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Posters - Schedules

Poster presentations at ISMB/ECCB 2021 will be presented virtually. Authors will pre-record their poster talk (5-7 minutes) and will upload it to the virtual conference platform site along with a PDF of their poster beginning July 19 and no later than July 23. All registered conference participants will have access to the poster and presentation through the conference and content until October 31, 2021. There are Q&A opportunities through a chat function and poster presenters can schedule small group discussions with up to 15 delegates during the conference.

Information on preparing your poster and poster talk are available at: https://www.iscb.org/ismbeccb2021-general/presenterinfo#posters

Ideally authors should be available for interactive chat during the times noted below:

View Posters By Category

Session A: Sunday, July 25 between 15:20 - 16:20 UTC
Session B: Monday, July 26 between 15:20 - 16:20 UTC
Session C: Tuesday, July 27 between 15:20 - 16:20 UTC
Session D: Wednesday, July 28 between 15:20 - 16:20 UTC
Session E: Thursday, July 29 between 15:20 - 16:20 UTC
Assessing understanding of simple bioinformatics algorithms with the Moodle quiz “formulas” question type
COSI: Education
  • Bruno Gaeta, UNSW Sydney, Australia

Short Abstract: One of the biggest hurdles in the shift to online education brought about by the current pandemic is the design of online, unsupervised summative assessment tasks that minimise the risk of cheating and plagiarism. The quiz engine built into the Moodle Learning Management System includes a “Formulas” question type that allows scripting questions where the answer needs calculating from a set of randomly generated values. During the test or exam, Moodle provides each student with a different set of random numbers for the wildcards to be used in the formulas, which makes cheating by sharing of answers more difficult. Although the Formulas question type was designed for assessing relatively simple problems, its syntax allows for some simple logic functions.

As part of an introduction to bioinformatics course, this framework was harnessed to design a series of questions that test students’ understanding of sequence alignment, UPGMA and graph-based sequence assembly algorithms. In addition to minimising opportunities for cheating, the setup allows the questions to be marked automatically as well as the generation of practice questions for the students to learn about the algorithms.

Bioin4girls 2020: Brazilian (women) symposium in Bioinformatics
COSI: Education
  • Ana Carolina de Moraes Mello, Universidade Federal do Rio Grande do Sul, Brazil
  • Ágnis Grefenhagen, Universidade Federal do Rio Grande do Sul, Brazil
  • Cristal Villalba, Universidade Federal do Rio Grande do Sul, Brazil
  • Lariane Frâncio, Universidade Federal do Rio Grande do Sul, Brazil
  • Mariana Botton, Universidade Federal do Rio Grande do Sul, Brazil
  • Marina Hentschke, Universidade Federal do Rio Grande do Sul, Brazil
  • Martiela Freitas, Universidade Federal do Rio Grande do Sul, Brazil
  • Paola Carneiro, Universidade Federal do Rio Grande do Sul, Brazil
  • Ursula Silveira Matte, Genetic Therapy Laboratory, Clinical Hospital of Porto Alegre, Brazil
  • Mariana Recamonde-Mendoza, Institute of Informatics, Universidade Federal do Rio Grande do Sul, Brazil

Short Abstract: Women are underrepresented in bioinformatics, despite its foundation by Margaret Dayhoff. Remarkable differences are observed between the gender ratio for bioinformatics' parent fields, with biology being more balanced than computer science. In Brazil, most workshops and scientific events feature only men as speakers. Even when females are represented, they are often the minority. Motivated by this background, we organized an online event called BioIn4Girls with talks spanning seven major topics in bioinformatics, all given by female researchers. Besides, 100% of the steering committee members were women. We sought to promote ethnicity and gender identity diversity among speakers and organizers. Talks were given in Portuguese, and the event audience comprehended 1705 registered attendees from 26 states of Brazil and 18 countries. An average of 1800 people watched the talks on Youtube. To our best knowledge, BioIn4Girls was the first symposium on bioinformatics in Brazil to feature women exclusively as speakers, with a great receptivity. The event gave visibility to brilliant women researchers and their contributions to bioinformatics and, at the same time, gave room to newcomers. In the future, we hope to continue promoting gender equity in science and bioinformatics by highlighting women as role models in the research field.

