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Data scientists for life
From one-off services to long-term collaborative support
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Collaborative support and services:
meeting your bioinformatics needs
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Biostatistics and bioinformatics analysis
Making your biological data speak

With more than 20 years' experience in applying data and computer science to biological questions, our specific areas of expertise include: biomarker identification; de novo assembly from sequencing data; genome comparative data analysis; targeted, exome and whole genome sequencing analysis; metagenomic data analysis; omics analysis; data integration from multiple sources; annotation and gene prediction; machine learning.

In practice:

  1. Human clinical data analysis: data analysis of the results of a clinical trial, looking at dietary supplementation with Urolithin A, a pomegranate metabolite, which could help slow down certain ageing processes by improving mitochondrial and cellular health in humans, in conjunction with EPFL and its spin-off, Amazentis.
  2. Identifying candidate biomarkers: data analysis from large amount of patient data in a pan-European project leading to the discovery of molecules, which could serve as biomarkers to detect type 2 diabetes (T2D) up to nine years before its onset, as well as to the identification of genes involved in the demise of diabetic beta cells.
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Data management
Organizing your data for long-term reuse

We assist you by defining and implementing your Data Management Plan (DMP) for research proposals; reaching data interoperability targets, from local to international scales, within academic or regulated environments; ensuring the long-term management and storage of scientific data.

In practice:

  1. Implementing semantic and technical interoperability within the Swiss Personalized Health Network (SPHN) initiative, aiming to make data from consenting patients available securely to researchers from across Switzerland’s hospitals and universities.
  2. Acting as a Data Coordination Centre in European public-private partnerships to fight diabetes, including through the identification of biomarkers of the disease. This includes the set-up of a federated data analysis system across multiple countries to enable access to large patient cohorts while addressing legal, ethical and FAIR principles.
  3. Extracting, reformatting and migrating patient-related data between systems for our clinical partners, to ensure data consistency and query traceability.
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Secure services for sensitive data
Dedicated, secure IT environment to process sensitive human data

Our encrypted information technology infrastructure conforms with all current data protection regulations (incl. GDPR) and IT security standards. You can therefore process and host both sensitive data - such as genomic information or health records - and non-sensitive data - with complete confidence. We use modern virtualization technologies such as OpenStack to protect our data and computing environments.

In practice:

  1. Secure Data Processing Platform: set-up by SIB as part of the nationwide secure infrastructure enabling the exchange of biomedical data between health institutions across Switzerland and researchers. This infrastructure has been set up as part of our BioMedIT Project in the context of the national initiative for personalized health, SPHN.
  2. Swiss Variant Interpretation Platform for Oncology (SVIP-O): to enable faster and more robust prioritisation of genetic variants, SIB is co-leading the development of a centralized, joint, curated database for clinical somatic variants coming from Swiss hospitals and related institutions, such as pathology institutes.
  3. Hypo-RESOLVE: hundreds of clinical trials transferred and hosted onto our secure central server, in the context of this pan-European project – supported by the Innovative Medicines Initiative (IMI) and including 23 leading academic experts, pharmaceutical and device manufacturers, as well as patients’ organizations – to find better solutions to alleviate the burden and consequences of hypoglycaemia, a common and serious complication of diabetes.
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Software engineering and tailoring
Developing engaging and customized software tools

Our software engineers and User eXperience specialists contribute to some of the world-leading databases and tools used by life scientists around the globe. We also develop tailored applications for personalized medicine in hospitals or industry settings. Our teams assist you in creating user-friendly software products – or tailoring existing ones to your in-house needs – based on the most up-to-date web technologies.

In practice:

  1. Oncobench ®: together with the Geneva University Hospitals, we launched a user-friendly platform that streamlines and automates the analysis of patient tumour DNA for cancer diagnosis, while ensuring the privacy of the patient’s data.
  2. Swiss Pathogen Surveillance Platform: we are co-leading the development of the Swiss Pathogen Surveillance Platform to enable near real-time sharing of pathogen whole genome sequences and their associated clinical/epidemiological metadata for surveillance of outbreaks.
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Expert biocuration
Generating high-quality, up-to-date annotations

Tap into our unique pool of biocuration experts, who excel in the art of generating knowledge from a growing body of publications, by ensuring the most adequate and informative evidence is reported. We can provide expert biocuration on specific data types (e.g. proteomics, lipidomics or transcriptomics), or help you with setting up expert-annotated resources, for a wide range of applications, such as understanding protein function, facilitating clinical interpretation of cancer variants or enabling biomarker discovery. Read more

In practice:

  1. Our Swiss-Prot team provides the manually annotated section of UniProt, the world-leading protein information resource (together with EMBL-EBI and PIR) accessed by thousands of users every day.
  2. The Swiss Variant Interpretation Platform (SPHN project) aims to harmonize the clinical interpretation of genetic variants across Swiss hospitals, and will combine clinical data from hospital partners with publicly available information from international projects (e.g. ClinVar, CIViC) and published literature, sourced by expert biocurators.
  3. We developed, in collaboration with SystemsX and LipidX, the SwissLipids knowledgebase – a comprehensive library of over 500,000 lipid structures enriched with expert-curated information on lipid metabolism, protein interactions and occurrence in organelles, cells, tissues and organs.
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Process optimization
Gaining efficiency, from analysis pipelines to quality control

Our experts help you to harmonize and optimize your internal data management processes, analysis pipelines or software tools. We also organize and support clinical benchmarking activities with Swiss or international partners.

In practice:

  1. Swiss-wide ring trial: SIB led the first nationwide quality-control test to benchmark and harmonize the current metagenomic workflows used at Swiss clinical virology laboratories, in collaboration with EPFL and the University of Zurich.
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Training
Boosting your bioinformatics skills

Whether you are a researcher or a healthcare professional, our comprehensive – and constantly evolving – course portfolio provides hands-on experience of the most up-to-date bioinformatics techniques and resources, including clinical applications. We offer over 100 course-days provided by 80 trainers each year.

In practice:

  1. Certificate of Advanced Studies (CAS) in Personalized Molecular Oncology: First of its kind in Switzerland, it is co-organized by SIB and the University Hospitals of Basel and Lausanne, and aims to establish a common language between the wide range of professionals involved in the personalized oncology process, from biologists and bioinformaticians to pathologists and clinicians, towards better informed use of genomic data for both routine clinical practice and clinical research.
  2. SIB was commissioned by the Food and Agriculture Organization of the United Nations (FAO) and the International Atomic Energy Agency (IAEA) joint programme to produce two e-learning modules, accessible via the dedicated website Viral Zone. These modules focus on (i) phylogenetics of animal viral pathogens and applications primarily dedicated to the veterinarians and molecular epidemiologists from diagnostic and research laboratories of developing FAO and IAEA member states and (ii) BLAST and multiple sequence alignment (MSA) programs.
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About SIB
The SIB Swiss Institute of Bioinformatics is an academic not-for-profit organization whose mission is to lead and coordinate the field of bioinformatics in Switzerland. Its data science experts join forces to advance biological and medical research and enhance health.
Contact
Quartier Sorge - Batiment Amphipole
1015 Lausanne / Switzerland
Tel: +41 21 692 40 50
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