Immersive Molecular Modelling Workshop

Immersive Molecular Modelling

Friday, October 19, 2018, 1 – 3:30* pm, University of Konstanz, Room C426

* As we will have basic hands-on demos included, it might take a bit longer than 3:30 pm.

In contrast to many other biochemical research areas where the applicability of immersive visualization and analysis still has to be proven, molecular data profits from spatial visualization since many years. In this workshop, a number of tools will be presented which fall into the area of molecular modelling, docking and simulation, making use of Virtual and Augmented Reality-related technologies.


  • 1:00 – 1:05 pm Welcome
  • 1:05 – 1:35 pm Marc Baaden
    • Immersive visual exploration of biomolecular systems in virtual reality
      • Abstract: For several years now, my team pursues the goal to study complex molecular assemblies through interactive visualization, manipulation and analysis approaches to aid hypothesis generation and exploration of complex datasets. The UnityMol framework [1] forms a central tool for these investigations and is based on the Unity3D game engine. A first line of research tries to help with the 3D context, for instance through content-guided navigation, exploded views and semantic links between molecular objects and their analysis data [2].
        Concerning the molecular representations, we extended the UnityMol repertoire to include specific visualizations for sugar molecules [3] and have now also included coarse-grained systems by default. These are particularly apt for interactive simulations, even in the classroom or via crowdsourcing. A particular focus lies on the integration of dedicated hardware such as large, high-resolution display walls, or more recently head-mounted virtual reality headsets or augmented reality setups.
        The latest version of our UnityMol VR implementation will be demoed.
        [1] Lv et al., Game on, Science – how video game technology may help biologists tackle visualization challenges, PLoS ONE 8(3):e57990, 2013
        [2] Trellet et al., Interactive Visual Analytics of Molecular Data in Immersive Environments via a Semantic Definition of the Content and the Context, IEEE VR 2016/VR 2016 Workshop on Immersive Analytics
        [3] Pérez et al., Three-Dimensional Representations of Complex Carbohydrates and Polysaccharides. SweetUnityMol: A Video Game Based Computer Graphic Software, Glycobiology 25, 2015, 483-491; doi: 10.1093/glycob/cwu133
      • CV: Marc Baaden studies membrane proteins using extensive large-scale simulations, such as for the bacterial GLIC ion channel (gating, anesthesia, …), a homolog of the nicotinic receptor. This is completed by innovative work at the interface between biology, chemistry and computer sciences (virtual reality and scientific visualization).
  • 1:35 – 2:05 pm Jens Krüger
    • Simulations on the de.NBI Cloud
      • Abstract: Research in life science greatly profits from all kind of simulation approaches. In particular insight on a molecular level helps to decipher mechanisms of function of enzymes, ion channels and all other kind of molecular machinery. The presentation will give an introduction to the highly flexible simulation platform called de.NBI Cloud. It offers compute and storage capabilities to all researchers in the life sciences with an affiliation to a German research institution. Taking the popular molecular dynamics application Gromacs as use case, the life cycle of data generation will be illustrated. The authentication process will be covered, as well as the configuration of the simulation environment, the setup of the simulation system, the molecular dynamics calculation itself, and its analysis. Detailed instructions will be provided to enable users to boost their research by using the de.NBI Cloud.
      • CV: Jens Krüger is group leader for High Performance and Cloud Computing at the University of Tübingen. He acquired his PhD at the University of Paderborn. He has more than a decade of experience in molecular dynamics simulation studies. As one of the driving forces behind the MoSGrid initiative (Molecular Simulation Grid), he is an expert in the development of cloud services in diverse scientific contexts.  He is involved in the excellence initiative of the University of Tübingen and in a number of chemoinformatics projects.
  • 2:05 – 2:30 pm
    • Coffee Break
  • 2:30 – 3:00 pm Michael Krone
    • Immersive Analytics for Molecular Dynamics Simulations
      • Abstract: Interactive visualization is commonly used as a tool for the analysis of molecular structures, especially for molecular simulations. Many different molecular models have been developed to show individual properties of the simulated molecules, resulting in complex three-dimensional depictions. Immersive technology such as stereoscopic rendering has been adopted for molecular visualization early on, as it makes it easier to understand the spatial relations between these complex structures. In my talk, I will show how we have applied immersive technologies to facilitate the visual analysis of biomolecular simulation data in the last 10 years, ranging from classical stereoscopic high-resolution tiled displays (so-called Powerwalls) to modern head-mounted displays that enable the use of Augmented Reality. Besides stereoscopic rendering, I will also briefly discuss the use of spatial audio as an additional immersive technology, which is to date rarely used in molecular visualization.
      • CV: Michael Krone is a junior professor (assistant professor) at the Eberhard Karls University of Tübingen in Germany, where he leads the Big Data Visual Analytics research group. He is also principle investigator in a Czech-German research project funded by the German Research Foundation. He received a diploma in Computer Science (equivalent to M.Sc. in CS) in 2008 and his Ph.D. in 2015 from the University of Stuttgart. In 2016 and 2017, he had appointments as guest lecturer for Computer Graphics at the Ludwig Maximilian University of Munich. His main research interests are in scientific visualization and visual analytics for life sciences, especially the interactive visual analysis of molecular structures, and GPU-accelerated computing. 
  • 3:00 – 3:30 pm Björn Sommer
    • Membrane Modeling with MembraneEditor
      • Abstract: The modeling of homogeneous membranes with a single lipid type is a quite simple task which can be done by writing a simple script compatible to tools like VMD. But if the membrane should contain multiple lipid types, different proteins, maybe lipid rafts and be of different shapes (like circular ones or vesicular), things are getting complicated. Then, the CELLmicrocosmos 2.2 MembraneEditor is a tool which has been already used for many publications to set up heterogeneous membranes or vesicles [1]. Moreover, the MembraneEditor supports stereoscopic visualization during the modeling process. The so-generated membranes can be used for molecular dynamic simulations with, e.g., Gromacs, and then analyzed with tools like APL@Voro [2],
        Here, we will give a short live intro to MembraneEditor. You may bring you laptop and preinstall Java and the MembraneEditor available from:
        [1] Sommer et al. CELLmicrocosmos 2.2 MembraneEditor: a modular interactive shape-based software approach to solve heterogeneous membrane packing problems, Journal of chemical information and modeling: 51(5):1165-1182, 2011.
        [2] Lukat et al. APL@Voro: A Voronoi-Based Membrane Analysis Tool for GROMACS Trajectories, Journal of chemical information and modeling: 53(11):2908-2925, 2013.
      • CV: Bjorn Sommer is a Research Fellow with the Department of Computer & Information Science of the University of Konstanz. He studied Media Informatics & Media Sciences at Bielefeld University, Germany, made his PhD in Bioinformatics, and was working as researcher at the Bio-/Medical Informatics Department. From 2015 to 2016, he was working as Research Fellow in the Immersive Analytics initiative of Monash University, Melbourne. Together with his students he developed the CELLmicrocosmos project. 


  • Marc Baaden (IBPC Paris)
  • Jan Byška (University of Bergen)
  • Michael Krone (Tübingen University)
  • Jens Krüger (High Performance and Cloud Computing, IT Center Tübingen)
  • Björn Sommer (University of Konstanz)


Please register here and choose: “Immersive Molecular Modeling Workshop”:

Please note that you can choose another workshop in the morning session as there will be no morning session for our ImmMolMod.