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ECCB2020: the 19th European Conference on Computational Biology

Year: 2020

Type: article

Abstract: This volume of Bioinformatics includes the proceedings papers of the 19th European Conference in Computational Biology (ECCB), an annual international conference for research in computational biology and bioinformatics. The conference is being held jointly with the Intelligent Systems for Molecular Biology (ISMB) Conference in the odd-numbered years and independently in the even-numbered years. This year, the 19th ECCB (ECCB2020) took place virtually from 31 August to 8 September, 2020. Health concerns and travel restrictions due to the COVID-19 pandemics have made ECCB2020 the first edition of the conference held virtually. Indeed, ECCB2022 is planned to be held in-person in the same localization (Sitges, Barcelona, Spain) as ECCB2020. Information on the ECCB2020 main conference as well as satellite meetings can be found at eccb20.org and will be later archived at the EBI website. With more than 850 participants from academia and industry in this virtual format, ECCB is the leading European Conference on Computational Biology and Bioinformatics, and the second largest internationally, next to ISMB. The work presented in ECCB is related to all domains of the field of computational biology and bioinformatics, ranging from molecular to systems biology level. The proceedings papers present new computational methodologies and tools for addressing challenging problems in the field, including research in single cell dynamics, 3D organization of the genome, new cancer therapies using big-data approaches and others. Adjusting the conference format to a virtual one led to producing a compact but yet attractive program. Due to the reduced format, the traditional Highlights and Applications tracks were not carried out. Previous ECCB editions were organized in Basel, Switzerland (Bromberg et al., 2019); Athens, Greece (Hatzigeorgiou et al., 2018); Prague, Czech Republic (Beerenwinkel and Bromberg, 2017); The Hague, The Netherlands (Heringa and Reinders, 2016); Dublin, Ireland (Moreau and Beerenwinkel, 2015); Strasbourg, France (Devignes and Moreau, 2014); Berlin, Germany (Ben-Tal, 2013); Basel, Switzerland (Schwede and Iber, 2012); Vienna, Austria (Gaasterland and Vingron, 2011); Ghent, Belgium (Moreau and Heringa, 2010); Stockholm, Sweden (Gusfield and Tramontano, 2009); Cagliari, Italy (Tramontano, 2008); Vienna, Austria (Lengauer et al., 2007); Eilat, Israel (Wolfson and Safer, 2007); Madrid, Spain (Guigo et al., 2005); Glasgow, UK (Thornton et al., 2004); Paris, France (Lenhof and Sagot, 2003); and Saarbrücken, Germany (Lengauer, 2002). ECCB2020 continues the 19-year tradition and was held under the auspices of the Spanish National Bioinformatics Institute (http://inb-elixir.es), founded in 2003, which is the node of ELIXIR in Spain since 2015, and the bioinformatics technology platform of the Carlos III Health Institute (‘Instituto de Salud Carlos III’) since 2018. The Life Sciences department at the Barcelona Supercomputing Center (BSC) has been the main organizer of this year’s conference. BSC is the national supercomputing center in Spain with more than 700 R&D experts and professionals distributed across four fields: Computer Sciences, Life Sciences, Earth Sciences and Computer Applications in Science and Engineering. The Life Sciences department comprises more than 120 professionals including MSc and PhD students, post-doctoral researchers and research engineers. The department’s mission is to understand living organisms by means of theoretical and computational methods, e.g. molecular modeling, genomics, proteomics, as well as contributing to the development of research infrastructures in the frame of different European projects, organizations and international efforts. ECCB2020 received a record number of 203 applications for proceedings talks from institutions across 33 countries. The submissions were organized in five themes, according to their topic: (i) data (organization, integration, knowledge discovery and multi-scale modeling), (ii) genes (expression, function, editing and geno/phenotype), (iii) Genome (sequence analysis, evolution, phylogeny and microbiome), (iv) proteins (structure, function, alterations and drug design) and (v) systems (molecular pathways, signaling and metabolomics). All proceedings submissions were subjected to a rigorous peer-review process (2–4 reviews per paper), organized by the members of the ECCB2020 Programme Committees of the corresponding theme. The Programme Committees consisted of a Theme Chair (Josep Lluís Gelpí, Ana Conesa, Toni Gabaldón, Modesto Orozco, Patrick Aloy, respectively) and up to three co-chairs per theme (Artemis Hatzigeorgiou, Jacques van Helden, Mark Robinson, Stephane Rombauts, Mark Wass, Amelie Stein, Pedro Beltrao). For the