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Session A: (July 22 and July 23)	Session B: (July 24 and July 25)
Presentation Schedule for July 22, 6:00 pm – 8:00 pm A) 3DSIG B) BioVis C) Function D) HitSeq E) RegSys F) SysMod G) TransMed H) Special Session (SST01): Text Mining for Biology and Healthcare Presentation Schedule for July 23, 6:00 pm – 8:00 pm I) Bio-Ontologies J) CompMS K) EvolCompGen L) Microbiome M) NetBio	Presentation Schedule for July 24, 6:00 pm – 8:00 pm P) BOSC Q) CAMDA R) Education S) MLCSB T) RNA U) VarI V) General Computational Biology
Session A Poster Set-up and Dismantle Session A Posters set up: Monday, July 22 between 7:30 am - 10:00 am Session A Posters should be removed at 8:00 pm, Tuesday, July 23.	Session B Poster Set-up and Dismantle Session B Posters set up: Wednesday, July 24 between 7:30 am - 10:00 am Session B Posters should be removed at 2:00 pm, Thursday, July 25.

Short Abstract: The ELIXIR Training Platform is tasked with providing a high-quality, coherent, timely, and impactful training program across the ELIXIR network. As part of the ELIXIR-EXCELERATE grant, the Quality and Impact subtask was set up to develop a framework to assess the quality of ELIXIR-badged training courses in the short term (i.e. directly after a training event) and training impact in the long term (i.e. six months to one year after a training event). So far, a common feedback collection approach has been approved and endorsed by ELIXIR Head of Nodes, and commented on, adopted, and implemented by the vast majority of ELIXIR Training Coordinators, to standardise collection of a core set of feedback metrics, across ELIXIR Nodes. Data has been collected since September 2015 showing promising results. We are currently designing and implementing a Training Metrics Database to streamline collection, storage, visualisation, and reporting of ELIXIR training-related statistics and feedback. Here we will present the results of the work done so far as well as discuss future plans. Training quality and impact assessment activities within other EU grants, such as EOSC-life and the European Joint Project on Rare Diseases, will be based on the strategy here presented.

Short Abstract: UNSW Sydney (The University of New South Wales) has been offering undergraduate degrees in bioinformatics since 2001, including a Bachelor of Engineering (Bioinformatics Engineering) and more recently a Bachelor of Science (Bioinformatics). These degrees include a number of dedicated bioinformatics courses, some of which are focused on the application of bioinformatics towards biological research, with the others emphasizing the theory and engineering of bioinformatics software systems. The applied bioinformatics courses have made heavy use of supervised computer lab sessions where students get to apply and compare a range of bioinformatics software tools and approaches. With the increase of popularity in these courses, supervised labs have become increasingly impractical due to lack of resources, including large enough computer laboratories and qualified tutors to supervise and mark the lab reports. This is driving a shift towards blended learning and “flipped” laboratory sessions. The supervised lab sessions are gradually being replaced by self-guided computer exercises followed by a laboratory-based consultation session where students can bring their questions to the lecturers. The self-guided exercises are implemented using the Moodle Learning Management System, allowing automatic marking and efficient student feedback at a much larger scale than in supervised laboratories.

Short Abstract: During the past decade, concern about bioinformatics/computational skills gaps amongst life-scientists has been growing. Opportunities for training are available worldwide, but international surveys have shown that training is often only sought at the ‘point-of-need’; typically, skills acquired at this late stage are quickly lost. The earlier computational thinking is introduced and bioinformatics skills are engrained, the more likely they are to be retained. This argues for investment in training at undergraduate level – or sooner – so that data-analysis and scripting become fundamental skills for biologists. Initiatives to incorporate bioinformatics even earlier in the education cycle are gaining traction. Here, we present some of these: the 4273π project in Scotland; SIB’s bioinformatics education outreach programme; the Dutch Bioinformatics at school programme (from the global Amgen Biotech Experience programme); and high-school teacher workshops co-organised by bioinformatics.ca and GOBLET. We highlight a range of open, standardised Critical- and Practical-Guides (from the Introduction to Bioinformatics, and Bringing Bioinformatics into the Classroom series) being developed by the GOBLET Foundation to support these and other educational enterprises. Together, we aim to help prepare a new cohort of more computationally minded life-scientists, to give them confidence to manage the scripting and analytical components of their research.

