Molecular Visualization Day - my talks
Beyond Ball-and-Stick – Representation and Perception in Chemistry Visualization
The morning talk was about:
- Representational conformism in chemistry visualization software
- How a good representation could enhance understanding
- How all the chemistry representations are metaphorical
- How standard representation could limit insight
- All this with examples of strange, new representations and how standard representations could be chosend with different criterias.
From Tradition to Insight Support – What we can demand from our Chemistry Visualization Tools
The final talk was on tools. I presented my tools survey that covers:
- Usability problem with visualization tools
- Divorce between the chemists' mental process and what a tool offers.
- And how visualization tool are mostly used for presentation and not for discovery
- As an example I cite Photoshop as one example of perfect tools in its field. Someone said that it is considered perfect because it is the bestseller of its category. Chicken and egg problem... anyway, the best seller draw the path and must stay in the top. That means it is forced to be perfect every time more in my opinion.
- Is there any universal data file format? Yes! It is called CML (Chemystry Markup Language) but unfortunately no one care about it.
- Why instead of doing more, the tools try to do less? That means, why the tools does not try to be built around components? Good suggestion. One example is OpenBabel. It tries to create a component devoted to data file input/output and nothing more. Good idea, but has shortcomings.
- Visualization for the disabled. In UK if a blind person asks to take a visualization course you are forced to take him. I never had this kind of problem, but nonetheless it is something worth thinking about. For example studying auralization or considering broadly visualization as perceptualization.
- How do you show something that is missing? (from the Stefano Leoni talk). For example it is difficult to show a vacancy or where water transforms into vapor.
- An image is worth 10.000 words, but should be the right 10.000 words!
Labels: chemistry visualization, conferences and talks, data formats, visualization tools
posted by mario @ 11:38
2 comments
2 Comments:
Open Babel's motto should be "Not Just File Conversion!". Open Babel is in fact a C++ library for cheminformatics, which has bindings in several popular scripting languages (and Java). 'babel' is a command-line executable that uses the Open Babel library to convert files, filter the contents of files, add hydrogens, center the coordinates and so on. But everyone hears "Open Babel" and thinks "File Conversion!" and nothing else. It's a victim of its own success :-)
BTW, Inkscape is also probably the best in its field. Looks good. Beautiful output. Very intuitive to use. But it's open source, so everyone thinks Adobe Illustrator must be better.
Interesting to know.
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