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Education: Computational Biology Education

COSI Track Presentations

Schedule subject to change
Wednesday, July 24th
10:15 AM-10:20 AM
Welcome and Introduction
  • Russell Schwartz
10:20 AM-11:20 AM
Keynote talk: Training, Teaching, Technology, Togetherness – Promoting Knowledge Exchange in Life Sciences Through Communities of Practice
  • Jason Williams

Presentation Overview: Show

As the pace and scope of research in the life sciences accelerates, education in new methods (especially computational ones) has been a pressing concern. At the undergraduate level, many institutions are working to introduce bioinformatics and data science into the curriculum. Our research on undergraduate bioinformatics education in the U.S. revealed that although 95% of undergraduate faculty/educators believe bioinformatics should be integrated into their teaching, only 40% manage to do so (with clear disparities for faculty at less-resourced institutions). At the graduate and post-graduate level, training on a number of data related topics is also in high demand. Our survey of US National Science Foundation-funded investigators in the biological sciences concluded that training in several areas of bioinformatics are the most unmet need for established researchers.

Some of the most recent and successful educational efforts in the life sciences implicitly (or explicitly) borrow from a “Community of Practice” model. One source defines a Community of Practice (COP) as “groups of people who share a concern or a passion for something they do and learn how to do it better as they interact regularly.” The Carpentries (Software, Data, Library) – a global group of nearly 2000 volunteer instructors working to build data and software skills – are an explicit community of practice and have had tremendous impact on the life sciences. Several other communities (too many to list: e.g. GOBLET, Galaxy, H3ABioNet, etc.) could be viewed not just organizations with educational objectives as, but COPs.

Drawing on several efforts (including those mentioned above), this talk explores the potential role for COPs as an ideal way to promote knowledge exchange in the life sciences – a discipline that is rapidly progressing, but also rapidly specializing into many sub-domains across several scales (from ecological understanding of artic climates to single-cell transcriptomics). While the need for education within a discipline is neither new, nor unique to biology – a COP model may be flexibly applied to this use case to address challenges: 1) Teaching – revising formal education curricula, 2) Training – creating career-long learning and scaling train-the-trainer networks; and also to take advantage of an foster opportunities 1) Togetherness – aligning researchers by discipline needs and within affinity groups (diversity), 2) Technology – harnessing the power of technology to make open education resources and cyberinfrastructure accessible, and use communication vehicles to empower even small and/or remote groups.

11:20 AM-11:40 AM
Clinical Bioinformatics education to the masses: enabling change in healthcare
  • Frances Hooley, The University of Manchester, United Kingdom
  • Rebecca Bennett, The University of Manchester, United Kingdom
  • Angela Davies, Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom
  • Andy Brass, Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom

Presentation Overview: Show

Introduction
Genomics is revolutionising healthcare, enabled by next generation sequencing, requiring workforce transformation to improve genomic literacy and data analysis skills. Here we demonstrate how development of the world’s first Massive Online Open Course (MOOC) in Clinical Bioinformatics has educated thousands of healthcare professionals, patients and public.

Methodology
Hosted by FutureLearn the MOOC explores bioinformatic fundamentals to clinical working practices, ethics and tools. Social discourse is embedded throughout, enabling knowledge exchange and development between learners, "follow", “like” and "bookmark" functions to enable applauding of specific comments.

Results
The course has attracted 17, 000 learners, the largest from the UK, Egypt, India and USA, of those stating their profession, 31%, the largest group, identified as working in health and social care and was most popular with participants aged 18-35, educated to at least degree level. Evaluation showed 78% of 145 learners liked/strongly liked social learning, enjoying online discussions and interacting with other learners, 92% of 80 learners agreed/strongly agreed that the course had increased their understanding of clinical bioinformatics.

Conclusions
This course has provided knowledge and skills in clinical bioinformatics and improved genomic literacy at a global scale, providing a unique platform for discussion between clinicians and the public.
https://www.futurelearn.com/courses/bioinformatics

