SIB Profile 2023: 25 years of data scientists for life

Open Research Data

SIB is one of the federal government's instruments to support research and innovation in Switzerland, and to promote the country internationally.

Personalized health

We set up solutions on the national and international level to make consented patient data available to researchers, to foster personalized health.

SEE P. 14

Forewords

At SIB, we know that expertise in life science data is critical to solving the world's most pressing challenges—healthy living, biodiversity preservation, food security, and the digital transformation.

Twenty-five years after its creation, our institute is more needed than ever. SIB’s three areas of activity provide solutions to the pressing challenges of data-intensive biological and biomedical science. Our centre of excellence leverages our data science expertise and network to accelerate discovery and innovation. Our coordination activity enables collaboration across institutions, disciplines, and national boundaries, and helps establish the common standards needed to make open data and knowledge universally understandable and AI ready. And not least, our open resources (databases, knowledgebases, and software tools) are depended upon by millions of researchers worldwide, and continue to embody the Swiss values of quality, innovation, and openness.

Our vision is brought to life by our wonderful community, which is becoming more connected every year. Together, we unleash the potential of biological data to make a better future. •

Exemplified by the European Open Science Cloud, ELIXIR projects or the National Open Research Data Strategy: the public domain is increasingly looking to better manage data. The same need also arises in the private sector, with start-ups and multinational companies alike striving to unlock innovation and competitiveness.

Better managing data is thus topical for all actors in the life sciences. It involves integrating multiple streams of data, making them FAIR, streamlining computing workflows, knowledge representation, etc. These skills also happen to have been the core expertise of SIB for 25 years.

Christophe Dessimoz Executive Director

Independent and excellence-driven, SIB’s complete service offering is thus a timely boon for any company, healthcare provider, research group or international consortium. I am already impressed by the number of European organizations seeking high-value collaborations in Switzerland and with SIB. With the institute’s strong track record in health-related applications and fundamental research, it will be exciting to see new collaborations emerging in other domains that rely on Big Data. •

Jérôme Wojcik Chairman of the Board of Directors

“At SIB, we know that expertise in life science data is critical to solving the world's most pressing challenges.”

Switzerland can be proud of its long history of excellence in the life sciences. It is home to world-class research institutions and companies, leading the way from discovery to innovation. But to maintain our position as a global leader, key challenges need to be tackled. And life science data specialists such as SIB’s are essential in this context.

One such challenge is the increasing complexity and volume of data generated by research activities. The promises of Open Research Data (ORD) for society and the economy have been recognized at the academic as well as at the political level. Democratizing access to data has become a priority to ensure their full potential is exploited and public investments are optimized. SIB directly supports this ambition through world-leading bioinformatics resources, projects and expertise.

Over the years, SIB’s work has impacted society in many ways, including its contribution to pandemic management. The topics of agriculture and biodiversity being close to my heart in both my political commitments and professional activities, I am particularly impressed by how bioinformatics can benefit them. By integrating and analyzing large datasets of genetic and ecological information, it provides insights into the drivers of biodiversity loss and helps identify the most effective conservation measures.

Another key challenge is the need for collaboration and interdisciplinary research. Advances and innovation in life science increasingly rely on expertise from multiple disciplines, including biology, chemistry, computer science and engineering, which can be split between the academic and private sectors. SIB’s position as an independent partner with expertise spanning these areas is a clear booster for collaborations.

Over the past 25 years, the institute has established itself as the Swiss reference for biological and biomedical data science. I am honoured and delighted to play an active role in shaping its future and positioning Switzerland as a global leader in life science research. •

Simone de

President of the Foundation Council

Montmollin

“Over the past 25 years, the institute has established itself as the Swiss reference for biological and biomedical data science.”

Data scientists for life

We are multidisciplinary experts who safeguard data and make it speak to solve biological questions. Discover how we work and the highlights of the year from our members and teams.

What kinds of data are we talking about?

Bioinformatics deals with a broad spectrum of complex data types.

Bioinformatics: a definition

Life scientists and clinicians have long tried to assemble data and evidence to find the right answers to fundamental questions. Today, however, there is no shortage of data, and we find ourselves with a different issue. New technologies are producing data at an unprecedented speed, and in such quantity and variety that they can no longer be interpreted by the human mind alone.

Enter bioinformatics.

Bioinformatics is the application of computer technology to better understand and effectively use biological and biomedical data. It is the discipline that stores, analyses and interprets the Big Data generated by life-science experiments, or collected in a clinical context. This multidisciplinary field is driven by experts from a variety of backgrounds: biologists, computer scientists, mathematicians, statisticians and physicists.

Bioinformatics encompasses:

DATABASES for storing, retrieving and organizing curated information to maximize the value of biological data;

SOFTWARE TOOLS for modelling, visualizing, interpreting and comparing biological data;

ANALYSIS of complex biological datasets or systems using novel statistical approaches or machine learning techniques;

RESEARCH harnessing computational methods in a wide variety of biological fields to develop solutions in diverse areas, from agriculture to precision medicine; (SEE P. 32)

COMPUTING AND STORAGE

INFRASTRUCTURE to process and safeguard large amounts of biological data.

Expression data, such as the level of expression of a gene in a sample

Thanks to computer-based approaches, researchers can improve their understanding of complex systems.

BRINGING BIOINFORMATICS TO SOCIETY

From precision medicine to drug design and DNA testing: bioinformatics is increasingly tied to health and societal issues.

Through outreach activities, SIB regularly communicates on advances made in this field and on their importance to the general public. A special focus is given to young people and girls in particular, to foster their interest in STEM* disciplines.

The website, In the Light of Evolution, an SNSF-Agora-funded project developed by SIB Employees and Members, shows the real-life implications of evolutionary biology through interactive stories. This year, stories delved into questions such as: “Have all the dinosaurs actually disappeared?” and “What can we learn from the DNA left behind by ancient Greeks?” More than 1,500 people benefited from this project through classroom visits and science fair events in 2022.

In 2022

2,500 participants took part in over 90 activities and events, including:

Workshops on the coronavirus “Hunting SARS-CoV-2, its variants and its origin”

TecDays

organized by the Swiss Academy of Engineering Sciences SATW for students aged 15-20 Nuit de la Science in Geneva, a science fair with the theme “And yet”

Explore our other interactive outreach websites, such as ChromosomeWalk.ch, to discover our genome and PrecisionMed.ch to understand how increased knowledge of our individual genomes can improve and personalize healthcare.

Mystères de l’UNIL, the University of Lausanne’s open day with the theme “Life paths”

Expanding your horizons in Geneva, an event dedicated to providing young girls with experiences in STEM* and encourage them to see it as a future option.

* Science, Technology, Engineering and Mathematics (STEM)

The Protein Spotlight comic strip tells stories of proteins for a lay audience written by Vivienne Baillie Gerritsen, with illustrations by Aloys Lolo. In 2022, 12 comics were published with articles in French and English.

proteinspotlight.org/comics/

More activities and news on Facebook, our dedicated outreach channel in French and English goo.gl/4c6xCZ

SIB in brief

SIB is a high-quality partner enabling innovation in academia, hospitals and industry by leveraging its data science expertise, resources, national network, and independent non-profit status.

As a centre of excellence, SIB offers its services to researchers, institutions and private companies in a range of areas such as data stewardship and bioinformatics training as well as software engineering. (SEE P. 27);

It builds high-quality national bioinformatics platforms, such as the Swiss Pathogen Surveillance Platform (SPSP), to allow the analysis and near real-time sharing of epidemiological and molecular data from pathogens;

It enables the secure sharing of sensitive patient data through novel techniques, such as federated analysis. A unique network of data from over 60,000 patients with type 2 diabetes was thus made available for research in the RHAPSODY Europe initiative to fight diabetes.

88 groups

900 members, including

190 employees

28

institutional partners across Switzerland

200 databases and software tools developed by our members and accessible via the Expasy web portal

516

peer-reviewed articles and preprints published in 2022

As of 1 January 2023

A leading organization in biological and biomedical data science, SIB functions through three complementary pillars, with infrastructure tightly embedded in research.

Open databases and software tools

SIB provides long-term access to the most useful, reliable and precise biodata resources made in Switzerland to scientists all over the world, ensuring they meet the highest standards for research.

It provides a portfolio of 14 SIB Resources (SEE P. 23), which explore a wide variety of biological processes and address various needs such as tracking pathogen evolution, information on cell lines, and computer-aided drug design. Four biodata resources from SIB are supported on the European level as ELIXIR Core Data Resources and three are recognized worldwide as Global Core Biodata Resources.

It has its portfolio reviewed every four years by the Scientific Advisory Board, which ensures the highest quality resources are offered to as many communities as possible as well as society.

It supports them throughout their life cycle with a range of dedicated expertise, including user interface and experience, IT security, tech transfer and licensing.

We tailor these resources to the specific needs of our partners in the private sector.

SIB maximizes the impact of projects and investments by making data FAIR (Findable, Accessible, Interoperable and Reusable) and developing common standards to facilitate collaboration and allow data to be as open as possible. This in turn benefits the entire research landscape.

