InVADo: Interactive Visual Analysis of Molecular Docking Data

based on MegaMol

Switch to branch `VS2026_and_CUDA13.1` for a version that
works with Visual Studio 2026, CUDA 13.1, and CMake 4.2.

This repository includes MegaMol with InVADo contained in the prolint plugin.

Install steps and additional data: https://github.com/MarcoSchaeferT/InVADo_setup

The repository 'InVADo_setup' contains the specific requirements and instructions how to build and run InVADo.

ACKNOWLEDGMENTS

This work was partially funded by the German Research Foundation (DFG) as part of the Project No. 437702916 "Illustrative Visualization of Uncertainty in Dynamic Molecular Structures". It was also supported by the Czech Ministry of Education (grants ESFRI RECETOX RI LM2018121, ESFRI ELIXIR CZ LM2018131, e-INFRA LM2018140) and by the National Institute for Cancer Research (Programme EXCELES, ID Project No. LX22NPO5102) - Funded by the European Union – Next Generation EU.

Special thanks go to the experts from Loschmidt Laboratories, Masaryk University, Brno, for their participation in the evaluation and thorough and valuable feedback. We also thank Frank Böckler and his team from the Molecular Design and Pharmaceutical Biophysics group, University of Tübingen for providing task descriptions and feedback on the initial design of InVADo.

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MegaMol is a visualization middleware used to visualize point-based molecular data sets. This software is developed within the ​Collaborative Research Center 716, subproject ​D.3 at the ​Visualization Research Center (VISUS) of the University of Stuttgart and at the ​Computer Graphics and Visualization Group of the TU Dresden.

MegaMol succeeds ​MolCloud, which has been developed at the University of Stuttgart in order to visualize point-based data sets. MegaMol is written in C++, and uses an OpenGL as Rendering-API and GLSL-Shader. It supports the operating systems Microsoft Windows and Linux, each in 32-bit and 64-bit versions. In large parts, MegaMol is based on VISlib, a C++-class library for scientific visualization, which has also been developed at the University of Stuttgart.

Changelog

​See changelog for newly available features in the current version of MegaMol.

Building MegaMol

Linux

1. Clone the MegaMol repository

2. Create a build folder

3. Invoke cmake inside the build folder

4. Execute make to build MegaMol

5. Run make install to create your MegaMol installation

6. Test Megamol with

   $ ./megamol.sh -p ../examples/testspheres.lua
   

Windows

1. Clone the MegaMol repository

2. Use the cmake GUI to configure MegaMol

   1. The configuration creates a sln file inside the build folder

3. Open the sln file with Visual Studio

4. Use the ALL_BUILD target to build MegaMol

5. Use the INSTALL target to create your MegaMol installation

6. Test Megamol with

   > mmconsole.exe -p ..\examples\testspheres.lua
   

MegaMol Configurator

MegaMol offers a configurator GUI (C#) that runs with .Net Framework 4. It runs also on Linux with Mono 3.2.8 (except for the analysis function and indirect-start functions).

How to use MegaMol

For a detailed description have a look at the manual.

Using the plugin template

1. Copy the template folder
2. Rename the copied folder to the intended plugin name
3. Execute the instawiz.pl script inside the new folder
   1. The script detects the plugin name
   2. Autogenerate the GUID
4. Remove instawiz.pl
5. Add libraries/dependencies to CMakeLists.txt (optional)
6. Implement the content of your plugin
7. Write a Readme.md for your plugin (mandatory)
8. Add the folder to your local git

Citing MegaMol

Please use one of the following methods to reference the MegaMol project.

MegaMol – A Comprehensive Prototyping Framework for Visualizations
P. Gralka, M. Becher, M. Braun, F. Frieß, C. Müller, T. Rau, K. Schatz, C. Schulz, M. Krone, G. Reina, T. Ertl
The European Physical Journal Special Topics, vol. 227, no. 14, pp. 1817--1829, 2019
doi: 10.1140/epjst/e2019-800167-5

@article{gralka2019megamol,
    author={Gralka, Patrick
    and Becher, Michael
    and Braun, Matthias
    and Frie{\ss}, Florian
    and M{\"u}ller, Christoph
    and Rau, Tobias
    and Schatz, Karsten
    and Schulz, Christoph
    and Krone, Michael
    and Reina, Guido
    and Ertl, Thomas},
    title={{MegaMol -- A Comprehensive Prototyping Framework for Visualizations}},
    journal={The European Physical Journal Special Topics},
    year={2019},
    month={Mar},
    volume={227},
    number={14},
    pages={1817--1829},
    issn={1951-6401},
    doi={10.1140/epjst/e2019-800167-5},
    url={https://doi.org/10.1140/epjst/e2019-800167-5}
}

MegaMol – A Prototyping Framework for Particle-based Visualization
S. Grottel, M. Krone, C. Müller, G. Reina, T. Ertl
Visualization and Computer Graphics, IEEE Transactions on, vol.21, no.2, pp. 201--214, Feb. 2015
doi: 10.1109/TVCG.2014.2350479

@article{grottel2015megamol,
  author={Grottel, S. and Krone, M. and Muller, C. and Reina, G. and Ertl, T.},
  journal={Visualization and Computer Graphics, IEEE Transactions on},
  title={MegaMol -- A Prototyping Framework for Particle-based Visualization},
  year={2015},
  month={Feb},
  volume={21},
  number={2},
  pages={201--214},
  keywords={Data models;Data visualization;Graphics processing units;Libraries;Rendering(computer graphics);Visualization},
  doi={10.1109/TVCG.2014.2350479},
  ISSN={1077-2626}
}

Coherent Culling and Shading for Large Molecular Dynamics Visualization
S. Grottel, G. Reina, C. Dachsbacher, T. Ertl
Computer Graphics Forum (Proceedings of EUROVIS 2010), 29(3):953 - 962, 2010

@article{eurovis10-grottel,
  author = {Grottel, S. and Reina, G. and Dachsbacher, C. and Ertl, T.},
  title  = {{Coherent Culling and Shading for Large Molecular Dynamics Visualization}},
  url    = {https://go.visus.uni-stuttgart.de/megamol},
  year   = {2010},
  pages  = {953--962},
  journal = {{Computer Graphics Forum}},
  volume = {{29}},
  number = {{3}}
}

Optimized Data Transfer for Time-dependent, GPU-based Glyphs
S. Grottel, G. Reina, T. Ertl
In Proceedings of IEEE Pacific Visualization Symposium 2009: 65 - 72, 2009

@InProceedings{pvis09-grottel,
  author = {Grottel, S. and Reina, G. and Ertl, T.},
  title  = {{Optimized Data Transfer for Time-dependent, GPU-based Glyphs}},
  url    = {https://go.visus.uni-stuttgart.de/megamol},
  year   = {2009},
  pages  = {65-72},
  booktitle = {{Proceedings of IEEE Pacific Visualization Symposium 2009}}
}

MegaMol™ project website
https://megamol.org

@misc{megamol,
  key  = "megamol",
  url  = {https://megamol.org},
  note = {{MegaMol project website \url{https://megamol.org}}},
}