Detalle de: ECCB2022: the 21st European Conference on Computational Biology

This volume of Bioinformatics includes the proceedings papers of the 21st 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 21st ECCB (ECCB2022) took place in a hybrid format in Sitges (Barcelona, Spain) from September 12 to September 21, 2022, under the motto of Planetary Health and Biodiversity. The positive experience of running ECCB2020 in a virtual format due to the COVID-19 pandemic and the still existing health concerns and travel restrictions have made ECCB2022 the first edition of the conference held in a hybrid format. Information on ECCB2022 and the conference’s satellite meetings can be found at http://eccb2022.org. With more than 850 in-person participants from academia and industry, 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, with a strong presence of predictive modelling approaches and multi-omics data integration (Fig. 1). Recovering the traditional in-person format allowed us to open the calls for Highlight Papers, Applications and Posters that were not included in the ECCB2020 programme. Word cloud representing the most frequent keywords accompanying the submissions received. The keywords ‘machine learning’, ‘deep learning’, ‘cancer’, ‘gene expression’ and ‘data integration’ were the most frequently used keywords ECCB2022 leveraged experiences from previous editions, including the last two ones, held online despite being initially programmed to be hosted in-person in Lyon, France (Dessimoz and Przytycka, 2021, ISMB/ECCB 2021) and Sitges, Barcelona, Spain (Capella-Gutierrez et al. 2020, ECCB2020). This was the second time that ECCB was hosted in Spain after the successful experience of the fourth edition back in 2005 in Madrid, Spain (Guigo et al., 2005, ECCB 2005). ECCB2022 was held under the auspices of the Spanish National Bioinformatics Institute (INB; http://inb-elixir.es), founded in 2003, which has been the node of ELIXIR in Spain since 2015. The Life Sciences Department of the Barcelona Supercomputing Center (BSC) was the main organiser of 2022’s conference. BSC is the national supercomputing facility in Spain with more than 800 R&D experts and professionals distributed across four domains: Engineering, Computer, Earth and Life Sciences. The Life Sciences Department includes more than 160 professionals, ranging from MSc and PhD students to postdoctoral researchers and research engineers. The department’s mission is to understand living organisms through theoretical and computational methods, from genomics, structural bioinformatics, molecular and cellular modelling and biomedical research infrastructures, all of them in the framework of European projects and infrastructures (ELIXIR in particular). ECCB2022 received manuscripts for Proceedings talks from institutions across 39 countries. The submissions were organised in five themes: (1) Data (organisation, management, categorization, integration, analysis of data, knowledge discovery), (2) Genes (expression, function, regulation, transcription, translation, geno-phenotype), (3) Genomes (sequence analysis, alignment, evolution, phylogeny, genetics, epigenetics, 3D conformation) (4) Proteins (structure, function, alterations, assemblies, interactions, design, proteomics) and (5) Systems (systems biology, pathways, molecular networks, dynamics, signalling, multi-scale modelling). All proceedings submissions were subjected to a rigorous peer-review process (two to four reviews per paper), organised by the members of the ECCB2022 Programme Committee of the corresponding theme. The Programme Committee, chaired by Ana Conesa and the respective area chair: Josep Lluís Gelpí, Artemis Hatzigeorgiou, Toni Gabaldón, Mark Wass and Patrick Aloy and one to three co-chairs per theme (Heidi Peterson, Rory Johnson, Irene Papatheodorou, Sonia Tarazona Campos, Stephane Rombauts, Shilpa Garg, Franca Fraternali, Jolanda van Leeuwen and Anaïs Baudot) and a Programme Committee with 185 reviewers (see the Supplementary File ‘ECCB2022 Committees’). The review process was handled by the EasyChair system (www.easychair.org), focusing on the impact and reproducibility of the submitted research, as well as its suitability for the ECCB2022 audience. Once the review was completed, the committee chairs and co-chairs selected 25 papers to be included in the ECCB2022 proceedings with an acceptance rate of 17.4% across the different areas. All Proceedings papers and supplementary files are freely available in the electronic form of Oxford University Press journal Bioinformatics as a special issue of September 2022 (https://academic.oup.com/bioinformatics/issue/38/Supplement_2). The ECCB2022 call for Highlight Papers invited in-person presentations of recently published works, i.e. up to 1 year since its publication. The track received a total of 79 submissions