Postdoc/PhD Positions, Parallel Computing, Extreme-Scale Systems, Umeå University

Department of Computing Science at Umea University, Sweden invites excellent candidates to apply for postdoctoral and PhD positions. The successful candidate(s) will join NLAFET, which is one of the high-profile extreme-scale computing projects funded by the European Commission within the recent FET-HPC call under Horizon 2020. NLAFET is coordinated by Umea University with international partners from INRIA (France), University of Manchester and STFC-RAL (UK).

Future extreme-scale supercomputers will be heterogeneous and lead to new and challenging demands for efficient numerical algorithms and parallel software libraries. The aim of NLAFET is to tackle these challenges and ultimately deliver new scalable numerical libraries for fundamental problems in numerical linear algebra, including the
solution of dense and sparse systems of equations and eigenvalue problems. Achieving this requires a co-design effort including developing novel algorithms, exploration of advanced scheduling strategies and runtime systems, offline and online autotuning, as well as avoiding communication and synchronization bottlenecks.

The positions will focus on design, implementation, and evaluation of parallel algorithms for matrix eigenvalue problems with regards to the extreme-scale challenges. The research will be done in close collaboration with recognized researchers and PhD students in the research group as well as with other partners in NLAFET.

For complete information of the positions see (dead-line for applications is August 17, 2015):
Postdoc-English:
https://umu.mynetworkglobal.com/en/what:job/jobID:69387/where:4/
PhD-English:
https://umu.mynetworkglobal.com/en/what:job/jobID:69520/where:4/

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/

UPPMAX publishes report on hadoop for NGS data analysis

Researchers affiliated with UPPMAX and financed by the Strategic Research Program eSSENCE published a report on the applicability of Hadoop for analyzing next-generation sequencing data.

Siretskiy A, Sundqvist T, Voznesenskiy M, Spjuth O.
A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data.
Gigascience. 2015 Jun 4; 4:26. doi: 10.1186/s13742-015-0058-5
http://www.gigasciencejournal.com/content/4/1/26
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Swedish e-Science Education graduate school (SeSE) courses: Autumn 2015

The Swedish e-Science Education graduate school (SeSE) now announces its graduate courses of autumn 2015.

The courses are listed at the SeSE website:

http://sese.nu/courses-autumn-2015/

SeSE gives basic training in fields where the use of e-Science is emerging and where such education can have an immense impact on the research as well as advanced training for students in fields that are already computer-intensive. The course curriculum is tailored to meet a broad set of prerequisites and will foster collaborations between Swedish researchers, possibly opening up for new research fields utilising e-Science tools and methods and also making it possible for inter- disciplinary collaborations on a Nordic level.

Swedish e-Science Education graduate school (SeSE) courses: spring 2015

The Swedish e-Science Education graduate school (SeSE) now announces its graduate courses of spring 2015.

The courses are listed at the SeSE website:

http://sese.nu/courses-spring-2015/

SeSE gives basic training in fields where the use of e-Science is emerging and where such education can have an immense impact on the research as well as advanced training for students in fields that are already computer-intensive. The course curriculum is tailored to meet a broad set of prerequisites and will foster collaborations between Swedish researchers, possibly opening up for new research fields utilising e-Science tools and methods and also making it possible for inter- disciplinary collaborations on a Nordic level.

Postdoc in structural bioinformatics of GPCRs – Development of GPCR-ModSim

Postdoc opening in structural bioinformatics of GPCRs
Development of GPCR-ModSim, http://gpcr-modsim.org

The platform GPCR-ModSim is one of the first and most complete web-based solutions for the modeling and simulation of GPCRs (see http://gpcr-modsim.org). The GPCR-ModSim project is now part of the Computational and Systems Biology program at the Cell and Molecular Biology department in Uppsala University, one of the most vibrant and dynamic Universities in Europe. Our research on G-protein coupled receptors (see
http://www.icm.uu.se/forskning/csb/aqvist/projekt/membrane-channels/ ) is currently funded by several private and public sources. In particular, the development of GPCR-ModSim is supported by a grant from the Carl Trygger Foundation (Stockholm), and we are looking for a talented postdoc to join this project in the spring 2015. If you have recently finished your PhD (or you are about to in the very next future) in bioinformatics, computer science, computational chemistry or similar disciplines, you are encouraged to send us an application for this position. Simply send a CV and a motivation letter by e-mail to hugo.gutierrez@icm.uu.se.

