Posters
Poster presentations at ISMB 2020 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.
All registered conference participants will have access to the poster and presentation through the conference and content until October 31, 2020. There are Q&A opportunities through a chat function to allow interaction between presenters and participants.
Preliminary information on preparing your poster and poster talk are available at:
https://www.iscb.org/ismb2020-general/presenterinfo#posters
Ideally authors should be available for interactive chat during the times noted below:
View Posters By Category
Poster Session A: July 13 & July 14 7:45 am - 9:15 am Eastern Daylight Time |
Session B: July 15 and July 16 between 7:45 am - 9:15 am Eastern Daylight Time |
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| July 14 between 10:40 am - 2:00 pm EDT |
Short Abstract: BioExcel is the leading European Centre of Excellence for computational biomolecular research. Its training programme is based on a competency profile and aims to develop computational abilities related to structural biology and molecular modelling. In 2019, BioExcel started to include remote courses in the programme as a way to lower the barriers for both delivering and attending a course, i.e., we offer short courses that we would not offer face-to-face and we allow people to participate without travelling. But remote training poses several challenges to provide an enriching learning experience, including high computational demands in the case of biomolecular software. To address these challenges, we work with virtual machines, breakout rooms, interaction with participants and the combination of presentations and exercises. We gather feedback from both trainers and trainees after each course to learn how to keep improving our remote training programme. We are developing a living document for trainer guidelines along the programme. Here we present the lessons learned so far and the challenges that we continue working on in areas such as social interaction, hands-on activities, computational demands or instructions for participants.
Short Abstract: High-throughput sequencing technologies, and the bioinformatics software required to analyze their output, evolve rapidly. As a result, many biological scientists either lack the skills to analyze these data sets or are challenged to keep pace with constant changes in technology and analysis tools. The High-Performance Computing in Biology (HPCBio) group at the Roy J. Carver Biotechnology Center fills this gap by providing training and consulting services to students, postdocs, staff, and faculty members via workshops and externships. Over the past eight years, HPCBio has developed skill- and application-based workshops that empower researchers to analyze their own sequencing data. These workshops are targeted toward researchers on the University of Illinois at Urbana-Champaign campus. HPCBio has also delivered services to other campuses such as Millikin University and Fisk University with development of a non-computational, hands-on workshop that provides a conceptual overview of bioinformatics for undergraduate students. Workshop development utilizes core resources and methods for generating active and practical learning materials that flexibly meet the needs of attendees regardless of their computational experience, genomics knowledge, age, career status, scientific discipline, and biological system of interest. Workshop delivery emphasizes outcomes-assessment methods that provide the data needed to drive continuous improvement of training materials.
Short Abstract: The life sciences education community has long recognized the need to provide more rigorous quantitative and computational training essential to current research practice. Here we describe an effort to meet this need for a cohort of experimental life sciences graduate students assumed to have no prior biostatistics or bioinformatics training. We sought to provide a practical and accessible introduction via a course organized around analyzing real primary experimental data in series of modules, each covering a distinct biological domain and data type. The course in part uses lecture material on biological problems and data sources as well as cross-cutting topics in bioinformatics and biostatistics. These are brought into practice with hands-on analysis in class and in homework of primary data in R. Assessment suggests that the course produces modest gains in reasoning correctly about problems in biological data analysis and experimental design, particularly via increasing ability to draw on quantitative knowledge. Future work will aim to extend students' ability for more complex coding tasks, incorporate new modules, and better develop course materials for export.
Short Abstract: Bioinformatics education is essential for supporting R&D in Latin America; consequently, it is imperative to understand its status and to support challenged audiences. The number of bioinformatics programs in LatAm is low compared with developed countries; ~16% non-biotechnological undergraduate programs in life sciences offer bioinformatics. A project aimed at analysing the current status of bioinformatics education in LatAm and supporting training for undergraduate programs in life sciences is presented herein. It is a secondment project supported by CABANA (www.cabana.online) that comprises: 1) undergraduate training modules in Spanish and, 2) status analysis and trainer support. Modules: LatAm trainers assigned high-level competency requirements to undergraduates in life sciences for basic and applied biology, and scientific computing skills using the ISCB Competency Framework. Accordingly, face-to-face and online training modules are being created, will be peer-reviewed by CABANA partners and evaluated in test groups. Status and trainer support: A status analysis of bioinformatics programs is being performed jointly with LatAm researchers. Status analysis of undergraduate programs in life sciences samples one country, Mexico. A train-the-lecturer program is being created for support and knowledge exchange and to promote the creation of a community of practice for bioinformatics trainers and educators.
