Six new postdoc positions are funded by eSSENCE in Uppsala in 2017-2018. The projects and the principal investigators are
- Computational modeling, parameterization, and evaluation of the spread of antimicrobial resistance (Stefan Engblom)
- Automatic handwritten text recognition (Anders Hast)
- New e-science tools for in silico craniofacial development (Andreas Hellander)
- Functional networks for systems biology modelling: The tool and its validation for leukemia and diabetes (Jan Komorowski)
- Task based parallelization of electromagnetic scattering problems (Elisabeth Larsson)
- Modelling opinion dynamics at individual level (Ilkka Mäkinen)
The first project is data driven and a collaboration between Uppsala and Lund Universities. In the second project, machine learning will be used for semi-automatic interpretation of handwritten material in collaboration with the University Library. Computational methods will be applied to problems in developmental biology in the third project in a collaboration with Karolinska Institute. The Departments of Cell and Molecular Biology and Information Technology work together to improve functional network models in the fourth project. The multipole method will be implemeted on parallel computers in an industrial collaboration in the fifth project, Methods from statistical physics will be applied to electoral data from Stockholm city in the last project. New partnerships and new applications for eSSENCE are found in all projects.
The spring 2017 introductory course on Pharmaceutical Bioinformatics (7.5 ECTS credits; start January 16, 2017) given by Uppsala University is now open for late application.
The course, which is free of charge for EU/EAA-citizens, is suited for researchers who are interested to learn how complex chemical and biomedical processes can be investigated even down to their finest chemical details using informatics, and how this can be used for the development of novel drugs.
To receive further information please visit www.pharmbio.org.
On request of many previous participants we now also offer two additional courses:
I. Applied Structural Pharmaceutical Bioinformatis (5 ECTS credits; start January 16, 2017)
II. Applied Pharmaceutical Bioinformatics (5 ECTS credits; start April 3, 2017)
More information is available at www.pharmbio.org/pages/other_courses .
To apply to the courses, please follow this link:
Per Lötstedt, Director of eSSENCE, was interviewed by the Uppsala newspaper, UNT. In an article entitled “The laboratory has moved into the computer” Per took the opportunity of introducing e-Science to the public and describing the eSSENCE research program.The article was published on September 7, 2016 (in Swedish).
If you have a subscription you can read the article here.
“Recommendations on e-infrastructures for next-generation sequencing”
O. Spjuth, E. Bongcam-Rudloff, J. Dahlberg, M. Dahlö, A. Kallio, L. Pireddu, F. Vezzi, and E. Korpelainen,
GigaScience, vol. 5, no. 1, pp. 1-9, 2016.
With ever-increasing amounts of data being produced by next-generation sequencing (NGS) experiments, the requirements placed on supporting e-infrastructures have grown. In this work, we provide recommendations based on the collective experiences from participants in the EU COST Action SeqAhead for the tasks of data preprocessing, upstream processing, data delivery, and downstream analysis, as well as long-term storage and archiving. We cover demands on computational and storage resources, networks, software stacks, automation of analysis, education, and also discuss emerging trends in the field. E-infrastructures for NGS require substantial effort to set up and maintain over time, and with sequencing technologies and best practices for data analysis evolving rapidly it is important to prioritize both processing capacity and e-infrastructure flexibility when making strategic decisions to support the data analysis demands of tomorrow. Due to increasingly demanding technical requirements we recommend that e-infrastructure development and maintenance be handled by a professional service unit, be it internal or external to the organization, and emphasis should be placed on collaboration between researchers and IT professionals.
The citation for his nomination reads; “Bo Kågström is Professor of Numerical Analysis and Parallel Computing and Director of High Performance Computing Center North (HPC2N) at Umeå University. Kågström has 25 publications in SIAM books and journals. He was a corresponding editor of the SIAM Journal on Matrix Analysis and Applications, was awarded the SIAM/SIAG Linear Algebra Prize in 2000, and has served on multiple SIAM prize committees, among other involvements. Kågström is being honored for contributions to the understanding of matrix pencils and for leadership within the European high performance computing community.”
