MOTIVATION: Software plays a crucial and growing role in research. Unfortunately, the computational component in Life Sciences research is often challenging to reproduce and verify. It could be undocumented, opaque, contain unknown errors that affect the outcome, or be directly unavailable and impossible to use for others. These issues are detrimental to the overall quality of scientific research. One step to address this problem is the formulation of principles that research software in the domain should meet to ensure its quality and sustainability, resembling the FAIR (findable, accessible, interoperable, and reusable) data principles. RESULTS: We present here a comprehensive series of quantitative indicators based on a pragmatic interpretation of the FAIR Principles and their implementation on OpenEBench, ELIXIR's open platform providing both support for scientific benchmarking and an active observatory of quality-related features for Life Sciences research software. The results serve to understand the current practices around research software quality-related features and provide objective indications for improving them. AVAILABILITY AND IMPLEMENTATION: Software metadata, from 11 different sources, collected, integrated, and analysed in the context of this manuscript are available at https://doi.org/10.5281/zenodo.7311067. Code used for software metadata retrieval and processing is available in the following repository: https://gitlab.bsc.es/inb/elixir/software-observatory/FAIRsoft_ETL.

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

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

The Quest for Orthologs (QfO) is an open collaboration framework for experts in comparative phylogenomics and related research areas who have an interest in highly accurate orthology predictions and their applications. We here report highlights and discussion points from the QfO meeting 2015 held in Barcelona. Achievements in recent years have established a basis to support developments for improved orthology prediction and to explore new approaches. Central to the QfO effort is proper benchmarking of methods and services, as well as design of standardized datasets and standardized formats to allow sharing and comparison of results. Simultaneously, analysis pipelines have been improved, evaluated and adapted to handle large datasets. All this would not have occurred without the long-term collaboration of Consortium members. Meeting regularly to review and coordinate complementary activities from a broad spectrum of innovative researchers clearly benefits the community. Highlights of the meeting include addressing sources of and legitimacy of disagreements between orthology calls, the context dependency of orthology definitions, special challenges encountered when analyzing very anciently rooted orthologies, orthology in the light of whole-genome duplications, and the concept of orthologous versus paralogous relationships at different levels, including domain-level orthology. Furthermore, particular needs for different applications (e.g. plant genomics, ancient gene families and others) and the infrastructure for making orthology inferences available (e.g. interfaces with model organism databases) were discussed, with several ongoing efforts that are expected to be reported on during the upcoming 2017 QfO meeting.

MOTIVATION: Multiple sequence alignments are generally reconstructed using a progressive approach that follows a guide-tree. During this process, gaps are introduced at a cost to maximize residue pairing, but it is unclear whether inferred gaps reflect actual past events of sequence insertions or deletions. It has been found that patterns of inferred gaps in alignments contain information towards the true phylogeny, but it is as yet unknown whether gaps are simply reflecting information that was already present in the guide-tree. RESULTS: We here develop a framework to disentangle the phylogenetic signal carried by gaps from that which is already present in the guide-tree. Our results indicate that most gaps are incorrectly inserted in patterns that, nevertheless, follow the guide-tree. Thus, most gap patterns in current alignments are not informative per se. This affects different programs to various degrees, PRANK being the most sensitive to the guide-tree. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

SUMMARY: Multiple sequence alignments are central to many areas of bioinformatics. It has been shown that the removal of poorly aligned regions from an alignment increases the quality of subsequent analyses. Such an alignment trimming phase is complicated in large-scale phylogenetic analyses that deal with thousands of alignments. Here, we present trimAl, a tool for automated alignment trimming, which is especially suited for large-scale phylogenetic analyses. trimAl can consider several parameters, alone or in multiple combinations, for selecting the most reliable positions in the alignment. These include the proportion of sequences with a gap, the level of amino acid similarity and, if several alignments for the same set of sequences are provided, the level of consistency across different alignments. Moreover, trimAl can automatically select the parameters to be used in each specific alignment so that the signal-to-noise ratio is optimized. AVAILABILITY: trimAl has been written in C++, it is portable to all platforms. trimAl is freely available for download (http://trimal.cgenomics.org) and can be used online through the Phylemon web server (http://phylemon2.bioinfo.cipf.es/). Supplementary Material is available at http://trimal.cgenomics.org/publications.