11:40 AM-12:00 PM
FAIR Training in ELIXIR Europe
  • Gabriella Rustici, University of Cambridge, United Kingdom
  • Mateusz Kuzak, Dutch Techcentre for Life Sciences, ELIXIR-Netherlands, Netherlands
  • Sarah L Morgan, EMBL-European Bioinformatics Institute, United Kingdom
  • Melissa L Burke, EMBL-European Bioinformatics Institute, United Kingdom
  • Celia van Gelder, DTL, Netherlands
  • Patricia M. Palagi, SIB Swiss Institute of Bioinformatics, Switzerland
  • Peter McQuilton, University of Oxford, United Kingdom
  • Pascal Kahlem, ELIXIR Hub, United Kingdom
  • Kim Gurwitz, University of Cambridge, United Kingdom
  • Victoria Dominguez Del Angel, French Institute of Bioinformatics, France
  • Niall Beard, The University of Manchester, United Kingdom
  • Ricardo Arcila, EML-EBI, United Kingdom
  • Bérénice Batut, University of Freiburg, Germany
  • Leyla Jael García Castro, EMBL-EBI, United Kingdom
  • Denise Carvalho-Silva, EMBL-EBI | Open Targets, United Kingdom
  • Fotis Psomopoulos, INAB|CERTH, Greece
  • Paula Martinez, ELIXIR-Belgium, Belgium

Presentation Overview: Show

ELIXIR [1] is an intergovernmental organization that brings together life science resources across Europe. These resources include databases, software tools, training events and materials, cloud storage, and supercomputers. ELIXIR's activities are divided into the following five areas Data, Tools, Interoperability, Compute and Training known as “platforms”. The ELIXIR Training Platform coordinates training activities, trains life-science researchers, and helps scientists and developers to find the training they need. One of the goals of ELIXIR is to coordinate these resources so that they form a single interconnected infrastructure. This infrastructure makes it easier for scientists to find and share data, exchange expertise, and agree on best practices, such as best practices for developing and sharing training materials.
The FAIR Training Working Group was first informally formed after the “How to make training FAIR” workshop held at the ELIXIR All Hands Meeting in Berlin in 2018. During the workshop, it became clear that there are two different but interdependent topics (1) availability and findability of training materials about FAIR Data Stewardship, (2) making training resources FAIR. Within the Working Group, two Task Forces have been established, and their activities will be highlighted in this talk.
[1] https://elixir-europe.org/

12:00 PM-12:20 PM
Towards a community-endorsed data steward description for life science research
  • Salome Scholtens, UMCG, Netherlands
  • Petronella Anbeek, UMCU, Netherlands
  • Jasmin K. Böhmer, UMCU Bioinformatics Expertise Core, Netherlands
  • Mirjam Brullemans, Radboudumc, Netherlands
  • Marije van der Geest, UMCG, Netherlands
  • Mijke Jetten, Radboud University, Netherlands
  • Christine Staiger, Dutch Techcentre for Life Sciences (DTL), Netherlands
  • Inge Slouwerhof, UMCG, Netherlands
  • Celia van Gelder, DTL, Netherlands

Presentation Overview: Show

In a ZonMw funded 1-year project we are working to make the data steward function concrete, to create consensus on the function description and required competencies, and to develop tailored education. Sustainable implementation of the outcomes of the project and alignment with existing education is ensured by close collaboration with our consultation committee that has representatives of a.o. LCRDM, NFU, Data4lifesciences, ZonMw, the HANDS handbook, SURFsara, DTL/ELIXIR-NL and HBO institutes. The project has delivered the first version of a community endorsed Life-sciences data steward function matrix (DOI: 10.5281/zenodo.2561723). This matrix is based on an analysis of existing competency frameworks for data stewardship in recently published reports from EOSCpilot, EDISON and Purdue, complemented with a review of over 40 published vacancies texts and experiences of persons working as data experts. The next step is to formulate an agreed set of knowledge, skills and abilities (KSAs) which will be translated into concrete learning objectives, which in turn will be used to develop an education line for data stewards (including a design for an eLearning module). All project outputs will be shared with the community on https://zenodo.org/communities/nl-ds-pd-ls/about/.

12:20 PM-12:40 PM
Proceedings Presentation: scOrange – A Tool for Hands-On Training of Concepts from Single Cell Data Analytics
  • Martin Stražar, University of Ljubljana, Slovenia
  • Anup Parikh, Naringi Inc., United States
  • Andrew Lamire, Howard Hughes Medical Institute, United States
  • Menon Vilas, Howard Hughes Medical Institute, United States
  • Gad Shaulsky, Baylor College of Medicine, United States
  • Janez Demšar, University of Ljubljana, Slovenia
  • Anže Starič, University of Ljubljana, Slovenia
  • Pavlin Poličar, University of Ljubljana, Slovenia
  • Aleš Erjavec, University of Ljubljana, Slovenia
  • Vesna Tanko, University of Ljubljana, Slovenia
  • Jaka Kokošar, University of Ljubljana, Slovenia
  • Lan Žagar, University of Ljubljana, Slovenia
  • Blaž Zupan, University of Ljubljana, Slovenia

