SWEDISH e-SCIENCE ACADEMY 2015

Dates: Wednesday lunch October 14 – Thursday lunch October 15
Location: Quality Airport Hotel Arlanda, Arlandastad

Keynote talk: “The Dutch e-Science Initiative” by Frank Seinstra,
Director eScience Program at The Netherlands eScience Center

PRELIMINARY AGENDA


WEDNESDAY OCTOBER 14

10:00 Arrival, coffee and sandwiches, hanging of posters
11:30 Starting lunch
12:30 Swedish e-Science Academy Words of Welcome
Ingela Nyström, Director of eSSENCE, UU
 12:45 Keynote talk: “The Dutch e-Science Initiative”
Frank Seinstra, Director eScience Program at The Netherlands eScience Center Abstract:
Science and society are inextricably linked. The grand societal challenges of the coming years, such as climate change, resource scarcity, and increased urbanization will require innovative scientific and technological interventions. This revolutionizing of scientific practice will depend for a large part on our capacity to harness the power of ‘big’ compute, data, and analytics technologies.
Modern data-driven and compute-intensive research requires scientists to rapidly develop ICT skills that may currently be foreign to them. For many scientists, the prospect of developing the skills needed to engage increasingly diverse and complex e-infrastructure is daunting. eScience can provide discipline focussed scientists the tools, personnel and support needed to lower this barrier and ensure developments in computing and data science are readily applied in other research areas.
To this end, the Netherlands eScience Center (NLeSC) has been set up as a collaboration between NWO, the principle Dutch scientific funding body and SURF, the Dutch higher education and research partnership for ICT. NLeSC funds and participates in multidisciplinary projects, with academia and industry, having optimized data-handling, efficient computing and big-data analytics at their core.In this presentation, I will discuss NLeSC’s goals, strategy, and approach and highlight some of the results achieved since the center’s launch in 2011.
 13:30 “Parallel Numerical Linear Algebra for Future Extreme-Scale Systems”
Bo Kågström, UmU
 13:50 “Modelling materials and chemistry – in an eSSENCE and a European context”
Kersti Hermansson, UU Abstract:
A Holy Grail of scientific modelling is the ability to design, in silico, materials and molecules with enhanced properties that can ensure a sustained, and sustainable, economic and societal growth. To achieve such impact, we will need to know how to model systems of great complexity (e.g., chemical complexity) with both sufficient accuracy and sufficient speed. Moreover, widely different length and time scales may need to be considered and linked. The development of new, more reliable models and modelling workflows is therefore essential – as realised at the onset of the eSSENCE program. I will discuss efforts and successes in the development of multi-scale materials modelling (with a chemical touch) enabled by eSSENCE, and place them in a broader European perspective.
 14:10 “Talk 3”
Tomas Lundqvist, LU
 14:30 “Talk 4”
Chalmers
14:50  Coffee Break and Check-in
 15:30 “Autonomous Resource Management for Robust, Efficient, and High-Performance Cloud Computing”
Erik Elmroth, UmU
 15:50  Two accepted papers for presentations at IEEE e-Science 2015, Munich
 “SeSE – Swedish e-Science Education – a Graduate School in e-Science”
Anders Hast, Director of SeSE, UU Abstract
Swedish eScience Education (SeSE) is a national graduate school in eScience in Sweden. It comes from the collaboration between two major research initiatives in eScience and the school has turned out to be very successful. It has made it possible for students at different universities to get access to education that is not normally available at their home universities. With SeSE they get access to education by the top experts within their respective field. We argue why such graduate school is important and how it is different from training offered by many HPC centres in Europe. Furthermore, examples of courses and their structure is discussed as well as lessons learned from SeSE and its two predecessors in Sweden.
 “e-Science in Cancer Research: Identification of Biomarkers and Signatures in Protein Data”,
Torbjörn Nordling, UU  Abstract
The correct diagnosis of cancer patients conventionally depends on the pathologist’s experience and ability to distinguish cancer tissue from normal tissue under a microscope. Advances in technology for measuring the abundance of, e.g., proteins and mRNAs in tissue samples make it interesting to search for an optimal subset of these for classification of samples as cancer or normal. This search for an optimal subset of molecules is in Statistics and Machine learning known as variable selection, features selection, and subset selection.
It is typically computationally intensive and biomarker discovery benefit from an e-Science approach. In this talk, I give a brief introduction to biomarker discovery in cancer research. I discuss issues of identification of biomarkers that provide distinct signatures for prediction of tissues as cancer or normal, exemplified by a recent study of cancer signalling signatures in human colon cancer. More precisely, I discuss ranking of individual features versus combinations of features, model over-fitting, and confidence evaluation. I show that the optimal subset for separation of cancer tissues from normal tissues does not contain any of the proteins in the top quintile in terms of significant difference between the groups according to Mann-Whitney U-test or correlation to the diagnosis. I also demonstrate how Monte Carlo simulations of the separation with random class assignment can be used to calculate p-values for observing any specific separation by chance and selection of the optimal number of proteins in the subset based on these p-values. Both selection of the optimal number of biomarkers and calculation of p-values corrected for multiple hypothesis testing are essential to obtain a subset of biomarkers that yield robust predictions for clinical use.
 16:30-
18:30
 Poster Session and Drinks & Snacks
 19:00  Dinner and Discussions