It federates the bioinformatics community of Switzerland and connects it to the world, with links to global organizations such as ELIXIR, the Global Biodata Coalition and the Global Alliance for Genomics & Health (GA4GH);

It acts as the Data Coordination Centre in several pan-European public-private consortia tackling diabetes, cancer or obesity;

It coordinates clinical research data as the Data Coordination Centre in the Swiss Personalized Health Network (SPHN) across all actors involved, from hospitals to researchers and experts, and set up the secure national computer network BioMedIT;

It brings the community together to promote Swiss bioinformatics in events such as the Basel Computational Biology Conference [BC]2 and the SIB days, as well as by supporting other events and facilitating collaborations with the industry.

Coordination

Massive amount of data of various types: genetics, text, biochemical, imaging, etc.

SIB

Swiss Institute of Bioinformatics

Centre of Excellence

Leveraging data science expertise, resources, national network, and independent non-profit status

Coordination

Developing common standards to facilitate collaboration and allow data to be as open as possible

Open databases and software tools

Sharing access all over the world to the most reliable and precise biodata resources made in Switzerland

Dedicated multidisciplinary experts

25 YEARS OF DATA SCIENTISTS FOR LIFE

SIB’s work is helping us to better understand our environment by developing solutions and guiding decisions towards a sustainable world. Our biodata resources are being used in food security and to understand the impact of air pollution (SEE P. 22) SIB Members are also involved in large-scale initiatives that are transforming our understanding of biodiversity and informing actions for conservation (SEE P. 42)

Supporting the development of personalized health

Since 2017, SIB has co-led key initiatives to ensure citizens benefit from findings in personalized medicine driven by research projects: the national secure network for the processing of health data, BioMedIT, and the Swiss Personalized Health Network (SPHN) for which we act as the Data Coordination Centre (SEE P. 53). Our scientists are also advancing precision oncology by developing clinical software solutions such as Oncobench®, used since 2016 to manage and analyse data from routinely sequencing cancer genomes. They built the Swiss Variant Interpretation Platform for Oncology (SVIP-O) for sharing cancer variants, and are involved in educating health professionals in this fast-evolving area with the first Swiss CAS in Precision Molecular Oncology.

Equipping researchers and policymakers to fight pandemics

Much of the infrastructure and expertise developed over many years at SIB came into the spotlight with the recent pandemic. Among the SIB Resources, V-Pipe is used, for instance, by international researchers to detect novel variants in wastewater, while Nextstrain enables real-time tracking of virus evolution, whether SARS-CoV-2, Ebola or Zika. Several SIB Group Leaders are also active members of the Scientific Advisory Panel to advise the government on mitigating COVID-19. The Swiss Pathogen Surveillance Platform (SPSP), co-led by SIB with the potential to host any pathogen sequences of public interest, also acts as the Swiss SARS-COV-2 Data hub with the support of the Federal Office of Public Health (FOPH).

Twenty-five years ago, bioinformatics was a niche discipline. Anticipating it would become central to advancing biology and medicine, a team of scientists came together with a vision to reinforce it: SIB was born.

Working towards a better environment for all

“Switzerland is well positioned, thanks to infrastructure like that of SIB.”

Felix Gutzwiller Former President of SIB’s Foundation Council in an interview on Big Data in health in the Neue Zürcher Zeitung am Sonntag

“At a time of revolutionary advances in biology and biomedicine, both in scientific research and its applications, with direct implications for society and the economy, the role of SIB is even more important and central than ever.”

Scientific Advisory Board review, January 2022

Over its 25 years of existence, SIB has seen an extraordinary growth in its numbers of affiliated groups and their outputs in publications.

Promoting and maintaining excellence in science

Since its creation in 1998, SIB has made substantial contributions to fostering research data quality, integrity and reproducibility by providing essential infrastructure to support advances in the life sciences and fostering Open Research Data. This includes the portfolio of SIB Resources, 14 leading Open Science databases and software tools, as well as the centre of excellence providing researchers with services of the highest quality. As a recognized provider of bioinformatics training, SIB increases the skills of researchers in good research practice. Methodological excellence is also actively encouraged through the SIB Bioinformatics Awards and the annual conferences organized by SIB on the most important developments in the field.

From a network to a fully fledged organization

SIB began as an association of like-minded scientists with a common passion: to ensure the progress of life science research in Switzerland. It is now a nationwide organization that can be relied on for professional services, with a structure and governance to cater for the multiple needs of the life science community and inform key decisions on its future, such as on Open Research Data.

SIB has grown into a major organization with far-reaching societal impact.

Organization and governance

The unique structure of SIB’s governance forms the basis of its strength.

SIB's unique governance structure ensures a high level of efficiency by embedding solutions into research and leveraging Switzerland's network of bioinformatics competences.

Scientific Advisory Board

Acts as an independent consultative body, providing recommendations to the Board of Directors and the Council of Group Leaders. Its main tasks consist of monitoring service and infrastructure activities, such as the SIB Resources.

(SEE P. 23)

Define and implement the institute's strategic goals as well as representing the organization at the national and international level. Support functions include finance & grant services, legal & technology transfer, human resources, information technology, cyber security, coordination of biodata resources, and communication & scientific events.

Foundation Council

Highest authority in the institute, with supervisory powers. Its responsibilities include changes to SIB’s statutes, nomination of Group Leaders, and approval of the annual budget and financial report.

Board of Directors

Takes the decisions necessary to achieve the aims of the institute, such as defining the scientific strategy and internal procedures, and allocating federal funds to service and infrastructure activities.

Council of Group Leaders Management & support functions

Discusses all matters relating to SIB Groups as a whole, and proposes new Group Leadersfor nomination. The Council also elects its representatives on the Board of Directors.

SIB Hub

Staffed and headed by SIB Employees, this focuses on SIB’s three core activities, coordination, open resources and centre of excellence.

(SEE P. 28-29)

Affiliated Groups

Academic member groups from partner institutions across Switzerland, which can also include SIB Employees. They participate in the community by sharing and benefiting from scientific expertise, and take part in collaborative projects and resources fostered by SIB (SEE P. 30).

President Simone de Montmollin

Member of the National Council

Founding Members

Prof. Ron Appel

Former SIB Executive Director

Prof. Amos Bairoch

Group Leader, SIB and University of Geneva

Dr Philipp Bucher

Affiliate Group Leader, SIB

Prof. Denis Hochstrasser

Former Vice-Rector, University of Geneva

Prof. C. Victor Jongeneel

Carl R. Woese Institute for Genomic Biology, University of Illinois, USA

Prof. Manuel Peitsch

Chief Scientific Officer Research at Philip Morris International

Ex officio Members

Prof. Hugues Abriel

Vice-rector for Research, University of Bern

Prof. Cezmi A. Akdis

Director, Swiss Institute of Allergy and Asthma Research (SIAF)

Mr Thomas Baenninger

Chief Financial Officer, Ludwig Institute for Cancer Research

Prof. Claudia Bagni

Vice Dean for Research and Innovation, Faculty of Biology and Medicine, University of Lausanne

Prof. Christian Berthold

Managing Director, Cardio-CARE

Prof. Hervé Bourlard

Director, IDIAP

Prof. Edouard Bugnion

Vice President for Information Systems, EPFL

Prof. Emmanuele Carpanzano

Director, Department of Innovative Technologies, SUPSI

Prof. Carlo Catapano

Director, IOR Institute of Oncology Research

Prof. Alex Dommann

Head of Department “Materials meet Life”, Swiss Federal Laboratories for Materials Science and Technology (Empa)

Prof. Estelle Doudet

Vice Rector “Research”, University of Lausanne

Prof. Katharina Fromm

Vice Rector, University of Fribourg

Prof. Cem Gabay

Dean, Faculty of Medicine, University of Geneva

GOVERNING BODIES

The Foundation Council

Each of SIB’s partner institutions is represented on the Council. Composition as of 1 January 2023

Prof. Patrick Gagliardini

Vice Rector for Research at the Universita della Svizzera italiana (USI);

Prof. Brigitte Galliot

Vice Rector, University of Geneva

Prof. Antoine Geissbühler

Vice Rector, University of Geneva

Head of eHealth and Telemedicine Division, Geneva University Hospitals (HUG)

Dr Corinne Jud

Head of the Competence Division

Method Development and Analytics, Agroscope

Prof. Jérôme Lacour

Dean, Faculty of Science, University of Geneva

Dr Vincent Peiris

Dean, School of Business and Engineering Vaud (HEIG-VD), HES-SO

Prof. Jean-Marc Piveteau

President, Zurich University of Applied Sciences (ZHAW)

Prof. Alexandre Reymond

Centre for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne

Prof. Davide Robbiani

Director, Institute for Research in Biomedicine (IRB)

Prof. Patrick Ruch

Head of Research, School of Business Administration (HEG-Geneva), HES-SO

Prof. Gebhard Schertler

Head of Biology and Chemistry Division

PSI – Paul Scherrer Institute

Prof. Falko Schlottig

Director, FHNW School of Life Sciences

Prof. Dirk Schübeler

Co-Director, Friedrich Miescher Institute for Biomedical Research (FMI)

Prof. Torsten Schwede

Vice President of Research and Talent Promotion, University of Basel

Prof. Elisabeth Stark

Vice President Research, University of Zurich

Prof. Juerg Utzinger

Director, Swiss Tropical and Public Health Institute

Prof. Detlef Günther

Vice President Research and Corporate Relations, ETH Zurich

Co-opted Member

Prof. Alfonso Valencia

ICREA Professor

Life Sciences Department Director

Barcelona Supercomputing Centre, Spain

The Board of Directors (BoD)

The BoD consists of two Group Leaders elected jointly by the Council of Group Leaders and the BoD, two external members elected by the Foundation Council on the recommendation of the BoD, and the SIB Executive Directors. Members of the BoD are appointed for a renewable five-year period.