Presentation Overview: Show

MOTIVATION: Single-cell RNA sequencing allows us to simultaneously profile the transcriptomes of thousands of cells and to indulge in exploring cell diversity, development and discovery of new molecular mechanisms. Analysis of scRNA data involves a combination of non-trivial steps from statistics, data visualization, bioinformatics, and machine learning. Training molecular biologists in single-cell data analysis and empowering them to review and analyze their data can be challenging, both because of the complexity of the methods and the steep learning curve.
RESULTS: We propose a workshop-style training in single cell data analytics that relies on an explorative data analysis toolbox and a hands-on teaching style. The training relies on scOrange, a newly developed extension of a data mining framework that features workflow design through visual programming and interactive visualizations. Workshops with scOrange can proceed much faster than similar training methods that rely on computer programming and analysis through scripting in R or Python, allowing the trainer to cover more ground in the same time-frame. We here review the design principles of the scOrange toolbox that support such workshops and propose a syllabus for the course. We also provide examples of data analysis workflows that instructors can use during the training.

2:00 PM-3:00 PM
Keynote talk: TBA
  • Daniel Barker
3:00 PM-3:20 PM
Scaffolding undergraduate student learning with video instruction - a case study
  • David Martin, University of Dundee, United Kingdom

Presentation Overview: Show

Computational Biology is now mainstream in high quality undergraduate curricula in the Life Sciences. This can come as a challenge to undergraduates enrolled on a biology degree who may not have an advanced (post 16) mathematical qualification. They are then faced with computational biology and research methods courses that require them to gain skills in data analysis and statistics. Entry level classes are typically large (>100 students) with a broad range of abilities and prior knowledge. Teaching a class like this effectively is challenging - students learning new concepts need to build and use new mental models in order to retain and understand the materai. If an instructor does not wish to abandon the slower students, and pauses to deal with issues, this forces an interruption in concentration for the rest of the class and a subsequent loss of these new constructs and hence poor learning.
In this presentation I will show how we have addressed this challenge through the use of video led workshops, enabling students to study at their own pace without forced interruptions. I will discuss where these methods can be effectively used and where they are less desirable.

3:20 PM-3:40 PM
Challenges and solutions to teach structural bioinformatics to biochemistry undergraduate students in short university modules
  • Ozlem Tastan Bishop, Rhodes University, South Africa

Presentation Overview: Show

In South Africa, the bachelor (BSc) degree is three years. Students may continue with one-year Honours studies (BSc Honours) to get a further degree. Honours studies provide a bridge to the postgraduate studies, and involve course work as well as a mini research project. Although Rhodes University gives Bioinformatics degree at MSc and PhD levels via studies performed at the Research Unit in Bioinformatics (RUBi), it has not been established as a separate discipline at the undergraduate and Honours levels. RUBi, which is located in the Department of Biochemistry and Microbiology, collaborates with the Biochemistry division and teaches short modules at 3rd year and Honours levels. The teaching time is very short, students are unfamiliar with bioinformatics related topics, and their background is inadequate for technical details; thus, over the years various teaching approaches were developed to tackle these challenges. The main education question is – What is the best way to make students familiar with basic terminology and approaches in structural bioinformatics in short modules? This presentation will summarize the approaches applied to 3rd year biochemistry and Honours students.

3:40 PM-4:00 PM
Meet-U : Educating through Research Immersion
  • Anne Lopes, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, UPSay, France
  • Elodie Laine, Sorbonne Université - Laboratory of Computational and Quantitative Biology (LCQB, CNRS-SU), France

Presentation Overview: Show

Biology is undergoing a revolution thanks to high-throughput technologies and increasing computing resources. To keep up with this evolution, we need to prepare students for collaborative work . We propose Meet-U, a new educational initiative that mimics the setup of collaborative research projects and takes advantage of the most popular tools for collaborative work and of cloud computing. Students are grouped in teams of 4–5 people and have to realize a project from A to Z that answers a challenging question in biology. Meet-U promotes "coopetition," as the students collaborate within and across the teams and are also in competition with each other to develop the best final product. Meet-U promotes students’ success by immersing them into the research “ecosystem”. Specifically, a final meeting day, open to everyone, is organized to showcase the students’ projects and gather the scientific community. Students have the opportunity, for the first time, to present their work in front of a jury of researchers and create their first network. Meet-U has been running for 3 years as a collaborative course between 3 universities from Paris area. It is easily transferrable to other universities and disciplines.