You should:

  • Have experience in computer simulations and/or protein modeling and/or bioinformatics
  • Have programming skills in Python and be familiar with Unix systems,
    web servers and databases.
  • Be interested in the development and implementation of novel computational methodologies within structural biology and ligand design.
  • Have demonstrated capacity of collaboration and ability for multidisciplinary
    communication.

We offer:

  • A one year, tax-free fixed postdoctoral position, with possibilities to extend our funding.
  • An extensive network of collaborations. We are part of the EU-COST action GLISTEN, which agglutinates the major GPCR research labs and industries in Europe, and maintain several collaborations with top medicinal chemists, structural biologists and pharmacologists in the field (see http://gpcr-modsim.org/publications).
  • A vibrant international environment in one of Europe’s top universities.

Applications or further inquiries are welcome until 31st January to the project leader:

Hugo Gutierrez de Teran, PhD.
Dept. of Cell and Molecular Biology
Uppsala University (SWEDEN)
Phone: +46(0)18 471 5056
e-mail: hugo.gutierrez@icm.uu.se
http://gpcr.usc.es

2015 IEEE 11th International Conference on e-Science

Do you want to be an eSSENCE ambassador for Swedish e-Science?
The eSSENCE programme council encourages researchers in the eSSENCE community to submit papers to this international multidisciplinary e-Science conference. Persons whose papers are accepted will be eligible for funding, provided that eSSENCE is acknowledged (see http://essenceofescience.se/publications/). Funding includes:
* conference fee
* travel
* accommodation

Call for papers
Submission deadlines: March 8, 2015 for abstracts and March 15, 2015 for papers
11th IEEE International Conference on e-Science
31 August – 4 September, 2015
Munich, Germany

To the conference website

——————–
The IEEE international e-Science conference series is a yearly event that takes place in different cities around the world.

IEEE-2011 IEEE-2011 in Stockholm
IEEE-2012 IEEE-2012 in Chicago
IEEE-2013 IEEE-2013 in Beijing
IEEE-2014 IEEE-2014 in Sao Paulo
IEEE-2015IEEE-2015 in Munich

Swedish Theoretical Chemistry Meeting, Uppsala, 27-29 Oct 2014

We invite you to participate in the following conference:

Swedish Theoretical Chemistry Meeting 2014 – New Horizons
at the Ångström Laboratory, Uppsala University, Sweden
27–29 October 2014 (lunch to lunch)

Room: Häggsalen at the Ångström Lab, Uppsala University
Website: https://sites.google.com/site/stkmuu14
Deadline for abstracts and registration: 26 September 2014
Among the invited speakers are:

  • Prof. Roberto Car (Princeton U, USA)
    “Water, ice, dynamics and hybrids”
  • Prof. Martin Head-Gordon (UC Berkeley, USA)
    “The next generation of electronic structure theories”
  • Prof. Sally Price (UCL, UK)
    “Crystal-polymorphs prediction for pharmaceutical development – a challenge for force-field development and our understanding of crystallization”
  • Prof. Joost VandeVondele (ETH Zurich, CH)
    “Exploring the frontiers in sampling, large-scale models, and electroncorrelation using petascale computing and CP2K.”
  • Dr. Horst Weiss (BASF, DE)
    “Driving innovation for materials in the chemical industry – modelling needs and opportunities”

For this meeting we define theoretical chemistry in a broad sense, encompassing theory and computation from all fields of chemistry and its interfaces with physics, biology, materials science, and so on. The meeting is subtitled “New Horizons”, and the presentations will discuss new methods and directions, from fundamental concepts of bonding to calculations for industrial applications.

We welcome your participation and your oral or poster contributions!

/Kersti Hermansson and co-organisers