SIG BioExcel is a major venue for knowledge exchange and networking for the computational biomolecular research community. It brings together stakeholders of 1) core applications that are supported by the center – HADDOCK (integrative modelling), GROMACS (molecular dynamics simulations) and CPMD (hybrid QM/MM methods) and 2) worklow environments and platforms for data integration and analysis such as Galaxy, Taverna, Open PHACTS, COMPSs and Copernicus. These include:

  • Academic scientists whose research depends heavily on software for biomolecular simulations (e.g. users and developers)
  • Industrial users of such software, especially from pharmaceutical, chemical or food industries
  • Independent software vendors of biomolecular modeling/simulation applications or platforms
  • Resource providers for biomolecular simulations (HPC centers, commercial Cloud/HPC/Grid system providers)
  • International projects and initiatives in the area of biomolecular simulations

This year’s meeting will take place as a satellite event during ECCB2016 on 4th September in the Hague.  The event will host invited talks by top-scientists, flash presentations of the highest quality abstracts from the poster session, and lunchtime hands-on presentation of cutting-edge high-end (HPC and HTC) systems.

The venue will provide opportunities to participants to:

  • Showcase their success stories (posters and selected flash talks)
  • Discuss upcoming challenges and how they might be addressed
  • Share experience and best practices to develop standards
  • Create networking and collaboration opportunities with each other
  • Provide input into the development of improved software and workflows


Contributions for poster presentations and flash talks are invited on all topics related to computational biomolecular research , including, but not limited to:

  • methods and algorithms for atomistic modelling and simulations
  • docking and integrative modelling
  • high-performance (HPC) and high-throughput (HTC) techniques and methods
  • ab initio and hybrid QM/MM methods for biomolecular systems modelling
  • coarse grained and multi-scale simulation methods
  • workflows and platforms for biomolecular simulations and data integration
  • distributed systems for modelling and simulations
  • data management for biological sciences – formats, databases, repositories, integration
  • industrial applications of biomolecular modelling and simulation
  • computer aided drug design
  • virtual screening
  • free energy calculations
  • Use cases of HADDOCK, CPMD, GROMACS and other modelling and simulation applications
  • Training and education in biomolecular modelling and simulation

Keynote speakers

Carole_Goble Carole Anne Goble is a Professor of Computer Science at the University of Manchester in the UK. She has spent over 25 years working in Research Infrastructures for science, undertaking pioneering work in Scientific Workflows, Semantic Web and knowledge technologies and ontologies, data/model collaboration environments and reproducible research. She lead the development of the Apache Taverna Workflow System, the workflow sharing resource myExperiment, coordinates the FAIRDOM Initiative for Systems Biology data/model sharing and has driven the Research Object approach to workflow reproducibility. She is ELIXIR-UK Head of Node and co-leads the ELIXIR Interoperability Platform. She is a co-founder and investigator for the UK’s Software Sustainability Institute..
Alexandre_Bonvin Alexandre Bonvin is a full Professor of Computational Structural Biology in Utrecht University since 2009. Research within his computational structural biology group focuses on the development of reliable bioinformatics and computational approaches to predict, model and dissect biomolecular interactions at atomic level, as implemented in the widely used HADDOCK software for the modelling of biomolecular complexes (
erik-lindahl Erik Lindahl is a Professor of Theoretical and Computational Biophysics at Royal Institute of Technology and Stockholm University. He is one of the main developers of GROMACS, a highly optimized, scalable, efficient and popular code for molecular dynamics simulations.
gert vriend Gert Vriend is head of department of the Nijmegen Centre for Molecular Life Sciences. He has developed numerous widely used tools in the area of biomolecular modelling such as WHATIF.


Start End Title
Presenter name (Affiliation)
9:00 9:30 Introduction and Welcome

BioExcel Center of Excellence
Rossen Apostolov (KTH Royal Institute of Technology, SWEDEN)

9:30 10:00 Advances in Molecular Simulations
Erik Lindahl (KTH Royal Institute of Technology, SWEDEN)
10:00 10:30 Advances in Intergrative Modelling of Biomolecular Complexes
Alexandre Bonvin (University of Utrecht)
10:30 11:00 Poster session + networking coffee break
11:00 11:30 Application of Computational Methods in Industry: “NMR structural biology at ZoBio
Eiso Ab (ZOBIO BV)
11:30 12:00 Flash talks selected from abstracts
Damien Larivière
András Szilágyi
12:00 12:30 Advances in Computational Biomedicine
Agastya Bhati (University College London)
12:30 13:30 Lunch-on demonstrations of cutting-edge high-end (HPC and HTC) computational systems
13:30 14:00 Application of Computational Methods in Industry

Linda Kaldenberg (MERUS N.V.)

14:00 14:30 Advances in workflow environments
Carole Goble (University of Manchester)
14:30 15:00 Flash talks selected from abstracts
Po-chia Chen
Tomas Bastys
15:00 15:30 Poster session + networking
15:30 16:00 Only interoperability can generate Hope for the future
Gert Vriend (
Netherlands Society on Biomolecular Modelling)
16:00 16:50 Panel discussion on challenges in computational biomolecular research
16:50 17:00 Closing remarks

Important Dates

Submission Deadline (abstract): June 25, 2016
Notification: June 22 27, 2016
Early-bird registration: July 29, 2016
Registration deadline : August 19, 2016
Workshop Date: September 4, 2016


SIG BioExcel is a satellite meeting of ECCB’16 and registration should be done through


  • Rossen Apostolov, BioExcel Manager, KTH, Sweden
  • Alexandre Bonvin, Utrecht University, The Netherlands
  • Cath Brooksbank, Head of Training at EMBL-EBI
  • Ian Harrow (industry co-organizer), Director & Principal Consultant at Ian Harrow Consulting


Abstracts should be sent through the form below and may include published or already submitted material to other conferences, workshops or journals.

Additional information

If you have any questions regarding the SIG meeting, please contact us at