Dr Jérôme Wojcik (Chairman)

Industrial Data Scientist & Entrepreneur

Prof. Christophe Dessimoz SIB Executive Director

PD Dr Katja Baerenfaller Group Leader, SIB and Swiss Institute of Allergy and Asthma Research (SIAF)

Ms Martine Brunschwig Graf

Former National Councillor

Prof. Robert Waterhouse Group Leader, SIB and University of Lausanne

The Scientific Advisory Board (SAB)

The SAB is made up of at least five members, who are internationally renowned scientists from the institute’s fields of activity.

Prof. Alfonso Valencia (Chairman) ICREA Professor

Life Sciences Department Director Barcelona Supercomputing Centre, Spain

Prof. Søren Brunak Research Director, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark

Prof. Melissa Haendel Director of the Ontology Development Group, Oregon Health & Science University, Portland, USA

Prof. Claudine Médigue Head of the Laboratory of Bioinformatics Analyses for Genomics and Metabolism (LABGeM), Génoscope & CNRS, Evry, France

Prof. Alexey I. Nesvizhskii

Department of Pathology and Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, USA

Prof. Christine Orengo

Department of Structural and Molecular Biology, University College London, UK

Prof. Ron Shamir

Computational Genomics Group at the Blavatnik School of Computer Science, Tel Aviv University, Israel

Council of Group Leaders

The Council consists of the Group Leaders and the SIB Executive Director.

(SEE P. 30)

SIB is a not-for-profit organization combining employees and affiliated members from 28 partner institutions

 Powered by the Swiss Confederation

The largest and most stable funder of SIB is the State Secretariat for Education, Research and Innovation (SERI), which accounts for 39% of our institute’s income, excluding specific BioMedIT/SPHN funding.

 A unique funding model to sustain Open Resources

SERI’s contribution to our Open Resources (53%, CHF 7 million) is complemented by many additional funding sources, including competitive grants and contributions from the industry. In addition, most resources are also supported by short-term research funds held at partner institutions.

 One third of SIB’s income comes from competitive funds 32% (CHF 9.8 million) of the funds secured by SIB originate from competitive grants, collaborations and services. SIB’s independent status, the diversity of skills of its employees, and the full professional support they offer, from scientific expertise to project management, make the institute a desirable partner. This includes innovative projects with the industry (e.g. Innosuisse) and long-term collaborations in European public-private consortia (e.g. Innovative Medicines/Health Initiatives).

Find out how our funding from the government and from other competitive sources allows us to achieve our mission and position SIB as a reference for life science data.

Software developers Biocurators Researchers

 Keeping up with increasing demands

The loss (3%) is funded by reserves to support additional Open Resources, in accordance with the investment strategy for the 2021-2024 period.

 A Centre of Excellence that delivers

Our Centre of Excellence includes training and bioinformatics services to universities, private companies and hospitals (SEE P. 26) amounting to a total of CHF 8.4 million. It is mostly funded through collaboration and competitive grants - many international.

 Lean and effective management & support

Scienti c project managers

The management and support functions expenses (14%, CHF 4.2 million) cover day-to-day administrative, people and culture, finance, communication, legal and IT support. These support teams also contribute to projects in the key pillars, for which the funds are allocated to the relevant activities (e.g. legal expertise for SPHN is allocated to Coordination).

 Investing in people at the heart of research

77% (CHF 23.8 million) of SIB’s funding is invested in our people, of which 73% for employees at the SIB Hub and 27% for employees embedded in partner institutions. This reflects our unique and efficient model anchoring Open Science infrastructure in research.

 Bioinformatics: a variety of competences and shared life science data expertise

PEOPLE AND CULTURE

7

The median age at SIB is 44 years old, with a balanced age pyramid favouring knowledge exchange by bringing early-career scientists together with senior experts

Geneva

73 employees

6 groups

Lausanne

89 employees

8 groups including Management and support

Basel

23 employees

5 groups

Zurich

5 employees

2 groups

The median length of service is seven years, with 23% of employees having been at SIB for over 10 years

By providing data science expertise, developing essential resources, harmonizing practices, and supporting the institutes’ activities, our employees are the key to our impact.

“I joined the Swiss-Prot group in 2000, two years after the birth of SIB. Working at the institute means supporting the research community with internationally recognized tools and services. It also means working in a flexible and autonomy-driven environment. ”

Elisabeth Coudert Team Lead, Biocuration

at SIB

There are 94 women (49%) and 96 men (51%) working at SIB

SIB has 190 employees of 26 different nationalities *

* As of 1 January 2023

From measuring employee satisfaction and engagement…

In 2022, employees were asked how they felt about working at SIB. The survey, prepared jointly by the People and Culture team, the Staff Committee and the Diversity working group, had a high participation rate of 75%, which highlighted that:

91% felt that their group respected each individual person

98% appreciate the flexibility of working between home and office

89% found their work interesting

…to implementing follow-up actions

SIB is convinced that high motivation and great work contributions are linked to satisfaction in the workplace. The institute is therefore following up on the survey with a range of actions, including:

Fostering career progression opportunities through internal mobility, among other things;

Continuing to raise awareness on topics related to equality, diversity and inclusion, e.g. through unconscious bias as part of leadership training.

Open databases and software to study life and foster discoveries

Life at different scales to tackle global challenges with SIB Resources: from atomic interactions to populations.

ENVIRONMENT

Understanding the impact of air pollution

To evaluate diverse properties of molecules, scientists rely on accurate predictions at the atomic scale.

EXAMPLE

In an analysis of polluted versus clean air samples in the Maldives, SwissADME (part of SwissDrugDesign) was used to estimate the harmful properties of thousands of unknown chemicals. The study showed the importance of studying air composition at the molecular level to assess its effect on health and climate.

DOI: 10.1038/s43247-022-00365-1

AGRICULTURE Understanding cattle fertility

To infer if and how genes and their variants functionally affect specific traits, such as diseases or fertility, knowing in which tissue they are most expressed offers precious clues.

EXAMPLE

Bgee was used to support the hypothesis that a rare mutation of a gene in Angus bulls could lower sperm quality and thus affect their extensive use and economic importance for artificial insemination. Bgee indeed revealed that the gene, in cattle, is most highly expressed in the reproductive system.

DOI: 10.3389/fcell.2022.872740

Scientific impact of the SIB Resources in 2022

13,001 citations* in peer-reviewed papers

17.2 million users

9,000 mentions in patents

* citation of the respective SIB Resource's reference paper

AGRICULTURE

Promoting food security

Strategies to develop agriculturally promising traits, such as resistance to drought or pests, play a key role in ensuring food security. The genetic basis of these traits in hundreds of agronomic species can be inferred using knowledge from a handful of model species thanks to orthology, which relates genes between organisms.

EXAMPLE

OMA (part of SwissOrthology) was used to develop agriculturally desirable traits in crops such as soybean and wheat.

MEDICINE & HEALTH

Designing therapeutic tools

In-depth information on 3D structures, functions and ligands of proteins, carbohydrates or lipids are crucial to investigate their function in biological processes.

EXAMPLE

Glyco@Expasy was used to prove the ability of a predicted sugar-binding protein to form a pore (i.e. to ‘punch holes’) in the membrane of cancer cells, thus opening the way to designing therapeutic molecular tools.

DOI: 10.1038/s42003-022-03869-w

MEDICINE & HEALTH Tracking mpox (monkeypox)

Through the analysis and sharing of genomic sequences of pathogens such as bacteria and viruses, their evolution and spread can be unfolded and tracked in real time.

EXAMPLE

Nextstrain used publicly available data to provide a daily updated analysis of thousands of mpox virus genomes, enabling scientists to monitor its spread during the 2022 outbreak.

Measuring the impact of databases and software is no mean feat. The stories on this page highlight how resources are essential to the work of niche communities, with a strong impact on discoveries and innovation. Usage figures tell another part of the story.

This way for more stories…

The 14 SIB Resources

ASAP Automated single-cell analysis portal

BGEE Gene expression expertise

CELLOSAURUS Cell lines knowledge resource

GLYCO@EXPASY

Zooming in on webbased glycoinformatics resources

NEXTSTRAIN Real-time tracking of pathogen evolution

RHEA Knowledgebase of biochemical reactions

STRING Protein-protein interaction networks and functional enrichment analysis

SWISSDRUGDESIGN Widening access to computer-aided drug design

SWISSLIPIDS

Knowledge resource for lipids

SWISS-MODEL Protein structure homology-modelling SWISSORTHOLOGY

One-stop shop for orthologs

SWISSREGULON PORTAL Tools and data for regulatory genomics

UNIPROTKB/ SWISS-PROT Protein knowledgebase

V-PIPE Viral genomics pipeline

THE BEHIND THE SCENES OF RESOURCE SUSTAINABILITY

Aligned with Open Science principles and customizable to industry needs

All SIB Resources can also be tailored to specific needs or proprietary data. For instance, the orthology database OMA, part of SwissOrthology, was customized to the needs of the chemical company BASF. This enables them to develop various traits in crops such as soybean and wheat, by inferring homologous relationships between genes using both public and proprietary genome sequences.

