The SIB Training group ensures that Switzerland maintains a highly skilled workforce in the increasingly data-intensive life and health sciences. We do this by organizing training courses and fostering international collaborations. On this page you can also find out who we train and how we make our training Open and FAIR.
Focus on the group's mission
The SIB Training group, led by Patricia Palagi, coordinates the institute’s bioinformatics training and course offer. Throughout its activities, it ensures that the next generation of bioinformaticians and life scientists make the best of the latest advances in computational biology.
Our courses are unique: taught by experts, up-to-date, and practical. They complement the teaching at Swiss universities, with whom we collaborate. As leaders in open and FAIR* guidelines for teaching materials, we are also committed to empowering other trainers worldwide through standards development and capacity building.
Addressing training needs
From in-person and streamed classes to openly accessible materials, recordings and e-learning modules, a range of regularly updated content and topics are provided. They are designed to closely match the bioinformatics training needs of all life science actors, from the academia or the private sector, including PhD students, postdoctoral researchers and health professionals. Discover all upcoming courses and stay informed, and if you need training in an area of bioinformatics not currently covered, please let us know.
International collaborations
The Training group collaborates in pan-European and international training projects, together with the broader bioinformatics community of ELIXIR, GOBLET and ISCB. For instance, the Training group is co-leading or is involved in the following projects:
- ELIXIR-STEERS: contributing to empowering ELIXIR Nodes to provide better training courses.
- Pathogen Data Network (PDN): contributing to developing and delivering on target courses.
- EOSC-FIDELIS: contributing to promoting the development and operation of a European network of trustworthy repositories.
- ELIXIR-GOBLET Train-the-Trainer: co-leading the ELIXIR and GOBLET programme, which empowers researchers to deliver high-quality training.
- Co-leading the ISCB Education COSI, which fosters collaborations in bioinformatics education and training.
People
SIB training courses are developed and delivered collaboratively by the people working in the training group, SIB members, and national and international experts, ensuring world‑class education.
Who do we train?
We provide a rich course offering to students, researchers, bioinformaticians, programmers, technicians and clinical professionals, from academia and industry. Participants from Switzerland and beyond are thus able to hone their skills across the spectrum of bioinformatics techniques, methods and tools.
Courses for scientists
We offer courses for researchers at all levels: PhD students and postdocs, senior scientists, principal investigators, as well as research staff such as programmers, technicians or bioinformaticians, from Switzerland or abroad. Participants from industry are welcome to attend SIB courses to rapidly develop expertise in a specific area, such as genomics, proteomics and systems biology.
To specifically support the PhD students in Switzerland carrying out research in bioinformatics or computational biology, the institute runs the SIB PhD Training Network.
Are you looking for a new challenge or a career change? SIB courses are also open to participants with a scientific background, looking for additional training.
You can also find below the various academic diplomas available in Switzerland to become a bioinformatician.
Private courses for companies
Whether you are a startup, small or medium-sized enterprise, or a multinational corporation, SIB's course portfolio can be customized to suit the unique requirements of your business. These courses can be conducted either in-person or online.
Contact us to discuss any bioinformatics training you may require.
Courses for clinical professionals
Our courses are developed in collaboration with clinical stakeholders and are designed to seamlessly integrate into their continuing education programs. The primary objective of these courses is to equip clinical professionals, such as medical doctors, clinicians, and medical laboratory professionals, with a comprehensive understanding of fundamental bioinformatics concepts that are crucial for the analysis, interpretation, and management of molecular data, and their practical applications in clinical settings.
This regular course is:
- Certificate of Advanced Studies (CAS) in Personalized Molecular Oncology, in collaboration with the Basel and Lausanne University Hospitals and Basel University.
Academic degrees in Switzerland leading to a career in bioinformatics
- Bachelor’s degree in Computational Sciences – University of Basel
- Master’s degree in Bioinformatics and Computational Biology – University of Bern and University of Fribourg
- Master’s degree in Computational Biology and Bioinformatics – ETH Zurich, University of Zurich and University of Basel
- Master’s degree in Molecular Life Sciences specialization in Bioinformatics – University of Lausanne
- Master’s degree in Biology specialization in Bioinformatics and Biological Data Analysis – University of Geneva
The SIB Training group is dedicated to making training materials accessible and reusable by all. We do this not only by sharing our own course materials but also support others who do the same and participate in developing standards.
Open and FAIR training
We are dedicated to making training materials accessible and reusable by all. We do this not only by sharing our own course materials but also support others who do the same and participate in developing standards.
