The Swedish e-Science Academy is organised by eSSENCE and is open to anyone interested in e-Science. It is a lunch-to-lunch meeting and this year it will be at Elite Hotel Ideon in Lund (Room Tera).

The Swedish e-Science Academy represents a great opportunity to meet fellow e-scientists to discuss common issues and get inspired.

Meals and accommodation for the night between 16-17 October will be provided.

Just like last year, there will also be satellite meetings.

Preliminary Programme

Wednesday 16 October

12:00   Starting Lunch

13:15   Welcome: Stefan Engblom, Uppsala University

13:30   Keynote 1: "LINXS for the Exploitation of X-Ray & Neutrons in Hard Matter, Soft Matter, and Life Sciences – Opportunities for e-Science", Trevor Forsyth, Lund University / LINXS

14:10   "Developing Data-Driven Simulation of Protein Structural Dynamics", Magnus Andersson, Umeå University

14:30   "POLLENOMICS: Decoding the Farming History of Europe Using Advanced Statistics to Combine Ancient DNA with Paleo-Pollen Data", Behnaz Pirzamanbein, Lund University

14:50   Coffee/tea break

15:20   "Machine Learning for Physics-Based Force Fields", David van der Spoel, Uppsala University

15:40   Poster Blitz (45 seconds per poster, 1 slide)

16:20-18:00 Poster Session with Drinks and Snacks

19:00   Dinner and Discussions

Thursday 17 October

09:00   Keynote 2: "The Automation of Science", Ross King, Chalmers University of Technology

09:40   "Solving Ill Posed and Inverse Problems in Numerical PDE", Karl Larsson, Umeå University

10:00   Coffee/tea break

10:30   "Magnetic Materials Modelling", Erik van Loon, Lund University

10:50   "Artificial Intelligence for Experiment Design", Maria Andreina Francisco Rodriguez, Uppsala University

11:10   Panel Discussion: "What is the impact of e-Science?", Kersti Hermansson (UU), Ross King (Chalmers), Per Runesson (LU), Oxana Smirnova (LU), Kalle Åström (LU)

11:50   Closing Remarks: Stefan Engblom, Uppsala University

12:00-13:00     Lunch

Accommodation

There are prebooked rooms at Elite Hotel Ideon in Lund for the night between 16 and 17 October. To claim a room, just say "yes" to "I want accommodation ..." in the registration form, but since rooms are limited, register for the Swedish e-Science Academy as soon as possible to avoid missing out.

Registration

Registration is closed.

Poster format

Poster format is portrait A0 (width: 841 mm x height: 1189 mm).

Satellite Meetings

Interactive access and visualisation in HPC environments

Time: Tuesday 15 October, 13.00-17.00

Venue: Elite Hotel Ideon, Room Giga

Abstract

The need and ability to access HPC resources in new ways have increased in the recent years. Sizes of analysed data have increased significantly, making it more problematic to move data home for visualisation and analysis. Visualising data sets can also require special resources that are expensive and complicated to achieve with workstation hardware. Also, a remote desktop environment can provide tailored user interfaces for workflows, making it easier for new HPC users to take advantage of the resources. Another important interactive environment is the Jupyter Notebook. Providing a notebook environment that has access to data close to the HPC resources can be a very valuable tool in data analysis of data produced in simulation. It can also be an effective way of sharing analysis results within research groups.

By providing interactive and remote access to HPC environments, we can offer researchers a more efficient HPC environment that can be more productive.

Programme

13:00   "Introduction / LUNARC HPC Desktop and the GfxLauncher Framework", Jonas Lindemann, LUNARC, Lund University

• Since 2013 LUNARC has been working on providing interactive access to our computing resources. During the last years we have deployed our own solution based on GfxLauncher with Thinlinc as the transport layer. We currently have over 100 unique users and several thousands fo interactive applications running through SLURM. This talk will provide a description of the architecture and typical use of the interactive HPC and visualisation on the LUNARC resources.

13:15   "ThinLinc: Enabling Interactive Research Workflows in HPC Environments", Jean Zagonel / Pierre Ossman, Cendio

• The evolving landscape of High-Performance Computing (HPC) necessitates solutions that facilitate user-friendly and efficient access to resources for researchers. ThinLinc, a high-performance remote desktop solution developed by Cendio, addresses this need by providing a seamless and familiar desktop experience specifically tailored for HPC. Deployed by institutions including Indiana University, Purdue University, Lund University, and the Technical University of Denmark, ThinLinc enables researchers to interact with HPC systems through a persistent Linux desktop, accessible from various devices. This approach streamlines data management, job submission, and the use of interactive applications within HPC workflows. By offering a centralized platform that integrates with existing HPC infrastructure, ThinLinc empowers researchers of all experience levels to leverage the full potential of HPC for scientific exploration. This presentation will showcase ThinLinc's capabilities in addressing the demand for interactive HPC access and discuss its role in facilitating cutting-edge research.