that were ranked according to relevance and impact on biology and/or medicine, and their suitability to be presented in front of a large and heterogeneous audience. The existence of complementary work additional to the published paper was also considered positively. Finally, 30% of the submissions were presented at the conference. The conference programme included an Applications track in which participants were invited to present their works on software, services and infrastructures developed in a broader context of academia and industry. The proposals were evaluated by a committee of six members chaired by Javier De Las Rivas and co-chaired by Sara Aibar. A total of 15 out of 29 submissions were selected to be presented at the conference after ranking them based on their impact and potential in bridging different researcher and professional profiles together. ECCB2022 hosted two poster sessions where researchers introduced and discussed their work in person. The Posters track received 567 contributions from authors affiliated with 54 different countries. The submissions were reviewed by a committee of 28 members, chaired by R. Gonzalo Parra and co-chaired by Handan Melike Dönertaş and Alexander Miguel Monzon. Overall the ECCB2022 tracks received the participation of authors from 66 countries. The countries with the higher number of accepted submissions in ECCB2022 tracks (Fig. 2) were Germany, Spain, the UK and France, jointly contributing to half of the overall accepted submissions. Authors from Belgium, Switzerland, Italy and Poland followed the ranking adding up a comparable number of accepted proposals (∼25–30 submissions) and the USA and India were the non-European countries with the higher number of authors with accepted submissions. Proportion of countries’ affiliation from the authors with accepted submissions at ECCB2022. The Programme Committee accepted a total number of 626 submissions, most of which were authored by researchers affiliated with institutions from Germany, Spain, the UK and France The programme incorporated a new track aligned with the motto of the conference: Climate Crisis and Health. The track consisted of two sessions with talks from invited speakers on air quality, heat stress, infectious diseases and biodiversity. Taking advantage of the hybrid format, ECCB2022 hosted a dedicated track to foster the interactions between different geographically distributed communities. During this edition, two sessions were dedicated to fostering interactions between ELIXIR, the pan-European infrastructure for data in Life Sciences and Latin America Bioinformatics societies. The main topic revolved around research data management and how to facilitate the knowledge exchange between communities. These joint sessions just represented the starting point for further collaborations. The programme also included four ELIXIR sessions in which the speakers showcased the latest outputs and services on data integration and data management strategies developed in this European research infrastructure context. Additionally, the Quest for Orthologs consortium organised a satellite meeting on the scope of the conference, which included a day and a half meeting and an open workshop to discuss new approaches for improving orthology predictions. Six distinguished keynote speakers presented their work: Prof. Cesar Hidalgo from the Universities of Toulouse, Manchester and Harvard, Prof. Raul Rabadan from Columbia University, Dr Ana Freitas from the Institute for Systems and Computer Engineering, Technology and Science—Technical University of Lisbon, Dr Maria Rodriguez-Martínez from IBM Research Europe, Dr Graciela Gonzalez-Hernandez from the University of Pennsylvania and Prof. Mar Albà from the Catalan Institution for Research and Advanced Studies and Hospital del Mar Medical Research Institute. The keynotes covered broad and diverse research areas, including evolutionary genomics, personalized medicine and new methods in artificial intelligence and natural language processing for computational modelling of biological data. Following the pilot experience from ECCB2020, this edition also had a programme of virtual workshops and tutorials under the umbrella of New Trends in Bioinformatics by ECCB. This format allowed the spread of 3-h virtual sessions during the week before ECCB2022, enabling the participation of attendees in multiple sessions and making it easier for the global community to join them. For the 2022 edition, the New Trends in Bioinformatics by ECCB combined a total of 9 virtual sessions and 10 in-person sessions. The virtual events were programmed in two blocks, the first from 13.30 to 16.30 and the second from 17.00 to 20.00 following the Central European Summer Time. All sessions were recorded so participants could visit them again through the ECCB2022 virtual platform