Meeting Schedule

Monday 8 June

09:00 - 09:30

09:30 - 12:00

Workshops and Tutorials

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Organisers: Patricia Palagi and Marc Robinson-Rechavi

Description: Sharing, reusing and reproducing data, software and other digital objects are the basis for open science practices, and to ease this the scientific community has developed the Findable, Accessible, Interoperable and Reusable (FAIR) principles. FAIR principles are however not so simple to understand and adopt, and may be quite convoluted for some. The ELIXIR Training Platform has put up together a Ten Simple Rules which simplify the FAIR principles by breaking them down into very practical steps. Though these steps were described for training materials, they can be adapted to any kind of research data as well. In this workshop, we will first discuss issues and practical solutions in small groups per type of object (e.g. training/teaching materials, software, data). Then we will compare and provide feedback and improvements in how to put the FAIR principles in practice. The discussion will be structured around the Ten Simple Rules for FAIR training materials and software. The aims are (i) find solutions or lead towards solutions for the participants to put FAIR in practice; (ii) create a community of SIB members working towards such solutions, or eventually communities per object type (e.g. FAIR software, FAIR teaching materials).

Organisers: Patrick Rölli, Stefania Giacomello and Stephen Williams

Description: The relationship between cells and their relative locations within a tissue sample can be critical to understanding disease pathology. Spatial transcriptomics, including the Visium Spatial Gene Expression Solution, is a groundbreaking technology that allows scientists to measure all the gene activity in a tissue sample and map where the activity is occurring. Already this technology is leading to new discoveries that will prove instrumental in helping scientists gain a better understanding of biological processes and disease.

The workshop consists of three parts.
1) A short introduction to the technology (30min)
2) A short presentation of the loupe cell browser for non-bioinformatician users (30min)
3) A long hands on session for power users in R using the Seurat package to explore spatial data more in depth (1:30)

We will provide online Rstudio sessions with all the code, data and packages already loaded up for users to join and follow the session.
Code and data will also be available for users who prefer to run everything on their own computer.

Organisers: Kasun Samarasinghe and Pierre-Andre Michel

Description: All the data and knowledge resources have to integrate data from various external resources.

In order to accommodate large scale data, scalable data integration pipelines need to be developed. The aim of this workshop is to present the steps to build a scalable data integration pipeline using container technology and state-of-the-art workflow management tools.

Containerization is a mature technology, which is used in various different use cases, especially to isolate large systems into manageable and maintainable components. Such containerized components can be deployed to achieve scalability and load balancing. We will present a container-based architecture for data pipelines based on Docker and the use of such a containerized workflow in the Apache Airflow open source workflow management framework.

A hands-on session will be organized for the attendees to build a simple ETL (extraction, transformation and load) pipeline, ideally from a bioinformatics resource such as Ensembl. We will also share neXtProt’s experience on developing and improving our internal pipelines and the challenges faced during the process.

Finally, an open discussion will be conducted to exchange ideas, comments and possible collaborations to work on improvements of the presented system in a bioinformatics context.

Organisers: Tarcisio Mendes de Farias, Anne Morgat, Thierry Lombardot, Jerven Bolleman, Lydie Lane, Marco Pagni, Julien Mariethoz, Julien Wollbrett, Alain Gateau and Dmitry Kuznetsov

Description: Although many tools and programmatic interfaces have been developed by the SIB databases, bioinformaticians and biologists in general still struggle to know how to fetch and combine the information they are looking for in these databases.
To mitigate this problem, many SIB resources are modelling their knowledge with a common data model: the Resource Description Framework (RDF). Currently, nine independent SIB resources made their RDF data queryable and accessible through SPARQL query language services. These resources are GlyConnect, UniProt, Rhea, OrthoDB, OMA, Bgee, MetaNetX and NeXtProt.

In this workshop, we propose hands-on activities to answer questions based on individual needs of each user of the SIB databases. For example, how to extract the datasets of interest for users’ own research from SIB databases. The workshop will be composed of a quick introduction to SPARQL, and for each resource, we will show what kind of information is available. Afterwards, the arising biological questions and dataset needs by the attendees of this workshop will be treated case by case. Therefore, we expect that this workshop will significantly ease the attendees’ workflow to retrieve the data they need for the own research and to answer complex questions.