The benefits of sharing
Have you ever learned something from an open online tutorial or course? Well, you are not alone. Nowadays, freely available online educational materials are part of almost everyone’s learning journey. An increasing number of educators share their materials, because it widens their audience, encourages collaboration and allows them to get acknowledged for their work. However, sharing with reuse in mind is no easy task. For example, the material must be accessible with stable links, have standardized descriptions, and should be easy to find. The Open Research Data best practices and FAIR principles (Findable, Accessible, Interoperable, and Reusable) were developed to support the reuse of digital objects. At the SIB Training group, we apply and help others to implement these practices for training materials.
Open and FAIR training initiatives
The SIB Training group has been and continues to be involved in several initiatives to encourage open and FAIR training, both within and beyond SIB. Solid international collaborations are very important because describing and indexing training materials requires common standards with a large support base.
Current and past international collaborations and deliverables:
- Ten simple rules for making training materials FAIR: a landmark paper on making training materials FAIR. Developed by the ELIXIR Training Platform
- FAIR training handbook: A guide for making training materials FAIR. Developed by the ELIXIR Training Platform
- Co-leading the ELIXIR FAIR Training Working Group
- Bioschemas training profiles: A standard to describe training material and courses. Developed by the ELIXIR FAIR Training Focus group, GOBLET and ISCB.
Internal activities and deliverables:
- Open and FAIR SIB training materials
- Glittr.org: a database of open training materials hosted on GitHub and GitLab
- FAIR training task force: a group of FAIR training enthusiasts within SIB that aim to catalyze FAIR training practices within SIB, national and international institutions.
Are you looking for support to share your training materials? Do you want to know more about applying the FAIR principles to training materials or do you want to collaborate with us? Contact Geert van Geest.
Training Advisory Committee
In the Training Committee, the strategic outlook and the concept of training activities are discussed and decided upon. It comprises the SIB Group Leaders most involved in training activities, namely:
- Pedro Beltrao
- Rémy Bruggmann
- Marek Basler (Unibas)
- Alessandro de Simone (UNIGE)
- Christophe Dessimoz
- Pierre Farmer (Novartis)
- Mark Ibberson
- Raphaelle Luisier
- Patricia Palagi
- Mark Robinson
- Frédéric Schütz (Chair)
- Thierry Sengstag
- Vincent Zoete
- Report: Mining the potential of knowledge graphs for metadata on training Panouris, D. et al. OSF.
- Report: Data sharing and reuse under GDPR - BY-COVID Fest workshop report. Saldner, S. et al. Zenodo.
- Report: BY-COVID D6.2 Training efforts report. Palagi, P. et al. Zenodo.
- Article: Using Glittr.org to find, compare and re-use online materials for training and education. van Geest G. et al. PLoS ONE 19(12): e0308729.
- Article: The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity. Waterhouse, R. et al. F1000Res. 2024 May 22;12:ELIXIR-499.
- Article: A research data management (RDM) community for ELIXIR. D'Anna, F. et al. F1000Res; 2024.
- Article: ELIXIR fair training handbook. Holinski, A. et al. Zenodo; 2024. Read the news
- Article: Bioschemas training profiles: A set of specifications for standardizing training information to facilitate the discovery of training programs and resources. Castro LJ. et al. PLoS Comput Biol. 2023.
- Article: Grand challenges in bioinformatics education and training. Büşra Işık, E. et al. Nat Biotechnol. 2023.
- Article: An international consensus on effective, inclusive, and career-spanning short-format training in the life sciences and beyond. Williams, J. et al. PLoS One. 2023.
- Article: Beyond COVID - how the BY-COVID project is increasing European pandemic preparedness. Lauer, K. et.al (2023). Zenodo.
- Article: Ten simple rules for writing a PLOS Computational Biology quick tips article.Palagi PM, Schwartz R, Markel S, Ouellette BFF (2023). PLoS Comput Biol 19(12): e1011689.
- Article: Community-driven ELIXIR activities in single-cell omics. Czarnewski P, Mahfouz A, Calogero RA et al. Community-driven ELIXIR activities in single-cell omics [version 1; peer review: awaiting peer review]. F1000Research 2022, 11(ELIXIR):869
- Article: Ten simple rules for good research practice. Simon Schwab, Perrine Janiaud, Michael Dayan, Valentin Amrhein, Radoslaw Panczak, Patricia M. Palagi, Lars G. Hemkens, Meike Ramon, Nicolas Rothen, Stephen Senn, Eva Furrer, Leonhard Held. PLoS Computational Biology, 2022 June 23.
