Fabian Lehmann

Fabian Lehmann

Ph.D. candidate

Humboldt University of Berlin

Biography

I am Fabian Lehmann, a Ph.D. candidate in computer science at the Knowledge Management in Bioinformatics Lab at the Humboldt University of Berlin. I get my funding through FONDA, a collaborative research center of the German Research Foundation (DFG).

Since my bachelor studies, I have been fascinated by any complex, distributed system. I love to understand and overcome their limits. In my Ph.D. research, I focus on workflow engines, improving the execution of distributed workflows while analyzing large amounts of data. In particular, my goal is to improve scheduling and data management. Therefore, I work closely with the Earth Observation Lab at the Humboldt University of Berlin to understand real-world requirements.

Interests
  • Distributed Systems
  • Scientific Workflows
  • Workflow Scheduling
Education
  • Master of Science in Information Systems Management, 2020

    Thesis: Design and Implementation of a Processing Pipeline for High Resolution Blood Pressure Sensor Data

    Technical University of Berlin

  • Bachelor of Science in Information Systems Management, 2019

    Thesis: Performance-Benchmarking in Continuous-Integration-Processes

    Technical University of Berlin

  • Abitur (comparable to A Levels), 2015

    Hannah-Arendt-Gymnasium (Berlin)

Professional Experience

 
 
 
 
 
Knowledge Management in Bioinformatics Lab (Humboldt University of Berlin)
Ph.D. candidate (computer science)
Nov 2020 – Present Berlin, Germany
In my Ph.D. studies, I focus on improving the execution of large scientific workflows processing hundreds of gigabytes of data.
 
 
 
 
 
DAI-Labor (Technical University of Berlin)
Student Assistent
May 2018 – Oct 2020 Berlin, Germany
In my student job, we were working with time-series data in DIGINET-PS. For example, we predicted parking slot occupation.
 
 
 
 
 
University of Oxford
GeoTripNet - Case Study
Oct 2019 – Mar 2020 Oxford, England, United Kingdom
For the case study, we crawled restaurants' reviews on Google Maps to analyze the relations between different restaurants and examine gentrification in Berlin districts. One problem was to process and analyze the large amount of data in real-time.
 
 
 
 
 
Einstein Center Digital Future
Fog Computing Project
Apr 2019 – Sep 2020 Berlin, Germany
This project aimed to analyze SimRa’s bicycle rides. Therefore, we developed a distributed analysis pipeline. Moreover, we visualized the track information on an interactive web. We were able to classify risk hotspots for Berlin’s cyclists' tracks.
 
 
 
 
 
Conrad Connect
Application Systems Project
Oct 2017 – Mar 2018 Berlin, Germany
For Conrad Connect, we analyzed hundreds of gigabytes of IoT data. Moreover, I uncovered security vulnerabilities in their software.
 
 
 
 
 
Reflect IT Solutions GmbH
Semester Term Work
Mar 2016 – Apr 2016 & Sep 2016 – Oct 2016 Berlin, Germany
In my semester term work, I helped to develop the backend for a construction-progress-management system.
 
 
 
 
 
SPP Schüttauf und Persike Planungsgesellshaft mbH
Gap work between school and studies
May 2015 – Sep 2015 Berlin, Germany
Before I started my bachelor studies, I worked a few months, helping to manage a large construction project, gaining experience in dealing with different trades.

Computer skills

A small excerpt

JAVA
Python
Docker
Kubernetes
Spring Boot
Latex
SQL
React
JavaScript
Nextflow
Haskell
Excel

Software

Benchmark Evaluator

Benchmark Evaluator

The Benchmark Evaluator is a plugin for the Jenkins automation server to load benchmark data and decide on the success of a build accordingly.

Publications

Geoflow - Novel Workflow Implementations To Facilitate Big EO Data Workflows in Nextflow
FORCE on Nextflow: Scalable Analysis of Earth Observation data on Commodity Clusters

Modern Earth Observation (EO) often analyses hundreds of gigabytes of data from thousands of satellite images. This data usually is processed with hand-made scripts combining several tools implementing the various steps within such an analysis. A fair amount of geographers' work goes into optimization, tuning, and parallelization in such a setting. Development becomes even more complicated when compute clusters become necessary, introducing issues like scheduling, remote data access, and generally a greatly increased infrastructure complexity. Furthermore, tailor-made systems are often optimized to one specific system and cannot easily be adapted to other infrastructures. Data Analysis Workflow engines promise to relieve the workflow developer from finding custom solutions to these issues and thereby improve scalability, reproducibility, and reusability of workflows while reducing development cost at the infrastructure side. On the other hand, they require the workflow to be programmed in a particular language, to obey certain principles of distributed processing, and to properly configure and tune the execution stack, which puts additional burden to data scientists. Here, we study this trade-off using a concrete EO workflow for long-term vegetation dynamics in the Mediterranean. The original workflow was programmed with FORCE, a custom-made framework for assembling and executing EO workflows on stand-alone servers. We ported it to the scientific workflow system Nextflow, which is capable of seamlessly orchestrating workflows over a large variety of infrastructures. We discuss the pitfalls we faced while porting the workflow, advantages and disadvantages of such an approach, and compare in detail the efficiency of both implementations on various infrastructures. We quantify the overhead in execution time incurred by the workflow engine and give hints on how to deal with heterogeneous tasks. Overall, our Nextflow implementation shows promising behavior in terms of reusability and scalability, though this does not apply to all workflow stages.

Research Projects

FONDA

FONDA

Foundations of Workflows for Large-Scale Scientific Data Analysis

Contact