and, starting on January 1, 2023, through the ISCB.tv channel. Among the 19 scheduled events were 11 workshops, 7 tutorials and 1 session led by ELIXIR. The workshops aimed to provide participants with 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 11 workshops were selected out of a total of 17 applications. In contrast, the purpose of the tutorials program is to provide participants with specialized lectures and hands-on training on the most important and emerging topics in bioinformatics and computational biology research. The tutorials offered topics ranging from early and basic steps of computational analysis, e.g. machine learning, cellular processes modelling or data management, to advanced computational skills in important established topics, e.g. functional analyses of single-cell transcriptomics data. A total of 7 tutorials were selected as part of the New Trends in Bioinformatics by ECCB out of 10 applications. The programme of workshops and tutorials was round out by a workshop organised by ELIXIR on practical approaches for applying FAIR guiding principles in data reuse. 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 workshop contains an E, to form the events ID. NTB-T01 Computational challenges in phospho-proteomics and systems biology of cellular signalling, organised by Filipa Blasco Tavares Pereira-Lopes (Case Western Reserve University, USA), Marzieh Ayati (University of Texas Rio Grande Valley, USA), Serhan Yilmaz (Case Western Reserve University, USA), Daniela Schlatzer (Case Western Reserve University, USA), Mehmet Koyutürk (Case Western Reserve University, USA) and Mark Chance (Case Western Reserve University, USA). NTB-T02 To rarefy or not to rarefy microbiome data? What are the alpha diversity metrics?, organised by Violeta Larios-Serrato (Winter Genomics, México), Maira Nayeli Luis-Vargas (Winter Genomics, México), Karla Ruiz (Winter Genomics, México) and Kenya Contreras (Winter Genomics, México). NTB-T03 Deep learning for biological sequence data: from convolutional neural networks to transformers, organised by Panagiotis Alexiou (Masaryk University, Czech Republic), Petr Simecek (Masaryk University, Czech Republic), David Cechak (Masaryk University, Czech Republic) and Vlastimil Martinek (Masaryk University, Czech Republic). NTB-T04 Functional analysis of single-cell transcriptomics, organised by Pau Badia i Mompel (Heidelberg University, Germany), Robin Browaeys (VIB Center for Inflammation Research, Belgium) and Daniel Dimitrov (Heidelberg University, Germany). NTB-T05 Guidelines for the assessment and analysis of lrRNA-seq data for transcript identification and quantification (LRGASP challenge), organised by Ana Conesa (Institute for Integrative Systems Biology, Spain), Fairlie Reese (University of California at Irvine, USA), Dennis Mulligan (University of California at Santa Cruz, USA), Ying Chen (Genome Institute of Singapore, Singapore), Ralf Herwig (Max Planck Institute for Molecular Genetics, Germany) and Sílvia Carbonell-Sala (Center for Genomic Regulation, Spain). NTB-T06 Boost your data management planning, organised by Helena Schnitzer (ELIXIR Germany and Forschungszentrum Jülich, Germany) and Daniel Wibberg (ELIXIR Germany and Forschungszentrum Jülich, Germany). NTB-T07 Software containerization in bioinformatics: how to make reproducible, portable and reusable bioinformatics software and pipelines, organised by Giacomo Baruzzo (University of Padova, Italy), Barbara Di Camillo (University of Padova, Italy), Marco Cappellato (University of Padova, Italy), Giulia Cesaro (University of Padova, Italy), Mikele Milia (University of Padova, Italy). NTB-W01 Machine learning good practices—DOME recommendations for better machine learning in computational biology, organised by Jennifer Harrow (ELIXIR, UK), Fotis E. Psomopoulos (CERTH, Greece), Silvio Tosatto (University of Padova, Italy) and Leyla Jael García-Castro (ZB MED Information Centre for Life Sciences, Germany). NTB-W02 FAIRification of multi-omics metadata, organised by Gary Saunders (EATRIS-ERIC Data Director, The Netherlands), Emanuela Oldoni (EATRIS-ERIC Scientific Programme Manager, The Netherlands) and Anna Niehues (Bioinformatician at Radboud University Medical Center, The Netherlands). NTB-W03 Simulating cellular behaviours: advancing HPC-enabled computational biology, organised by Arnau Montagud (BSC, Spain), Marta Lloret-Llinares (EMBL-EBI, UK), Renata Giménez (BSC, Spain) and Mariola Tàrrega-Moltó (BSC, Spain). NTB-W04 Spatial transcriptomics and cell–cell communication modelling: new opportunities to study the cellular dynamics of biological systems, organised by Giacomo Baruzzo (University of Padova, Padova, Italy), Enrica Calura (University of Padova, Italy), Davide Risso (University of Padova, Italy), Chiara Romualdi (University of Padova, Italy), Gabriele Sales (University