review, the EasyChair system (www.easychair.org) was used by 208 reviewers, recruited by the Programme Committees. Reviewers evaluated the impact and reproducibility of the presented research, as well as its suitability for the ECCB2020 audience. Once the review was completed, the committee chairs and co-chairs selected 41 papers to be included in the ECCB2020 proceedings with an acceptance rate of 20.2%, ensuring proportion to the initial theme submissions. The accepted works required, in some cases, minor revisions and the authors had 2 weeks to modify them accordingly. All Proceedings Track papers and any supplementary files accompanying them are freely available in the electronic form of Oxford University Press journal Bioinformatics, as a special issue of December 2020. Due to the virtual format, ECCB2020 did not have a dedicated session to posters where researchers could introduce their works to the whole community in-person. In contrast, the conference proposed a newly established format to get to know research activities from far and from near under the umbrella of the Glimpse into Global Bioinformatics Communities. ECCB2020 held two of these sessions, one dedicated to Latin America and another one to Europe. The aim of the Iberoamerican Society for Bioinformatics session served to bridge the gap with the Latin American communities by highlighting emerging researchers from different countries working on a broad range of topics, including national initiatives on precision medicine, city-scale genomic cartographies for infectious diseases response, molecular modeling and novel transcriptional regulatory interactions. The aim of the ELIXIR session as European representatives was to showcase the latest outputs and services developed in the context of this research infrastructure. Presentations had a strong focus on the response of ELIXIR to the challenges posed by the spread of COVID-19 from different angles including the development of specific ontologies, data management strategies to the release of dedicated structural and functional data for the SARS-CoV-2 proteome. Six distinguished keynote speakers presented their work: Prof. Modesto Orozco from Institute from Research in Biomedicine (IRB Barcelona), Prof. Geneviève Almouzni from Institut Curie, Science Academy in France and LifeTime Initiative, Assistant Prof. Debora Marks from the Harvard Medical School, Prof. Fabian Theis from Institute of Computational Biology at Helmholtz Zentrum München, Prof. Bissan Al-Lazikani from The Institute of Cancer Research and Prof. Londa Schiebinger from Stanford University. Keynotes covered broad and diverse areas of research including single cell genomics modeling, probabilistic generative modeling of genetic variation and gender in research, policy and practice. During ECCB2020, 11 exhibitor and career virtual booths were set up, namely: BSC, INB/ELIXIR-ES, ELIXIR, EMBL-EBI, GOBLET, the International Society for Computational Biology (ISCB), Genes-MDPI, Saint Jude Children’s Research Hospital. Exhibitors showcased the latest trends in computational biology and bioinformatics technology, in training and scientific literature, as well as in high-performance computing. The organizing committee invited participants to visit the exhibition area and the career fair to support these community-minded organizations, who deliver a strong message in supporting the Computational Biology and Bioinformatics scientific field. For the 2020 edition, the organizing committee designed a tailored format for virtual workshops and tutorials under the umbrella of the brand-new New Trends in Bioinformatics by ECCB. New Trends in Bioinformatics by ECCB aims to create virtual spaces for closer interactions among participants in specific areas of Bioinformatics and Computational Biology for this and future editions. Rather than having many parallel 1 or 2 days long face-to-face sessions prior to the main conference, this new format aims to facilitate 3-h long virtual workshops and tutorials during the week prior to ECCB. By programing those sessions considering the different time-zones of participants, it is possible to have a truly global audience taking part in these activities. For the 2020 edition, the New Trends in Bioinformatics by ECCB programed a total of 19 events in 2 parallel tracks and 2 blocks, the first from 13.30 to 16.30 and the second from 17.00 to 20.00, all following the Central European Summer Time. All sessions were recorded so participants can visit them at any time through the ECCB2020 virtual platform and, starting on 1 January, 2021, through the ISCBtv channel. Among the 19 events, there were 5 Workshops including 2 from Special Interest Groups—SIGs, 10 Tutorials and 4 sessions led by ELIXIR. The aim of workshops was to provide participants the opportunity to discuss different perspectives on the cutting edge of a selected research area through