REDCap Webinar Recording

On 6 July, the eResearch Office held a webinar on REDCap, a powerful tool for electronic data capture and management. The session was facilitated by Director of the eResearch Office Prof Vaccari, and included presentations from members of the eResearch Office, as well as two informative and inspiring presentations from UWC researchers who make regular use of REDCap for their research – Faheema Kimmie-Dhansay and Tamryn Frank.

REDCap (Research Electronic Data Capture) is a browser-based, metadata-driven Electronic Data Capture (EDC) software and workflow methodology for designing clinical and translational research databases. It is widely used in the academic research community: the REDCap Consortium is a collaborative, international network of more than 2400 institutional partners in over 115 countries, with more than 590,000 total end-users employing the software for more than 450,000 ongoing research studies. REDCap users can benefit from a broad range of data collection functionality, and take control of their data collection work. It is a powerful tool for secure methods of flexible and robust data collection, and although it was originally developed for the Health Sciences, it can be used in any discipline.

Watch a recording of our REDCap webinar.

About our Guest Presenters

Faheema, a Biostatistician with qualifications in Dentistry and Clinical Epidemiology, is currently working at UWC’s dental faculty and is pursuing her PhD in the risk factors associated with the incidence of caries in children under 6. She has a special interest in the detection of caries in adults and children, alike, and is interested in statistical models analysing time-varying covariates.

Tamryn is a researcher at the UWC’s School of Public Health (SoPH). She works in the food environment policy space, in the field of obesity- and NCD prevention. This informs her current PhD research, which is in the area of obesity prevention policies in low income settings. She is currently serving on the research working group advising the South African National Department of Health on Front-of-Package labelling. Prior to joining the SoPH, Tamryn worked as a primary health care dietitian for eight years for the Department of Health. Her masters research focused on human rights and food security.

The State of Open Data Survey 2021

Every year, Figshare, in partnership with Digital Science and Springer Nature, conducts the largest survey of its kind to discover global attitudes towards open data.

Researchers from around the world are invited to participate in The State of Open Data Survey 2021.

The aim of the survey is to find out about global experiences and attitudes towards sharing data, how researchers handle research data, the challenges that researchers and institutions face in regard to data, and its impact on workload and resources.

Read about the results of the 2020 survey here.

Survey completion time: approximately 20 minutes
Closing date: Friday 30th July
Prize draw: One of five $100 gift cards

Take the survey

Upcoming REDCap Webinar: Take Control Of Electronic Data Capture And Workflow

The eResearch Office invites researchers and students to participate in a webinar on REDCap on Tuesday 6 July at 11am.

REDCap (Research Electronic Data Capture) is a browser-based, metadata-driven Electronic Data Capture (EDC) software and workflow methodology for designing clinical and translational research databases. It is widely used in the academic research community: the REDCap Consortium is a collaborative, international network of more than 2400 institutional partners in over 115 countries, with more than 590,000 total end-users employing the software for more than 450,000 ongoing research studies.

REDCap users can benefit from a broad range of data collection functionality, and take control of their data collection work. It is a powerful tool for secure methods of flexible and robust data collection, and although it was originally developed for the Health Sciences, it can be used in any discipline.

The webinar will include an introduction to the REDCap platform and its main features, a demonstration on how REDCap data can be used for analysis and visualisation, as well as brief presentations of use cases by colleagues at UWC. We will conclude with questions directed at the panel.

We will also be addressing any UWC-specific related REDCap queries, and if there are any pressing questions that you would like to raise, please feel free to email us prior to the webinar at eresearch-support@uwc.ac.za

REDCAP Webinar Details

Date: Tuesday 6 July 
Time: 11:00 am
Register in advancehttps://uwc.zoom.us/meeting/register/tJUrdO6gqD4oGtX-_HRfWxFJIhbVWq-tAQSU

After registering, you will receive a confirmation email containing information about joining the meeting.

We look forward to seeing you there.

CarpentryConnect South Africa 2021

Registration is now open for CarpentryConnect South Africa 2021! 

The Carpentries is a non-profit organisation that teaches foundational computational, coding, and data science skills to academics, students and academic support staff worldwide. Carpentries workshops have been running at South African public universities and research institutions to hundreds of learners since 2014, and almost 100 instructors have been trained to teach digital and computational concepts to novices.

