New Horizons Magazine from Uppsala University • Issue 1
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NEW HORIZONS MAGAZINE FROM UPPSALA UNIVERSITY • ISSUE 1. 2014 theme: E-SCIENCE FROM THE CONTENT: MILLIONS OF IMAGES OF CANCER Page 10 GAME DESIGN IN RAPID DEVELOPMENT Page 26 HANS ROSLING REDRAWS THE MAP Page 36 1 NEW HORIZONS ISSUE 1. 2014 IN THIS ISSUE: THEME: E-SCIENCE 4 Large amounts of data require new tools 8 Computers calculate how the glaciers move 9 Language is difficult för Google’s computers 10 Millions of images of cancer New tools for large amounts of data . 4 He wants to redraw the map. 36 Resources for research 12 Genetic risk More and more information is stored Meet honorary doctor Hans Rosling, who wants AN INCREASINGLY IMPORTANT FACTOR for successful research and inn- 13 In focus: School on a downward slope digitally and is available to many. to show us our new world ovation, is the access to well-functioning research infrastructure. The research becomes more complex and dependent on different types of resources. Some 16 Positive trend for world peace of these are available at Uppsala University, others we gain access to through 20 Researcher profile: Erik Ingelssons driving force national and international collaborations. This ranges from major facilities to databases, libraries, biobanks, laboratories and data storage resources. 24 The shoal of fish is the model in studies of democracy Long-term planning and intelligent funding strategies are required in order for the research infrastructure to maintain a high level of quality. In recent 26 Report: Game design in Visby years, opportunities for external funding have declined. This means that a gre- 30 Student Kajsa Asplund: ”Psychologists are needed” ater financial responsibility for local infrastructure lies with the actual insti- tutions of higher education. We have therefore identified infrastructure as a 32 Innovation: The instrument that finds pathogens strategic priority area for the University of Uppsala in the coming years. Science for Life Laboratory (SciLifeLab) is an excellent example of a lar- 36 Alumni: Hans Rosling redraws the map ge-scale collaboration where the research infrastructures play a significant role. 38 Magician Johan Ståhl: ”Absolutely world class” It is a national centre for molecular biosciences aimed towards health and en- vironmental research. The centre is a collaboration between Karolinska Insti- tutet, the Royal Institute of Technology, Stockholm University and Uppsala Fish show the way. Game design in Visby. Student of the year. University, where both technology and knowledge are to be used as a national 24 26 30 resource. Other examples of joint national initiatives, which give Swedish research new opportunities include: Max IV Lab and ESS in Lund. For a small country such as Sweden, it is important to participate in international projects that give New Horizons is Uppsala University’s magazine about research our researchers the best conditions for high quality scientific work. Providing and education. It is issued twice a year, in English and in Swedish, Nya world-class infrastructures also contributes to increased mobility by attracting horisonter. The magazine can be ordered free of charge or down- loaded as a PDF at the address: www.uu.se/new-horizons outstanding researchers from other countries, which creates attractive meeting Address: Communication and External Relations Uppsala University The flow of data is increasing places and creative environments. Factors, which in turn, have positive effects P.O. Box 256, SE-751 05 Uppsala, SWEDEN on the quality of research and to society in general. n A FLOOD OF DATA STREAMS ACROSS THE WORLD. Environment and climate data, Editor: Annica Hulth, [email protected] electrical particles, DNA sequences and genetic information... Not to mention patient data, Editorial board: Magnus Alsne, Anders Berndt, Anneli Björkman, statistics on unemployment benefit and sickness benefit. Even web services such as Face- Eva Åkesson, Vice-Chancellor Helena Edström, Linda Koffmar, Anna Malmberg, Gunilla Sthyr, Anneli Waara. book and search engines like Google are based on the data volume. Executive editor: Urban Lindberg For research, it has meant that completely new issues can be studied and on a much Layout: Torbjörn Gozzi greater scale than before. In this issue, we discuss some examples: research on glaciers, how Printing: Danagård Litho computers can learn to understand language, the future of magnetic materials and cancer English translation: Svensk Språkservice treatment. To analyse all this data requires a wealth of computing power – both for data storage and to make calculations. In recent time resources have increased at Uppsala University, For a small country such as Sweden, it is especially for researchers in biology and medicine. With computer power researchers can investigate new questions, but also pick up old important