Bioinformatics capacity building for life sciences educators in Spanish-speaking Latin American countries
COSI: Education
  • Patricia Carvajal-López, EMBL-EBI, United Kingdom
  • Maria Bernardi, Universidad de Buenos Aires, Argentina
  • Zuami Villagrán-de la Mora, Universidad de Guadalajara, Mexico
  • Mindy Muñoz, Universidad Espíritu Santo, Ecuador
  • Piraveen Gopalasingam, EMBL-EBI, United Kingdom
  • Alejandra Escobar-Zepeda, EMBL-EBI, United Kingdom
  • Carolina Reyes, Universidad Nacional Agraria, Honduras
  • Teresa de Jesús Sandoval-Contreras, Tecnológico de Tepic, Mexico

Short Abstract: Bioinformatics education in Lower to Middle Income Countries faces many challenges, including the shortage of regional capacity in bioinformatics, the availability of materials and training in languages other than English and the additional burden of learning a second language. To address these challenges, we designed and delivered a virtual bioinformatics curriculum in Spanish over seven weeks to a group of lecturers in the Universidad Nacional de Agricultura (UNAG) in Honduras. Additionally, we delivered a virtual train the trainer workshop in Spanish to both UNAG lecturers and additional trainees across Latin America. Although EMBL-EBI has delivered these courses before in Latin America, this was the first time they were conducted in Spanish. These endeavours resulted in a group of lecturers trained in various bioinformatics topics, who were given additional skills in training design, both in-person and virtual delivery. Responses from trainees were positive and in the last year a number of trainees have advocated for more bioinformatics education in their department and course curricula, and are participating in projects with a larger bioinformatics component. We advocate for more training in Spanish and local languages to increase regional bioinformatics capacity.

Dutch roadmap towards national implementation of FAIR data stewardship
COSI: Education
  • Celia W.G. van Gelder, DTL, Netherlands
  • Mijke Jetten, DTL Dutch Techcentre for Life Sciences, Netherlands

Short Abstract: In the context of the Dutch National Programme Open Science, we have executed a project related to professionalising data stewardship, aiming to provide arguments and recommendations to ensure adequate data steward capacity in the Netherlands. It was a collaborative effort of over 30 representatives of universities, university medical centres, universities of applied sciences, service providers, and representatives of the major Dutch umbrella organisations. We performed a analysis of the data stewardship training and education landscape, based on case studies, we established the components of a job profile for data stewards (and research software engineers), we did an inventory of data-related trainings, including a pilot annotation of courses based on our data stewardship competency framework (doi.org/10.5281/zenodo.3471707), and we made a design for a data steward skills tool with navigation pathways. In February 2021 the end report of the project was published: Professionalising data stewardship in the Netherlands. Competences, training and education. Dutch roadmap towards national implementation of FAIR data stewardship (doi.org/10.5281/zenodo.4320504), ,which contains the outcomes, recommendations for all the stakeholders and next steps in the implementation trajectory, focusing on competences, training and education for data stewards.

Feedback analysis from in person and streamed SIB courses
COSI: Education
  • Monique Zahn, SIB Swiss Institute of Bioinformatics, Switzerland
  • Alessia Di Pietro, SIB Swiss Institute of Bioinformatics, Switzerland
  • Valeria Di Cola, SIB Swiss Institute of Bioinformatics, Switzerland
  • Wandrille Duchemin, SIB Swiss Institute of Bioinformatics, Switzerland
  • Isabelle Dupanloup, SIB Swiss Institute of Bioinformatics, Switzerland
  • Geert van Geest, SIB Swiss Institute of Bioinformatics, Switzerland
  • Diana Marek, SIB Swiss Institute of Bioinformatics, Switzerland
  • Gregoire Rossier, SIB Swiss Instititute of Bioinformatics, Switzerland
  • Frédéric Schütz, SIB Swiss Institute of Bioinformatics, Switzerland
  • Patricia M. Palagi, SIB Swiss Institute of Bioinformatics, Switzerland

Short Abstract: The SIB Swiss Institute of Bioinformatics Training group organizes courses, e.g. on data analysis and management, statistics, programming, machine learning, as well as specific applications in genomics and transcriptomics. These courses are characterized by being short, practical, and in-person (1).