The first South African CarpentryConnect took place in Johannesburg, South Africa in September 2018. The second will be held virtually and will bring together newer and more experienced community members to share knowledge, network, develop new skills, and develop strategies for building strong local communities around digital and computational literacy at universities. Workshop fees and mobile data for African participants are funded by Code for Science and Society Event Fund

We invite participants to register for the following events:

Data Carpentry: 6-10 September, 9:00-13:00 SAST. This is an introduction to R, designed for participants with no programming experience. Lessons begin with some basic information about R syntax and the RStudio interface, and then move through how to import CSV files, the structuring of data frames, how to deal with factors, how to add/remove rows and columns and how to calculate summary statistics from a data frame. The lessons also touch on plotting, which is an excellent introduction to data visualisation. Space is limited to 25 learners. Register here.

Instructor training: 13-17 September, 9:00-13:00 SAST. The Carpentries workshops are taught by trained, peer, volunteer instructors. All of our Instructors complete an Instructor Training program, which teaches instructional pedagogy as well as the practicalities of teaching a Carpentries workshop. Instructors can teach workshops in their local area, travel to teach or teach or teach online. We have held workshops in over 40 countries on every continent (including Antarctica). Space is limited to 20 learners. Register here. *Please use the code “ccza43”.

Other events include:

Keynote: CarpentryConnect South Africa’s blurb in 2021 will be delivered by Dr Kari L. Jordan, Executive Director at The Carpentries on Monday 6 September at 14:00 SAST. Register here.

Networking events: The CarpentryConnect South Africa organising team will also host two networking events (Tuesday 7 and Thursday 16 September at 14:00 SAST) for our Carpentries community. These will be great opportunities to connect with like-minded people in fun, collaborative and interactive online events. Register here.

Closing: On Friday 17 September at 14:00 SAST we would like to create a space for community members to offer feedback and lessons learned on CarpentryConnect South Africa 2021 at the end of the two weeks. Register here.

For more information visit https://za2021.carpentryconnect.org/ 

Please note: While the event is fully funded by the organisers you will be held liable for a R500 attendance fee should you fail to attend without cancelling more than 48 hours prior.

X-ray Observations Supporting MIGHTEE MeerKAT Science Project Unveiled

New X-ray map reveals the growing supermassive black holes in next-generation MeerKAT survey fields 

One of the largest X-ray surveys using the European Space Agency’s XMM-Newton space observatory has mapped nearly 12,000 X-ray sources across three large, prime regions of the sky. The X-ray sources represent active galactic nuclei and galaxy clusters, and the survey captures the growth of the supermassive black holes at the cores of these galaxies. This X-ray survey complements previous X-ray surveys, allowing the researchers to map active galactic nuclei in a wide range of cosmic environments.

The XMM-SERVS survey lays key groundwork for studying the cosmic history and physical  properties of active galaxies 

Figure 1: XMM-Newton image of the 4.6-square-degree W-CDF-S field reveals the wide, sensitive view of the X-ray sky provided by XMM-SERVS. The detected sources, most of which are growing supermassive black holes, are color coded according to the energies of the X rays detected (with red having the lowest energies and blue the highest). The white outline indicates the area of the Chandra Deep Field-South, a well-known ultradeep pencil-beam X ray survey. The image highlights how XMM-SERVS has now provided sensitive panoramic X ray imaging around this survey. The XMM-Newton image covers an area about 20 times larger than the apparent size of the full moon, shown to scale at upper left.
Figure 2: XMM-Newton image of the 3.2-square-degree ELAIS-S1 field, which is about 15 times larger than the apparent size of the full moon (shown to scale at lower right). XMM SERVS provides a wide, sensitive X-ray view of this region.

These X-ray observations will be invaluable to study the active galactic nuclei (i.e. black holes) and galaxy clusters (the largest cosmic structures bound together by gravity) detected by the MIGHTEE MeerKAT Large Survey Project (led by UWC Visiting Professor Matt Jarvis and UWC Research Chair Russ Taylor) in its ongoing mission to study the faint radio sky.

Qingling Ni and W. Niel Brandt from Penn State presented the results of the XMM-Spitzer  Extragalactic Representative Volume Survey (XMM-SERVS) at a press briefing during the 238th meeting of the American Astronomical  Society on 7 June. A paper describing the survey, authored by an international team of astronomers including UWC’s eResearch Director Prof Mattia Vaccari, has been accepted for publication in The Astrophysical Journal Supplement. A pre-print is also available on arxiv.org.