These questions can often only be answered by combining various SIB databases such as the following one that requires Bgee, OMA, and UniProt: “What are the human genes which have a known association to glioblastoma (a type of brain cancer) and which furthermore have an orthologous gene expressed in the rat’s brain”.

Organisers: Stefan Bienert, Pablo Escobar and Jaroslaw Surkont

Description: Going beyond the usual 20 minute Docker tutorial... lots of tutorials on the net leave the user at the point where they can run a simple application out of a single container. But how do you get your own full-blown web service in the cloud thereafter?

That requires multiple containers working together in the scope of container orchestration. In a real world setup, this requires the containers to be provided via a container registry. Finally, since no one likes to rebuild containers manually for every code change, the whole deployment should be automated by CI.

That is what we want to try to teach people in this workshop: Take a (Django) web app, distribute it into multiple containers and run it via Docker Compose as an entry-level orchestration tool. Of course, in the back everything should live in a Git repository and from there we want to add GitLab's CI functionality to our project. To not store confidential information like passwords inside the Git repository while using the CI, GitLab secrets will also be a topic. As usual we want the users to do the work.

Organiser: Romain Feron and Antonin Thiebaut

Description: Data analyses usually involves pipelines connecting tools and script to process the data. In recent years, workflow management systems have attempted to standardize these pipeline and provide many quality-of-life features for pipeline developers.
Snakemake is a popular workflow manager that works as a superset to Python. It implements a text-based workflow specification language and an execution environment allowing easy execution of workflows on local and remote computers and computational platforms.

Organiser: Charlotte Soneson, Federico Marini and Kevin Rue-Albrecht

Description: Exploratory analysis and visualization are integral parts of the analysis and communication of biological data, but are typically performed using static plots.

This workshop will demonstrate how to use the iSEE R package (https://bioconductor.org/packages/iSEE/) to instead create and customize interactive applications for the exploration of various types of biological data sets (e.g., bulk and single-cell RNA-seq, CyTOF, gene expression microarray), while maintaining reproducibility.

A running example of an app created with iSEE, including a tour guiding the user through the interface, is deployed at http://shiny.imbei.uni-mainz.de:3838/iSEE/.

The workshop will be presented as a lab session that combines an instructor-led live demo with hands-on experimentation guided by completely worked examples and stand-alone notes that participants may continue to use after the workshop.

Tuesday 9 June

09:00 - 09:30

09:30 - 09:45

Welcome speech

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09:45 - 10:15

Keynote lecture 1: Victoria Nembaware (Sickle Africa Data Coordinating Center)

Sickle Cell (a.k.a. Banana Cell) Africa Data Coordinating Center (SADaCC)

Sickle cell disease (SCD) is a life-threatening blood disorder that affects millions of people worldwide, with disproportionate incidence rates and mortality rates in the Sub-Sarahan (SSA) region. The Sickle Africa Data Coordinating Center (SADaCC) was created in 2017 to provide support to develop the largest multi-national SCD patient registry in SSA, data standardization, research capacity development, support improved healthcare and coordinate communications for the SCD in SSA Collaborative Consortium (SickleInAfrica). SADaCC envisions contributing to improved quality of care, quality of life and survival of people affected by SCD in Africa and globally. This presentation will highlight SADaCC’s strategy, lessons to date and key achievements.