Due to the COVID-19 pandemic, SIB courses starting early March 2020 were converted from in-person to online in record time. This was only possible thanks to the group member’s and trainers' flexibility and enthusiasm.

Twenty-nine SIB courses were streamed in 2020, and only four were cancelled. The online SIB Training courses received the SIB Remarkable Outputs 2020 award in recognition of outstanding achievement. From the teaching and training management perspectives, the lessons learned in the first months of streaming were reported in (2) and used to improve the following courses. The feedback received from trainers and trainees remained overall the same as for in-person courses, e.g., extremely positive, and the number of applications from Switzerland and worldwide, increased even further, indicating that our streamed courses remained on target, useful and appreciated.

We will present the feedback results from SIB courses held pre- and during-COVID-19.

References:
1. www.sib.swiss/training/past-training-courses#2020
2. f1000research.com/documents/9-1148

Innovative MOOCs for global bioinformatics training
COSI: Education
  • Rachel Berkson, Wellcome Connecting Science Courses and Conferences, United Kingdom
  • Dusanka Nikolic, Wellcome Connecting Science Courses and Conferences, United Kingdom

Short Abstract: Background/motivation for the review
Global access to high quality bioinformatics training is a key need. To reach as wide an audience as possible, we used the MOOC format, with short online courses that are free of cost, open to all, and allow thousands to be trained simultaneously. Here we discuss how we met the challenges of delivering bioinformatics training to a large, mixed audience.

Method and findings
We designed a range of courses using the FutureLearn platform, covering both general and specialized aspects of bioinformatics. We used social and conversational learning pedagogies to harness peer learning with an expert audience, as well as light touch facilitation by educators, to ensure an excellent educational experience for all learners. We relied on freely available online tools, made datasets available for learners to download, and created interactive exercises allowing learners to have hands-on experience outside the classroom. Over the past 3 years our courses have reached over 60,000 learners in 170 countries.

Conclusion
MOOCs provide a viable means for delivering bioinformatics training at scale, including in using specialist software for analysis. Many aspects of training such as social learning and hands-on experience can be successfully adapted to the online format.

Jalview School Workbook for Visualising DNA, RNA & Proteins
COSI: Education
  • Suzanne Duce, University of Dundee, United Kingdom
  • Benedict Soares, University of Dundee, United Kingdom
  • Mungo Carstairs, University of Dundee, United Kingdom
  • Jim Procter, University of Dundee, United Kingdom
  • Geoff Barton, University of Dundee, United Kingdom

Short Abstract: There are often limited opportunities to integrate practical exercises into the classroom despite it being widely accepted that a student’s learning experience is enhanced by practical activities that utilise their critical thinking skills [1]. Although developed as a research tool, Jalview’s (www.jalview.org) ease of use has made it ideal for teaching concepts in molecular biology and genetics that are often hard to communicate to school-age students. To help teachers, the Jalview Team developed several easy-to-use, web-based, hands-on exercises. They allow students to view protein and DNA sequences side-by-side, and interact with the 3D structures of DNA, RNA and protein molecules [2]. All that is required is a computer with a web-browser and internet access. Exercises are designed to reinforce principles being taught in the classroom. For example, students create a phylogenetic tree to compare protein sequences from different animals. They view the coding sequence, and codons, alongside the protein sequence. In Project 4, pupils can view the exons and introns in the gene involved in sickle cell anaemia, then identify the genetic mutation linked to this disease. These interactive projects have proved popular [3], last year they were run over 4,000 times.