of Padova, Italy), Luz García-Alonso (Wellcome Sanger Institute, UK), Roser Vento-Tormo (Wellcome Sanger Institute, UK), Julio Saez-Rodriguez (Heidelberg University, Germany) and Yvan Saeys (VIB, Belgium). NTB-W05 Building high-quality reference genome assemblies of eukaryotes, organised by Nadège Guiglielmoni (University of Cologne, Germany), Joanna Malukiewicz (Deutsches Primatenzentrum, Germany; University of Sao Paulo, Brazil), Lino Ometto (University of Pavia, Italy) and Robert (University of Lausanne and Swiss Institute of Bioinformatics, Switzerland). NTB-W06 Tools and techniques to make sensitive data discoverable (use-cases, hands-on session of Beacon implementation), organised by Babita Singh (European Genome-phenome Archive, Spain) and Lauren Fromont (European Genome-phenome Archive, Spain). NTB-W07 Sex and gender dimension in biomedical research, organised by Àtia Cortés (BSC, Spain), Davide Cirillo (BSC, Spain) and Fatemeh Baghdadi (BSC, Spain). NTB-W08 Integration of large-scale data for reference genome development in biodiversity, organised by Shilpa Garg (University of Copenhagen, Denmark) and Josiah Kuja (University of Copenhagen, Denmark). NTB-W09 Annual European Bioinformatics Core Community (AEBC2) workshop 2022, organised by Camille Stephan-Otto Attolini (IRB Barcelona, Spain), Dieter Beule (Berlin Institute of Health, Germany), Sven Rahmann (Saarland University, Germany), Sven Nahnsen (University of Tübingen, Germany) and Daniel J. Stekhoven (ETH Zurich, Germany). NTB-W10 Computational modelling of immunological mechanisms: from statistical approaches to interpretable machine learning, organised by María Rodríguez-Martínez (IBM—Zurich Research Laboratory, Switzerland), Anna Niarakis (University of Évry Val d'Essonne and University of Paris-Saclay) and Matteo Barberis (University of Surrey, UK). NTB-W11 Novel challenges in the quest for orthologs, organised by Ingo Ebersberger (Goethe University Frankfurt, Germany), Michael Hiller (Senckenberg Society for Nature Research, Germany), Thomas Rattei (University of Vienna, Austria), Paul D. Thomas (University of Southern California, USA) and Sofia Kirke Forslund (Max-Delbrück-Centre for Molecular Medicine, Germany). NTB-EW01 ELIXIR | FAIR applied: a practical FAIRification guide for life science data from FAIRplus, organised by Tony Burdett (EMBL-EBI, UK), Ibrahim Emam (Imperial College London, UK), Nick Juty (University of Manchester, UK), (University of UK), (University of and (EMBL-EBI, UK). The New Trends in Bioinformatics by ECCB in format in with the European The was organised by the European of the for and by researchers to a to exchange research ideas and The was co-chaired by from Spain, and Maria from are The work and of the and participants of the have led to a and successful the last 10 making the an part of ECCB. Following previous of a number of by were to students and postdoctoral with to members affiliated in or countries to their at the conference and the New Trends in Bioinformatics by ECCB. A total of were received from from countries. a were by the ECCB2022 Committee and The ECCB2022 Committee is to gender for better and in this was considered in all the steps of the the of review out of 10 chairs and 9 out of 15 co-chairs were the and the made an important to the review by as as and a for the keynotes represented four out of the six distinguished The programme included jointly organised with the to further to in the field of bioinformatics. the of the were after in the field of bioinformatics and a was to to further to their contributions in the ECCB2020 established a of which was leveraged and by ECCB2022. The ECCB2022 of a and to and had to to in had been a of the of The ECCB2022 Committee to through their work to the conference’s The co-chairs and reviewers have been the of the conference and workshops, manuscripts and talks for and making this conference a are to them. ECCB2022 are to the ECCB2022 Committee and the ECCB2022 Committee for their and during the of the of ECCB2022. are also to the to for their and for contributing to the of ECCB2022 at the international and for This conference not be the of and ELIXIR the conference as a was the and the poster also further Sciences and The and Spanish Supercomputing were of ECCB2022. to all for their and make ECCB2022 an and conference. A number of to the of ECCB2022. their call of to make this conference and as part of Conference were for the members of the and the Life Sciences Department at BSC this conference: and the the Finally, the of a conference is its the conference for its ECCB2022 all of for us at the first hybrid edition of ECCB. the and the of previous of ECCB with the of ECCB2022 to the next conference in Supplementary Supplementary data are available at Bioinformatics This paper was published as part of a special issue by ECCB2022. of