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.

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

PRACE 10th Call for Proposals

PRACE 10th Call for Proposals for Project Access including Multi-year, and Programmatic Access is Open

Important dates:

  • Opening date: 10 September 2014
  • Closing date: 22 October 2014, 12:00 (noon) CEST
  • Response of applicants to reviews: 15– 21 January 2015
  • Anticipated allocation decisions: last week of February 2015
  • Allocation start date of awarded proposals: 10 March 2015
  • Allocation end date of award: 9 March 2016
  • Type of access: Project Access, Multi-Year Project Access, Programmatic
    Access

PRACE HPC systems available:

  • “Curie”, Bull Bullx cluster (GENCI@CEA, France)
  • “Fermi”, IBM Blue Gene/Q (CINECA, Italy)
  • “Hornet” – Cray XC30 (GCS@HLRS, Germany)
  • “MareNostrum”, IBM System X iDataplex (BSC, Spain)
  • “SuperMUC”, IBM System X iDataplex (GCS@LRZ, Germany)

The mission of PRACE is to enable high impact scientific discovery and engineering research and development across all disciplines to enhance European competitiveness for the benefit of society. PRACE seeks to realize this mission by offering world class computing and data management resources and services through a peer review process.

Scientists and researchers from around the world can apply for access to PRACE resources.

Industrial users can apply if they have their head offices or substantial R&D activity in Europe.

Project Access:

Proposals can be based on a 12-months schedule, or, for Multi-year Projects, on a 24- or 36-months schedule. The allocation of awarded resources is made for 1 year at a time with provisional allocations awarded for the 2nd and 3rd year.

Additionally, the Call:

  • includes a pilot test case for Programmatic Access for 12-months
    allocations schedule only.
  • reserves 0.5% of the total resources available for this call for Centres of Excellence (CoE) as selected by the EC under the E-INFRA-5-2015 call for proposals.

The PRACE Access Committee, composed of leading European scientists and engineers, ranks the project proposals that will be awarded access to PRACE resources.

For more information and application forms see:
http://www.prace-ri.eu/prace-project-access/

If you need some extra information please feel free to contact PRACE directly via peer-review@prace-ri.eu

or

The following people at SNIC centers:

  • PDC – Lilit Axner lilit@kth.se
  • NSC – Chandan Basu cbasu@nsc.liu.se, Soon-Heum “Jeff” Ko
    sko@nsc.liu.se
  • HPC2N – Mikael Rännar mr@cs.umu.se, Jerry Eriksson jerry@cs.umu.se

SeSE course Autumn 2014

Please see the attached call for participation in the SeSE courses this autumn.

The courses are free for PhD students (in Sweden) and it is possible to get a travel grant of 6000skr.

These courses are so far scheduled:

  • Introduction to high performance computing/PDC summer school, August
  • Matrix Computations in Statistics and with Applications, September, v39
  • Introduction to programming in science and technology, September
  • Computational Python, October, v42
  • Numerical Linear Algebra, October, v42
  • Scientific Visualisation, November 3-21
  • Scientific Software Development Toolbox, December
  • Topics in CFD, December 1-19

Kind regards
Anders Hast
Director of SeSE
ps. Please note that it is possible to register to get news about courses via our subscribe function: https://lists.uu.se/sympa/subscribe/sese

Call for participation: SeSECall2014A.pdf