eSSENCE Multiscale Modelling Meeting, 3-5 June 2019 in Uppsala

– with “Physics-based and data-driven modelling” as a cross-cutting theme.
Venue:   The Ångström Laboratory of Uppsala University
Time:     3-5 June 2019, lunch-to-lunch
Multiscale modelling (coupling & linking of models) is a central theme in molecular and materials modelling of complex systems, and it is also a central theme of this meeting. Furthermore, this is the 2nd international EMMC-eSSENCE meeting with the sub-theme of physics-based & data-driven modelling.  How can physics-based insight and data-driven analysis  best work together (or at least how can they complement each other)? Will the reliability, accuracy and validity of our modelling results improve when data-driven approaches are mixed in with physics-based simulation techniques?
Registration is open! The deadline for registration and abstracts submission is 15th of May 2019.  Abstracts on the general theme of multiscale modelling (we use the term in a broad sense) and on the data-driven &. physics-based models theme are equally welcomeIt is of course also perfectly fine to participate without a presentation – there will be many opportunities to participate in discussions. The meeting is free of charge.
Very welcome to come and participate and discuss new trends in modelling!
Kersti Hermansson, Peter Broqvist

Researcher Position in Scientific Computing/Systems Biology

Uppsala University is an international research university focused on the development of science and education. Our most important assets are all the individuals who with their curiosity and their dedication make Uppsala University one of Sweden’s most exciting work places. Uppsala University has 40,000 students, 7,000 employees and a turnover of SEK 6,5 billion.

The Department of Information Technology conducts research and education in a spectrum of areas within Computer Science and Information Technology. The research is organized in five Divisions, and the research at the Division of Scientific Computing has a broad scope, ranging from numerical analysis over software development and high-performance computing to collaborative projects in Computational Science and Engineering and industrial applications.

The researcher will work in an research project funded by eSSENCE, a strategic collaborative research programme in e-science between three Swedish universities with a strong tradition of excellent e-science research: Uppsala University, Lund University and Umeå University. e-science promotes innovation in collaborative, computationally or data intensive research across all disciplines. In Uppsala, a number of projects are supported by the programme. Most of them are in computer simulation and data science in biology, chemistry, and physics. More information about eSSENCE is found at the homepage

The project, described below, will be conducted as part of a collaboration between the the research groups headed by associate professor Andreas Hellander, Uppsala University, see, and associate professor Igor Adameyko, Karolinska Institute, see

Read more… 

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

Postdoc opening in structural bioinformatics of GPCRs
Development of GPCR-ModSim,

The platform GPCR-ModSim is one of the first and most complete web-based solutions for the modeling and simulation of GPCRs (see 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 ) 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

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

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
  • 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

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
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

Multiscale materials modelling – 2014

The 2014 eSSENCE meeting on “Multiscale materials modelling”
at the Ångström Laboratory, 2-4 June 2014

You are very welcome to participate and contribute! Register until May 15 on the web! Book hotel room(s) before May 5 (if you want to make use of our pre-booked rooms).

PROGRAM: We use the word “materials” in a broad sense, i.e. including molecules, liquids and interfaces. Day 1 will start at 13.00 and end with a poster session, drinks and a buffet dinner (free of charge). Part of Day 2 will be focused around Quality issues like “Where are the bottlenecks?” “Does industry trust the result of modelling – and should
they?” “How can we improve the predictability of our results?” The meeting ends around 12.00 on Day 3.

There will be a number international and national invited speakers. There will also be contributed talks and poster presentations.

More info at:


UPPMAX 10 years on November 21


UPPMAX celebrates its 10th anniversary with a symposium and inauguration of UPPNEX new compute cluster Milou and storage system Pica.

Date: November 21, 2013
Time: 13-16
Place: Häggsalen, Ångström Laboratory.
UPPMAX (Uppsala Multidisciplinary Center for Advanced Computational Science) is Uppsala University’s resource of high-performance computers, large-scale storage and know-how of high-performance computing (HPC).

