News

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.

PI Lecture Series Part 6 (with guest!)

For our next set of Monday afternoon talks on March 3rd, Lars Grunske will give a talk on his research area “Understanding Software and DAW Input Spaces”, and we will have a guest lecture by Paul Ralph titled “Evidence Standards Improve Reliability in Scholarly Peer Review“. The talks will take place in the Humboldt-Kabinett of Johann-von-. Neumann-Haus, Rudower Chaussee 25, 12489, Berlin.

Abstract:

Background. Scholarly peer review is “the lynchpin about which the whole business of science is pivoted” (Ziman 1968). Most researchers believe peer review is effective (Ware 2008), but empirical research consistently shows that reviewers cannot reliable distinguish methodologically sound from fundamentally flawed studies (Cole 1981; Peters & Ceci 1982; Lock 1991; Rothwell and Martyn 2000; Price 2014; Ralph 2016). Consequently, we created comprehensive evidence standards and tools to improve peer review in software engineering and related fields. Objective. The objective of this study is to investigate the impact of evidence standards on scholarly peer review. Method. A randomized controlled experiment was conducted at an A-ranked software engineering conference. The program committee was randomly divided into two groups: one using a typical conference review process; the other using a standardized process based on the ACM SIGSOFT Empirical Standards for Software Engineering Research (https://acmsigsoft.github.io/EmpiricalStandards/) Results. Evidence standards significantly improve inter-reviewer reliability without harming authors’ or reviewers’ attitudes toward the review process. Reviewers using evidence standards gave more praise and focused more on research methods than style. Discussion. Asking reviewers to write free-text comments about a paper and score it on a 6-point scale from strong reject to strong accept produces data statistically indistinguishable from random noise. This means that decisions are determined entirely by reviewer selection, not the merits of the research. Conventional review processes are therefore scientifically and morally indefensible. While not a silver bullet, evidence standards significantly improve reliability, and the data collected in this study facilitates further refinement of the standards and tooling toward still greater reliability. 

Dr. D. Paul Ralph, PhD (British Columbia), B.Sc. / B.Comm (Memorial), is an award-winning scientist, author, consultant, and Professor of Software Engineering at Dalhousie University. His cutting-edge research at the intersection of software engineering, human-computer interaction, and project management explores the relationship between software teams’ social dynamics and success.

Photo of Paul Ralph in a blurry forest

PI Lecture Series Part 5

Our fifth set of PI-Lectures will be Monday Feb 24th starting at 15:00 in Adlershof – Rudower Chaussee 25, 12489 Berlin. We will meet in the Humboldt-Kabinett for talks regarding ongoing research by the following PIs:

  • Nicole Schweikardt – Logic in Computer Science
  • Matthias Weidlich – On Events and Processes
  • Claudia Draxl – From science to data and back
  • Knut Reinert – Hierarchical Interleaved Bloom Filter: Enabling ultrafast, approximate sequence queries

PI Lecture Series Part 4

Our fourth set of PI-Lectures will be Monday, February 17th starting at 15:00 in Humboldt-Universität zu Berlin’s main building, Unter den Linden 6. The following PIs will give talks about their ongoing research:

  • Anna-Lena Lamprecht – Workflomics
  • Florian Schintke – SIMD Vectorization of Positional Population Count
  • Dagmar Kainmueller – The Helmholtz Foundation Model Initiative

PI-Lecture Series Part 3

We had the third session of PI-Lectures on Monday, February 3rd. Tilmann Hickel presented on his work in computational materials science, “Workflows as an enabler for computational materials design”. This was followed by a tutorial on using the FONDA cluster by Vasilis Bountris, and the second part of Ulf Leser’s tutorial on workflow systems.

There will not be a lecture next week. We will meet again on February 17th at Unter den Linden 6 for our next set of talks.