Structure-based function prediction; Docking, analysis, prediction and simulation of biomolecular interactions such as protein-protein, protein-ligand and protein-nucleic-acid; Protein dynamics and disorder; Evolution studied through structures; Application of structure to systems biology; Macromolecular assemblies; Structural genomics; 3D databases and data mining; Molecular visualization; Relevant methods of structure determination particularly hybrid methods; Prediction and analysis of protein domains; Membrane protein structure analysis and prediction; The structural basis of immunology.

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Bio-Ontologies provides a vibrant environment for reporting novel methods and sharing experiences on the construction and application of ontologies in health care and the life sciences. The informal nature of the COSI offers a constructive environment to nurture discussion of innovative and scientifically sound work that range from preliminary to completed, from both young and experienced investigators alike. Bio-Ontologies participants also benefit from a strongly interdisciplinary setting, where ISMB attendees intermingle with members from American Medical Informatics Association (AMIA) and the W3C’s Healthcare and Life Sciences interest group (HCLSIG), thereby increasing impact through broader dissemination and enabling new and exceptional collaborations.

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The major goal of this COSI is to offer a community to people who manage and staff bioinformatics cores around the world. Topics of interest to this group for our ISMB workshop include topics that core members would find interesting or useful. This includes but is not limited to: management topics relevant to cores, core formation and setup, workflow development, reproducibility, best practices, training, or exploring analysis of new types of data.

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The rapid adoption of data-intensive biology approaches creates enormous challenges for computational visualization techniques, which are needed to enable researchers to gain insight from their large and highly complex data sets. The goal of this session is to bring together researchers from the visualization, bioinformatics, and biology communities with the purpose of educating, inspiring, and engaging bioinformatics and biology researchers in state-of-the-art visualization research, as well as visualization researchers in problems in biological data visualization.

Keywords
Visualisation, Visual Analytics, Education

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Launched in 2000 and held yearly since then, BOSC is organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community.

Keywords
Open source; Open science; Open data; Reproducible research; Interoperability; Data science; Workflows; Translational bioinformatics; Diversifying bioinformatics communities

You can learn more about the BOSC COSI here.

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The CAMDA track highlights and compares the latest methods and results in an international data analysis contest, with this year's topics including:

1. The Synthetic Clinical Health Records Challenge provides a rich set of highly realistic Electronic Health Records (EHR) tracing the diagnosis trajectories of diabetic patients, created with dual-adversarial auto-encoders trained on data from 1.2 million real patients in the Population Health Database of the Andalusian Ministry of Health. Predict relevant diabetes endpoints like blindness or cardiopathy from past diagnosis trajectories!
2. The Anti-Microbial Resistance Prediction Challenge features clinical isolates sequences. Predict resistance genes/markers and identify resistant bacteria!
3. The Gut Microbiome based Health Index Challenge features hundreds of WMS based taxonomic and functional profiles of healthy and unhealthy individuals.

Take advantage of the Theater of Activity concept and compete already existing taxonomy based metrics!

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Data-driven computational studies addressing fundamental or translational questions in immunology are also of interest. Potential topics may cover, but are not limited to:

• ingle-cell multi-omics for characterizing immune cell heterogeneity and regulatory mechanisms of immune cell function
• Spatial genomics for studying immune microenvironments and interactions among immune cells.
• Trajectory inference and lineage tracing in immune cells.
• Analysis of receptor-ligand interactions.
• Profiling, reconstruction, and analysis of T cell and B cell receptor repertoires.

We encourage researchers to submit abstracts showcasing innovative approaches and insights in these areas for consideration in our Special Session on Computational Immunology.

As such topics relevant for this Special Session include, but are not restricted to, genetics and genomics of agriculturally relevant species; plant and animal phenomics; AI/machine learning; image analysis; remote sensing; educational innovations; discoveries resulting from public-private partnerships; data sharing and FAIR data standards; biotechnology; and soil sciences.

A major goal of this COSI is to foster a mutually supportive, collaborative community in which bioscientists can share bioinformatics education and training resources and experiences, and facilitate the development of education programs, courses, curricula, etc., and teaching tools and methods.

Keywords
Education, training, training resources, curricula, competencies

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At the same time, evolutionary and comparative genomics are inherently “transversal” disciplines in that work in many other biological areas of research have some evolutionary component (e.g. cancer genomics, epidemiology, toxicology, population genetics, functional genomics, structural biology just to name a few). The scope of this COSI is intentionally kept broad. The track will feature a mix of proceedings, highlight, and invited talks. Priority will be given to contributions which are relevant to more than a single area of application, or to contributions which are not covered by more specialised COSIs.

Keywords
Evolution, phylogeny, phylogenomics, comparative genomics, genome rearrangements, orthology, paralogy, recombination, lateral gene transfer, genome variation, population genomics, comparative epigenomics, epidemiology, cancer evolution genomics, genome annotation

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The Function COSI features the Critical Assessment of Function Annotation, an ongoing community challenge aimed at improving methods for protein function prediction. The Function-COSI holds annual meetings alongside ISMB. Also, we are conducting the multi-year Critical Assessment of protein Function Annotation, or CAFA, experiment.