Short Abstract: Clinical Bioinformatics combines computer science with genomics in clinical practice. Trained clinical bioinformaticians are in short supply necessitating creative and flexibly-delivered education to fill the skills-gap. Our Introduction to Programming unit launched in 2019 as part of a PG-Cert teaching the fundamentals of Clinical Bioinformatics to a diverse cohort of distance learners.
The unit simulated real-world experiences by building a situated learning environment that used agile project methods and authentic problem-solving activities to emulate clinical programming best-practice. Clear instructions, signposting and support, ensured comfort with course materials delivered using Jupyter Notebooks via GitHub. This use of industry-standard platforms and downloadable content also encouraged post-course lifelong-learning.
The unit followed a social constructivist model geared to help students to learn individually and as a team. Synchronous online support from experienced facilitators helped encourage group-based peer-to-peer support which afforded more time for educators to support struggling students.
By prioritising pedagogy over technology, the learning design resulted in incremental coding activities supporting a variety of learners. Methods such as Sprints provided real-world problem-based learning using real user-stories. The students directly contributed to the clinical bioinformatics toolkit by developing resources for personal practice or for co-development of the VariantValidator software, used in clinical practice worldwide.
Short Abstract: In the current era of Big Data production and Artificial Intelligence development, one of the fastest growing scientific and professional areas that is generating petabytes of data is Life Sciences. In this context, many scientific and educational institutions recognize that it is no longer possible to carry out adequate studies and research in this area without well-trained computational biologists and bioinformaticians. GOBLET is an international organization, established in 2012, with the mission to cultivate a global community of bioinformatics trainers who support learning, education and training. GOBLET’s mission was defined under the vision that there is a clear worldwide need to harmonize bioinformatics training activities and to unite, inspire and equip bioinformatics trainers. This can only be achieved by developing active linkages and collaborations with many national and international institutions that work in the field of Life Sciences. Relevant activities conducted last year by GOBLET members, together with other international experts, include the initiation of a series of assets, standards and guidelines, to define competencies, promote best practices and provide high-quality resources for learning, education and training in bioinformatics and computational biology, worldwide. GOBLET's new website offers a comprehensive portal, providing many materials and resources for the international bioinformatics community.
Short Abstract: Background: Curriculum and instructional development should follow a formal process. Although the focus in formal curriculum theory is on long-term programs of study, the process is also applicable to shorter-form Learning Experiences (LEs) (single courses, lessons, or training sessions). Successful curricula and instruction support learners as they develop from entry-level performance to the minimum qualification for completing a program or course, articulated in terms of Learning Outcomes (LOs). These considerations have been encapsulated in an iterative model of curriculum and instructional design, with guidelines for its use.
Output and conclusion: The starting point is the articulation of target LOs: everything follows from these, including the selection of LEs, content, the development of assessments, and evaluation of the resulting curriculum/instruction. The iterative process can be used in curriculum and instructional development, and provide a set of practical guidelines for curriculum and course preparation. The essential features effective curriculum and instruction (i.e., that achieves its stated LOs for the majority of learners) is presented here, to offer practical guidance and support for devising and evaluating both short- and long-form teaching.
Short Abstract: Bioinformatics is an expanding field of vital importance in life sciences and the CABANA project (www.cabana.online) aims to support capacity building in this field for Latin America. An integral part of this project is providing guidance and development opportunities for bioinformatics trainers, training and delivery. This poster presents three strands of this work: a Latin American Trainer database; CABANA Workshop workflow guidance; and the implementation of a ‘train-the-trainer’ program in this region.
The Latin American Trainer database will map bioinformaticians and other professionals to their knowledge and expertise in training. This provides an opportunity for trainers to promote their work, share their skills and be part of the LatAm trainer community, whilst also enabling workshop organizers to find local experts and trainers.
To provide guidance to course developers, the CABANA workshop workflow provides pedagogical contextualization, organizational practises and recommendations for planning and delivering impactful workshops with a progressive timeline.
