Call for Papers

Important note: The submission deadline for full papers as well as short papers has been extended to March 12, 2018! Molecular visualization is one of the oldest branches of scientific visualization, which has been developing for over 50 years. Due to the continuous advances in both computational biology and computer graphics techniques, molecular graphics and visualization are still very active areas of research. Not only the ever-increasing dataset sizes yield a constant challenge for visual analysis, but also new technologies like advances in web-based graphics or augmented and virtual reality open new possibilities. In this half-day workshop, which is held for the first time in conjunction with EuroVis, we would like to initiate a multidisciplinary meeting which brings visualization researchers together working with molecular data. Whereas molecular graphics is an established topic since many years, the hybrid-dimensional visual analysis of molecular structures is still a quite new research field with a lot of potential. We would like to encourage submissions especially using new technologies, such as immersive analytics-related approaches. We invite short papers as well as full papers (2-4 pages for short and up to 8 pages for full papers, both with an additional page reserved for references). All papers will undergo a single-stage, double-blind peer review process. Accepted papers will be published in the EG digital library. Authors prepare their submissions as a PDF file using the EuroVis 2018 LaTeX2e template. The submission must be original work that has not been published previously in any conference proceedings, magazine, journal, or edited book. All papers are submitted using the Precision Conference System (PCS). The workshop will be held in Brno, Czech Republic, June 4th, 2018 as part of EuroVis 2018. Suggested topics include, but are not limited to:
  • Molecular Graphics
  • Visual Analysis of Molecular Data
    • e.g., molecular structures, biological networks and pathways, or omics data
  • Visualization of Dynamic Molecular Data
  • Visualization of Large Molecular Systems
  • Web-based Molecular Graphics and Visualization
  • Immersive Analytics approaches using, e.g., VR/AR technologies

Important Dates (Update!)

Paper Submission Deadline: March 12, 2018 (UPDATE!)
Notification of Acceptance: April 10, 2018
Camera-ready Deadline: April 20, 2018
Workshop Date: June 4, 2018


Chairs: Jan Byška, Michale KroneFist session: Computational analysis of dynamic molecular data.
14:20 - 14:25Opening
14:25 - 15:20 Invited talk: Visualization Challenges and Opportunities Posed by Petascale Molecular Dynamics Simulations
John E. Stone
15:20 - 15:40 (FP: 15min + 5min) An Accelerated Online PCA with O(1) Complexity for Learning Molecular Dynamics Data
Salaheddin Alakkari and John Dingliana
15:40 - 16:00 (FP: 15min + 5min) Atomic Accessibility Radii for Molecular Dynamics Analysis
Norbert Lindow, Daniel Baum, and Hans-Christian Hege
Chair: Björn SommerSecond session: Frameworks for molecular data visualization.
16:30 - 16:50 (FP: 15min + 5min) VIA-MD: Visual Interactive Analysis of Molecular Dynamics
Robin Skånberg, Mathieu Linares, Carolin Konig, Patrick Norman, Daniel Jönsson, Ingrid Hotz, and Anders Ynnerman
16:50 - 17:05 (SP: 10min + 5min) Mol*: Towards a common library and tools for web molecular graphics
David Sehnal, Alexander Rose, Jaroslav Koca, Stephen Burley, and Sameer Velankar
17:05 - 18:00 Invited talk: Visualizing Biomolecular Structures for Research and Outreach
Dr. Seán O’Donoghue
18:00 - 18:10Closing remarks

Invited Speakers:

John E. Stone

Bio: John Stone is the lead developer of VMD, a high performance molecular visualization tool used by researchers all over the world. His research interests include molecular visualization, GPU computing, parallel processing, ray tracing, haptics, and virtual environments. Mr. Stone is a Senior Research Programmer in the Theoretical and Computational Biophysics Group at the Beckman Institute for Advanced Science and Technology, and Associate Director of the NVIDIA CUDA Center of Excellence at the University of Illinois. He was inducted as an NVIDIA CUDA Fellow in 2010. In 2015 Mr. Stone joined the Khronos Group Advisory Panel for the Vulkan Graphics API. In 2017, Mr. Stone was awarded as an "IBM Champion for Power" for innovative thought leadership in the technical community. He also provides consulting services for projects involving computer graphics, GPU computing, and high-performance computing.