Becoming an SIB Resource: a robust selection process involving international experts

Every four years, our independent Scientific Advisory Board (SAB), (SEE P. 17) provides recommendations on Swiss bioinformatics resources to be developed and maintained, or newly included, in the SIB portfolio. Its recommendations are based on their scientific impact, scientific return on investment, and consistency with the institute’s portfolio and strategy. The SAB also provides guidelines for their continuous development. SIB’s Board of Directors then decides the allocation of funding through SIB Employees to develop the resources and implement their action plan.

Professional support to help SIB Resources reach long-term sustainability

Access to a range of services helps to reinforce the quality of the resource, thus creating a virtuous circle where it is more likely to receive additional funding from other sources. This unique offer in academia includes technical support, user experience research and design, best practices and knowledge sharing, infrastructure hosting, legal and data protection, human resources, and grant management.

Why do we need to foster best-in-class Open Science resources?

Massive volumes of data are produced by life science research and biomedical activities. The preservation of scientific knowledge and the reproducibility, impact and quality of science rely on open data resources. Recognizing this, since 2000 the State Secretariat for Education, Research and Innovation has ensured stable funding for SIB to identify, support and develop essential bioinformatics resources.

Over 500 genomes have been uploaded since the implementation of the new feature in STRING, including from the organisms depicted here

To reach and maintain the highest level of usefulness, accuracy and reliability, the scientific input of SIB Resources relies on professional support.

Assessment and monitoring of the SIB Resources is done across a set of 27 indicators

To ensure that resources remain at the cutting edge of research, the Biodata Resource team (part of SIB’s central services) helps set up surveys, fosters collaborations within the portfolio and with the SIB network, improves UX design, and initiates funding projects to develop new scientific ideas, etc. A recent example:

Based on a recommendation from the SAB, a STRING user survey was crafted;

500 answers from around the globe helped the team to prioritize efforts, in particular with regard to increasing the number of species in the database;

To address this need, a new feature was developed to predict protein interactions and to annotate the function of proteins of any fully sequenced genome. This makes STRING the only resource offering such a complete service. This feature was described in a recent paper.

DOI: 10.1093/nar/gkac1000

International recognition as biodata infrastructure

Among the 14 SIB Resources, several are recognized outside of our borders as of fundamental importance to the worldwide life sciences community. A great tribute to the SIB Groups developing them, to SIB’s commitment to life science infrastructure and to Switzerland’s leading expertise in biological data.

EUROPE:

In March 2022, SIB launched an internal call for innovative projects using AI to add features to the SIB Resources and foster collaboration and knowledge exchange within the network. Five projects were selected, and include the development of scoring functions to predict the damaging effect of mutations on protein structures, and the implementation of AI-guided annotation of gene expression data from single cells or cell lines.

Four SIB Resources are recognized as ELIXIR Core Data Resources (Cellosaurus, Rhea, UniProt and STRING)

WORLDWIDE:

Three SIB Resources were recognized in 2022 as Global Core Biodata Resources (GCBRs), with Rhea, UniProt and STRING included in the very first set of GCBRs by the Global Biodata Coalition.

And there will be more to join these top leagues with the upcoming calls…

Enabling trusted research on human data

Biomedical research, and in particular personalized health research, relies on a critical mass of heterogenous sensitive data from patients or clinical trials spread across institutions and sometimes countries. We draw on our extensive experience in large European public-private consortia and national initiatives to enable the secure sharing and processing of interoperable data.

SOFTWARE DEVELOPMENT

Developing engaging and customized tools

We harmonize and optimize internal data handling processes through the customization and development of analysis pipelines or software tools. This includes a multi-site data processing tracking pipeline, diagnostic tools and more. Our teams also contribute to world-leading Open Science databases and tools for life sciences, which can be adapted as necessary for the needs of partners

(SEE P. 22)

BIOSTATISTICS AND BIOINFORMATICS ANALYSIS

Making sense of life science data

We manage, integrate and analyze all kinds of data from a range of technologies to enable discoveries in life sciences. Our areas of expertise include molecular imaging analysis; de novo assembly of sequencing data; functional analysis, multiomics data integration, machine learning and more.

DATA STEWARDSHIP AND MANAGEMENT

Organizing data for long-term reuse

We assist with defining and implementing Data Management Plans (DMP) for research proposals and funding applications as well as reaching data interoperability targets, from local to international scales. We do this within academic or regulated environments and ensure long-term management, expert annotation and storage of biological data. This involves making data FAIR and harmonizing datasets.

Successful Innosuisse partnerships

TRAINING

Boosting bioinformatics skills

Our comprehensive course portfolio provides hands-on experience of the latest bioinformatics techniques and resources, including clinical applications for researchers. We offer about 100 training days per year and design specific courses for companies.

All our services, case studies and practical examples

In collaboration with the start-up Lunaphore and the Geneva University Hospitals, the Clinical Bioinformatics group generated machine learning solutions to power the analysis of molecular imagery to support the characterization of tumour microenvironments.

The Computer-Aided Molecular Engineering group and the Molecular Modelling group used molecular docking, in collaboration with Cellestia Biotech, to support the design of transcription factor inhibitors as part of a cancer drug discovery programme.

MEET OUR TEAMS

Comprising and headed by SIB Employees, our teams at the SIB Hub harness their expertise to collaborate with external partners and other SIB Groups in activities across our three pillars – Coordination, Centre of Excellence and Open Resources (SEE P. 10).

COORDINATION

Clinical Bioinformatics

Valérie Barbié

Personalized Health Informatics

OPEN RESOURCES

Swiss-ProtKnowledgebases

Alan Bridge

“We support health professionals from hospitals and the pharma industry to make the most of an exponential fow of data, in order to enhance diagnostics and to foster optimal patient care and well-being. We do this through dedicated tools and methods, benchmarking and practice harmonization.”

EXAMPLES

Diagnostic applications (cancer, genetic diseases, etc.) for the medical and pharmaceutical domain. Collaborative platforms to enable data sharing for research or clinical purposes.

TAGS Human genetics; interoperability; infectious disease; oncology; outreach; personalized medicine; training

“We are convinced that in order to ensure high-quality care and patient safety in the long term, healthcare and research must go hand-in hand. In the context of the Swiss Personalized Health Network (SPHN), we have thus made healthrelated data in Switzerland available for research in a lasting way. This is done through their FAIRification* and the creation of the national secure IT infrastructure BioMedIT.”

EXAMPLE

BioMedIT, the national infrastructure for the secure handling of health data, which can be jointly used by Swiss universities, research institutions and hospitals.

TAGS information security; interoperability; personalized medicine; training

“As a competence centre for biocuration and knowledge management we develop, annotate and maintain internationally renowned knowledge resources such as UniProtKB/ Swiss-Prot. Our resources provide an essential framework for biological data science.”

EXAMPLES

Some of our flagship resources include: UniProtKB/Swiss-Prot, ENZYME, Rhea, SwissLipids, HAMAP, PROSITE and ViralZone.

TAGS biochemistry; database curation; lipidomics; metabolomics; ontology; proteomics; proteins and proteomes; semantic web; systems biology

Katrin Crameri

CENTRE OF EXCELLENCE Training

CENTRE OF EXCELLENCE

Vital-IT –Computational biology

Supporting all groups and activities at SIB: a range of specialized teams

SIB’s activities and diverse network require specialized support teams dedicated to serving its projects and activities:

BIODATA RESOURCES

Coordinates the portfolio of SIB Resources, from selection to key indicators monitoring and dedicated support (SEE P. 23).

COMMUNICATIONS & SCIENTIFIC EVENTS

Ensures the transmission to scientific audiences and society of the advances made possible by the science of biological and biomedical data.

FINANCE & GRANTS MANAGEMENT

“Thanks to the unique pool of leading experts making up SIB’s scientific network, we are able to provide a rich nationwide training offer across the spectrum of bioinformatics techniques, methods and tools, and thus support the fast-evolving needs of researchers.”

KEY FIGURES 2022

60 courses offered to the community by groups from across Switzerland and bioinformatics domains

67 experts and trainers

1,400 participants

“As both computational biologists and software developers, we understand data and how to manage them, as well as the underlying biological questions. Our focus is on finding innovative approaches to data analysis, such as overcoming constraints related to sensitive data.”

EXAMPLE

Setting up a federated data analysis system across several countries to enable access to large patient cohorts while addressing legal, ethical and FAIR principles*.

TAGS data management; data mining; genome reconstruction; knowledge representation; machine learning; mass spectrometry; next-generation sequencing; personalized medicine; software engineering; systems biology

*FAIR: a set of guiding principles to improve the Findability, Accessibility, Interoperability, and Reuse of digital assets

Manages allocated funds (SEE P. 18), including reporting to funders and advising Principal Investigators on financial management of grants.

IT

Builds reliable technology platforms to ensure secure and seamless access to information resources and high-quality technology services.