Another key element is a regional “train-the-trainer” program providing training tools and techniques and promoting the creation of a Latin American community of practice for bioinformatics trainers and educators
The work presented here is intended to support capacity growth efforts through trainer community building and people development.
Short Abstract: Reconstructing genomes from DNA sequencing reads - genome assembly - is a fundamental task in genomics that is the foundation for many downstream analyses. Genome assembly also reveals the power provided by the combination of biology and computer science - innovations in assembly algorithms were critical to the genomic revolution. To introduce these concepts to the general public and to illustrate computational thinking paradigms related to assembly algorithms, we developed a simple word game similar to magnetic poetry kits.
The game involves reconstructing repetitive phrases from fragments printed on magnets. The size of the fragments and complexity of the phrases can be varied to adjust the level of difficulty. Using a metal whiteboard as a backing for the game also creates the opportunity for introducing graph-based solutions to the genome assembly problem, while collaborative team teaching within a classroom setting also enables a discussion of parallel algorithms.
In our presentation, we will describe lesson plans built around this game and highlight our experiences in deploying them at Maryland Day (an open house event organized at the University of Maryland each spring) and within a summer camp aimed at introducing K-12 students to computer science.
Short Abstract: In March 2020, the COVID-19 pandemic triggered an unprecedented and rapid transition to remote teaching and learning at all U.S. colleges and universities. Instructors were challenged to flip undergraduate lecture and lab courses online at mid-semester and strategically adapt summer courses. This radical pedagogical shift presented an opportunity to engage students in the science of COVID-19 by leveraging online bioinformatics platforms. We rapidly developed and implemented two inquiry-based bioinformatics modules in undergraduate molecular biology courses. In preparation for these interactive sessions, students analyzed emerging scientific literature on the novel coronavirus, SARS-CoV-2, which enhanced their understanding of the central dogma of molecular biology. During synchronous class meetings, students explored coronavirus genome sequences using NCBI Virus and framed research questions about the origins of SARS-CoV-2. Evaluation of mutation fitness and virus phylogeny was demonstrated with the T-BioInfo Platform. In addition, the viral spike glycoprotein was investigated as a critical target for neutralizing antibodies and vaccine development. Completion of these modules resulted in gains in perceived learning about the novel coronavirus and an increased understanding of sequencing data. We recommend incorporation of similar modules into undergraduate courses to enhance remote learning and increase opportunities for research training during and beyond the pandemic.
Short Abstract: Sharing, reusing and reproducing data, software and other digital objects forms the cornerstone of open science practices. Such practices are guided by the Findable, Accessible, Interoperable and Reusable (FAIR) principles. Implementing FAIR principles is not always straightforward, especially in the context of Bioinformatics training. If we are to meet worldwide demand for such training, adhering to the FAIR principles is vital not only for data and software, but also for training materials (any digital object used in a training context, such as slide presentations, exercises, datasets). To facilitate this process, and break the principles down into practical steps, the ELIXIR Training Platform community has put together ten simple rules for making training materials FAIR. Above all is the need to plan to share your training materials online from the outset. Amongst the remaining rules is the importance of describing materials properly, assigning unique identifiers, registering them online, defining access criteria, and using interoperable formats. The full set of ten rules is presented here.
Short Abstract: To approach the evaluation of teaching content in Harvard Medical School’s Masters in Biomedical Informatics program (MBI) we generalized program goals into an objective set that can be used to evaluate the quality of fit of classes into the curriculum. Using principles of backward design, we developed a set of 6 core program themes each of which was further subdivided into sub-topics and a resulting 49 competencies. These competencies represent our objectives for student improvement across all areas as they complete the program. Each program course was evaluated using these competencies to identify areas of weakness, redundancies between courses, and assess the fit of the course within the Master’s Program. Additionally, this process can be used further to compare student and faculty perceptions of the communicated course content to improve the quality of education within the program. We believe this could be replicated in other departments seeking to streamline their curriculum.
Short Abstract: EMBL-EBI’s online learning platform, Train online has a new look. Since it’s development in 2011 it has grown into a resource accessed by nearly 600,000 people per year globally. Containing over 80 courses, it provides training on EMBL-EBI data resources and tools, and basic concepts in bioinformatics and data analysis.
Our aim in re-development was to provide increased interactivity and improved performance for our learners, along with an updated style. This enables online learning from EMBL-EBI to be more engaging, user friendly and ultimately have greater learner impact.