presenting technical issues, exchanging research ideas and sharing practical experiences. The five workshops of the 2020 edition were selected out of a total of 14 applications. In contrast, the purpose of the tutorial program is to provide participants with specialized lectures and hands-on training to the most important and emerging topics in bioinformatics and computational biology research. The tutorials offered skills ranging from early and basic steps of computational analysis, e.g. machine learning, cellular processes modeling or data visualization, to advanced computational skills in important established topics, e.g. epigenomics and RNA-seq analysis using long-reads. A total of 10 tutorials were selected as part of the New Trends in Bioinformatics by ECCB2020 out of 19 applications. This initial selection of workshops and tutorials was complemented by four events organized by ELIXIR, the strategic partner for the ECCB series of conferences. Specifically, ELIXIR organized three short workshops to share with the broad community advances in the development of standards and reference implementations for the use and re-use of research data even when data are under access control. Those workshops were complemented by a tutorial on integrating structural and functional data to support in silico predictions for drug design. The specific sessions for the New Trends in Bioinformatics by ECCB were as follows. Tutorials are denoted by a T, Workshops are denoted by a W and ELIXIR events contain an E to form the events ID. NTB-T01 machine learning and omics data: opportunities for advancing biomedical data analysis in Galaxy, organized by Anup Kumar, Alireza Khanteymoori and Björn Grüning (all at de. NBI, ELIXIR-DE, Germany) and Fotis Psomopoulos (INAB | CERTH, ELIXIR-GR, Greece). NTB-T02 powerful presentations tutorial—how to prepare, design and deliver high-impact presentations, organized by the Bioinfo4Women programme (BSC, Spain) and Grifols as strategic partner to the programme. NTB-T03 using deep learning for image and sequence analysis, organized by Petr Simecek and Panagiotis Alexiou (Central European Institute of Technology, Masaryk University, Czech Republic). NTB-T04 keeping up with epigenomic analysis: theory and practice, organized by Marcel Schulz (Institute of Cardiovascular Regeneration, Uniklinikum and Goethe University Frankfurt, Germany) and Ivan G. Costa (Institute for Computational Genomics, RWTH Aachen, Germany). NTB-T05 computational modeling of cellular processes: regulatory versus metabolic systems, organized by Anna Niarakis (Université d'Évry, Université de Paris-Saclay, France), Dagmar Waltemath (University Medicine, Greifswald, Germany),Pedro Monteiro (Universidade de Lisboa, Portugal), Vincent Noel (Institut Curie, France), Marta Cascante (Universitat de Barcelona, Spain) and Miguel Ponce de Leon (BSC, Spain). NTB-T06 reconstruction, analysis and visualization of phylogenomic data with the ETE Toolkit, organized by Jaime Huerta Cepas (Centre for Plant Biotechnology and Genomics, Spain) andFrançois Serra (BSC, Spain). NTB-T07 deep dive into metagenomic data using metagenome-atlas and MMseqs2, organized by Silas Kieser (PHYME, University of Geneva, Switzerland), Milot Mirdita and Johannes Söding (both at the MPI for Biophysical Chemistry, Germany), Martin Steinegger (Seoul National University, Korea) and Sofie Thijs (Hasselt University, Belgium). NTB-T08 full-length RNA-Seq analysis using PacBio long-reads: from reads to functional interpretation, organized by Ana Conesa (University of Florida, United State) and Elizabeth Tseng (Pacific Biosciences, United States). NTB-T09 introduction to structural bioinformatics for evolutionary analysis, organized by Claudia Alvarez Carreño (Georgia Institute of Technology, United States) and Alma Carolina Sanchez Rocha and Vyacheslav Tretyachenko (both at Charles University, Czech Republic). NTB-T10 biomedical data and text processing using shell scripting, organized by Francisco M. Couto (LASIGE, Universidade de Lisboa, Portugal). NTB-W01 CRISPR informatics for functional genomics, cancer targeting, and beyond, organized by Traver Hart (MD Anderson Cancer Center, United States) and Leopold Parts (Wellcome Sanger Institute, UK). NTB-W02 Annual European Bioinformatics Core Community (AEBC2) Workshop 2020, organized by Dieter Beule (Berlin Institute of Health, Germany), Sven Rahmann (University of Duisburg-Essen, Germany), Sven Nahnsen (University of Tübingen, Germany), Daniel J. Stekhoven (ETH Zurich, Switzerland), Camille Stephan Otto Attolini (IRB Barcelona, Spain) and Chris Evelo (Maastricht University, Netherlands). NTB-W03 BioNetVisA: biological network reconstruction, data visualization and analysis in biology and medicine, organized by Emmanuel Barillot, Inna Kuperstein, Cristóbal Monraz Gómez and Andrei Zinovyev (all at Institut Curie, France), Hioraki Kitano (RIKEN