LEGAL & TECHNOLOGY TRANSFER

Ensures compliance of SIB and transfer of its knowledge to partners, and provides skilled support for biomedical research.

PEOPLE & CULTURE

Nurtures an inclusive, respectful and stimulating working culture in which employees strive for excellence and develop themselves (SEE P. 20)

Mark Ibberson

Patricia Palagi

A GATEWAY TO SWISS-WIDE EXPERTISE

Through institutional partnerships and with our teams closely collaborating or nested within academic groups, we unlock access to national expertise.

incl.

employees (SEE P. 20), across 28 partner institutions

GENEVA LAUSANNE YVERDON BERN BASEL

MARTIGNY

WÄDENSWIL 2 GROUPS 19 MEMBERS

ST

GALLEN 1 GROUP 3 MEMBERS

Collaborative by design

VILLIGEN

FIELDS OF ACTIVITY AND APPLICATIONS

Genes and genomes

Life’s instruction manual

16

A genome is the sum of genetic material of an organism, including all of its genes. It is composed of DNA and contains all the information needed to create and maintain an organism, as well as the instructions on how this information should be expressed.

Bioinformatics develops tools to read genomes, store, analyse and interpret the resulting data.

Proteins and proteomes

More than meets the eye

7

A proteome is the sum of proteins expressed by a cell, a tissue or an organism, at a given time. Proteins are the products of genes, and are involved in nearly every task carried out within an organism –from carrying oxygen to fighting off pathogens.

Bioinformatics develops tools to understand the role of proteins.

17

Changes that occur in genomes tell life scientists how an organism has evolved over time. Comparisons made between genomes from different species or populations tell them how they are related to one another –this is the field of phylogenetics.

Bioinformatics develops tools to compare the genomes of organisms, as well as computational methods to reconstruct their past and build their ‘family’ trees.

Number of groups per domain (only the groups that gave these themes as their main activities are listed)

Key resources on Expasy.ch (218 tools and databases developed)

Our teams at the SIB Hub (SEE P. 28) collaborate with affiliated groups across all fields of activity.

Bioinformatics is an interdisciplinary field, where genetics, physiology, chemistry and physics meet, resulting in many fields of activity and applications.

Structural biology

The third dimension

8

Macromolecules such as DNA and proteins have specific 3D structures that are dictated by their sequence. A protein’s function is defined by its 3D structure, which in turn defines the way it interacts with other molecules.

Bioinformatics develops software to create 3D models of proteins to study their interactions with other molecules, such as drugs.

Machine learning

and text

mining

Rise of the machines

6

Machine learning (ML) techniques allow computers to learn from data without explicit instructions, and to draw inferences from data patterns. Text mining algorithms, often based on ML, are designed to recognize patterns within text, such as biomedical terms.

Bioinformatics is supported by and feeds into ML algorithms, with diverse applications including drug design, biomarker discovery and text mining to facilitate literature triage.

Systems biology

Never alone

16

Life occurs and is sustained by a mesh of interactions within and between cells, tissues, organisms and their environment. Understanding how these complex systems function allows scientists to predict what happens if one of the components changes or the conditions are altered.

Bioinformatics methods help to predict metabolic pathways.

Core facilities

The means to an end

12

The quantity of data generated by the life sciences has grown exponentially over the years and needs to be stored and processed. Researchers also need support in making sense of their data. Core facilities centralize research resources, and provide tools, technologies, services and expert consultation to this end.

Bioinformatics core facilities support researchers with specific issues relating to the management and analysis of their datasets to make the most of them.

…AGRICULTURE

from predicting the spread of bird flu outbreaks and understanding the lifecycle of agricultural pests, to improving crop productivity.

…BASIC RESEARCH

from unravelling the evolutionary processes that have shaped today’s biodiversity, to solving the equation behind a lizard’s scale colour pattern.

…ENVIRONMENTAL SCIENCES

from understanding how organisms adapt to climate change, to how microbial communities can be used to break down pollutants in oil spills.

…MEDICINE AND HEALTH

from designing optimized proteins in cancer immunotherapy, to creating biomedical decision-support tools.

LEVERAGING THE EXCELLENCE OF A SWISS-WIDE COMMUNITY

Discover the community initiatives making progress or being launched this year fostering shared values, culture and best practices across Swiss bioinformatics.

Looking into SIB’s impact on environmental sustainability

What is the environmental impact of SIB’s activities? How can current practices in computer science be more sustainable while preserving scientific competitiveness? An Environmental working group, bringing together members and employees from various locations and backgrounds has been launched to evaluate these questions and improve the impact of the organization.

Fostering exchanges and bioinformatics know-how among doctoral students

The PhD Training Network provides a supportive community for doctoral students undertaking bioinformatics research in Switzerland. Members take part in annual retreats where interactive sessions are combined with opportunities for them to present their work. In October 2022, 20 students from across Switzerland took part in a retreat in Fribourg on making the most of data visualization in presentations led by Group Leader Frédéric Schütz.

SIB days 2022: the Swiss Bioinformatics Summit – a lively community gathers in Biel

In June, the biennial scientific conference dedicated to members and employees took place in person for the first time since 2018. The scientific diversity of Swiss bio informatics was well represented, with 340 participants from over 70 affiliated groups across Switzerland attending the event and putting their heads together to tackle some of the cutting-edge challenges in the field of data science, from proteins and genes to the environment and evolution. Keynote speakers Antonella Santuccione Chadha and Johannes Rainer (Eurac Research) presented the work of the “Women’s Brain Project” and on the power of open software development respectively. A panel discussion was also held on “Who is afraid of data sharing?” in which promises of data sharing were put into perspective with the challenges and risks it poses for various stakeholders and how to mitigate them.

54 speakers

8

9 workshops and tutorials

Gathering to advance cutting-edge scientific topics

Focus groups have been established across the community to foster exchanges of knowledge and encourage collaborations across disciplines. For single-cell omics, members are coming together to share and discuss best practices for analyzing and visualizing single-cell data. Another group, dedicated to epigenomics, aims to propose recommendations on ensuring data generated in this field are aligned with FAIR principles. More groups will form as the need and interest arise.

Discussions around RDF: joining forces to align on an emerging technology

Resource Description Framework (RDF) is a key aspect of enabling interoperability and relationships between biodata resources towards a common language. In 2022, an SIBwide discussion took place around developments in RDF technologies with respect to resources developed at SIB. This group is now meeting monthly and collaborating actively.

Promoting values of diversity and inclusion

SIB is committed to fostering equality, diversity, and inclusion (EDI) for members of all backgrounds. The Diversity working group organized a workshop at the Swiss Bioinformatics Summit (SIB days 2022) to examine sex and gender biases in data science and artificial intelligence and how to address them. It also collaborated on the employee satisfaction survey and follow-up actions.

SCIENCE THROUGHOUT THE YEAR…

Enlightening

161,000 visitors to the SIB website

6,916 followers on Twitter

13,349 followers on LinkedIn

Using AI to extract new relationships between genes and diseases from the literature

What if information on genes involved in diseases could be automatically retrieved and annotated from scientific literature? By using melanoma, one of the most serious types of skin cancers, as a case study, over 2,000 new genes associated with this disease were found through using natural language processing techniques, a branch of Artificial Intelligence.

GROUP INVOLVED

BioMeXT: Biomedical Information

Extraction, led by Fabio Rinaldi

Published in the Journal of Biomedical Semantics

DOI: 10.1186/s13326-021-00251-3

How genomic deletions and duplications affect our health

Deletions and duplications in our genome can change the number of copies of specific genetic fragments, which can cause rare genetic syndromes. But do they also modulate traits in healthy individuals? By studying a large cohort of healthy volunteers, it was found that these mishaps, which are much more common than previously thought, can play a role in our physical traits and health.

GROUP INVOLVED

Statistical genetics, led by Zoltán Kutalik

Published in The American Journal of Human Genetics

DOI: 10.1016/j.ajhg.2022.02.010

The surprising molecular convergence in the venom factories of animals

Venomous animals like wasps and snakes have surprisingly similar molecular mechanisms to squirt toxins out of specialized cells. This was found through the first comparative analysis of gene expression profiles of venom glands across 20 species, with the SIB Resources Bgee, Swiss-Orthology and UniProtKB/Swiss-Prot supporting key steps. (SEE P. 43 FOR MORE)

GROUPS INVOLVED

Evolutionary bioinformatics, led by Marc Robinson-Rechavi and Frédéric Bastian

Evolutionary-Functional Genomics, led by Robert Waterhouse

Published in the Proceedings of the National Academy of Sciences

DOI: 10.1073/pnas.2111392119

findings of our members that were shared with the global scientific community and general public through science news, press releases and talks.

Computer-aided drug design to investigate immune resistance

Since the discovery of the role of the enzyme IDO1 in tumoral immune resistance, the search for its inhibitors has been intensely pursued, but eventually faded because of its complex biology. Leveraging 15 years of research on the topic, this study exploits the wealth of recent structural data on IDO1 and paves the way for its renaissance as a drug target in cancer or other pathologies.