[1] www.nature.com/articles/nrm1856
[2] www.jalview.org/sites/jalview.org/files/School-Workbook-%2829-04-2021%29.pdf
[3] cdn.rcsb.org/rcsb-pdb/general_information/news_publications/newsletters/2020q3/corner.html

Organising the EOSC-Life Remote training series: an exchange-of-experience forum for adapting face-to-face to remote training
COSI: Education
  • Daniel Thomas-Lopez, European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI) & ELIXIR-EBI, United Kingdom
  • Rebecca Ludwig, European Infrastructure for Translational Medicine (EATRIS), Netherlands
  • Vera Matser, European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI) & ELIXIR-EBI, United Kingdom

Short Abstract: The COVID-19 pandemic resulted in a sudden transition from face-to-face to remote training. We define virtual or remote events as events where there is a certain live interaction between participants and/or trainers. To support the EOSC-Life and Research Infrastructures (RI) community to transition to remote events, the EOSC-Life EU project developed a series of knowledge-exchange sessions for Life Science trainers and organisers.
The Remote training series started with a one-day workshop, attended by almost 70 participants, about how to adapt your event to a virtual setting. Afterwards, we launched informal monthly sessions to exchange experiences, questions and opinions. Certain sessions include live demonstrations of relevant tools and platforms. A key objective is to share lessons learnt, what worked and did not work well with a specific tool, format or audience. Periodical announcements are disseminated through internal channels, and the recorded sessions are accessible to the participants through a Youtube unlisted playlist.
The series has proven to be valuable and has created a community of practice within the RI network. Furthermore, longer one-day workshops about ‘Remote access to RI physical machinery and services’, ’Hosting hybrid events’ and ‘Improving accessibility in remote training’ are being organised.

Redesign and FAIRification of EMBL-EBI’s training website
COSI: Education
  • Nikiforos Karamanis, EMBL-EBI, United Kingdom
  • Sarah Morgan, EMBL-EBI, United Kingdom
  • Anna Swan, EMBL-EBI, United Kingdom
  • Ajay Mishra, EMBL-EBI, United Kingdom
  • Prakash Singh Gaur, EMBL-EBI, United Kingdom
  • Mahfouz Shehu, EMBL-EBI, United Kingdom
  • Cindy Natassia, EMBL-EBI, United Kingdom
  • Adam Broadbent, EMBL-EBI, United Kingdom
  • Melissa Burke, EMBL-EBI, United Kingdom
  • Joseph Rossetto, EMBL-EBI, United Kingdom
  • Peter Walter, EMBL-EBI, United Kingdom
  • Carla Oliveira, EMBL-EBI, United Kingdom
  • Catherine Brooksbank, EMBL-EBI, United Kingdom

Short Abstract: Over the last 18 months, following user feedback around findability of our training, we have been redesigning EMBL-EBI’s training website to showcase what is on offer and ensure our training is findable, accessible, interoperable and reusable, using the FAIR principles to guide us.

EMBL-EBI offers a range of training in data-driven life sciences, including face-to-face and virtual courses, webinars, online tutorials and course materials. To improve the findability of training, the site includes some new features, including a search box to focus on a topic of interest, filters to target specific types of courses and short overviews of courses within the listings pages. Individual course pages were redesigned to provide all the required information to decide if a course is suitable and to understand how to participate. To aid in design and accessibility, we adhered throughout to the newly developed EMBL visual framework.

To ensure our materials are reusable, we have added a new section ‘Support for trainers’. This provides descriptions of how materials and online content can be reused, alongside information on competency frameworks, tailored courses and support to help individuals develop their training skills.

Further development of the website is planned, focusing on personalisation and collaboration of learners.

The de.NBI training platform (SIG3)
COSI: Education
  • Daniel Wibberg, de.NBI / ELIXIR-DE / CeBiTec / Bielefeld University, Germany

Short Abstract: The 'German Network for Bioinformatics Infrastructure' (de.NBI) provides bioinformatics services and training to users in life sciences research, industry and biomedicine. Training activities of de.NBI are focused on supporting and training end users. To effectively coordinate training courses of the consortium, de.NBI has established the Special Interest Group 3 (SIG3 - Training and Education) also known as the de.NBI training platform. SIG3 is composed of training experts from each de.NBI unit.
Different types of training activities are supported and organzied by de.NBI. First of all, the de.NBI summer schools provide training courses for undergraduate and graduate students in specific topics related to one or several de.NBI nodes. The respective nodes organize tool-specific training. In addition, online training was introduced in 2016 and intensified by the Corona pandemic in 2020. Online training enables users first insights into bioinformatics tools. Between 2015 and 2021, de.NBI organized more than 350 training courses with more than 7000 participants.
According to the recent administrative developments, Germany joined ELIXIR. The German ELIXIR Node will be run by de.NBI. As a result, de.NBI also joined the ELIXIR Training Platform and SIG 3 already started to establish collaborations with ELIXIR in training activities.