- Article: Ten simple rules in good research practice for early career researchers. Simon Schwab, Perrine Janiaud, Michael Dayan, Valentin Amrhein, Radoslaw Panczak, Patricia Palagi, Lars M. Hemkens, Meike G. Ramon, Nicolas Rothen, Stephen Senn. 2021,OSF Preprint.
- Article: ELIXIR‐EXCELERATE: establishing Europe's data infrastructure for the life science research of the future. Jennifer Harrow, John Hancock, Niklas Blomberg, Søren Brunak, Salvador Capella‐Gutierrez, Christine Durinx, Chris T Evelo, Carole Goble, Ivo Gut, Jon Ison, Thomas Keane, Brane Leskošek, Luděk Matyska, Johanna McEntyre, Célia Miguel, Arcadi Navarro, Steven Newhouse, Tommi Nyrönen, Patricia Palagi, Bengt Persson, Cyril Pommier, Jordi Rambla, Marco Roos, Gabriella Rustici, Andrew Smith, Alfonso Valencia, Celia van Gelder, Jiri Vondrasek, Nils Peder Willassen, Juan Arenas, Helen Parkinson, Robert D Finn, Sergi Beltran, Leslie Matalonga, Hannah Hurst, Paul Kersey, Ilkka Lappalainen, Pascal Kahlem, Gary Saunders, Sirarat Sarntivijai, Rachel Drysdale, Johnathan Tedds, Jeremy Lanfear. The EMBO Journal,40, 6, e107409, 2021.
- Report: Copyright Guidelines - How to acknowledge and be acknowledged in training material. Frédéric Schütz, Clement Parisato, Valeria Di Cola, Monique Zahn, Patricia M. Palagi. 2021 November 29.
- Presentation: Making training materials FAIR experiences, challenges, solutions. Saskia Hiltemann, Anna Swan, Verena Ras, Maria Doyle, Melissa Burke, Patricia M. Palagi, Celia W.G van Gelder. 2021 July 25.
- Presentation: Open and FAIR in bioinformatics and training. Patricia M. Palagi. 2021 March, Open Science Zurich, 04 March 2021, online.
- Report: Lessons learned when moving SIB Training courses from in-person to online – anything in bioinformatics can be taught online, but not anyhow. Patricia M. Palagi. 2020 September 17.
- Article: Biocuration - mapping resources and needs. Alexandra Holinski, Melissa L. Burke, Sarah L. Morgan, Peter McQuilton, Patricia M. Palagi. 2020 September 04.
- Article: Clinical bioinformatics for microbial genomics and metagenomics: an ESCMID Postgraduate Technical Workshop. Gilbert Greub, Patricia M. Palagi, David Dylus, Adrian Egli, Trestan Pillonel, John W. A. Rossen, Helena M. B. Seth-Smith, Aitana Lebrand. 2020 August 22.
- Article: A framework to assess the quality and impact of bioinformatics training across ELIXIR. Kim T. Gurwitz, Prakash Singh Gaur, Louisa J. Bellis, Lee Larcombe, Eva Alloza, Balint Laszlo Balint, Alexander Botzki, Jure Dimec, Victoria Dominguez del Angel, Pedro L. Fernandes, Eija Korpelainen, Roland Krause, Mateusz Kuzak, Loredana Le Pera ,Brane Leskošek, Jessica M. Lindvall, Diana Marek, Paula A. Martinez, Tuur Muyldermans, Ståle Nygård, Patricia M. Palagi, Hedi Peterson, Fotis Psomopoulos, Vojtech Spiwok, Celia W. G. van Gelder, Allegra Via, Marko Vidak, Daniel Wibberg, Sarah L. Morgan, Gabriella Rustici. 2020 July 23.
- Presentation: Applying best practices to enhance bioinformatics training in Switzerland. Diana Marek, Wandrille Duchemin, Isabelle Dupanloup, Grégoire Rossier, Margaux Roulet, Frédéric Schütz, Monique Zahn, Patricia M. Palagi. 2020 July 16.
