SWISS BIOINFORMATICS SIB NEWSLETTER - SEPTEMBER 2016
Prof. Ron Appel
Switzerland is home to an array of research institutes involved in many different fields of science. Bioinformatics is particular in that it is not only a scientific field per se but also a discipline, which is gradually becoming the backbone of the life sciences as a whole. With the number of SIB groups steadily growing – 65 groups today – and the increasing role of bioinformatics in today’s major scientific advances, SIB’s scope of action is expanding both on the national and the international level.
An important development in bioinformatics is its extension to the clinical environment. SIB therefore created a group to support clinical bioinformatics in the university hospitals across the country and its first diagnostic tool has already been installed. In the same vein, SIB is preparing for the official start of the Swiss Personalized Health Network (SPHN) initiative; the Institute will be collaborating with experts in the field of medical informatics to define the strategy and guidelines for data production, storage, interoperability and exchange in Switzerland.
At the European level, SIB is the Swiss node of ELIXIR – the pan-European bioinformatics programme whose mission is to build a sustainable European infrastructure for biological information.
We are proud of SIB’s ever-expanding role in the world of bioinformatics, and we hope you will enjoy reading all about it in this issue of our newsletter.
ON THE INTERNATIONAL SCENE
Open Data in Action: Researchers, funders and industry highlight the importance of life science open data for innovation
In February, the Open Data in Action conference took place in Brussels. The meeting brought together about 100 researchers, policy makers, research infrastructure managers and industry representatives to discuss the impact of life science open data on innovation. In his talk, Ron Appel, SIB Executive Director, mentioned the valuable contributions of SIB to scientific progress in the life sciences. He highlighted the need to develop a robust framework to secure the long-term sustainability and accessibility of life science data.
Indicators for ELIXIR’s Core Bioinformatics Resources
SIB is participating in the Horizon 2020 ELIXIR-EXCELERATE project. One of its objectives is the identification of the ELIXIR Core Data Resources – a set of European data resources that are of fundamental importance to the broad life science community – as well as the long-term preservation of biological data. Over the past months, SIB, the Swiss node of ELIXIR, has been working on the identification of indicators, which will enable careful evaluation of the multiple facets of the databases.
SIB’s expertise for the benefit of clinicians and patients
SIB’s first bioinformatics diagnostic pipeline has been installed in a hospital. The pipeline allows seamless transfer, storage, annotation and reporting of the genetic mutations of tumour samples analysed by next-generation sequencing. It was developed by SIB’s Clinical Bioinformatics and Vital-IT Groups, in close collaboration with the staff of the Geneva University Hospital. This opens a new chapter in the Institute’s history, where SIB’s expertise will directly benefit not only clinicians in hospitals but also their patients.
Swiss Personalized Health Network (SPHN)
SIB as well as other stakeholders are getting ready for the official start of the Swiss Personalized Health Network (SPHN). Torsten Schwede has accepted the role of Director of the Data Coordination Centre (DCC). The DCC will be in charge of nationwide data interoperability and organization. Torsten will be working with the Data Expert Group, composed of experts in the field of medical informatics, to define the strategy and guidelines for data production, storage, interoperability and exchange.
Hairs, feathers and scales have a lot in common
The potential evolutionary link between hairs in mammals, feathers in birds and scales in reptiles has been debated for decades.
Today, researchers at UNIGE and SIB demonstrate that all these skin appendages share a common ancestry.
After ten years of research, the genome of the deer tick has been sequenced by an international team of scientists, including SIB researchers. Studying the tick genome sheds light on how ticks function and will help to develop novel tick control programmes by interfering with the processes of disease transmission.
Harmful mutations have accumulated during early human migrations out of Africa
The further a population moves away from its place of origin, the more harmful mutations it will carry. This is the result of a study conducted by SIB Group Leader Laurent Excoffier, Professor at the University of Bern, and his team, as part of an international collaboration.
SIB’s Virtual Seminars available online and open to everyone
The Computational Biology seminars organized by SIB on the campus of the University of Lausanne are now available online and open to everyone. These seminars represent a great opportunity for life scientists and clinicians to learn more about SIB’s research, expertise and resources.
For more information, please visit the Virtual Seminar Series webpage and subscribe to our mailing list in order to receive future announcements.
On 7 and 8 June, the SIB Days 2016 took place in Biel/Bienne, Switzerland. SIB organizes this scientific event for its members every two years in alternation with the [BC]2- Basel Computational Biology Conference.
The programme included lectures relating to bioinformatics and other scientific fields, poster sessions, lightning talks by young researchers, keynote speakers as well as workshops.
The SIB Days are a unique opportunity for SIB members to meet and exchange with their peers.
SIB Founding group celebrates its 30th Anniversary
Coinciding with the Biocuration Conference 2016, the SIB Swiss Institute of Bioinformatics and the Swiss-Prot group celebrated the 30th anniversary of the UniProtKB/Swiss-Prot database on 10 April 2016 in Geneva.
This pioneering knowledgebase of extensively curated proteins is provided and maintained by the SIB Swiss-Prot Group together with their colleagues of the UniProt consortium, and now scores over 800,000 requests every month. Over the past 30 years, the database has become an essential source of information for the scientific community. With the arrival of novel high-performance technologies, the Swiss-Prot knowledgebase has also evolved substantially without ever compromising on quality. It has adapted to 21st century science and is resolutely focused on the future.
A series of articles was written for the occasion and is also available on our dedicated webpage.
BIOINFORMATICS FOR ALL
The Metagenomic Pizza Workshop 2016
SIB offers a number of activities including online workshops. These workshops are at the disposal of teachers, students as well as the layman and are in English, French or German. They introduce the audience to the key role played by bioinformatics in the life sciences today. In April, an article on one of SIB's most popular workshops - "The Metagenomic Pizza" - presenting the world of bioinformatics to the layman and students, was published in EMBnet.journal.
We are not alone. From the day we are born, we carry with us hordes of microorganisms which, if all is going well, live off us while giving something in return. This micro-universe, which is an integral part of our physiology, has been called the microbiome. In the recent years, scientists have demonstrated the importance a microbiome has on our overall health; how it can influence our well-being as it can be at the heart of a disease. Take our mouths for instance. A mouth is home to billions of microorganisms with whom we share our life on a daily basis.Read More
SIB’s scope of activities continues to grow in all fields of bioinformatics – from proteomics and genomics to metabolomics and the crucial domain of personalized health. One of its 2015 highlights was its appointment as Reference Centre for Bioinformatics by the Food and Agriculture Organization of the United Nations (FAO). During the course of 2015, five new research groups joined SIB as well as one new partner institution, demonstrating not only SIB’s importance within the life science environment but also the necessity for such an infrastructure.
The SIB Swiss Institute of Bioinformatics is an academic not-for-profit organization. Its 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 by (i) providing the national and international life science community with a state-of-the-art bioinformatics infrastructure, including resources, expertise and services; (ii) federating world-class researchers and delivering training in bioinformatics. It includes some 65 world-class research and service groups and some 800 scientists in the fields of genomics, transcriptomics, proteomics, evolution, population genetics, systems biology, structural biology, biophysics and clinical bioinformatics.