Prior to redesign, we worked with trainees and authors to identify challenges to taking and writing a course. A number of platforms were considered and we ultimately decided on WordPress. This provides a clean, modern look for trainees and simple course development for trainers. Increased interactivity has been added using H5P, enabling quick creation of games, quizzes and other interactive content to support and assess learning.
Feedback on the first updated course has been extremely positive, indicating improved engagement and retention of trainees. It was also pivotal to our design revisions before finalising the new look.
Further development of Train online is planned, focusing on personalisation and collaboration in online learning.
Short Abstract: Data stewardship and managing data skills are essential in research. To our knowledge, a coherent approach and dedicated education for data stewardship on the (inter)national level is currently lacking. The lack of consensus on the responsibilities, knowledge and skills of data stewards, combined with the lack of sufficient funding, hampers adequate capacity building, defining recruitment procedures and building career paths for data stewards. In 2019, two complementary Dutch projects* created the basis for the current NPOS-F project on professionalising data stewardship, embedded in the Dutch National Programme Open Science (www.openscience.nl). Its objectives are: 1) national coordination on competences and learning outcomes, 2) formal agreement by stakeholders and willingness to implement, 3) enable developers of educational programs to develop curricula. The project team consists of representatives of universities, UMCs and universities of applied sciences, and works in a bottom-up approach toward these common goals. The team is supplemented by representatives of umbrella organisations, including educational associations, funding bodies and infrastructure providers, which ensures embedding of the outcomes in the national data landscape. * Data stewardship on the map, doi.org/10.5281/zenodo.2669149; Towards FAIR data steward as profession for the lifesciences, zenodo.org/communities/nl-ds-pd-ls
Short Abstract: The European Bioinformatics Institute (EMBL-EBI) is part of EMBL. We have a large number of staff developing databases and tools to host, analyse and share data and analytic results openly in the life sciences. Staff training to adopt new technologies such as cloud computing is very challenging. We have defined the long-term strategy to adopt cloud infrastructure to provide better access to scientists in Europe and around the world to accelerate their research with the diverse data stored, verified and visualised by EBI.
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As a result, many research and service teams have launched their projects with the new skills in the clouds. This team has been invited to deliver cloud workshops for EU projects in person for EOSC-Life and remotely for BioExcel with additional projects in the near future. The Cloud Roundtable forum has now been extended to include participants from Wellcome Sanger Institute to foster closer cooperation in using cloud technologies with a new joint project proposed. With this systematic staff education, we have made our first step to lead EBI and EU projects to adopt cloud technologies.
Short Abstract: Four years ago, our university introduced a new undergraduate major in Quantitative Biology. The students take courses in biology, chemistry, physics, computer science, mathematics, and statistics. Further, the students take major-specific courses in genomics, structural biology, systems biology, and computational analysis of biological data. In addition, the students gain individual research experience under the guidance of principal investigators. I will discuss the curriculum for this major, the challenges in starting a new major, and what our first cohort of graduates is doing after graduation this spring. I will also discuss projects from the computational analysis of biological data course. Some of these projects used publicly available data, for example, comparing Neanderthal and human genomes, and other projects using the UCSC Genome Browser and the 1,000 Genome Project. For another project, the students collected local water samples, we then did shotgun metagenomic sequencing and analyzed the results.
Short Abstract: We are five faculty members who teach in Frontiers of Science, the Columbia College science core course. Like most of our colleagues around the world, we turned to online teaching in mid-March. To stay true to our name – Frontiers of Science, we modified our curriculum to make room for teaching about the evolution of SARS-CoV-2 using genomic data. After an introduction on the evolution of coronaviruses and genomics studies, we conducted an online activity, where students worked in teams to investigate the evolution of the SARS-CoV-2 using the Nextstrain.org website.
First, students thoroughly examined phylogenetic graphs and discussed how these trees are created. Next, students calculated the virus’ substitution rates per site and compared it to that of the other pathogens, such as Influenza. The class ended with discussions revolving around infectious diseases and the role of genomics in treatment and vaccine development.
We hope that other faculty may be able to use or adapt the activity that we have developed on SARS-CoV-2 and some of the ideas that have guided our modified online curriculum. If there ever was a topic that all students would deem to be relevant to their lives, this is certainly one.