Short Abstract: 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/.

Short Abstract: The 4273pi bioinformatics education project develops and delivers free bioinformatics workshops for secondary school students across Scotland. We have reached ~140 schools directly (e.g. visits to whole classes) or indirectly (teacher CPD events). Our workshops are educational and include a public engagement component, going beyond the curriculum in areas such as nutrition and food safety. With biology classes, we reach an almost entirely new and largely female audience for scientific computing. Our workshop "Bioinformatics: The Power of Computers in Biology" links to the SQA Higher Biology and Higher Human Biology curricula, which include bioinformatics and mutations (students typically 15-18 years old). In a case-study of the GULO gene/pseudogene, students run BLAST at the NCBI Web site, then at the Linux command-line on Raspberry Pi computers. Our workshop "Bioinformatics: Food Detective" links to the SQA National 4 and National 5 Biology curricula, which include DNA (students typically 13-16 years old). This workshop uses BLAST via the NCBI Web site in a DNA barcoding exercise, identifying to species level a sample of DNA sequence reads from a handmade pork sausage. Materials will reach a wider audience through contribution as Practical Guides to the GOBLET Foundation. We outline our workshops and feedback received.

Short Abstract: Mitochondrial biology is integral to our fundamental understanding of human health and many diseases. Despite a large volume of existing knowledge and increased public interest, its access and comprehension remain largely unavailable to the scientific community and public at large. The GeneWiki project, an effort within Wikipedia, was established to bridge the gap between esoteric and common knowledge. However, many mitochondrial proteins remain inadequately represented and poorly annotated. We have taken a concerted effort to identify and address these deficiencies. We have identified pages for update, trained students on concepts of mitochondrial biology and their scientific writing, and the results are astonishing. With the participation of 35 high school summer interns, 10 undergraduate college students, and 2 graduate students we have accomplished significant results: creating 75 new pages, improving 466 pages, enhancing and enriching the content of 2,432 sections, incorporating 5,674 references and 18,386 semantic links, with an overall contribution of 4,030 kB. In conclusion, we have improved 541 Wikipedia articles on mitochondrial proteins and biomolecules (e.g. metabolism, OXPHOS, redox), introduced basic bioinformatics and biocuration tools and strategies to students, and instilled FAIR Principles in the next generation of scientists, clinicians, and researchers.

Short Abstract: Findable, Accessible, Interoperable and Reusable (FAIR) principles provide a framework of minimum elements required for an effective management of digital resources. Some of the main aspects are: persistent and global identification, licensing and longevity commitment policies. Using metadata is one of the FAIR pillars; however, metadata requirements can vary from one digital resource to another, making the implementation of the FAIR principles challenging.For example, rich descriptions using a plurality of attributes and meeting community standards can be found without further clarification. The ELIXIR Training Platform established a FAIR-focused working group opened to participants from 23 ELIXIR nodes. Here, we report on 10 recommendations to make your training materials FAIRer. We consider for Findability, keywords, versioning and publication in specialized registries; for Accessibility, using public repositories together with clear access and contribution rules; for Interoperability, references to other elements used or related to the training material as well as trainee-oriented elements such as learning outcomes, prerequisites, and required skills; for Reusability, license, citation and contact details plus some trainer-oriented elements such as audience, instructions and easy-to-reuse formats, e.g. markdown rather than PDF. This effort will contribute to FAIRness for people (trainers, trainees) and machines for the benefit of science.

Short Abstract: 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.

Short Abstract: 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/

Short Abstract: Knowledge of your audience is key to developing appropriate training for specific learning needs. This can be challenging for open online training where we may not have concrete knowledge of our audience and their motivations. Gathering information on online trainees is particularly difficult when they are anonymous, as is the case with many of EMBL-EBI’s Train online users. This makes methods used for gathering information in face-to-face training, such as surveys and personal feedback, difficult to implement. We instead rely on hypotheses based on our face-to-face audience to shape the training, and various metrics as indicators of users’ behaviour and course popularity. While useful, these statistics leave us wondering about the trainees’ learning experience and the subsequent impact on their work. At EMBL-EBI we have embarked upon a project to address these questions. We are employing a variety of approaches including web analytics and user research. Here we present an outline of these approaches, our preliminary findings and how this information will feed back into our course development cycle.

