News

Snakemake Tutorial with Johannes Köster

FONDA has invited Professor Johannes Köster to give a tutorial on Snakemake, a widely used, python based workflow management system. Snakemake allows users to create scalable, human readable, reproducible workflows for scientific data analysis.

Professor Köster the leader of the Bioinformatics and Computational Oncology group at the Institute for AI in Medicine at the University of Duisburg-Essen, where his work focuses on reproducibility and bioinformatics workflows. He is the author and lead developer of Snakemake.

The full-day tutorial will be on July 02, 2025 starting at 9 am. Please contact Tobias Price if you are interested in attending.

NUMA, Portability, and AI: Three Bites of HPC

Guest Lecture by Ruben Laso

Date, time, and location:
Tuesday, July 1st, 11:15 am in the Humboldt-Kabinett (aka HUK, Rudower Chaussee 25, 1st floor)

Abstract:
In this presentation, we will cover three past and ongoing projects related to High-Performance Computing (HPC).

The first part will focus on NUMA (Non-Uniform Memory Access) systems, showing how process and memory placement can be improved to reduce execution times.

The second part will discuss the feasibility of using standard C++ for performance-portable HPC applications, showing how C++ can be used to write code that runs efficiently on different hardware architectures without sacrificing performance.

Finally, we will explore the optimisation of GPU-GPU communication to improve the performance of AI applications. As modern workloads often involve significant data movement, there is an opportunity to tune communication libraries for better performance.

Bio:
Ruben Laso is currently a postdoctoral researcher at the Research Group for Scientific Computing at the University of Vienna. He holds a PhD in High-Performance Computing (2023), a Master’s in Industrial Mathematics (2019), and a Bachelor’s in Computer Science (2017), all from the Universidade de Santiago de Compostela. His research interests include parallel computing, with a particular focus on manycore and NUMA systems, as well as performance portability in scientific codes.

Ruben will be visiting FONDA until mid-July.

Tutorial on Human-Computer Interaction with Thomas Weber

On June 12th from 10:00 -13:00 we will have a Tutorial on Human-Computer Interaction with Thomas Weber from LMU Munich. The event will be in the Humboldt-Kabinett. Everyone is invited to attend!

The abstract and bio Dr. Weber provided for the event can be found below.

Abstract:

Artificial Intelligence, especially Large Language Models, have proven
highly successful in many domains, including software development. New AI-powered tools not only increase the productivity of professional and novice software developers alike, they also enable completely new, highly flexible ways to interact with software. In this workshop, we will have a hands-on exploration of these capabilities and how they can enable and enhance rich and flexible interaction. However, integrating AI into interactive systems is not without challenges. Thus, we will also discuss how to design and evaluate AI-powered interactive systems to make sure they are both usable and useful.

Bio:

Thomas Weber is a post-doctoral research at LMU Munich. In his research, he investigates how AI-powered systems affect the lives and behavior of software developers from two perspectives: first, considering the rapid pace at which new and improved AI-powered tools emerge, how can developers use these tools productively to create high-quality software? However, software developers not only use AI but are also the ones building and shaping it. Thus secondly, how do requirements differ for building AI systems compared to traditional systems and how does this affect the behavior of developers.

To answer these questions, he combines methods from both software engineering research and human-computer interaction.

FONDA PhD Defense: Jonathan Bader on “Task Resource Prediction for Efficient Execution of Scientific Workflows”

Jonathan Bader defended his doctoral dissertation “Task Resource Prediction for Efficient Execution of Scientific Workflows” with distinction on June 4th, 2025. He is a member of the group “Distributed and Operating Systems” at TU Berlin, where he worked on FONDA subproject B1. His work focuses on predicting which tasks in a workflow are most resource intensive in order to dynamically adjust resource allocation and scheduling.

As part of this research, he introduced Lotaru and Sizey, two novel methods for predicting task run-time and memory requirements, respectively. Lotaru allows researchers to create a sensible baseline resource allocation profile for a workflow based on the task requirements and target infrastructure. Sizey continuously predicts the amount of memory each task requires and adjusts the memory allocation during runtime to minimize over-allocation while also preventing failures. Both outperform previous methods and improve the efficiency of workflow execution.

Congratulations Jonathan!

Data Aware Scheduling Method Now Available for Nextflow

With the latest release of the nf-cws Nextflow-Plugin, Fabian Lehmann and Friedrich Tschirpke introduce the WOW scheduling method as a production-ready feature. This release marks the transition of the WOW approach from a research prototype to a usable software component, fully integrated with the official Nextflow versions (v24.04.0 up to v25.02.3-edge).

Key Features:

  • WOW Scheduling for Nextflow: The Workflow-Aware data movement and task scheduling (WOW) method is now available as part of nf-cws. This enables dynamic coordination of data transfers and task execution, reducing network congestion and workflow runtime.
  • Seamless Integration: The nf-cws plugin can be used directly with Nextflow’s Kubernetes executor, requiring no experimental patches or custom setups.
  • Production Use: The improvements demonstrated in the original publication can now be leveraged by all Nextflow users in real-world scenarios.

-Fabian Lehmann

FONDA Integrated Research Training Group Courses

The Integrated Research Training Group (IRTG) has been very active in the past month providing courses and workshops for FONDA’s doctoral researchers. On April 28th and 29th Seqera, the company which supports the open source workflow engine “Nextflow” provided a tutorial using Nextflow to write and evaluate bioinformatics workflows. On May 7th, the IRTG members participated in a training course in Good Scientific Practice, especially geared towards computational sciences.

Future courses include a tutorial on GitLab with scientists from the German Aerospace Center on May 20th and 21st, a course on gender bias awareness on June 17, along with courses on workflow simulator WfCommons, and python-based workflow execution engine “Snakemake”.

FONDA Spring Retreat 2025

FONDA had its spring 2025 retreat on April 8th and 9th at the beautiful Schloss Lübbenau! All of the subprojects presented their progress so far, and our phase II Teams (T6-T9) had the chance to kick off their collaborations.

FONDA PhD student Martin Kuban successfully defends his dissertation on “Classification of materials based on similarity measures”

Martin Kuban defended his doctoral thesis on April 15, 2025. He is a member of the Theoretical Solid-State Physics group at Humboldt-Universität zu Berlin. His work focused on extracting comparable “fingerprints” for materials from heterogeneous data sources in order to identify compounds which may have similar properties. As part of this work, he developed MADAS, a python framework providing a modular and extendable interface for similarity calculations in material science.

His contributions to subproject A3 in FONDA include automating this technique as a workflow to calculate similarity between different instances of the same material in an open source repository, where its features have been calculated using different sets of parameters. This allows for the automated detection of parameters which produce reliable results, and identification of those which introduce artifacts.

His excellent work and presentation earned the grade summa cum laude – with highest honors. Congratulations Martin!

PI-Lecture Series Part 8

The final installment of FONDA’s PI-Lecture Series will take place on March 17th from 15:00-17:30 in Adlershof (Humboldt-Kabinett, Rudower Chaussee 25). The following PIs will give talks on their ongoing research:

  • Henning Meyerhenke – Workflow Scheduling and (Other) Graph Algorithms for Parallel & Distributed Systems
  • Thomas Kosch – TBA
  • Ulf Leser – Knowledge Management in Bioinformatics
  • Björn Scheuermann – Modern Web Transport Protocols (online)

We have had a lot of excellent talks over the last few months. The purpose of this lecture series was to introduce all of our new FONDA members to the research areas of the PIs. Based on the quality of questions and conversations, this has been very successful!

I’m looking forward to more conversations about science with everyone at our upcoming spring retreat.