Keywords
Protein function prediction, machine learning, performance assessment

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We seek contributions on any topic involving HTS data analysis including: genome assembly and haplotype phasing; transcriptome analysis; genetics and epigenetics variation; metagenomics and microbiome analysis; and new HTS platform data analysis (e.g. synthetic reads, long reads, nanopore). In addition to general sessions, we propose to have two specialized sessions to focus on current hot topics: a) long sequencing and mapping techniques, b) single cell sequencing applications, c) non-linear genome representations. Both of these topics have generated an enormous amount of interest recently.

Keywords
Sequencing, next generation, high throughput, algorithms, assembly, phasing, variation discovery, genotyping, metagenomics, microbiome, long reads, short reads, nanopre, pan-genomes, graph genomes

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The goal of the Integrative RNA Biology session is to bring together experts in computational and experimental aspects of research in RNA Biology to cover new developments across this broad field of research. The meeting focuses on two major areas:

1. The development of computational and high-throughput experimental methods
2. the application of such methods to break new grounds in the study of RNA biology and disease.

We aim to educate and inspire researchers in the field, novice and seasoned alike, by meshing together different aspects of Computational RNA Biology, and promoting cross-disciplinary collaborative research.

Keywords
Transcriptomics, RNA processing, post-transcriptional regulation, non-coding RNA, RNA 2D/3D structure, alternative-splicing, alternative polyadenylation, RNA translation degragation and localization, genetic variants effect on RNA processing, RNA and disease.

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It therefore guides users in the selection and application of methods and in their proper interpretation. Furthermore, the COSI provides a platform for exchange and networking between method developers, and provides valuable information allowing them to identify promising directions for their future work.

Keywords: microbiome, computational metaomics, microbial networks, pathogens, symbionts, (meta)omics-based diagnostics, microbial ecology and evolution

The MICROBIOME Community of Special Interest aims at the advancement and evaluation of computational methods in microbiome research, especially metaomic approaches.

Keywords
Microbiome, genome reconstruction, metagenomics, metatranscriptomics, metaproteomics, microbial networks, microbial traits, symbionts, pathogens, genome-based diagnostics

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Molecular biology and all the biomedical sciences are undergoing a true revolution as a result of the emergence and growing impact of a series of new disciplines and tools sharing the -omics suffix in their name. These include in particular genomics, transcriptomics, proteomics and metabolomics, devoted respectively to the examination of the entire systems of genes, transcripts, proteins and metabolites present in a given cell or tissue type. Taking advantage of this wealth of genomic information has become a conditio sine qua non for whoever has the ambition to remain competitive in molecular biology and in the biomedical sciences in general. Machine learning naturally appears as one of the main drivers of progress in this context, where most of the targets of interest deal with complex structured objects: sequences, 2D and 3D structures or interaction networks. At the same time, bioinformatics and systems biology have already induced significant new developments of general interest in machine learning, for example in the context of learning with structured data, graph inference, semi-supervised learning, system identification, and novel combinations of optimization and learning algorithms.

Keywords
Machine Learning, Data Mining, Deep Learning, Artificial Intelligence in Bioinformatics and Computational Biology

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Keywords
networks, pathways, systems, network analysis, disease networks, disease pathways

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An important goal of the meeting is to foster a collaborative community wherein scientists convene to solve difficult research problems in all areas of computational regulatory genomics.

Keywords
1. Genomic and epigenomic regulatory elements (transcription factors, enhancers, histones, gene promoters, regulatory motifs, non-coding RNAs, etc.)
2. NGS methods in regulatory genomics (e.g., ChIP-seq, RNA-seq, ATAC-seq)
3. Epigenetics and epitranscriptomics
4. Alternative splicing
5. Regulatory networks and pathway analysis
6. Genetic, molecular, and phenotypic variation in human disease
7. DNA shape
8. Single-cell transcriptomics (and other single cell assays)
9. 3D genomics (e.g., Hi-C and ChIA-PET)
10. Regulatory evolution or comparative regulatory genomics

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The meeting is open to the full range of methods used in systems modeling, including qualitative and quantitative modeling, dynamical and steady-state modeling, as well all applications of systems modeling including basic science, bioengineering, and medicine.

Keywords
Computational modeling, constraint-based models, logical models, kinetic models, multi-scale models

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This opens the debate on current state-of-the-art data infrastructures for translational medicine data integration and analysis. A variety of computational approaches are currently being used to harmonize and relate molecular data to clinical outcomes in order to better understand disease conditions. These methods also have the potential to discover biomarkers for early detection of disease, and targets for drug discovery, and to be used predictively to help to suggest personalised therapeutic strategies for patients. In this session we will bring scientists from both academia and industry to exchange knowledge and foster networking, to help in building up of the translational medicine community.

Keywords
Translational medicine; clinical and ‘omics data integration; curation and harmonization; stratification of patients; informatics for integrating biology and the bedside; medical informatics; ontology-driven data representation; patient centered outcomes research; cohort data; deep learning

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The meeting aims to organize a research network (VarI-COSI) facilitating the exchange of ideas and the establishment of new collaborations between researchers with different expertise. The VarI-COSI meeting is broadly divided in two sessions (“Genetic variants as markers: evolution, populations, GWAS” and “Genetic variants as effectors: function, structure, and regulation”) that encompass the four major research topics of the field:

1. Databases, data mining algorithms and visualization tools for variants analysis.
2. Methods for predicting regulatory/structural/functional impacts of SNVs.
3. Personal Genomics, GWAS studies and SNV prioritization.
4. Population genomics and phylogenetic analysis.

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