Title: Visualization Challenges and Opportunities Posed by Petascale Molecular Dynamics Simulations

Abstract: The combination of experimental structure information, molecular dynamics (MD) simulation, and high-fidelity visualization techniques with HPC computing resources creates a powerful "computational microscope" that permits molecular scientists to view the structure and dynamics of biomolecular complexes in atomic detail within realistic cellular environments. Advanced simulation methodologies such as multiple-copy MD, hybrid quantum mechanics / molecular mechanics (QM/MM), data-guided hybrid structure modeling simulations, and multi-scale modeling techniques each pose new challenges for selection, interaction, and visualization. I will describe analytical and visualization challenges that have arisen for state-of-the-art molecular dynamics simulations and opportunities for visualization tools and techniques to contribute to their ultimate success.

Dr. Seán O’Donoghue

Bio: Seán O’Donoghue is a Senior Principal Research Scientist in Australia's Commonwealth Scientific and Industrial Research Organisation (CSIRO), Sydney. He is also a Laboratory Head and Senior Faculty Member at the Garvan Institute of Medical Research in Sydney. He was also recently appointed as a Conjoint Professor in the School of Biotechnology and Biomolecular Science (BABS), University of New South Wales. He received his B.Sc. (Hons) and PhD in biophysics from the University of Sydney, Australia. Much of his career was spent in Germany, where he worked both in the Structural and Computational Biology programme at the European Molecular Biology Laboratory (EMBL), and at Lion Bioscience AG. He has been awarded a C. J. Martin Fellowship from the National Health & Medical Research Council of Australia, an Achievement Award from Lion Bioscience, and was recently elected a Fellow of the Royal Society of Chemistry. He is leading several projects, including: and Reflect, a browser plug-in designed to help in understanding life science literature widely used by life scientists (first prize, Elsevier Grand Challenge); VizBi, an international initiative aimed at improving data visualization and user experience in bioinformatics software; VizbiPlus, aimed at educating and inspiring the general public about cutting-edge biomedical research (Finalist, 2015 NSW Emerging Creative Talent Award); and Aquaria (first prize, 2015 NSW iAward for Research and Development), a resource that simplifies discovery and insight from protein structures.

Title: Visualizing Biomolecular Structures for Research and Outreach

Abstract: Molecular graphics has entered a new era; it is now used much more widely, and for an increasingly wide variety of applications. In this talk I will highlight challenges and opportunities arising with web-based deployment, how we can learn from past mistakes in our field, and how we can formally evaluate alternative visualisation methods. I will also showcase several applications in which molecular graphics is helping interpret cutting-edge biomedical datasets, including large-scale sequencing studies of specific diseases (e.g., cancer), as well as large-scale modeling studies of the 'protein structure universe'. I will briefly discuss challenges presented by the 'dark' proteome of structural biology. Finally, I will discuss the use of molecular graphics for educating and inspiring the broader public about breakthroughs in molecular medicine.

Organizers & Contact

Jan Byška, University of Bergen, Norway
Michael Krone, University of Tübingen (formerly University of Stuttgart), Germany
Björn Sommer, University of Konstanz, Germany
If you have any question, please contact us:

International program committee

Marc Baaden (Laboratoire de Biochimie Théorique, France)
Daniel Baum (Zuse Institute Berlin, Germany)
Matthieu Chavent (IPBS, France)
Martin Falk (Linköping University, Sweden)
Alejandro Giorgetti (University of Verona, Italy)
Pedro Hermosilla Casajus (Ulm University, Germany)
Barbora Kozlíková (Masaryk University, Czech Republic)
Jens Krüger (University of Tübingen, Germany)
Peter Mindek (TU Wien, Austria)
Kay Nieselt (University of Tübingen, Germany)
Timo Ropinski (Ulm University, Ulm, Germany)
Alexander Rose (RCSB, United States)
Cagatay Turkay (University of London, United Kingdom)
Pere-Pau Vázquez (Universitat Politècnica de Catalunya, Spain)