“X-ray surveys are the best way to find growing supermassive black holes, which are located at  the cores of many large galaxies,” said Ni, a graduate student at Penn State and lead author of  the paper. “With this massive new survey, we can access population data about growing  supermassive black holes to better understand their physical properties and evolution over cosmic history.” 

“This survey represents key foundational work upon which, I suspect, hundreds of studies will  be built over the next decade or two,” said Brandt, Verne M. Willaman Professor of Astronomy  and Astrophysics and professor of physics at Penn State, and one of the leaders of the study.  “XMM-Newton was the best mission to gather these data, and we needed to invest a lot of  observation time for this study—with a total combined exposure of nearly 60 days—because it  will be so important for active galaxy studies, galaxy cluster studies, and for understanding  large-scale structures in the universe. It required a multiyear, multinational effort and it’s  incredibly gratifying to get it done. We are most grateful to the European Space Agency and  NASA for their long-term support of this work.” 

Caption from featured image: XMM-Newton image of the 5.3-square-degree XMM-LSS field, which is about 25 times  larger than the apparent size of the full moon (shown to scale at lower right). XMM-LSS was the  first XMM-SERVS field to have been observed by XMM-Newton. Chien-Ting Chen, a former postdoctoral researcher at Penn State who is now an astronomer at USRA, led the work for this  field (see Chen et al. 2018, Mon. Not. Roy. Ast. Soc.). XMM-SERVS provides a wide, sensitive X ray view of this region

NITheCS Colloquium: Prof Mattia Vaccari, The Ilifu Cloud Computing Facility & X-Informatics Data Intensive Research

Monday, 7 June, 4pm.

NITheCS (National Institute for Theoretical and Computational Sciences) is hosting a colloquium featuring UWC’s Director of the eResearch Office, Prof Mattia Vaccari.

Abstract

Over the past decade, the global science enterprise has been transformed by the data generating capabilities of our instruments. Distributed science collaborations creating datasets too large to manage for individual researchers are becoming the norm, and in response, X-Informatics, or the application of data science techniques to different science fields, has evolved into a new and exciting field of applied computer science. In this new big data era, institutions and national communities that have the capacity to design and implement the solutions to effectively extract knowledge from data will play a lead role in science. Those that do not, will not.

The Ilifu project was set up to address this challenge in Astroinformatics and Bioinformatics. Ilifu is building cross-disciplinary teams to undertake research and development in technologies and big data science to build capacity for South African researchers to be globally competitive in the era of big data.

In this presentation, Prof Vaccari will talk about Ilifu, its partnership model, goals and research programs, with a particular focus on multi-wavelength galaxy evolution studies, and outline a vision for a federated South African Data Intensive Research Cloud that empowers researchers to work with and collaborate on big data science projects.

Register for the event, or read more.

Five Years of FAIR

The Future of FAIR

Five years since the formal publication of the FAIR data principles, a newly published white paper, Springer Nature’s The Future of FAIR, looks at the real-world impact of FAIR. An international cohort of research data professionals share their opinions and offer commentary on the impact of the FAIR data principles to date, as well as what the next steps in research data management are.

Varsha Khodiyar on the Springboard blog writes that the “burgeoning open science (or open research) movement aims to make public and charity funded research as transparent and accessible as possible, and available for use to all to use, extend and build on. Research data is central to this vision, and to many policies and initiatives launched in recent years encouraging the adoption of open science practices. The impact of the FAIR data concept on open science advocates, position statements, policies and funding opportunities is unmistakable”.

Read more about the FAIR data principles, find out more about the study, and download The Future of FAIR white paper.

eWorkshop: Command Line Interface for Genomics Beginners

Forensic DNA Lab UWC

The Forensic DNA Lab (FDL, UWC) will be running an eWorkshop (online workshop) on using the Command Line Interface, Unix, shell and other tools for genomics. 

The course will run from 10 June to 15 July with once a week lessons.  The course is aimed at graduate students and research scientists who will work with genomic and bioinformatic datasets for the first time. We will help attendees get started in using the CLI for performing genomic workflows. Attendees require no previous experience in CLI tools.

