| 1. |
- Hast, Anders, et al.
(författare)
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Swedish eScience education : A graduate school in eScience
- 2015
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Ingår i: Proceedings - 11th IEEE International Conference on eScience, eScience 2015. - : IEEE. - 9781467393256 ; , s. 31-35
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Konferensbidrag (refereegranskat)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.
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| 2. |
- Nordling, Torbjörn E. M., et al.
(författare)
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Identification of Biomarkers and Signatures in Protein Data
- 2015
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Ingår i: 2015 IEEE 11Th International Conference On E-Science. - 9781467393256 ; , s. 411-419
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Konferensbidrag (refereegranskat)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. We discuss issues of identification of biomarkers that provide distinct signatures for prediction of tissues as cancer or normal, exemplified by our recent study of cancer signalling signatures in human colon cancer characterised with regards to protein abundance using high sensitivity isoelectric focusing. We 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. Actually, one of the proteins belongs to the tertile with the lowest significance and correlation. This highlights the weakness of the practice of only looking for significant differences in the abundance of individual proteins and raises the question of how many lifesaving discoveries that have been missed due to it. We 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.
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| 3. |
- Zhao, Zhiming, et al.
(författare)
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Reference model guided system design and implementation for interoperable environmental research infrastructures
- 2015
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Ingår i: Proceedings - 11th IEEE International Conference on eScience, eScience 2015. - 9781467393256 ; , s. 551-556
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Konferensbidrag (refereegranskat)abstract
- Environmental research infrastructures (RIs) support their respective research communities by integrating large-scale sensor/observation networks with data curation services, analytical tools and common operational policies. These RIs are developed as pillars of intra-and interdisciplinary research, however comprehension of the complex, pathologically interconnected aspects of the Earth's ecosystem increasingly requires that researchers conduct their experiments across infrastructure boundaries. Consequently, almost all data-related activities within these infrastructures, from data capture to data usage, needs to be designed to be broadly interoperable in order to enable real interdisciplinary innovation. The Data for Science theme in the EU Horizon 2020 project ENVRIPLUS intends to address this interoperability challenge as it relates to the design, implementation and operation of environmental science RIs, the theme focuses on key issues of data identification and citation, curation, cataloguing, processing, optimization, and provenance, supported by a generic cross-infrastructure reference model.
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