10:15 - 10:45

"Meet-the-Speaker(s)" and coffee break-out sessions

10:45 - 11:45

Parallel Session 1 & 2

Franziska Singer (Group: Daniel Stekhoven)
Single-cell RNA analysis deciphers tumor heterogeneity and the immune microenvironment
Fabian Arnold (Group: Valérie Barbié)
MTPpilot: an interactive software for NGS results analysis for molecular tumor boards ‘Enriched’ data analysis & presentation
Iulian Dragan (Group: Mark Ibberson)
dsSwissKnife: Enabling federated data analysis for biomedical research
Maria Famiglietti (Group: Alan Bridge)
Linking genome and variation data with knowledge of protein function and disease: Enhanced integration of UniProtKB/Swiss-Prot, ClinVar and PubMed
Gerard Aubach (Group: Bart Deplancke)
Regulatory role of a non-coding variant in chronic lymphocytic leukemia
Marija Dmitrijeva (Group: Christian von Mering)
Strain-resolved Dynamics of the Lung Microbiome in Patients with Cystic Fibrosis
Imant Daunhawer (Group: Julia Vogt)
Enhanced early prediction of clinically relevant neonatal hyperbilirubinemia with machine learning
Xinrui Lyu (Group: Gunnar Rätsch)
Mutational Signatures used Supervised Negative Binomial Non-Negative Matrix Factorization

11.00 - 11.25: 1x25 min

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11.50 - 12.05 1x15 min

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Lucas Paoli (Group: Shinichi Sunagawa)
Exploring uncharted phylogenomic diversity reveals novel chemistry in the global ocean microbiome
Carlos-Andrés Peña (Group: Carlos-Andrés Peña)
Quantitative biomonitoring of agricultural soils using protist communities
Silas Kieser (Group: Evgeny Zdobnov)
A complete picture of the mouse gut microbiome
João Matias Rodrigues (Group: Christian von Mering)
Ecological insights from the analysis of the Microbe Atlas Project dataset, a global reference set of a million microbiome samples
Samuel Neuenschwander (Group: Anna-Sapfo Malaspinas)
What can we learn from the saliva of Aboriginal Australians

11:45 - 12:15

"Meet-the-Speaker(s)" - Q&A break-out rooms for Parallel Session 1 & 2

12:15 - 13:30

Lunch Break

13:30 - 14:30

Parallel Session 3 & 4

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Gabriel Schweizer (Group: Andreas Wagner)
Genotype networks of 80 quantitative Arabidopsis thaliana phenotypes reveal substantial phenotypic evolvability despite pervasive epistasis
Luciano Cascione (Group: Luciano Cascione)
Transcribed ultra-conserved regions model drug response in the NCI60 cell line panel
Jeremie Breda (Group: Mihaela Zavolan)
Realizing Waddington’s metaphor : Inferring regulatory landscapes from single-cell gene expression data
Abdullah Kahraman (Group: Christian von Mering)
Pathogenic impact of transcript isoform switching in 1209 cancer samples covering 27 cancer types using an isoform-specific interaction network

François Bonnardel (Group: Frédérique Lisacek)
Prediction of carbohydrate-binding proteins in microbial proteomes
Luciano Abriata (Group: Matteo Dal Peraro)
State-of-the-art web services for modeling the structures of proteins that lack clear templates in the PDB
Olivier Bignucolo (Group: Stephan Kellenberger, embedded in the groups of Olivier Michielin and Vincent Zoete)
Responses of ion channels to pH fluctuations investigated through molecular dynamics
Andrea Cavalli (Group: Andrea Cavalli)
Machine learning predicts immunoglobulin light chain toxicity through somatic mutations
Marta Perez (Group: Vincent Zoete)
Addressing challenges in cancer immunotherapy with structural bioinformatics approaches
Erblin Asllanaj (Group: Torsten Schwede)
Enabling structure-guided life science research with the SWISS-MODEL Repository

14:30 - 15:00

"Meet-the-Speaker(s)" - Q&A break-out rooms for Parallel Session 3 & 4

15:30 - 16:30

Poster Session 1 (poster and software demonstrations)

List of poster and software presentations

17:00 - 17:45

Get sporty!