13:30   "Plans for interactive HPC at HPC2N", Björn Torkelsson / Åke Sandgren, HPC2N, Umeå University

13:45   "The Evolution of Interactive Accesses and Services at UPPMAX", Jayant Yadav, UPPMAX, Uppsala University

• This talk covers the current and future state of interactive access and visualization at UPPMAX. We will discuss various graphical tools and applications on different platforms, including ThinLinc and X-forwarding. Key topics include accessing tools like Rstudio, Matlab, and Jupyter notebooks, and building custom applications in collaboration with other departments. We will also discuss about future of visualizing data via disposable sessions for broader university services, highlighting the future of interactive services at UPPMAX and nationwide.

14:00 "OpenOndemand at Alvis", Mikael Öhman, C3SE, Chalmers University of Technology

• Live demonstration of the OpenOndemand setup for Alvis.
  After authenticating via SUPR users on Alvis and Vera can use the OpenOndemand portal and with a few simple clicks run interactive web applications on compute nodes; Jupyter, MATLAB proxy, RStudio, VSCode, CARTA, TensorBoard.
  In addition users can also start interactive desktop sessions on compute and login nodes, where they can run all linux desktop applications, including 3D accelerated graphics when using a GPU node.

14:15 "Interactive HPC in a NAISS Context", Gert Svensson, NAISS

14:30   Coffee/tea break

14:45 "UCloud: Empowering Researchers with Seamless HPC Access", Claudio Pica, uCloud, University of Southern Denmark

• UCloud is an advanced, open-source platform designed to deliver a comprehensive, on-premise cloud solution for academic institutions. By providing secure, scalable, and user-friendly access to Denmark’s national HPC infrastructure, UCloud enables researchers to tap into powerful computing resources across multiple data centers with ease. Currently supporting over 11,000 users, UCloud caters to both novice and expert users with its intuitive web-based interface, simplifying the execution of interactive applications, management of research environments, and secure collaboration. This presentation will showcase UCloud's key features, its impact on advancing research across disciplines, and its future plans.

15:00 "Illuminating Ancient Social Dynamics: Using I-HPC for Lighting Simulations in a Reconstructed Roman House", Danilo Campanaro, Archeology, Lund University

• This research explores the intersection of archaeology, social theory, and technology through the application of Interactive High-Performance Computing (I-HPC) to lighting simulations in a reconstructed house in Pompeii. By simulating historical lighting conditions, the project investigates the role of light in shaping social interactions, status, and the use of space within Roman domestic architecture. I-HPC enabled the processing of complex models and real-time interaction with simulation parameters, providing new insights into how light influenced daily activities and social dynamics. This approach demonstrates the potential of I-HPC in archaeological studies, offering a novel methodology for modelling and investigating lived experiences in ancient environments.

15:15 "Image Analysis: From Interactive Setup to HPC Bulk Processing", Erika Tudisco, Structural Mechanics / Geomechanics, Lund University

• Image analysis often requires interactive work to prepare images and fine-tune parameters for further analysis. At the same time, it involves computationally intensive tasks, especially when working with large datasets. Therefore, it is crucial to have a tool that supports interactive testing of custom code and/or graphical interface-based software, while also enabling large-scale analysis on high-performance computing (HPC) systems such as supercomputers or multi-core systems.
  In this work, I used ImageJ and Ilastik (an AI-based software) for image preparation. The analysis was performed using an in-house Python code. I developed and tested the Python scripts in Visual Studio Code, refining parameters for each image set. After optimizing the analysis on a small subset of images, I ran the code on the full dataset (around 3,000 images) using SLURM job scheduling on an HPC system.

15:30 Discussions

16:15 Closing

Registration

Registration is closed.

Computational social science: linking social theory and big data

Time: Wednesday 16 October, 08.30-12.00

Venue: Elite Hotel Ideon, Room Giga

Abstract

The social sciences have a long and strong history of developing theory for understanding social phenomena and dynamics. In contrast to for example economics, the social sciences have strived to understand the immense complexity of society at scales from the individual to the globe, and more recently also how the social dynamics at various scales interact with nature, e.g. in terms of climate change. Profound theoretical understanding has taken priority over empirically based evidence. The prominent sociologist, Michael Mann, famously described society as a patterned mess, and that “societies are much messier than our theories of them” (Mann 1986: The sources of Social Power, Vol. 1, p.4). Recent advances in the access to and compilation of large datasets on a wide range of social phenomena, combined with the progress of AI-based tools for analysis, have opened new opportunities for linking social theory and empirical data (that may reduce Michael Mann’s messiness) and pave the way for a new social science that can better both tell and show how social phenomena and processes matter. 