GROUP INVOLVED

Molecular modelling group, led by Olivier Michielin and Vincent Zoete

Published in the Journal of Medicinal Chemistry

DOI:10.1021/acs.jmedchem.1c01665

Clarifying the origins of the world’s first farmers

The question of the origin of agriculture and sedentism has occupied researchers for over 100 years. This study showed that the first farmers represented a mixture of Ice Age hunter-gatherer groups, spread from the Near East all the way to south-eastern Europe. The method they developed could help reveal other human evolutionary patterns with unmatched resolution.

GROUPS INVOLVED

Computational and Molecular Population Genetics, led by Laurent Excoffier

Statistical and Computational Evolutionary Biology, led by Daniel Wegmann

Published in Cell

DOI: 10.1016/j.cell.2022.04.008

The origins of the proteins that fuse sperm and egg cells

The protein responsible for fusion between sex cells, and thus sexual reproduction in plants and animals, may have appeared long before the organisms that rely on it for this purpose. Through combining AI with protein domain prediction, the origins of this protein where found in the bacteria-like microorganisms called archaea, about three billion years ago.

GROUP INVOLVED

Computational Evolutionary Biology and Genomics, led by Christophe Dessimoz

Published in Nature Communications

DOI: 10.1038/s41467-022-31564-1

SIB REMARKABLE OUTPUTS

2022

Discover the 10 best achievements and work produced by our scientists over the last year.

Annotating biologically relevant ligands in UniProtKB

DOI:10.1093/bioinformatics/btac793

GROUP INVOLVED

Swiss-Prot, led by Alan Bridge, Geneva

WHAT THE COMMITTEE SAID ABOUT THE WORK

“Using the ChEBI small molecule ontology, UniProt curators reannotated ligand binding sites. This standardization enables easier and rational analysis, improving the quality of protein structure and drug target prediction.”

A comprehensive catalogue of the mouse microbiota genome

DOI:10.1371/journal.pcbi.1009947

GROUP INVOLVED

Computational Evolutionary Genomics, led by Evgeny Zdobnov & Evgenia Kriventseva, Geneva

WHAT THE COMMITTEE SAID ABOUT THE WORK

“An excellent functional and taxonomic summary of the mouse gut metagenome, built using a solid bioinformatics pipeline. This is a great resource for researchers translating results from mouse to human.”

Staying abreast of the latest advances and bright ideas emerging in a field as diverse as bioinformatics is challenging. The SIB Remarkable Outputs provide the global community with a shortlist of outstanding works produced during the year by our members. These outputs, selected by the SIB Award committee, can include peer-reviewed publications, preprints, software tools, databases, outreach programmes, science advocacy, etc.

FAIR principles in practice for health data

sphn.ch/training/fair-principles-in-practicefor-health-data/

GROUP INVOLVED

Personalized Health Informatics, led by Katrin Crameri, Basel

WHAT THE COMMITTEE SAID ABOUT THE WORK

“An excellent resource for FAIR data training and awareness. It is a valuable general introduction, presenting the guiding principles in a well-structured format with practical explanations.”

Kutalik, Lausanne

WHAT THE COMMITTEE SAID ABOUT THE WORK “This work represents the most comprehensive examination to date of the relationships between copy-number variations and human phenotype traits through the use of computational methods.”

Enabling real time recording of gene expression in single cells

DOI:10.1038/s41586-022-05046-9

GROUP INVOLVED Systems Biology and Genetics, led by Bart Deplancke, Lausanne

WHAT THE COMMITTEE SAID ABOUT THE WORK “Live-seq is a truly novel and innovative approach enabling experiments for profiling gene expression in live, individual cells over time, in ways that were previously impossible.”

Gunnar Rätsch, Zurich.

WHAT THE COMMITTEE SAID ABOUT THE WORK “Using a customized bioinformatics pipeline, over 26,000 genomes from all over the planet were analyzed to highlight their biosynthetic features. The Ocean Microbiomics Database provides access to these data.”

Detecting variants of the SARS-CoV-2 virus in wastewater

DOI:10.1038/s41564-022-01185-x

GROUP INVOLVED

Computational Biology, led by Niko Beerenwinkel, Basel

WHAT THE COMMITTEE SAID ABOUT THE WORK “A remarkable example of how tools and databases developed by SIB Groups can

the world’s first farmers

Computational and Molecular Population

Bern, and Statistical and Computational Wegmann, Fribourg

WHAT THE COMMITTEE SAID ABOUT THE WORK “This study makes a significant contribution to our knowledge of human history and agricultural origins. It emphasizes the crucial role that informatics and genomics play in uncovering our shared history.”

Determining inheritance of genes in biobanks without parental genomes

DOI:10.1038/s41467-022-34383-6

GROUPS INVOLVED Systems and Population Genetics, led by Olivier Delaneau, and Statistical Genetics, led by Zoltán Kutalik, Lausanne

WHAT THE COMMITTEE SAID ABOUT THE WORK “A clever computational approach making it possible to infer which genes an individual inherited from their parents without having any information on them. This allows us to study whether the parental origin of a gene makes a difference for diseases and other traits.”

Bioinformatics for a biodiverse future

As a result of human activities, we find ourselves on the brink of a sixth mass extinction. The UN Biodiversity Conference (COP15) led to a landmark agreement to guide global action to address biodiversity loss. Here is how SIB is contributing to this effort.

Studying biodiversity to better protect it

How can studying the DNA of species inform us about the state of an ecosystem? Bioinformatics is helping us to unlock the mysteries of the natural world,

through genomics

Biodiversity Genomics Europe (BGE) is a pan-European project that combines the efforts of two key initiatives on DNA barcoding (BIOSCAN Europe) and genomics (European Reference Genome

University of Lausanne

harmful effects on agriculture.”

Sara Mitri

SIB Group Leader,

Microorganisms in our oceans, a source of new natural products

Group Leader Shinichi Sunagawa explores the biodiversity of microorganisms in oceans. In an article published in Nature, the team reveals a new family of bacteria, which they named Eudoremicrobiaceae, and discovered the abilities of these and other marine bacteria to form compounds that had not been previously observed. These products have potential in many areas,

How do species interact and coexist?

Extracting millions of species interactions from the literature to answer biodiversity and health questions

Knowing and making full use of available information on relationships between species in an ecosystem is essential for decisions on how to conserve species biodiversity. The Biodiversity Community Integrated Knowledge Library (BiCiKL) is building a database that draws from information on millions of relationships between species from the literature to make them readily accessible. It can show, for example, the relationships between predator and prey in a certain habitat – or how bats in South-East Asia interact with viruses, or answer direct questions such as “What species causes malaria infection?” This can be important to infer possible risks of zoonosis or for identifying keystone species. SIB's Patrick Ruch is involved in building this database through text mining and is ensuring the data generated align with FAIR principles.

How do species adapt to their environment?

Discovering the commonalities between species within diversity

The group led by Marc RobinsonRechavi and Frédéric Bastian was able to demonstrate that animals as different as wasps, spiders and snakes produce venom using surprisingly similar methods. This was possible thanks to SIB Resources such as OrthoDB (part of Swiss-Orthology) to group similar genes between species, Bgee to reveal how the genes are expressed and UniProtKB/

How shifting environments affect (microbial) diversity

Sara Mitri's group studies the impact of different species of microorganisms on each other in a changing environment, and of the factors driving microbial invasions, to better prevent them. Her team showed, for instance, that if an environment fluctuates to a certain state, even the fittest species could go locally extinct. They are also developing a database of interactions between microbes to better understand what happens in a microbial ecosystems. Such information can, for example, be used to increase the diversity of microorganisms in the soil, which is essential for agricultural success.

DOI:10.1038/s41396-022-01314-8

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Using AI to determine which species and areas to protect as a priority

Not only is it important to know which species should be protected, but it is also crucial to know which areas to protect as a priority. The team led by Daniele Silvestro used artificial intelligence to solve this problem by developing the software package CAPTAIN. It integrates biodiversity data and the budget allocated to conservation, together with information on human pressure and climate change. For a given budget, it offers solutions that protect more species than alternative methods. Building on this work, the team was also able to predict the risk of extinction and possible threats across almost 6,000 species of plants in Madagascar, as part of an international call for measures to better protect biodiversity on the island.

DOI: 10.1038/s41893-022-00851-6

DOI: 10.1126/science.adf1466

DOI: 10.1126/science.abf0869

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Where should conservation efforts be focused?

“At COP15, the UN Biodiversity conference, it was agreed that 30% of the Earth’s land and ocean area will be protected by 2030, but we still need to decide which areas need to be protected first. By combining AI with data collected on biodiversity and other factors in the environment, we can predict extinction risk for many species and prioritize actions in ways that were not possible before.”

Species

Species reintroduction efforts can be jeopardized by risks of genetic incompatibilities when different populations interbreed. These incompatibilities can lead to reduced fitness in the resulting offspring.

Claudia Bank and her team develop methods to identify such incompatibilities. For their most recent work they applied their method to naturally interbreeding populations of swordtail fish in Mexico.

DOI :10.1371/journal.pgen.1010120

Molecule

Molecular

Spectra

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It is all connected. As shown here, connecting knowledge on very different levels enables us to derive even more knowledge about species in relation to their environment, with a far-reaching potential for impact. (Image from the project detailed on P. 51) Protein

Bioactivity

“The data being generated and integrated now will enable us to develop models that can monitor biodiversity in space and over time, predicting changes while we continue to feed them with updates from observations.”