Franziska Singer (Group: Daniel Stekhoven)
Single-cell RNA analysis deciphers tumor heterogeneity and the immune microenvironment
Fabian Arnold (Group: Valérie Barbié)
MTPpilot: an interactive software for NGS results analysis for molecular tumor boards ‘Enriched’ data analysis & presentation
Iulian Dragan (Group: Mark Ibberson)
dsSwissKnife: Enabling federated data analysis for biomedical research
Maria Famiglietti (Group: Alan Bridge)
Linking genome and variation data with knowledge of protein function and disease: Enhanced integration of UniProtKB/Swiss-Prot, ClinVar and PubMed
Gerard Aubach (Group: Bart Deplancke)
Regulatory role of a non-coding variant in chronic lymphocytic leukemia
Marija Dmitrijeva (Group: Christian von Mering)
Strain-resolved Dynamics of the Lung Microbiome in Patients with Cystic Fibrosis
Imant Daunhawer (Group: Julia Vogt)
Enhanced early prediction of clinically relevant neonatal hyperbilirubinemia with machine learning
Kjong-Van Lehmann (Group: Gunnar Rätsch)
Mutational Signatures used Supervised Negative Binomial Non-Negative Matrix Factorization

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11.40 - 11.50: 2x5 min

11.50 - 12.05 1x15 min

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Lucas Paoli (Group: Shinichi Sunagawa)
Exploring uncharted phylogenomic diversity reveals novel chemistry in the global ocean microbiome
Xavier Brochet (Group: Carlos Peña)
Quantitative biomonitoring of agricultural soils using protist communities
Silas Kieser (Group: Evgeny Zdobnov)
A complete picture of the mouse gut microbiome
João Matias Rodrigues (Group: Christian von Mering)
Ecological insights from the analysis of the Microbe Atlas Project dataset, a global reference set of a million microbiome samples
Samuel Neuenschwander (Group: Anna-Sapfo Malaspinas)
What can we learn from the saliva of Aboriginal Australians

Off the carbs, off the couch!

It’s been another long day in front of a computer screen? You are feeling the urge to move, to work out a bit and to not only use your brain, but also your leg, arm and other body muscles? Then join us for this CrossFit session!

CrossFit is a fitness sport that combines elements from weightlifting, gymnastics, calisthenics and plyometrics with a healthy lifestyle philosophy and diet. The team of MAYAMA CROSSFIT will introduce you to the world of CrossFit and lead you through a short 45 minute programme with a range of exercises to loosen up your muscles.

Get into your sport clothes, find a free spot in your room or outside and join this workout session with your fellow SIB Members!

Take a deep breath and relax!

It’s been another long day in front of a computer screen? You just want to get your mind off for a few minutes, relax, but ideally together with your partner, kids or family? Then join us for this Yoga session and bring your loved ones along. The session is adapted for families and kids, but you can also join alone.

Yoga is a set of physical, mental, and spiritual practices or disciplines to strengthen your mind and body. Ana Rangel from the Sattva Yoga Institute will guide you through this Yoga session and help you to relax your mind and body after a long day of presentations.

All you need to join this session is a Yoga mat, blanket or similar and a little bit of space (either inside or outside your apartment).

Wednesday 10 June

09:30 - 12:00

Workshops and tutorials

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09:00 - 09:45

Morning Yoga: a perfect way to welcome the new day!

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12:40 - 13:30 in Kongresssaal

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12:40 - 13:30 in Vereinsaal

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The sun has risen, society and nature are waking up and you find yourself thinking about this new day and all the events and challenges it might bring…. join this Yoga class and put yourself in the right mindset to master them!

In this Yoga class by Ana Rangel from the Sattva Yoga Institute, you will discover the idea of mindfulness mediation combined with breathing methods and Yoga exercises to prepare your body and mind for the day to come.

All you need to join this session is a Yoga mat, blanket or similar and a little bit of space (either inside or outside your apartment).

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10:00 - 10:45

Facing the COVID-19 crisis as bioinformaticians: four perspectives

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12:40 - 13:30 in Vereinsaal

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Session Chairs: Julien Roux & Maïa Berman

The COVID-19 pandemic is now slowing down in most European countries, but it will leave profound marks on society. Many SIB members played a significant role in fighting against COVID-19 by developing or maintaining key resources that were necessary for the scientific community (e.g., Nextstrain, ViralZone).