Preliminary programme

08:30 – 08:50 "Introducing the new LU Social Science Methods Centre (SSMC)", Åsa Lundqvist, Department of Sociology and SSMC, Lund University

08:50 – 09:30 "Computational social science – potentials and perils", Robert Klemmensen, Department of Political Science and SSMC, Lund University

09:30 – 10:00 "Computational social science – perspectives from mathematics", Alexandros Sopasakis, Centre for Mathematical Sciences, Lund University

10:00 – 10:20 Coffee/tea break

10:20 – 10:35 "Deliberation in the Age of Deception: Measuring Sycophancy in Large Language Models", Minahil Malik, SSMC, Lund University

10:35 – 10:50 "Populist political communication on Instagram: a comparison between Matteo Salvini and Carlo Calenda. An investigation of political communication using topic modeling, sentiment analysis and object detection.", Maria Luchetta, SSMC, Lund University

10:50 – 11:05 "Linking social theory and data for understanding the agrochemical industrial complex", Lennart Olsson, LUCSUS, Lund University

11:05 – 11:20 "Studying political polarization in the Swedish Riksdag using computerized text analysis techniques", Hanna Bäck, Department of Political Science, Lund University

11.20 - 11.35 "Using computational methods for exploring how women’s right to vote influenced perceptions of womanhood", Mia Liinason (LU), Haim Dubossarsky (Queen Mary University of London), and Pierluigi Cassotti (GU)

11:35 – 11:55: Discussion on future potentials and directions of CSS led by Hanna Bäck, Robert Klemmensen, and Lennart Olsson

11:55 – 12:00: Closing remarks and way forward for CSS at LU, Robert Klemmensen and Åsa Lundqvist

Registration

Registration is closed.

Common challenges in large-scale code development

Time: Thursday 17 October, 13.00-17.00

Venue: Elite Hotel Ideon, Room Giga

Abstract

The development and maintenance of large-scale codes in the field of natural science is challenging. Many codes have grown ‘organically’ within scientific communities, relying on self-made programming knowledge. The satellite meeting aims to address the challenges associated with development and maintenance of large scale codes in natural science by bringing together code maintainers, software developers and researchers from Swedish universities. The goal of the meeting is to create a network of code developers to share the experiences in development and maintenance, and transfer the knowledge to the next generation.

The topics include

• Management of medium/large-sized software project
• Setting up a Continuous Integration pipeline
• Strategies for automatic testing
• Support for the software development
• Funding opportunities
• Toolboxes (code analysis, benchmarks, etc.)

Programme outline

The half-day workshop will begin with short presentations from established codes/projects and software engineers, followed by a panel discussion.

Registration

Registration is closed.

Scientific visualisations – from machine learning to XR

Time: Thursday 17 October, 13.00-16.00

Venue: Elite Hotel Ideon, Room Mega

Abstract

InfraVis is a Swedish national infrastructure that provides advanced visualisation services on research data from any scientific domain. Effective as of 2022, InfraVis aims at supporting Swedish scientific advancement and is funded by the Swedish Research Council.

Lund University is one of the nine Swedish universities forming the InfraVis constellation that with Chalmers as lead partner got national infrastructure funding from the Swedish Research Council. The Infravis@LU Team draws upon the breadth of knowledge at LU, with key elements being located in four faculties and is coordinated by the LU Research Infrastructure ‘Correlative Image Processing and Analysis’ (CIPA).

This event is open to anyone who is potentially interested in using InfraVis.

Preliminary programme

13.00 - 13.15 Welcome and introduction to InfraVis labs and experts, Emanuel Larsson, Lund University

Expert presentations

13.15 - 13.45 "Machine Learning-based segmentation", Alexandros Sopasakis, Lund University

13.45 - 14.05 "Creating visualizations using Python", Jonas Lindemann, Lund University

14.05 - 14.25 "Scientific Visualizations in VR", Jonas Ahlstedt, Lund University

14.25 - 14.55 Coffee/tea break

User Presentations

14.55 - 15.10 "Machine learning-based segmentation of microfossils scanned with Synchrotron X-ray microtomography", Helena Filipsson, Lund University

15.10 - 15.25 TBA

15.25 - 15.40 "Visualization of vegetation demographic processes within a Dynamic Global Vegetation Model", David Wårlind, Lund University

15.30 - 16.00 Open Discussion and Summary

Registration

Registration is closed.