 

THURSDAY OCTOBER 15

08:30 “Multi-scale Modeling of Spin Dynamics”
Gunilla Kreiss, UU Abstract
We are working on how to combine atomistic and continuum models for dynamic magnetization to get a computational technique, which combines the efficiency of a continuum model with the accuracy of an atomistic model. Difficulties include very large differences in temporal and spatial scales and construction of non-reflecting  interface conditions.
 08:50 “Talk 7”
Stefan Lindgren, LU
 09:10 “Talk 8”
Pär Strand, Chalmers
 09:30 “e-Science for Cancer Prevention and Control – Enabling Translational Medicine with e-Science”
Ola Spjuth, KI Abstract
New molecular technologies and computational methodology allow for an improved understanding of the mechanisms for initiation and progression of disease. eScience for Cancer Prevention and Control (eCPC) is a flagship project and joint collaboration between the Swedish e-Science initiatives SeRC and eSSENCE. The aim is to (a) support cancer biomarker discovery and use, and (b) translate discovery into individualized diagnostics, prevention and screening strategies. A modular framework for cancers of the prostate, breast and cervix has been developed, which includes prediction models for cancer initiation and progression coupled with a microsimulation to evaluate of cost and benefit of various screening scenarios. These e-Science tools have e.g. been used in the landmark STHLM3 diagnostic trial for prostate cancer screening. A system for translating next-generation sequencing to clinical diagnostics has also been developed and is now in use for early detection of mutation frequencies in chronic myelogenous leukemia (CML). The e-Science components identified and used in the eCPC projects include data integration, data security, image analysis, modeling and simulation, and automation of analysis workflows on high-performance e-Infrastructures.
 09:50  Coffee break
 10:20 “e-Science in the Galleries – From Martian Meteorites to Mummies”
Anders Ynnerman, LiU Abstract
In the last decades imaging modalities have advanced beyond recognition and data of rapidly increasing size and quality can be captured with high speed. This talk will show how e-Science methodology can be used to provide public visitor venues, such as museums, science centers and zoos with unique interactive learning experiences.  By combining large data visualization techniques with technologies such as interactive multi-touch tables and intuitive user interfaces, visitors can conduct guided browsing of large volumetric image data. The visitors then themselves become the explorers of the normally invisible interior of unique artifacts and subjects. The talk will take its starting point in the current state-of-the-art in CT and MRI scanning technology. It will then discuss the latest high-quality interactive volume rendering and multi-resolution techniques for large scale data and how they are tailored for use in public spaces.  Examples will then be shown of how the inside workings of the human body, exotic animals, natural history subjects, such as the martian meteorite, or even mummies can be explored interactively, bringing e-Science enabled data exploration to the public.  The recent mummy installation at the British Museum will be shown and discussed from both a curator and visitor perspective and results from a 3 month trial period in the galleries will be presented.
 10:40 “Nordic e-Science Actions”
Sverker Holmgren, Programme Director for NeGI
 11:00 Panel Discussion: “Swedish e-Science in an International Perspective”Moderator:Panel:

  • Anders Hast, SeSE
  • Juni Palmgren, SeRC
  • Frank Seinstra, international
  • Pär Strand, Chalmers
 Preliminary Questions:

  • How can a small country like Sweden play a role internationally in e-Science?
  • What role does the Universities play to establish and define e-Science initiatives?
  • How should we educate and spread knowledge about e-Science to young researchers?
  • questions of interest from the panel
 12:15 Swedish e-Science Academy Closing Words
Ingela Nyström, Director of eSSENCE, UU
 12:30  Farewell Lunch

 

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