Enabling integrative cross-biobank research: the SAIL method for harmonizing and linking biomedical and clinical data across disparate data archives
O. Spjuth, J. Hastings, J. Dietrich, J. Heikkinn, N. Pedersen, J. Hottenga, S. Ripatti, P. Burton, I. Fortier, C. van Duijn, E. Wichmann, J. Rung, M. McCarthy, M. Allen, E. Raulo, I. Prokopenko, J. Karvanen, M. Perola, M. Kolz, E. J.C. de Geus, G. Willemsen, P. Magnusson, J-E. Litton, J. Palmgren, M. Krestyaninova, and J. Harris.
European Journal of Human Genetics advance online publication 26 August 2015; doi:10.1038/ejhg.2015.165
A wealth of biospecimen samples are stored in modern globally distributed biobanks. Biomedical researchers worldwide need to be able to combine the available resources to improve the power of large-scale studies. A prerequisite for this effort is to be able to search and access phenotypic, clinical and other information about samples that are currently stored at biobanks in an integrated manner. However, privacy issues together with heterogeneous information systems and the lack of agreed-upon vocabularies have made specimen searching across multiple biobanks extremely challenging. We describe three case studies where we have linked samples and sample descriptions in order to facilitate global searching of available samples for research. The use cases include the ENGAGE (European Network for Genetic and Genomic Epidemiology) consortium comprising at least 39 cohorts, the SUMMIT (surrogate markers for micro- and macro-vascular hard endpoints for innovative diabetes tools) consortium and a pilot for data integration between a Swedish clinical health registry and a biobank. We used the Sample avAILability (SAIL) method for data linking: first, created harmonised variables and then annotated and made searchable information on the number of specimens available in individual biobanks for various phenotypic categories. By operating on this categorised availability data we sidestep many obstacles related to privacy that arise when handling real values and show that harmonised and annotated records about data availability across disparate biomedical archives provide a key methodological advance in pre-analysis exchange of information between biobanks, that is, during the project planning phase.
Link to article full text: http://www.nature.com/ejhg/journal/vaop/ncurrent/full/ejhg2015165a.html
In the EU COST Action SeqAhead, researchers lead by eSSENCE researcher Ola Spjuth have conducted a large survey on the use of scientific workflows in data-intensive bioinformatics.
Experiences with workflows for automating data-intensive bioinformatics
Ola Spjuth, Erik Bongcam-Rudloff, Guillermo Carrasco Hernández, Lukas Forer, Mario Giovacchini, Roman Valls Guimera, Aleksi Kallio, Eija Korpelainen, Maciej M Kańduła, Milko Krachunov, David P Kreil, Ognyan Kulev, Paweł P. Łabaj, Samuel Lampa, Luca Pireddu, Sebastian Schönherr, Alexey Siretskiy and Dimitar Vassilev
Biology Direct 2015, 10:43 doi:10.1186/s13062-015-0071-8
High-throughput technologies, such as next-generation sequencing, have turned molecular biology into a data-intensive discipline, requiring bioinformaticians to use high-performance computing resources and carry out data management and analysis tasks on large scale. Workflow systems can be useful to simplify construction of analysis pipelines that automate tasks, support reproducibility and provide measures for fault-tolerance. However, workflow systems can incur significant development and administration overhead so bioinformatics pipelines are often still built without them. We present the experiences with workflows and workflow systems within the bioinformatics community participating in a series of hackathons and workshops of the EU COST action SeqAhead. The organizations are working on similar problems, but we have addressed them with different strategies and solutions. This fragmentation of efforts is inefficient and leads to redundant and incompatible solutions. Based on our experiences we define a set of recommendations for future systems to enable efficient yet simple bioinformatics workflow construction and execution.
Link to full text: http://www.biologydirect.com/content/10/1/43
Software X: A new open-access journal from Elsevier for scientific software. The journal publishes peer-reviewed software and also allows for post-publication updates and metadata.
Two presentations from eSSENCE scientists Anders Hast and Torbjörn Nordling from Uppsala University have been accepted at the “11th IEEE International Conference on e-Science” in Munich, Germany, 31/8 – 4/9 2015.
Welcome to the eSSENCE conference “Swedish e-Science Academy”:
Date: 14-15 October, 2015 (lunch to lunch)