The PerMedCoE competency framework to guide the training programme
COSI: Education
  • Vera Matser, European Bioinformatics Institute (EMBL-EBI), United Kingdom
  • Marta Lloret-Llinares, European Bioinformatics Institute (EMBL-EBI), United Kingdom
  • Joaquim Calbo, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology & Universitat Pompeu Fabra (UPF), Spain
  • Jose Carbonell-Caballero, Barcelona Supercomputing Centre (BSC), Spain
  • Javier Conejero, Barcelona Supercomputing Centre (BSC), Spain
  • Esther Dorado-Ladera, Barcelona Supercomputing Centre (BSC), Spain
  • Damjana Kastelic, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Spain
  • Ana María Morales, ATOS, Spain
  • Henrik Nortamo, CSC – IT Center for Science (CSC), Finland
  • Daniel Thomas-Lopez, European Bioinformatics Institute (EMBL-EBI), United Kingdom
  • Miguel Vazquez, Barcelona Supercomputing Centre (BSC), Spain
  • Alessandra Villa, KTH Royal Institute of Technology, Sweden

Short Abstract: PerMedCoE is a European Centre of Excellence (CoE) for High Performance Computing (HPC) that aims at providing an efficient and sustainable infrastructure to support personalised medicine, adapting cell-level simulation methods to pre-exascale systems to translate omics data into molecular disease models. One of the activities to achieve this consists of a training programme to educate professionals in life sciences and HPC communities about the capabilities of PerMedCoE developments.

We created a competency framework to define the training needs and, based on them, implement a training programme. A competency is an observable ability of any professional, integrating multiple components such as knowledge, skills and behaviours. The PerMedCoE framework lists the competencies for professionals within the scope of the CoE: developing cell-level simulation tools with the long-term vision of using them in the clinical context.

The competency framework will enable the definition of different professional profiles within its area of application, which can help people identify the abilities needed for working in a specific role (e.g. bioinformatician, tool developer), and therefore, inform their professional development.

We will present the structure of the PerMedCoE competency framework, the first profiles created within it and how to explore it in the EMBL-EBI Competency Hub.

Train the trainer as an effective model for sustainable bioinformatics training and capacity building
COSI: Education
  • Alice Matimba, Wellcome Connecting Science, United Kingdom
  • Dusanka Nikolic, Wellcome Connecting Science, United Kingdom
  • Rachel Berkson, Wellcome Connecting Science, United Kingdom
  • Treasa Creavin, Wellcome Connecting Science, United Kingdom
  • Darren Hughes, Wellcome Connecting Science, United Kingdom

Short Abstract: Background
Bioinformatics training in low and middle-income countries (LMICs) was historically led by researchers and experienced trainers based elsewhere. This may not reflect the intended impact and is increasingly becoming unsustainable due to limited trainer availability, high costs of travel and environmental effects.

Methods
Three Train-the-trainer (TtT) models were applied to address this challenge. Firstly, experienced trainers collaborated with experts from LMICs who were interested in training and who then learned while co-developing the courses. The second model developed mini TtT modules for over 320 participants during 16 bioinformatics courses. This enabled participants to reflect on their learning and develop post-course action plans to apply the tools provided and effectively pass on their expertise to others. Finally, dedicated TtT courses have also been developed in face to face and online formats.

Results and Conclusion
Over 90% of the LMICs courses we offer are now led or co-led by instructor trainees from the respective regions in Africa, Asia and Latin America. Trainees have also established new training courses in their home institutions and nationally. Increased training capacity and building networks contributes to sustainable training models to empower subject area experts with requisite skills for tailoring bioinformatics training in their local contexts.



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