Center for Integrative Medical Sciences, Japan), Alfonso Valencia (Spanish National Bioinformatics Institute, Spain), Samik Ghosh (Systems Biology Institute, Japan) andRobin Haw (Ontario Institute for Cancer Research, Canada). NTB-W04 advances in computational modeling of cellular processes and high-performance computing, organized by Anna Niarakis (University Evry, University of Paris-Saclay, France), Arnau Montagud and Miguel Ponce de León (both at the BSC, Spain). NTB-W05 computational pangenomics: algorithms & applications, organized by Solon P. Pissis (Centrum Wiskunde & Informatica, The Netherlands) and Yuri Pirola (Università degli Studi di Milano-Bicocca, Italy). NTB-EW01 ELIXIR | Workshop on FAIR Computational Workflows, organized byIgnacio Eguinoa and Frederik Coppens (both at VIB & ELIXIR-BE, Belgium), Björn Grüning (University of Freiburg & ELIXIR-DE, Germany), Carole Goble and Stian Soiland-Reyes (both at The University of Manchester & ELIXIR-UK, UK) and Salvador Capella-Gutierrez (BSC & ELIXIR-ES, Spain). NTB-EW02 ELIXIR::GA4GH: advancing genomics through expedited data access enabled by standards and ontologies, organized by Gary Saunders (ELIXIR Hub, UK), Melanie Courtot (EMBL-EBI, UK), Michael Baudis (University of Zurich, ELIXIR-CH, Switzerland), Tommi Nyronen (CSC, ELIXIR-FI, UK) and Jordi Rambla (CRG, ELIXIR-ES, Spain). NTB-EW03 ELIXIR | Biological data analysis using InterMine, organized by Rachel Lyne and Daniela Butano (both at the University of Cambridge, UK). NTB-ET01 ELIXIR | 3D-Bioinfo: integrating structural and functional data to support in silico predictions in drug design, organized by Christine Orengo (University College London, UK), Preeti Choudhary (Protein Data Bank in Europe, UK) and Vincent Zoete (University of Lausanne, Switzerland). The New Trends in Bioinformatics by ECCB was followed by the Sixth European Student Council Symposium (ESCS 2020), which preceded the ECCB2020 main conference. This event was organized by the Student Council of the ISCB for and by early-stage researchers aiming to create a space to exchange research ideas and establish future networks. The event was chaired by Gabriel Olguín Orellana, from ISCB Student Council (ISCBSC)-Regional Student Groups (RSG) Chile and by the co-chair Sofia Papadimitriou, from ISCBSC-RSG Belgium. RSG are student groups of the ISCBSC. ESCS 2020 highlights will be published in F1000Research via the ISCBSC channel. The enthusiasm, hard work and genuine scientific interest by the organizers and participants of the ESCS series have led to a continuous and successful collaboration over the last 10 years, which in turn has made the ESCS an inseparable part of ECCB. Following previous editions of ECCB, a number of attendance waiver fellowships, sponsored by ISCB, were given to students and post-doctoral fellows with priority going to members from low or middle-income countries to attend the conference and the New Trends in Bioinformatics by ECCB. A total of 38 applications were received from scientists from 19 countries. After a careful review process, 31 registration fellowships were awarded by the ECCB2020 Organizing Committee together with ISCB. The conference ran under the ECCB2020 Code of to a and to at all and to have to turn to in there had been a to the Code of The ECCB2020 Organizing Committee to who through their work to this virtual Conference a the The and as well all the reviewers, who have been the of the Conference and workshops and this Conference a are truly to ECCB2020 organizers are to the ECCB2020 Committee and the ECCB for their and continuous support during the of the organization of ECCB2020 including the of for the of ECCB2020 into a virtual to ECCB for the support and knowledge on the organization of a conference of are to the ISCB, to for their and support in the of a newly format, in contributing to the of ECCB2020 at the international and for student This Conference not be possible the support of and was the of ECCB2020. ELIXIR the conference as ISCB, Spanish Supercomputing Jude Children’s Research and Bioinfo4Women programme were Genes-MDPI, University Press and Grifols were A to all for their and for to ECCB2020 an and A number of to the organization of ECCB2020. their of for this conference and as part of Conference were for the registration virtual technical and members of the and the Life Sciences at BSC this the of a conference is its presentations, the conference for its ECCB2020 organizers all of for at the first virtual edition of ECCB. the and ECCB2022 will the of previous editions of ECCB together with the of ECCB2020 to a face-to-face conference in the same localization (Sitges, Barcelona, Spain) planned for ECCB2020. The Spanish National Bioinformatics Institute is the Bioinformatics is by of the Salud of the de a de by the de Salud Carlos III and European of

Source: Bioinformatics

DOI: 10.1093/bioinformatics/btaa979