Robert Waterhouse

SIB Group Leader, University of Lausanne

“Studying the genetics of populations can give us information on the threats that they may face either from a lack of diversity but also from efforts to regenerate diversity by introgressing genetic material from related populations or species. This can inform management decisions and action plans.”

Claudia Bank

SIB Group Leader, University of Bern

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How do we restore healthy populations?

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Revealing the factors preventing the recovery of species

Open research data: becoming

Open Research Data: a vision becoming reality

SIB at the forefront of Open Research Data in Switzerland

The infrastructure and expertise at SIB are key to enabling the value chain of Open Research Data, starting with individual projects and leading to grand discoveries.

Every day, an astonishing amount of biological and biomedical data is generated. This is only set to increase in future. By creating possibilities to store these data and make them accessible and reusable with the right safeguards where necessary, they can be built upon for even more scientific progress at a faster rate. Openly sharing annotated data generated in labs is now creating opportunities for grand discoveries to be made in larger-scale initiatives. SIB has a role at the centre of this, with it aggregating and enabling the sharing of data to make this all possible.

A top priority for Switzerland, from academic policy to the political arena

In Switzerland, motions have been set by parliament for legislation to enable the secondary use of data recognizing that its greatest value lies in its almost unlimited potential for reuse. Since 2016, the Swiss National Science Foundation has also called for research data to be made freely available. After being commissioned by the State Secretariat for Education, Research and Innovation (SERI), swissuniversities, the ETH domain, the Swiss National Science Foundation and the Swiss Academies of Arts and Sciences jointly adopted a National Open Research Data Strategy in 2021. With it came the recommendation that data acquired from publicly funded research should be openly available and adhere to FAIR principles. This also came with an action plan that included a call for proposals for research projects that foster Open Research Data to be granted support. The Open Science revolution is finally going mainstream.

Tools and databases to enable building for discoveries and a better future

By maintaining openly available resources over a range of fields and biological needs, SIB Resources have a crucial role in fostering tomorrow’s discoveries. They aggregate the very best data from massive numbers of individual projects. Through expert curation and FAIRification, they ensure this wealth of knowledge can be understood across different areas of research, and mined by human and machines in ways that benefit society at large.

Catalyzing ORD in Switzerland with concrete projects

Several collaborative projects involving or led by SIB Members were selected for funding as part of 2022 swissuniversities calls to support the National ORD strategy. These show the close synergies of SIB Members with researchers generating data in institutions across Switzerland. The projects are also aligned with the principles of the SwissBioData ecosystem (SBDe), a proposed initiative to store biological research data from institutions all over the country (SEE NEXT PAGE). Find some of these projects detailed here.

Standardizing the management of the vast amounts of data generated through single cell genomics

There are increasingly many methods to generate data on transcriptomes at the single cell level, for all kinds of species in various conditions. scFAIR aims to create standards and a platform so that these data can be seamlessly shared and collaboratively annotated. It thus firmly establishes ORD practices in the single cell genomics community.

SIB GROUP LEADERS INVOLVED

Marc Robinson-Rechavi and Frédéric Bastian, University of Lausanne (leading house), Bart Deplancke, EPFL

An infrastructure to efficiently harness vast streams of large-scale biomedical data

Multi-level or multi-omics data on individual organisms, from genome sequences to mRNA and protein abundances, can now be routinely obtained. Yet an infrastructure for standardized multi-omics data analysis, which would enable the extraction physical quantities to model and understand the biological system under study, is lacking. This project aims to build such an infrastructure to ultimately boost biomedical research.

SIB GROUP LEADERS INVOLVED

Mihaela Zavolan and Erik von Nimwegen, University of Basel (leading house).

OTHER INSTITUTION INVOLVED EPFL

“The breadth of topics these projects cover, from omics and structural data to training and botanical collections, highlights the urgent transversal need for making data sharable and reusable in life sciences”

Christophe Dessimoz Executive Director

Plants from Swiss botanical gardens: Sanguisorba minor, Polypodium vulgare, Nelumbo nucifera

Open science solutions to manage information from botanical collections

The Digital Botanical Gardens Initiative aims to explore and establish robust workflows to digitalize chemical and biological diversity from botanical collections to global wild ecosystems. This will focus on defining a large-scale library to characterize chemicals found in plants. The resulting data and metadata will be represented through knowledge graphs, enabling faster discoveries, such as contributing towards biodiversity conservation.

SIB INVOLVEMENT

Ana Claudia Sima and Tarcisio Mendes de Farias.

OTHER INSTITUTIONS INVOLVED

University of Fribourg (leading house), University of Neuchatel, Swiss Federal Institute of Technology Zurich (ETHZ).

Towards a first Certificate of Advanced Studies and national network for Data Stewards

Data Stewards have a key role in ensuring that ORD principles are implemented (SEE NEXT PAGE). A first goal of the project is to provide a nationwide definition of the role’s curriculum, in terms of the skills required and its expectations. As well as this, a Certificate of Advanced Studies (CAS) is being developed, with SIB leading the life science work package. This project also involves the development of the Swiss Data Stewardship Network (SDSNet) in which individuals trained in this domain can continuously update their knowledge and discuss developments in group practices.

SIB INVOLVEMENT

Patricia Palagi, Head of Training.

OTHER INSTITUTIONS INVOLVED

University of Lausanne (leading house), Haute Ecole Pedagogique Vaud (HEP Vaud), University of Geneva, Geneva School of Business Administration (HEG Geneva), Swiss Centre of Expertise in the Social Sciences (FORS), University of Zurich, Zurich University of Applied Sciences (ZHAW).

Making computerpredicted protein structures openly available

By building and expanding on current ORD best practices, ModelArchive aims to become the reference repository to share structures of proteins determined through computational modelling. It will complement the Protein Data Bank, which currently stores data on protein structures determined experimentally. Combining experimental structures with computational models provides structural biologists with a treasure trove of data to foster new discoveries.

SIB GROUP LEADERS INVOLVED

Torsten Schwede, University of Basel (leading house), Andrea Cavalli, Institute for Research in Biomedicine, Vincent Zoete and Olivier Michielin, University of Lausanne and Matteo Dal Peraro, EPFL.

OTHER INSTITUTIONS INVOLVED

RCSB, Rutgers University (USA), European Bioinformatics Institute (EMBL-EBI) (UK), University of California San Francisco (USA).

Value creation through Open Research Data

The vision to transform data-intensive research in Switzerland

2022 brought some promising developments to the SwissBioData ecosystem proposal submitted to SERI's Roadmap for Research Infrastructure. This vision is a decentralized space where biological data from institutions all over Switzerland can be shared and reused to encourage reproducible science through greater transparency. It is the outcome of decades of collaborative projects and in-depth expertise around Open Science and FAIR principles. SIB acts as the Data Coordination Centre of this academic venture on unparalleled scale, with the University of Bern as leading house: altogether 18 institutions, including ETH Zurich, the University of Basel and the University of Geneva, are involved. The proposal received the top score in a scientific evaluation by the Swiss National Science Foundation, and was deemed a very much needed infrastructure that will enable Switzerland to “carry out rocket science”.

Knowledge, models

...and many other projects to come over the years.

Individual researchers

Clinicians

Supporting researchers through Data Stewards and training

Most researchers would like to increase their impact by making their data FAIR, but often lack the time, skills, and human or technical resources to achieve this. This is where Data Stewards come in.

Data Stewards are multidisciplinary experts who use skills in IT, coordination, data management, and curation to ensure scientists are able to make their data accessible and reusable. They support researchers within and across different fields and institutions. Their national coordination will be a key objective of the SwissBioData ecosystem.

Realizing the promise of Open Research Data requires up-skilling through courses and continuing education for researchers, for stewards, for data producing and data processing core facilities, as well as for trainers themselves. In collaboration with key partners the SIB Training group tackles this challenge nationally (SEE P. 51) and internationally.

Making data FAIR: a key skill of SIB

To facilitate the efficient and informative sharing of data and to foster large-scale collaborative projects, data need to be made FAIR: Findable, Accessible, Interoperable and Reusable.

SIB’s role as Data Coordination Centre in a range of large-scale endeavours, from the Swiss Personalized Health Network (SPHN) to European publicprivate projects, reflect its know-how on this topic.

– The BioMedIT network and SPHN have successfully been established as FAIR, sustainable national infrastructure enabling responsible sharing of health data for research purposes. In 2022 the SPHN connector tool was launched to enable faster sharing of clinical data in the standard format adopted nationwide.

– Data are harmonized and FAIR principles implemented in numerous large international projects (e.g. the Innovative Medicines Initiative) to tackle cancer, diabetes and obesity. SIB is ready to provide its services to partners in the private sector as described on P. 27.

SIB also contributed to the development of the ELIXIR RDMkit, an online guide containing good data management practices applicable to research projects in academia and industry, released in 2022.

“Thanks to the SPHN connector tool, we spend significantly less time and effort to share consented and interoperable data to feed research, ultimately speeding up the discovery process from large-scale projects.”