- Article: Ten simple rules for making training materials FAIR. Leyla Garcia, Bérénice Batut, Melissa L. Burke, Mateusz Kuzak, Fotis Psomopoulos, Ricardo Arcila, Teresa K. Attwood, Niall Beard, Denise Carvalho-Silva, Alexandros C. Dimopoulos, Victoria Dominguez del Angel, Michel Dumontier, Kim T. Gurwitz, Roland Krause, Peter McQuilton, Loredana Le Pera, Sarah L. Morgan, Päivi Rauste, Allegra Via, Pascal Kahlem, Gabriella Rustici, Celia W. G. van Gelder, Patricia M. Palagi. 2020 May 21
- Report: Report on training provided across the ELIXIR community. Attwood Terri, Ben-Avraham Daniel, Beard Niall, Dominguez del Angel Victoria, Fernandes Pedro, Gurwitz Kim, Kahlem Pascal, Korpelainen Eija, Leskošek Brane, Lindvall Jessica, Morgan Sarah, Nygard Stale, Palagi Patricia, Peterson Heidi, Rustici Gabriella, Sansone Susanna-A, Thurston Milo, van Gelder Celia, Via Allegra. 2019 August 23
- Presentation: FAIR Training in ELIXIR Europe. Mateusz Kuzak, Leyla García Castro, Bérénice Batut, Ricardo Arcila, Niall Beard, Melissa Burke, Denise Carvalho-Silva, Victoria Dominguez Del Angel, Kim Gurwitz, Pascal Kahlem, Paula Martinez, Sarah Morgan, Peter McQuilton, Patricia Palagi, Fotis Psomopoulos, Gabriella Rustici, Celia van Gelder. 2019 July 24.
- Presentation: ELIXIR-Training-2018-ELIXIR-CZ-Conference. Celia van Gelder, Patricia M. Palagi, Gabriella Rustici, Pascal Kahlem. 2018 November 24.
- Presentation: Challenges in adopting FAIR principles in Training. Patricia M. Palagi, Pascal Kahlem, Gabriela Rustici, Celia W. G. van Gelder. 2018 October 29.
- Article: A new pan-European Train-the-Trainer programme for bioinformatics: pilot results on feasibility, utility and sustainability of learning. Allegra Via, Teresa K. Attwood, Pedro L. Fernandes, Sarah L. Morgan, Maria Victoria Schneider, Patricia M. Palagi, Gabriella Rustici, Rochelle E. Tractenberg. 2017 September 26.
- Article: The ELIXIR-EXCELERATE Train-the-Trainer pilot programme: empower researchers to deliver high-quality training . Sarah L. Morgan, Patricia M. Palagi, Pedro L. Fernandes, Eija Koperlainen, Jure Dimec, Diana Marek, Lee Larcombe, Gabriella Rustici, Teresa K. Attwood, Allegra Via. 2017 August 24.
- Article: Developing a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot action. Aleksandra Pawlik, Celia W.G. van Gelder, Aleksandra Nenadic, Patricia M. Palagi, Eija Korpelainen, Philip Lijnzaad, Diana Marek, Susanna-Assunta Sansone, John Hancock, Carole Goble. 2017 Jun 03.
- Article: BioCIDER: a Contextualisation InDEx for biological Resources discovery. Carlos Horro, Martin Cook, Teresa K. Attwood, Michelle D. Brazas, John M. Hancock, Patricia M. Palagi, Manuel Corpas, Rafael Jimenez. Bioinformatics. 2017 Apr 12. doi: 10.1093/bioinformatics/btx213.
- Conference poster: GOBLET Standards Committee: best practices and standards in bioinformatics and biocuration. Maria Victoria Schneider, Teresa K. Attwood, Manuel Corpas, Mike Charleston, Saravanan Dayalan, Pascale Gaudet, Judit Kumuthini, Sarah Morgan, Patricia M. Palagi, Gabriella Rustici. ISB 2017 Mar.
- Report: Defining a lingua franca for the ELIXIR/GOBLET e-learning ecosystem. Teresa K. Attwood, Brane Leskosek, Jure Dimec, Sarah Morgan, Nicola Mulder, Celia W. van Gelder, Patricia M. Palagi. 2016 Nov 13.
- Report: Report on the training needs identified across the ELIXIR community. Celia van Gelder, Sarah Morgan, Allegra Via, Rita Hendricusdottir, Eija Korpelainen, Chris Ponting, Terri Attwood, Patricia Palagi. 2016 Sep 2.
- Article: The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. SIB Swiss Institute of Bioinformatics Members. Nucleic Acids Res. 2016 Jan 4;44(D1):D27-37. doi: 10.1093/nar/gkv1310. Epub 2015 Nov 28.
Article: GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training
Teresa K. Atwood, Erik Bongcam-Rudloff, Michelle E. Brazas, Manuel Corpas, Pascale Gaudet, Fran Lewitter, Nicola Mulder, Patricia M. Palagi, Maria Victoria Schneider, Celia W. G. van Gelder, and the GOBLET Consortium. PLoS Computational Biology 04/2015; 11(4):e1004143. DOI:10.1371/journal.pcbi.1004143
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