UPPMAX  is one of the six centra in the national metacenter Swedish National Infrastructure for Computing (SNIC)

Formal Program
13.00 Welcome, Hans Karlsson, Director UPPMAX
13.02 Presentation by the vendors: HP/GoVirtual (Milou) and Hitachi/SouthPole (Pica)
13.15 UPPMAX 10 years in 9 minutes, Hans Karlsson, Director UPPMAX
13.24 UPPMAX from the perspective of SNIC, Jacko Koster, Director SNIC
13.33 UPPMAX from the perspective of SciLifeLab, Karin Forsberg Nilsson, Scientific director SciLifeLab
13.42 UPPMAX and Next Generation Sequencing, Ola Spjuth, UPPNEX
13.51 UPPMAX and Uppsala University, Eva Åkesson, Vice Chancellor, Uppsala University

Inauguration of Milou and Pica

Coffee and cake

Scientific Program
14.30 Siv Andersson: A drop in the oceans: Single cell- and meta-genomic analyses of aquatic ecosystems
14.50 Kim Bolton: Piezoelectric and barrier properties of polymer composite systems
15.10 Lynn Kamerlin: Computational Protein Evolution: Progress and Pitfalls
15.30 Jörg Tiedemann: Data-driven Natural Language Processing
15.50 David van der Spoel: Concluding remarks


Associate Senior Lecturer in High Energy Physics

at the Department of Physics and Astronomy.
Application no later than 2013-05-15. UFV-PA 2013/349

Duties: The position includes teaching, research and administration. Teaching duties include course responsibility, course administration and supervision of post graduate students.The holder shall also keep abreast of developments within the subject area and the developments in wider community that are significant for the work at the university. A position as associate senior lecturer aims to qualify for a teaching position with higher assessment criteria.

The research relates to participation in the ATLAS experiment at CERN’s Large Hadron Collider (LHC) with data analysis to search for new physics beyond the standard model, including charged Higgs bosons. The work also includes the operation of the ATLAS experiment  and development of e-Science for simulation and analysis. Continue reading

Postdoc position in computer science or bioinformatics with focus on Hadoop for large scale sequence analysis

at the Department of Information Technology
Application no later than 2012-10-15. UFV-PA 2012/2414

Background: The emerge of high-throughput technologies such as next-generation sequencing has turned life science into a data-intensive domain, which places high demands on an e-infrastructure in order to be analysed. UPPMAX ( is UppsalaUniversity’s center for high performance storage and computations that via the project UPPNEX ( offers resources for storage, computations, software and user support in bioinformatics and primarily sequence analysis. We are now seeking a Postdoc to evaluate how technologies like cloud computing and Hadoop can complement the current infrastructure and offer improved services in storage and analysis of bioscience data. Continue reading


The bioinformatics community is adopting novel cloud computing technologies to cope with the challenges set forth by complex data integration tasks and NGS data masses. The hackathon will focus on next challenges that cloud adoption poses: massively distributed data processing frameworks such as Hadoop, distributed cloud databases and distributed bioinformatics applications.

The event will continue from topics raised during the previous hackathon in March in Finland where we familiarised ourselves with the relevant questions of Hadoop based data processing and proceeded to benchmark different deployment scenarios, some bioinformatics tools and generic cloud computing tools.

The next steps are: proceeding into bioinformatics specific computational challenges (mapping, variant calling, etc.) and discussing the mechanisms that allow easy deployment of new tools into a cloud platform (CloudBioLinux, VM images, Chef, etc.).

The event is aimed at bioinformaticians and software developers who are using or planning to use Hadoop or similar cloud computing frameworks. It will be organised around practical problem solving and group work.
The event is organized by the EU COST Action SeqAhead (, and kindly sponsored by UPPMAX ( and eSSENCE (
Organisers: Ola Spjuth, Aleksi Kallio, Eija Korpelainen.

Uppsala: Registration to CSC2012 – This summer in Uppsala

The 35th CERN School of Computing will be held at the Uppsala University, Sweden
from Monday 13th of August to Friday 24th August 2012

Programme highlights
The CERN School of Computing 2011 is organised around 3 thematic themes, each theme comprising lectures and exercises.

  • Do you know how to bridge Grids and Clouds using virtualization technology?
  • Is it possible to simplify LHC physics analysis using virtual machine?
  • How can reliable storage services be built from unreliable hardware?
  • Why are tapes still used in high energy physics data storage?
  • How can I write code for tomorrow’s hardware, today?
  • Do you want to see your software with attacker’s eyes?
  • Can you hack your own code?
  • Do you know what do ‘code injection’ and ‘integer overflow’ have in common?
  • What’s so special about High Energy Physic’s data format?
  • What are the key statistical methods used in physics data analysis?

All the answers at CSC2012 Continue reading