PASC18 Call for Submissions

The PASC18 Organizing Team is pleased to announce that submissions are now open for minisymposium, paper and poster contributions. We look forward to receiving your submissions through the online submission portal. Please note that the November 26th deadline for minisymposia proposals is rapidly approaching!  

CONFERENCE

PASC18 is the fifth edition of the PASC Conference series, an international platform for the exchange of competences in scientific computing and computational science, with a strong focus on methods, tools, algorithms, application challenges, and novel techniques and usage of high performance computing. 

The theme of PASC18 is Fast and Big Data, Fast and Big Computation, emphasizing our vision of the close coupling of data and computation. Exposing and expressing massive and irregular parallelism in computational problems are key challenges for exploiting the massive and heterogeneous parallelism available in current, and expected in future, HPC systems, as well as to find new ways of generating scientific insight from data and models. Through its rich and interactive program, PASC18 aims to highlight the computational approaches that computational scientists, computer scientists, and practitioners employ today and will employ over the next decades to address these challenges. 

CONTRIBUTIONS

PASC18 welcomes submissions for minisymposium, paper, and poster contributions that demonstrate innovative research in scientific computing related to the following scientific domains:

  • Chemistry and Materials
  • Life Sciences
  • Physics 
  • Climate and Weather
  • Solid Earth Dynamics 
  • Engineering
  • Computer Science and Applied Mathematics
  • Emerging Applications Domains (e.g. Social Sciences, Finance,…)

 Upcoming Submission Deadlines

  • Minisymposia: November 26, 2017
  • Papers: January 19, 2018
  • Posters: February 4, 2018

 
Minisymposia
A minisymposium at PASC18 is a two-hour session of four presentations on a topic of current importance in computational science that showcases research related to domain science, applied mathematics, computer science or software engineering. Proposals should describe research that is of significant current interest to a given PASC scientific domain, and ideally, have potential application to additional domains. Proposals should include speakers from multiple institutions and/or countries, and be designed such that the speakers bring a range of different perspectives to the topic. PASC18 encourages gender balance and diversity. 

Papers
The goal of the PASC papers program is to advance the quality of interdisciplinary exchange between the various specific fields of computational science and engineering. We welcome high-quality contributions of original research related to scientific computing in any of the eight PASC scientific domains. Papers will be evaluated by domain experts primarily on their significance, technical soundness, originality, and quality of communication. Papers accepted for PASC18 will be presented as talks, and published in the Proceedings of the PASC Conference, accessible via the ACM Digital Library. A selection of the highest quality papers may be given the opportunity of a plenary presentation. In selecting papers for plenary presentation, the Scientific Reviewing Committee will place particular weight on impact, interdisciplinarity and interest to a broad audience.  

Following the conference, authors will have the opportunity to further develop their PASC papers for publication in a relevant, computationally focused, domain-specific journal. Authors thus stand to benefit from the rapid and broad dissemination of results afforded by the conference venue and associated published proceedings, as well as the impact associated with publication in a high-quality scientific journal. 

Posters
Poster presentations provide an ideal opportunity for the exchange of ideas and expertise within and between the various computational science domains represented at the conference. Poster submissions should describe topical research related to domain science, applied mathematics, computer science or software engineering. Poster presenters will be given the possibility to “pitch” their posters to the conference audience in a rapid-fire flash session, and posters with the most stimulating content will be recognized in an award ceremony on the final day of the conference.  

Submission guidelines: pasc18.pasc-conference.org/submission/submissions-portal/

Papers, Minisymposia, and Posters Program Chairs
Sabine Roller (University of Siegen, Germany) 
Jack Wells (Oak Ridge National Laboratory, US) 

Two former eSSENCE PIs receive Big data grants from SSF

Congratulations to Sven Nelander and Carolina Wählby!

Sven Nelander and Carolina Wählby from Uppsala University receive 30 MSEK and 29 MSEK, respectively, from the Swedish Foundation for Strategic Research for projects in big data and scientific computing, see http://stratresearch.se/pressmeddelande/200-miljoner-till-big-data-och-berakningsvetenskap/ Both Sven and Carolina have been PIs in projects funded by eSSENCE, see http://essenceofescience.se/cancer-landscapes-an-interactive-global-map-of-regulation-in-human-cancer/ and http://essenceofescience.se/large-scale-analysis-of-live-cells/ In Carolina’s project, Ola Spjuth and Andreas Hellander will participate. Both Ola and Andreas have been supported by eSSENCE, see http://essenceofescience.se/predictive-modeling-in-drug-discovery/ and http://essenceofescience.se/development-of-escience-methods-for-drug-discovery/

 

New postdoc and researcher positions at Uppsala University

Six new postdoc and researcher positions are funded by eSSENCE in Uppsala in 2017-2018. The projects and the principal investigators are

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.

Free Internet Courses on Pharmaceutical Bioinformatics

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:

https://www.universityadmissions.se/intl/search?period=VT_2017&freeText=Pharmaceutical+bioinformatics&semesterPart=0

eSSENCE in the media – UNT 2016-09-07

eSSENCE in the media

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.

eSSENCE and SeRC researchers publish manuscript on “Recommendations on e-infrastructures for next-generation sequencing”

 

“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.
DOI: 10.1186/s13742-016-0132-7

URL: http://www.gigasciencejournal.com/content/5/1/26

Abstract
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.

Bo Kågström appointed SIAM Fellow 2016

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.”

http://www.teknat.umu.se/english/news//.cid266722

eSSENCE scientist Ola Spjuth publishes manuscript on cross-biobank data integration

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

Abstract

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

eSSENCE researchers publish article on workflows for automating data-intensive bioinformatics

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

ABSTRACT
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

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.

http://www.journals.elsevier.com/softwarex/