P R E S E N T A T I O N S

09:15

Ricardo Rocha, CH

CERN

Using the Cloud to scale out compute workloads

Ricardo is a software engineer at CERN currently part of the CERN cloud team, focusing primarily on networking and container based deployments. Previously he helped develop and deploy several components of the Worldwide LHC Computing Grid, a network of ~200 collaborating sites around the world helping to analyze the Large Hadron Collider data.

 

Ricardo has presented his and his teams work in different international conferences - Computing for High Energy Physics (CHEP), IEEE NSS/MIC, IEEE MSST, DockerCon, Kubecon and multiple OpenStack summits.

10:00

Björn Grüning, DE

Inst. of Computer Sciences  - Freiburg University

Running and deploying a cross community data science portal on-top of public compute infrastructures across Europe.

Dr Björn Grüning works at the Bioinformatics Group at Albert-Ludwigs-Universität Freiburg, in Freiburg Germany, where he heads the Freiburg Galaxy Project. His contributions include several that feature reproducible and accessible research prominently. He is a prominent contributor to, and is a driving force in, the Galaxy community. He is core member of the conda-forge, Bioconda and BioContainer community and is running the European Galaxy server together with an international team of researchers. His research interests include data visualisation, computational chemistry, and epigenetics.

10:45

Lighting up fluorescence microscopy with DSLs

Birthe Van den Berg, BE

Dept. Computer Science - KULeuven

Birthe van den Berg obtained her Master's degree in Computer Engineering from KU Leuven in 2019. As a follow-up on her Master's thesis entitled "Type Inference for Disjoint Intersection Types", she joined the programming languages group of Tom Schrijvers as a PhD researcher. Central to her research is the design of a domain-specific programming language for facilitating fluorescence microscopy experiments, in collaboration with the KU Leuven Lab for Nanobiology.

11:15

Laurent Lemmens, BE 

Ghent Quantum Chemistry Group

The electronic structure DSL for sustainable development and reproducible research

Laurent Lemmens is currently in the final year of his PhD in chemistry at the University of Ghent, working in the Ghent Quantum Chemistry Group of Patrick Bultinck. With a special interest in solving problems sustainably, Laurent is the lead developer of a domain-specific language for electronic structure calculations:  the Ghent Quantum Chemistry Package (https://gqcg.github.io/GQCP/).

11:45

Victor Vloemans, NL

Philips Research

15 years of agile software development within a research environment, lessons learned

Victor is an experienced architect with a background in desktop, mobile, and cloud development, high complexity content (algorithms, adaptive interfaces and clinical decision support), both in a research and product development context. Victor has worked as a project leader, where he strives for structure, clarity, and predictability. Victor is an Agile afficionado, currently working as Principal Architect for the IGT program at Philips Research in Eindhoven, the Netherlands.

13:15

Clémence Joseph, BE

Rega Institute - KULeuven

CellScanner, a tool developed in cooperation with biologists to meet their needs.

Clémence Joseph is a PhD student working on microbial metabolic modelling in the lab of microbial systems biology under the supervision of Karoline Faust at KU Leuven. She studied biotechnology and biochemistry for four years before joining an engineering school in bioengineering and modelling of biological systems in Sophia Antipolis (France). Clémence acquired her informatics skills during her education and her internships. She worked with sequence alignment tool at the Institute for Glycomics in Australia and discovered metabolic modelling in Bioaster (France). Her background helps her to develop new tools such as CellScanner.

13:45

Thibault Lestang, UK

University of Oxford

Reproducible research with GNU Emacs and Org-mode

Thibault is computational physicist turned research software engineer, currently member of the Oxford Research Software Engineering group at the University Of Oxford.  He is involved in various scientific software projects across the University, working hand in hand with research groups to make sure their work is supported (or leads to) high quality research software. Thibault is also an advocate for open research practices, and is involved in local initiatives providing training to researchers at all levels in writing sustainable research software, as well as the computing skills required for a research that remains open, reproducible and easy to build upon for others.

14:30

Pieter Verschaffelt, BE

Ghent University

From web app to cross-platform desktop tool in 3 easy steps

Pieter Verschaffelt is a PhD-student who started working on the Unipept project as a master student in 2018. He graduated as a computer scientist from Ghent University in 2019 and started as an FWO research fellow in November, 2019 to continue working on Unipept. His main research objective at this point is to increase the analysis throughput of metaproteomics data analysis pipelines and to provide support for proteogenomics analysis in the near future.

Twitter: @p_verschaffelt

15:00

Wim Vranken, BE

Bio2Byte - VUB Brussels

Challenges and pitfalls of integrating research software: a Bio2Byte case study

Wim got interested in programming when a Commodore 64 appeared at home in his early teens - close to magic in those days! After progressing through several other computers, he forgot all about programming when studying organic chemistry and finishing his Ph.D. on the conformation of peptides with Nuclear Magnetic Resonance (NMR)  in Gent, Belgium. The NMR work continued in Montréal, Canada, and during a postdoc year at the Université Libre de Bruxelles (ULB), Belgium, he rediscovered programming to move into the computational aspects of NMR and bioinformatics. This was the core of his work whilst at the Protein Data Bank Europe (PDBe) at the European Bioinformatics Institute (EBI) at Hinxton, Cambridge, UK. He is now professor at the VUB, where he heads the Bio2Byte group (http://bio2byte.be), with computational research focussing on how the dynamics, conformational states and available experimental data of proteins relates to their amino acid sequence.

15:45

Theodoros Chatzigiannakis, GR

Disney Streaming Services

Safety and Performance

Theodoros was born in Greece. He was taught programming in primary school and continued learning and experimenting on his own ever since. He became an active contributor to developer resources such as Stack Overflow, writing technical articles on his blog, and occasionally helping in open source software. He got an integrated master's degree in Electrical and Computer Engineering from the University of Patras. 

Currently, he is working at Disney Streaming Services on next-generation native client infrastructure for media streaming platforms.

W O R K S H O P S

09:45

James Collier, AU

VIB Bioinformatics Core

Build a Web Application with Elm

James Collier is a professional software developer with more than 10 years of experience working on software ranging from tiny embedded devices through to high-performance and web applications. He completed his PhD at Monash University in Australia and now works on scientific software within the VIB Bioinformatics Core Facility.

This workshop is scheduled to last 2h.

13:15

Birthe Van den Berg & Tom Schrijvers

Dept. Computer Sciences - KULeuven

On a date with DSLs: what domain-specific languages can do for you

Birthe van den Berg obtained her Master's degree in Computer Engineering from KU Leuven in 2019. As a follow-up on her Master's thesis entitled "Type Inference for Disjoint Intersection Types", she joined the programming languages group of Tom Schrijvers as a PhD researcher. Central to her research is the design of a domain-specific programming language for facilitating fluorescence microscopy experiments, in collaboration with the KU Leuven Lab for Nanobiology.

Tom Schrijvers graduated as master of engineering in computer science at KU Leuven in 2001. He obtained his PhD at the KU Leuven Department of Computer Science in 2005 and was postdoctoral researcher of the FWO from 2006 until 2010 when he became lecturer at UGent. In 2014 he returned to KU Leuven as senior research professor. His team studies programming languages and the functional programming paradigm in particular.

This workshop is scheduled to last 2h30. 

 
 

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