Annual eSSENCE multiscale modelling meeting went digital in 2020

Facts and  numbers

The meeting had 599 registered participants from 51 countries. Over 210 academic institutions were represented as well as 78 companies worldwide ranging from large international ones like Johnson Matthey, Dassault Systemes BIOVIA, AstraZeneca, Northvolt AB, Sandvik, BASF SE, Solvay SA, Ansys Granta, Unilever, etc. , to smaller ones such as Thermo-Calc Software AB, OrionX.net, Evonik Industries AG and Materials Design S.A.R.L.  At any point in time during the meeting high attendance was noted (50-60% of registered participants during the first half of the meeting and the attendence continued to be high throughout the meeting). This was the first virtual version of the eSSENCE multiscale modelling meeting (but not the last). In the midst of the spring the meeting was changed to an online meeting, entailing a pile of extra challenges.

Below, the main conference organizers, Professor Kersti Hermansson and Docent Peter Broqvist in the Structural Chemistry Program at Uppsala University, share what kind of decisions and preparations were needed to make the virtual conference happen.

“For good and for bad, we had to re-think most of the normal conference concepts”, they say. “Like what components are necessary, what is not necessary, how does one create a social ambiance in the webinar form, and so on.  All this needed to be planned as we were 2 months into the pandemic and 6 weeks before the meeting!”.

From a conventional conference to a modern webinar

“First of all, we had to decide whether to postpone, skip or pursue the event. After some deliberation we opted for the latter, checked the willingness of the speakers to switch to webinar mode, sent out a new set of announcements to all the forums already contacted, and – most of all –we needed to teach ourselves all the technical bits and pieces needed to run a smooth online meeting, and the functional website to go with it. This was a new and challenging experience to the members of our research group.”

“Overall, our philosophy was to make the on-line conference as similar as possible to an in-real-life meeting. That is, we wanted to include all the same scientific ingredients as in a usual conference: keynote presentations of international and national experts, invited talks, poster session with break-out rooms, panel discussion, + some sparse participants on site to create a meeting atmosphere and where the Zoom presentations could also be followed on big screens”.

Scientific program and a European perspective

The overall focus of the eSSENCE multiscale meeting is methods & model development in connection with multi-scale modelling and the meeting had “Physics-based vs data-driven” as an explicit sub-theme. This theme continues to be of prime interest to the modelling community and here we strive for a balanced mix of the physics-based and data-driven strands of multi-scale modelling. The meeting website is reachable at https://sites.google.com/site/emultiscale2020.

Two large new European programmes were also highlighted in the programme. Thus the computational aspects of the large-scale research initiative Battery 2030+ (launched 2020) was the topic of the first key-note lecture, given by Professor Tejs Vegge (Technical U of Denmark). The new European Materials Modelling Council (launched 2019) was highlighted in the invited talk by Dr. Gerhard Goldbeck (executive secretary, Brussels).

“At the same time, and at least as important”, says Kersti, “is the fact that the national attendance was great. The Swedish participation came from eSSENCE, from SeRC (SU, KTH, LiU), from the e-science communities at CTH and GU, as well as from Högskolan in Gävle, Malmö Högskola, Örebro University and the Technical University of Luleå. And as usual eSSENCE@Lund was greatly supportive in the planning, and also took an active part in the implementation.”

Outlook, 2021

An on-line survey was sent out after the meeting. Fig 2 displays the answer distributions for the question “The scientific quality of the event was….” (5 was best). Another question was: “How likely are you to attend our event next year if it were to be held via Zoom?” where 67% gave 5. The question “How likely are you to come to Uppsala in person to attend our event next year?” also gave a high score: 55% gave 5 or 4. For the question “Given both options, which do you prefer?” 52% answered: “in person attendance.”

With the notable success of the conference, the organizers will keep the digital format for 2021, possibly together with in-person attendance. The hybrid approach would allow to combine the best of both forms and provide strong visibility of eSSENCE. Stay tuned for more information

Rapporteur:  Fil lic Ageo Meier de Andrade

(Strucural chemistry, Uppsala University)

Call for graduate course in Machine Learning or/and Artificial Intelligence

Call for graduate course in Machine Learning or/and Artificial Intelligence

SeSE is a Swedish initiative for PhD level education in the field of e-Science. SeSE was founded and is supported by the Swedish e-Science Research Centre (SeRC) and the Swedish e-Science Collaboration (eSSENCE). SeSE offers education in the form of academic courses for PhD students in fields where the use of e-Science is emerging and also e-Science education for students in fields which are already computing-intensive.

The graduate school has identified large interest in the area of Artificial Intelligence and Machine Learning and is calling for developing, or offering an already existing, advanced level course in format of the school in the Autumn term of 2019 or in the following year of 2020.  

Course format

  • The course material should correspond, but is not strictly limited, to an equivalent of 3 hp (högskolepoäng) at University PhD level.
  • Typical format of a course at the graduate school consists of
    • one week of preparatory work e.g., literature studies, carried out at the university where the student is enrolled (home university)
    • one week on campus with lectures and exercises (where the course is offered)
    • one week of work after the course is completed, typically project work and examination

For more details on the activities organized by the graduate school, mission and organization, please visit the SeSE web page at http://sese.nu/

You expression of interest application should contain a brief overview of the course topics, target audience, name and affiliation of the teacher(s) and a 2-page CV of the course responsible teacher.

You can submit your express your interest by emailing the SeSE coordination team before 30.09.2019. Please contact us if you need more information.

Contact information:

Pavlin Mitev, Director and administration
e-mail: pmitev@kemi.uu.se

Arvind Kumar, Vice director and coordinator
e-mail: arvkumar@kth.se

SeSE-course-call-ML_AI.pdf

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


– with “Physics-based and data-driven modelling” as a cross-cutting theme.
 
Website:  https://sites.google.com/site/emultiscale2019/home 
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
 
Kemi-Ångström

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.