In this session we will meet and discuss with some of them, looking back at what went on behind the scenes over the past months. What were the immediate effects of the COVID-19 crisis on their work and teams? What were the main challenges to overcome? Which lessons were learned for the future, and how do they envision the evolution of their resources in the next few months?

Our discussion will revolve around the themes of communication, training, biocuration, open science, collaboration and sustainability of resources.

Our panel speakers are:

- Emma Hodcroft, Postdoctoral researcher at the Biozentrum, University of Basel (Nextstrain)

- Patricia Palagi, Head of the SIB Training Group

- Philippe Le Mercier, Project Manager at the SwissProt Group, University of Geneva (ViralZone)

- Fabio Rinaldi, Group Leader at the University of Zürich and Dalle Molle Institute for Artificial Intelligence Research, Lugano

We will end the session by a Q&A, allowing you to ask them your questions.

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Keynote lecture 2: Flora Graham (Science and Technology Journalist for Nature)

Getting it out there: Science communication for bioinformaticians

To make an impact, your research has to reach the experts, policymakers and members of the public it's designed to help. But how do you get your research noticed? And how do you contribute to the wider conversation -- even if you don't have 'news' to share? Science journalist and broadcaster Flora Graham, who writes the influential Nature Briefing newsletter for the journal Nature, will introduce you to science communication for scientists. She will throw back the curtain on how science journalism works, how to reach the people you're aiming for, how to grapple with social media, and how to measure success.

11:15 - 11:45

"Meet-the-Speaker(s)" and coffee break-out sessions

11:45 - 13:00

Lunch Break

13:00 - 14:00

Parallel Session 5 & 6

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Natalia Zajac (Group: Christophe Dessimoz)
Gene duplication and gain in Atriophallophorus winterbourni and other major parasitic trematodes contributes to adaptation
Alejandro V Cano (Group: Joshua Payne)
Modeling the effects of mutation bias on adaptive evolution
Julija Pecerska (Group: Marie Anisimova)
Impact of MDR-TB strain background on transmission fitness loss
Victor Rossier (Group: Christophe Dessimoz)
Phylogeny-driven and alignment-free protein family assignment is an accurate and scalable alternative to methods relying merely on closest sequence
Mathilde Foglierini (Group: Luciano Cascione)
AncesTree: an interactive immunoglobulin lineage tree visualizer
Diana Ivette Cruz Dávalos (Group: Anna-Sapfo Malaspinas)
Ancient population genomics of Brazilian Botocudo groups
Kimberly Gilbert (Group: Laurent Excoffier)
Transition from Background Selection to Associative Overdominance Promotes Diversity in Regions of Low Recombination
Tristan Cumer (Group: Jérôme Goudet)
Genomic tales: An history of European barn owls

Joern Petzold (Group: Bart Deplancke)
Postnatally developing epigenomic landscape defines immuno-modulatory properties across lymph node stromal cell subsets
Roman Vetter (Group: Dagmar Iber)
Modelling cell organization in epithelial tissue
Anastasiya Boersch (Group: Mihaela Zavolan)
Rodents as models of human sarcopenia: a comparative analysis reveals conserved modulators of aging-dependent muscle loss
Marco Pagni (Group: Mark Ibberson)
MetaNetX/MNXref 4.0 - a reconciliation of metabolites and biochemical reactions
Xavier Richard (Group: Christian Mazza)
On the use of game engines to perform stochastic simulations of bacterial interaction

14:00 - 14:30

"Meet-the-Speaker(s)" - Q&A break-out rooms for Parallel Session 5 & 6

14:30 - 15:30

Parallel Session 7 & 8

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Markus Muller (Group: Mark Ibberson)
NewAnce: identifying non-canonical HLA peptides in tumor immunopeptidomes
Marthe Solleder (Group: David Gfeller)
Mass spectrometry based immunopeptidomics leads to robust predictions of phosphorylated HLA class I ligands
Lionel Breuza (Group: Alan Bridge)
Representing the human metabolome in UniProtKB using Rhea
Philippe Le Mercier (Group: Alan Bridge)
Bioinformatic analysis of SARS-CoV-2
Maarten Reijnders (Group: Robert Waterhouse)
CrowdGO: a wisdom of the crowd-based Gene Ontology annotation tool
David Lyon (Group: Christian von Mering)
aGOtool.org web-tool for protein-centric enrichment analysis, featuring many functional categories, abundance-correction, and regular updates
Roman Mylonas (Group: Mark Ibberson)
Pumba: a web resource to verify antibody based results