4:40 PM-5:00 PM
Crossing continents, experience of using video sharing services to deliver biological sequence analysis and visualisation training around the world
  • Suzanne Duce, University of Dundee, United Kingdom
  • Ben Soares, University of Dundee, United Kingdom
  • Mungo Carstairs, University of Dundee, United Kingdom
  • James Procter, University of Dundee, United Kingdom
  • Geoff Barton, University of Dundee, United Kingdom

Presentation Overview: Show

Bioinformatics plays a crucial role within life science research, and provides platforms for annotating, analysing, visualising and interpreting biological data. As the power and sophistication of these bioinformatics platforms increases, unsurprisingly, so does the demand for bioinformatics training. Yet studies show that there is a serious training deficit, including an acute shortage of skilled trainers and training courses. Finding ways to meet the global demand for bioinformatics education and provide high-quality training to research scientists is a major challenge facing the bioinformatics community. Jalview (www.jalview.org) is one of the most widely used applications in education and research for visualising and analysing multiple sequence alignments. We describe how the Jalview team have utilised popular video sharing platforms (YouTube and Vimeo) to deliver training. The Jalview Online Training channel has over 60,000 views from over 140 countries. Of these countries, at least 80 are Low-and-Middle-Income (LMIC) countries and they account for 25% of the views. As we continue to review and revise our training videos in line with new developments in the Jalview platform, we need to ask the question: Where to next? We look forward to sharing our experiences and discussing the potential offered by other engagement approaches.

5:00 PM-6:00 PM
The African Genomic Medicine Training Initiative: Showcasing A Community-Driven Genomic Medicine Competency-Based Training Model for Nurses in Africa (Travel Fellowship funded by GOBLET)
  • Vicky Nembware
Thursday, July 25th
8:35 AM-8:40 AM
WEB Introduction
  • Cath Brooksbank, EMBL-European Bioinformatics Institute, United Kingdom
8:40 AM-9:40 AM
Keynote: Developing guidelines and resources for bioinformatics trainers and educators
  • Nicola Mulder, University of Cape Town, South Africa

Presentation Overview: Show

Bioinformatics training and degree programs have been developed world-wide to address the gaps in skilled students and personnel able to develop algorithms and/or analyze biological data. Bioinformatics is a broad topic, with trainees entering from a broad range of backgrounds. This makes development of appropriate training or degree programs challenging. Additionally, the field is moving rapidly so it is important for trainers to keep their training materials current. Not all bioinformatics trainers and educators have had prior experience in designing courses that are able to transfer the necessary skills and develop relevant competencies in trainees. While many bioinformatics training resources and materials exist, these are spread over different websites and may not be easy to find. To overcome some of these challenges, bioinformatics trainers and academics designing new bioinformatics degree programs gathered at a Bioinformatics Education Summit in Cape Town to develop guidelines and resources for trainers, including competency frameworks, guidelines for developing courses based on competencies, a train-the-trainer curriculum, trainer guideline documents and a trainer portal. Here I will discuss some of the community-driven outputs and the development of a community of trainers and educators.

10:20 AM-10:40 AM
The Mastery Rubric for Bioinformatics: a tool to support curriculum design and evaluation
  • Rochelle E. Tractenberg, Georgetown University Medical Center, United States
  • Jessica M. Lindvall, NBIS, Sweden
  • Teresa K. Attwood, The University of Manchester, United Kingdom
  • Allegra Via, IBPM-CNR, Italy

Presentation Overview: Show

As the life sciences have become more computational and data-intensive, the pressure to incorporate the requisite training into life-science education and training programmes has increased. To facilitate curriculum development, various sets of bioinformatics competencies have been articulated; however, these have proved difficult to implement in practice. Addressing this issue, we have created a curriculum-design and -evaluation tool – the Mastery Rubric for Bioinformatics (MR-Bi) – to support the development of specific Knowledge, Skills and Abilities (KSAs) that promote bioinformatics practice and the achievement of competencies.
12 KSAs were extracted via formal analysis, and stages along a developmental trajectory were identified. The KSAs and their performance level descriptors at each stage were formulated, ultimately yielding the MR-Bi.
The MR-Bi prioritises the development of independence and scientific reasoning. It can be used by developing or practicing scientists at all career stages to direct their (and their team’s) acquisition of new, or to deepen existing, bioinformatics KSAs. It can be used to strengthen teaching and learning and for curriculum building. It can thereby contribute to the cultivation of a next generation of who can design reproducible and rigorous research, and to critically analyse results from their own, and others’, work.

10:40 AM-12:40 PM
WEB Workshop Session
  • Cath Brooksbank, EMBL-European Bioinformatics Institute, United Kingdom