Patrick Hirschi Head of Clinical Data Platform for Research, University Hospital Zurich

INDEX OF SIB GROUP AND TEAM LEADERS

AAhrens Christian Proteins and proteomes

Anisimova Maria Evolution and phylogeny

Arguello Roman Evolution and phylogeny

Agroscope

Zurich University of Applied Sciences (ZHAW)

University of Lausanne

BBaerenfaller Katja Proteins and proteomes

Bairoch Amos Proteins and proteomes

Bank Claudia Evolution and phylogeny

Barbié Valérie Core facilities and services

Bastian Frédéric Evolution and phylogeny

Baudis Michael Genes and genomes

Beerenwinkel Niko Evolution and phylogeny

Bergmann Sven Genes and genomes

Beltrao Pedro NEW Systems biology

Bitbol Anne-Florence Evolution and phylogeny

Boeva Valentina Systems biology

Borgwardt Karsten Text mining and machine learning

Bridge Alan Proteins and proteomes

Bruggmann Rémy Core facilities and services

Buljan Marija Systems biology

SIAF – University of Zurich

University of Geneva

University of Bern

SIB Hub – Geneva

University of Lausanne

University of Zurich

ETH Zurich, D-BSSE

University of Lausanne

ETH Zurich

EPFL

ETH Zurich

ETH Zurich

SIB Hub – Geneva

University of Bern

Empa

CCarmona Santiago Systems biology

Cascione Luciano Core facilities and services

Cavalli Andrea Structural biology

Chopard Bastien Systems biology

Ciriello Giovanni Systems biology

Correia Bruno Structural biology

Crameri Katrin Competence centres and services

University of Lausanne

Institute of Oncology

Research

Università della Svizzera

italiana

University of Geneva

University of Lausanne

EPFL

SIB Hub – Basel

DDal Peraro Matteo Structural biology

Delaneau Olivier Genes and genomes

Deupi Xavier Structural biology

Deplancke Bart Genes and genomes

Dessimoz Christophe Evolution and phylogeny

EPFL

University of Lausanne

Paul Scherrer Institute (PSI)

EPFL

University of Lausanne

EExcoffier Laurent Evolution and phylogeny

University of Bern

FFalquet Laurent Genes and genomes

Fellay Jacques Genes and genomes

University of Fribourg

EPFL

GGervasio Francesco Luigi NEW

Structural biology

Gfeller David Proteins and proteomes

Glover Natasha NEW Evolution and phylogeny

Gonnet Gaston Evolution and phylogeny

Goudet Jérôme Evolution and phylogeny

Gottardo Raphael Core facilities and services

University of Geneva

University of Lausanne

University of Lausanne

ETH Zurich

University of Lausanne

University of Lausanne

IIbberson Mark Core facilities and services

Iber Dagmar Systems biology

Ivanek Robert Systems biology

SIB Hub – Lausanne

ETH Zurich, D-BSSE

University of Basel & University Hospital Basel

KKahraman Abdullah Core facilities and services

Kriventseva Evgenia Genes and genomes

Kutalik Zoltán Genes and genomes

University Hospital Zurich

University of Geneva

University of Lausanne

LLane Lydie Proteins and proteomes

Lisacek Frédérique Proteins and proteomes

Luisier Raphaëlle NEW Genes and genomes

University of Geneva

University of Geneva

IDIAP

MMalaspinas Anna-Sapfo Genes and genomes

Mazza Christian Systems biology

Michielin Olivier Structural biology

Miho Enkelejda Systems biology

Milinkovitch Michel Systems biology

Mitri Sara

Evolution and phylogeny

University of Lausanne

University of Fribourg

University of Lausanne

FHNW University of Applied

Sciences and Arts

Northwestern Switzerland

University of Geneva

University of Lausanne

NNeher Richard Evolution and phylogeny

Ng Charlotte Systems biology

University of Basel

University of Bern

PPalagi Patricia Training

Panse Christian Core facilities and services

Payne Joshua Evolution and phylogeny

Pedrioli Patrick Proteins and proteomes

Peña-Reyes Carlos-Andrés Text mining and machine learning

Pivkin Igor Systems biology

SIB Hub – Lausanne

ETH Zurich

ETH Zurich

ETH Zurich

HEIG-VD

Università della Svizzera

italiana

RRätsch Gunnar

Rehrauer Hubert

Riedi Marcel

Rinaldi Fabio

Rinn Bernd

Robinson Mark

Text mining and machine learning

Core facilities and services

Core facilities and services

Text mining and machine learning

Core facilities and services

Genes and genomes

Robinson-Rechavi Marc Evolution and phylogeny

Ruch Patrick

Text mining and machine learning

ETH Zurich

ETH Zurich, University of Zurich

University of Zurich

SUPSI

ETH Zurich, D-BSSE

University of Zurich

University of Lausanne

HES-SO - Geneva School of Business Administration (HEG)

SSchütz Frédéric Core facilities and services

Schwede Torsten Structural biology, Core facilities

University of Lausanne

University of Basel and services

Sengstag Thierry Core facilities and services

Silvestro Daniele Evolution and phylogeny

Snijder Berend Systems biology

Stadler Michael Genes and genomes

Stadler Tanja

University of Basel

University of Fribourg

ETH Zurich

Friedrich Miescher Institute for Biomedical Research

Evolution and phylogeny

Stekhoven Daniel Core facilities and services

Stelling Jürg Systems biology

Sunagawa Shinichi Genes and genomes

ETH Zurich, D-BSSE

ETH Zurich

ETH Zurich, D-BSSE

ETH Zurich

Vvan Nimwegen Erik Genes and genomes

Vogt Julia Text mining and machine learning

von Mering Christian Proteins and proteomes

University of Basel

ETH Zurich

University of Zurich

WWagner Andreas Evolution and phylogeny

Waterhouse Robert Genes and genomes

Wegmann Daniel Evolution and phylogeny

Wollscheid Bernd Proteins and proteomes

University of Zurich

University of Lausanne

University of Fribourg

ETH Zurich

ZZavolan Mihaela Systems biology

Zdobnov Evgeny Genes and genomes

Ziegler Andreas NEW Core facilities and services

Zoete Vincent

Structural biology

University of Basel

University of Geneva

Cardio-Care

University of Lausanne

ACKNOWLEDGEMENTS

We gratefully acknowledge the following funders, sponsors and partners for their financial support and encouragement in helping us fulfil our mission in 2022.

The Swiss government and in particular: The State Secretariat for Education, Research and Innovation SERI

The Swiss National Science Foundation (SNSF)

Innosuisse

Our institutional partners

The European Commission

The National Institutes of Health (NIH)

The Research for Life Foundation

We also thank all industrial, public health and academic partners who trust SIB’s expertise – and all employees and members who contributed to this edition of the SIB Profile.

IMPRESSUM

© 2023 – SIB Swiss Institute of Bioinformatics

ILLUSTRATION BY Davide Bonazzi / Salzmanart davidebonazzi.com

DESIGN AND LAYOUT BY Bogsch & Bacco, bogsch-bacco.ch

IMAGE CREDITS

(from top to bottom and from left to right)

The cover image is derived from the work of SIB Group Leader Daniele Silvestro (University of Fribourg)

DOI:10.1038/s41893-022-00851-6

Inside cover

1 Keystone / Pool / Pascal Lauener

2 Cliff Hide Travel / Alamy Stock Photo

P. 1 Keystone / Science Photo Library / Zephyr

P. 2 Nicolas Righetti / lundi13

Valentin Luggen

P. 4 Jon Benedictus / Alamy Stock Photo

Davide Bonazzi

Espen Rekdal / Espen Rekdal Photography

Nicolas Righetti / lundi13

P. 14 Nicolas Righetti / lundi13

P. 23 Davide Bonazzi

P. 24 Espen Rekdal / Espen Rekdal Photography

P. 25 Picture Partners / Adobe Stock

Neosiam / Adobe Stock

Motohiro Sunouchi

P. 28 Nicolas Righetti / lundi13

P. 35 Frédéric Burdet

Selvanegra / iStock

P. 36 The Natural History Museum / Alamy Stock Photo

P. 37 molekuul.be / Alamy Stock Photo Keystone / Science Photo Library / Christian Jegou Publiphoto Diffusion

Keystone / Science Photo Library / Eye of Science

p. 38 Eric Isselee / Shutterstock

P. 39 CC0 1.0 Universal Public Domain CDC

P. 42 Felix Imhof

Davide Bonazzi

P. 44 Boris Egger

P. 45 Felix Imhof

P. 49 Davide Bonazzi

P. 50 Imagebroker / Alamy Stock Photo Jon Benedictus / Alamy Stock Photo

P. 51 Nicolas Righetti / lundi13

Russotwins / Alamy Stock Photo

P. 52 modelarchive.org

P. 60 Keystone / Gaetan Bally

Epidemics

We equip Switzerland to face epidemics thanks to collaborative tools that have been tried and tested during COVID-19, and Open Resources.

SEE P. 22

Open Resources

Our open software and databases are recognized and used across the world to accelerate research, boost innovation and tackle global challenges, from pollution to food security.

SEE P. 22

Identifying priority areas for biodiversity conservation with AI Heatmap of Madagascar generated using the artificial intelligence software CAPTAIN, to maximize the number of species protected under a given budget. Colours range from red (highest priority) to blue (lowest priority).

SIB Swiss Institute of Bioinformatics

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