Charlotte Soneson (Group: Michael Stadler)
Preprocessing choices affect RNA velocity results for droplet scRNA-seq data
Andre Kahles (Group: Gunnar Rätsch)
Metagraph: Representing sequence data at a petabyte scale
Anna Koroleva (Group: Maria Anisimova)
Towards creating a new knowledge base for literature-based discovery
Yannis Nevers (Group: Christophe Dessimoz)
HOTs Hierarchical Orthologous Transcripts
Elena Montegro Borbolla (Group: Carlos Peña)
A machine learning approach on "signalomics" data to improve decision making at the ICU"
Mariia Bilous (Group: David Gfeller)
Coarse-graining of single-cell RNA-seq data preserves clustering and improves detection of gene correlations
Maciej Bak (Group: Mihaela Zavolan)
A novel approach to detect the influence of RNA-binding proteins on pre-mRNA processing
Fabio Rinaldi (Group: Fabio Rinaldi)
Fast Efficient Accurate Entity Recognition for biomedical applications

15:30 - 16:00

"Meet-the-Speaker(s)" - Q&A break-out rooms for Parallel Session 7 & 8

16:00 - 17:00

Poster Session 2 (poster and software demonstrations)

15:05 - 16:35

Poster session and coffee

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17:05 - 17:20

Closing Remarks

Keynote speakers

Vicky Nembaware - Project Manager / Researcher, SADaCC

Dr. Nembaware is the Project Manager for the Sickle Africa Data Coordinating Center (SADaCC). SADaCC’s mandate is to coordinate research capacity development and training in Sickle Cell Disease specifically in study design, Data Management Plans, Big Data Analytics, ontology development and application.

In addition, the SADaCC center is responsible for coordinating Sickle Cell Disease stakeholders and promoting public and community engagement. Previous positions held by Vicky include being the H3Africa Training Coordinator, mHealth and M&E specialist for a non-profit organization and was also a visiting post-doctoral fellow at Stanford University.

She earned her first degree in Chemistry and Microbiology from the University of Cape Town and then graduated Cum Laude for her Hons and MSc degrees from the University of Western Cape (South African Bioinformatics Institute). Vicky was awarded a PhD in Bioinformatics in 2008 from the University of Cape Town.

In addition to her didactic training in Bioinformatics and Monitoring and Evaluation, Vicky has research experience in Bioinformatics, Genomics and in the Public Health field. She also has experience in designing, monitoring and evaluation of projects in the Information Communication Technology field (particularly in mHealth). Vicky has conducted numerous mHealth projects.

She has also developed a mobile phone app (mGenAfrica) in collaboration with various stakeholders which aims primarily to train researchers how to engage and educate the general public on heredity and health in Africa.

Another noteworthy project she helps coordinate is the African Genomic Medicine Training Initiative. She is the current Secretary of the African Society of Human Genetics (AfSHG).

Flora Graham - Senior Editor, Nature Briefing

Flora Graham is a science journalist who writes the Nature Briefing, the daily news email from the world's leading science journal.

She was previously Digital Editor at New Scientist, and wrote for the BBC, CBC, and CNET, among others. She has appeared as a commentator on technology for news outlets in the UK, Europe and North America. As a speaker and chair, she has appeared at events at the Royal Institution, Imperial College and the Shangai Science Hall.

Flora has a Bsc in physics and English from the University of British Columbia and a Msc in science communication from Imperial College.

Favourite topics include physics, creative non-fiction, mobile technology, radio and why you'll never get a fridge that orders your groceries.

Poster & Demo sessions

Here is an overview of the preliminary programme for the SIB Days 2020.

Social activities

To Be Confirmed

Meeting Schedule

Poster & Demo sessions

Social activities

Data scientists for life