyber vulnerability incidents greatly affect the education sector, due to the fact that this sector holds more Personal Identifiable Information (PII) than many other sectors. The PII ranges from (but is not limited to) ID numbers and financial account numbers, to biomedical research data.

In response to growing threats, the General Data Protection Regulation (GDPR) was approved by the European Union (EU) in April 2016, and following the two-year post-adoption grace period, became enforceable in May 2018. This regulation applies to organisations (both within, and outside of the EU), that process personal data of EU citizens, or, who want to share data and/or collaborate with EU organization/institutions. In South Africa, a similar regulation strategy will be implemented, with a view to mitigate cybercrime and information security vulnerabilities. The Protection of Personal Information Act (POPIA), was designed to protect any personal information of South African citizens, which is processed by both private and public organisations (including universities). The Act was signed into law in November 2013, and following the proclamation date by the information regulator, organizations will only have a one-year grace period to comply, before the regulator starts to impose fines.

The extent to which African institutions, and specifically the South African universities, have embraced and respond to these two information security regulations (GDPR and POPIA) is not yet clear and will be a matter of great importance for bio-medical researchers. The core activities of bio-medical research includes the collection and processing of PII, to perform health-related research, which can be geared toward (but is not limited to) disease diagnosis, disease prevention and treatment, and disease epidemiology. In order to maintain confidentiality of associated data and personal information which may be captured in a biomedical study, effective information security practices must be developed and implemented within the university setting.

This research study aims to conduct a qualitative exploratory analysis of information security management across the four universities in the Western Cape Province, namely the University of the Western Cape, Cape Peninsula University of Technology, Stellenbosch University and the University of Cape Town. The study will use a TOE (Technology, Organizational, and Environmental) model as a theoretical model, to investigate the factors which may influence the effectiveness of information security measures. Moreover, the study will aid in assessing whether the participating universities have proper and reliable information security management practices in place, as well as whether these are in line with international standards. Findings will assist in elucidating the current status, issues and challenges which face information security practitioners at universities, particularly in the South African context. This study is poised to make a significant contribution in increasing the body of research related to the adoption, practices and management of information security at universities, and may assist with the development of a Management Model for security practitioners and a framework for information management of biomedical data.

Presenters

Oluwafemi Peter Abiodun Mr. Abiodun, a Nigerian by nationality, holds two Honors degrees; one in Computer Science and another in Information Systems (IS). The former was obtained from Nigeria’s Adekunle Ajasin University, the latter was completed at the Department of Information Systems at the University of the Western Cape (UWC). He is currently a full time registered MSc student at the South African National Bioinformatics Institute (SANBI) at the University of the Western Cape.

Professor Alan Christoffels is the Director of the South African National Bioinformatics Institute, and the DST/NRF Research Chair of the South African Medical Research Council Bioinformatics Capacity Development Research Unit. He holds a PhD in bioinformatics from the University of the Western Cape, and following which, completed a 3-year postdoctoral fellowship in Singapore. He then established a research laboratory at Temasek Life Sciences Laboratories (TLL) in Singapore, for 3 years before returning to South Africa. In 2009 he received the DST/NRF Research Chair in Bioinformatics and Public Health Genomics. His research work focuses on host-pathogen interactions with reference to tuberculosis, and developing tools for analyzing next generation sequencing data.

Dominique Anderson is currently a Post-Doctoral fellow and Project Analyst at the South African National Bioinformatics Institute. She holds a PhD in Metagenomics from the University of the Western Cape. Dominique spent a number of years in the biotechnology industry specializing in recombinant protein expression, fermentation and purification, before returning to UWC to specialize in biobanking and Laboratory Information Management Systems. Dominique is a co-chair of the DST Medical Biocollections committee and interested in regulatory standards for biological sample collection and associated bioinformatics software tools.

Wednesday, 17 April 2019

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