More about the eWorkshop

Command line interface (CLI) and graphic user interface (GUI) are different ways of interacting with a computer’s operating system. The CLI allows you to control your computer using commands entered with a keyboard instead of controlling graphical user interfaces (GUIs) with a mouse/keyboard combination.

The CLI is important for proficiency in genomics as most bioinformatics tools use the shell and have no graphical interface. Importantly, CLI is essential for using remote high performance computing centers e.g. ILIFU, CHPC.

After the course, participants should be able to:

  1. Discuss practical differences between Unix and Windows;
  2. Navigate and manipulate files and folders using standard bash commands;
  3. Write basic scripts for bash including piping between commands;
  4. Access the ILIFU HPC and submit simple scripts to SLURM; and
  5. Discuss folder/directory structure for genomic projects.

The course registration is now closed.

Research Opportunity Announcement: Data Generation Projects for the Bridge to Artificial Intelligence (Bridge2AI) Program

The NIH (US National Institute of Health) Common Fund’s Bridge to Artificial Intelligence (Bridge2AI) program is designed to help propel biomedical research forward by setting the stage for widespread adoption of artificial intelligence (AI) and machine learning (ML) that tackles complex biomedical challenges beyond human intuition. It is a new NIH Common Fund program, and will tap into the power of AI to lead the way toward insights that can ultimately inform clinical decisions and individualize care. AI, which encompasses many methods, including modern machine learning (ML), offers potential solutions to many challenges in biomedical and behavioral research.

The Bridge2AI program plans to support several interdisciplinary Data Generation Projects (OTA-21-008) and one complementary cross-cutting Integration, Dissemination and Evaluation (BRIDGE) Center (NOT-RM-21-021) to generate flagship data sets and best practices for the collection and preparation of AI/ML-ready data to address biomedical and behavioral research grand challenges. 

It also plans to support the formation of teams richly diverse in perspectives, backgrounds, and academic and technical disciplines. The current Research Opportunity Announcement (ROA) for Data Generation Projects for the Bridge to Artificial Intelligence (Bridge2AI) Program (OT2) (OTA-21-008) requires a Plan for Enhancing Diverse Perspectives (PEDP)—a summary of strategies to advance the scientific and technical merit of the proposed project(s) through inclusivity. Visit the Bridge2AI Program Resources page and Program FAQs for additional information on building diverse teams and for PEDP guidance.    To facilitate team building across communities and ensure responsiveness of proposals, NIH strongly encourages potential proposers to participate in the Grand Challenge Team Building Activities taking place in June 2021, please save the date for these upcoming events:    

Bridge2AI Program Town Hall
June 9, 2021
2:00-3:30pm ET
Bridge2AI Data Generation Project Module Microlabs
June 14, 16, and 18, 2021
2:00-4:00pm ET each day
Bridge2AI Grand Challenge Team Building Expo
June 23, 2021
11:00am-5:00pm ET


Further information about how to register and participate in these events, as well as an online networking platform, will be coming soon. Please check the Bridge2AI Scientific Meetings page for updates.    Please refer to the research opportunity announcement (OTA-21-008) for additional information on application submission and review. A Letter of Intent (LOI) is required, LOIs must be emailed to bridge2ai@od.nih.gov by 11:59 PM ET on or before July 20, 2021.   We encourage you to share the Bridge2AI listserv signup with your contacts and networks so they will receive updates on future funding announcements and the latest news from the Bridge2AI program. You can also keep up to date with the latest information by visiting the Bridge2AIwebsite. Questions can be sent to bridge2ai@od.nih.gov.

Read more about the vision for this new program in a recent NLM Director’s blog

PLOS and TCC Africa partner to support African researchers

The Open Access publisher PLOS, and the Training Centre in Communication, based at the University of Nairobi, Kenya, (known as TCC Africa) have announced a partnership to ensure that the interests and values of African research communities are represented in PLOS publications, policies, and services. The two organizations will work together to study and co-create pathways to Open Research that work for African researchers and stakeholders within the scholarly community ecosystem, while preserving the core tenets of Open Research.

“This is the beginning of an amazing partnership that will support higher education stakeholders in adopting open science, which will help increase their research visibility,” said Joy Owango, Executive Director TCC Africa. “PLOS and TCC Africa have similar objectives in supporting the research and academic community by  democratizing  research through effective adoption of open science.”

Find out more about the partnership.