Short Abstract: 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.

Short Abstract: 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.

Short Abstract: Replicating face-to-face training at distance presents numerous challenges, here we present our trials with two modes of distance training involving new technology and blended learning approaches. 1. Learner-at-distance At EMBL-EBI we often have a participant who, at last minute, cannot join us in Hinxton due to visa, monetary or illness issues. Thanks to developments in technology for children with long-term illness and our externally-accessible compute environment we have enabled learners to fully participate, including networking in discussions. This is thanks to a small robot avatar sitting in the training room as the eyes, ears and mouth of the trainee. 2. Trainer-at-distance To support several postgraduate courses in Latin America we developed a blended series approach using live webinars and EMBL-EBI online training materials. Trainers sit in Hinxton and deliver an initial introductory session before tasking students with online exercises (using local TA support if needed). Learners return the following day for detailed online Q&A session with trainers. Both modes have enabled us to reach audiences who would ordinarily be unable to join our f2f training. Though challenging at times, we have received extremely positive feedback and are now looking to roll these options out further over the coming year.

Short Abstract: Assessing training impact is a key element in measuring the success of a training programme, yet the methods used for such assessments are many and varied. At EMBL-EBI we collect a vast amount of data in relation to the training that we develop and deliver, enabling us to shape individual courses and the strategic direction of the whole programme. Our starting point was defining the impact we wanted to have: 1. Impact upon the individual learner (trainees gaining the skills and knowledge they wished to acquire); 2. Impact upon the global life science community (reach for face-to-face course applicants; location of off-site courses and users of online training) 3. Impact upon the organisation (what impact upon EMBL science / data resources; value of staff time in delivering training) By employing a mix of qualitative and quantitative indicators we have defined a set of potentially transformative measures that both inform us of our impact and areas of change or required review at trainee, course and programme level. These are collected via surveys, web analytics, application data and trainer self-reporting. This collection effort involves our entire training community and provides us with an understanding of impact across this community and beyond.

Short Abstract: With the increasing amounts of data produced in biomedical research, training of researchers in data skills is needed and in high demand. In 2018 we circulated an Expression of Interest around our institute to assess demand for acquiring data skills and received >100 responses. In response to the demand, we've provided training courses in R, Python and Galaxy and places have been filled in minutes. For the teaching content, we are making an effort to use material by others in the community where possible, and also adapting content to what we believe is most useful to our researchers. We've used a format of multiple short sessions, typically weekly, lasting a couple of hours. Short session format was used, rather than full day or multi-day sessions, to give attendees time to digest the information between sessions and to try to integrate the teaching more easily into schedules for both attendees, trainers and helpers. In the feedback form we ask whether the attendees would prefer a longer (day or multi-day) format and so far all attendees have said they prefer a short session format.

Short Abstract: 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.

Short Abstract: High-throughput sequencing technologies require scientists to learn and master new technical competences, and the use of High Performance Computing (HPC) machinery is one of them, creating a need for new training topics. While face-to-face courses remain essential for the sake of the human and lively interactions of trainees, their constraints in audience size, location and time availability are a challenge. To overcome these issues, the SIB Swiss Institute of Bioinformatics (the Swiss ELIXIR Node), has developed an e-learning module in HPC, in the context of the ELIXIR-EXCELERATE project. Composed of theory and quizzes, it aims at providing beginners the keys to properly understand the concept of HPC, its operation and rules, and data management and storage. This module was conceived as a self-learning product or as the electronic component of a blended training format (i.e. as a complement to a face-to-face course) necessary for new HPC cluster users. In this latter case, the module is aimed at equalizing the skill level prior to the face-to face course. Preliminary results confirm the usefulness of the e-learning module in this context. The module is available (guest access) on the SIB Training Portal at https://edu.sib.swiss/course/view.php?name=HPCeL.