to participate in international projects unresolved problems from the drawer. That’s according to Ingela Nyström who leads Es- By choosing this paper we have reduced our climate impact by more sence, a strategic research initiative on e-Science. This applies to many areas of research – that give our researchers the best conditions for than 35per cent. The paper is produced in Sweden, and the amount of water used in its production is uniquely low. The raw materials perhaps the majority. ‘In the future, perhaps we will not talk about e-science, but about “the Annica Hulth, editor high quality scientific work. come from “FSC forests”. science”,’ predicts Ingela Nyström. n [email protected] 2 NEW HORIZONS: ISSUE 1.2014 3 THEME: E-SCIENCE ‘A COMPLETELY NEW working method has He adds that they have invested a lot in sup- TEXT: ANNICA HULTH PHOTO: MIKAEL WALLERSTEDT, STAFFAN CLAESSON emerged over the past decade,’ says Ola Spjuth. port and training. Together with SciLifeLab, they He is a researcher at Science for Life Labora- offer a course where researchers have learned tory (SciLifeLab) in Uppsala and leads the Upp- the basics of using large-scale computer systems nex project. They have built up large computing and try to log in and use Uppnex. resources for what’s known as “next-generation ‘It is usually overbooked.’Very many rese- Large amounts of data sequencing” – i.e., large-scale gene analysis. arch groups employ bioinformaticians now, but The technology makes it possible to quickly research leaders also need to understand how it obtain the DNA sequence from samples from works.’ humans, plants and animals. It is useful in cancer Many projects are in progress for a long time. research, pharmaceutical research and biology – To map the genome of an organism, for example, REQUIRE NEW and generates lots of data. is just a starting point for further studies. Ola ‘One run on a single sample can generate bil- Spjuth envisions that the data volume will con- lions of bases (the letters A, T, C and G) and it’s tinue to increase. not like reading a book, but takes days, weeks or ‘Projects are getting bigger and more people The amount of data has in some instances months of calculations,’ says want to sequence. At the same time, the process TOOLS Ola Spjuth. is faster and we can get more and more data. increased tremendously over the past ten years. More ‘Suddenly, researchers were swimming in Projects expand 5–10 times on the drives during Ten years ago this data, hard drives were stacked up on the lab the analyses and biologists like to save all their was not possible, but and more information is stored digitally and is available benches so a decision was made to make a joint data. It’s a massive challenge to be able to scale effort to try to solve the problems.’ up storage and analyses.’ today we can do a to many. At the same time, there is a need of tools to analyse Uppmax was already in place at Uppsala Uni- lot more full-scale versity, with high-performance computers that CONSEQUENTLY, developments place new de- all this data and create new knowledge. This is especially served researchers in fields such as physics and mands on the research infrastructure. This con- experiments. chemistry. In 2010 the server room was expan- cerns both the ability to store data and to analyse true within biology, where new technology has led to an ded with Uppnex for biological research. It is the the information. part that has expanded the fastest and it’s still ‘We will need to develop new methods and explosion of data. growing. tools,’ says Ingela Nyström. INGELA NYSTRÖM She is a professor at the department of Infor- Professor at the department A NEW SERVER ROOM was recently opened at mation Technology and coordinator of Essence, a of Information Technology Ola Spjuth SciLifeLab, which is directly linked to Uppnex. strategic research initiative that is run from Upp- leads Uppnex in All in all there is currently data from over 800 sala University. Lund and Umeå Universities are Uppsala, which different projects and a storage capacity of 7 pe- also involved in the initiative. is a national tabytes, which is equivalent to 7000 times more ‘Essence assembles researchers who wish to resource for than will fit on a typical hard drive. improve their research with e-scientific methods. biologists who need to manage ‘We have recently increased the computing ca- Strong research both in the field and in method ever-increasing pacity three times and the storage capacity five ti- development are required in order for this to amounts of data mes, and apart from purchasing computers, we have work,’ says Ingela Nyström. in their research. built up a high level of expertise,’ says Ola Spjuth. She sees research being able to answer com- The new technical possibilities have led to a pletely new questions now that it’s possible to great deal of new research results, for example, process larger amounts of data.