3DMolSym

3DMolSym
http://www.molwave.com/software/3dmolsym/3dmolsym.htm
3DMolSym is an educational program designed to visualize the symmetry elements of molecules and to animate the corresponding symmetry operations in an interactive 3D environment.

HCI things I like

• The rotate controls update a small icon to show the axis around which it rotate
• Animation usage to explain symmetry
• Captured view with a simple click (the button then becomes the view selection button)
• The technology: it is a Shockwave web application.
• The usage of transparent elements to show movement, symmetry planes
  

What I do not like

• Captured view has a reset button that does not do the intuitive thing i.e. resetting the saved view.
• The small view for panning on the left is a duplicate of the main window useful only because the main window has no pan method (e.g. the three mouse button function for rotate/zoom/pan)
  

HCI and ChemViz

After a long hiatus, I'm back again.

Here at CSCS we are planning the development of a Molecular Structure Editor. There are so few free ones and our users ask for specific functionalities not found even in commercial ones.

But before starting we need to find funding and people, so I have time to study HCI (Human-Computer Interaction).

My plan is:

1. Use this blog to collect good/bad HCI ideas from existing Chemistry Visualization tools
2. Start from introductory HCI texts to have a foundation of the field
3. Prototype, prototype...

Grid vs. Visualization conferences

I'm just back from the first day of the EGEE'07 conference. I'm not a Grid fan, but I noted some differences between this and the visualization conferences I'm used to attend.
At the Grid conference I found, respect to a visualization one:

• more Italian participants
• more women
  
• more gadgets available at the exhibition
  
• more food and more beer and wine offered

Well, it is not a scientific comparison. It is also biased by the location (mostly US the visualization conferences, instead this was in Hungary). But the differences attracted my attention.
The reason for the differences could be:

• More money from industry, they see commercial opportunities
• Young field
• In Italy we have discovered an empty field in which we are not behind the other countries, sadly
• (my biased opinion) more vaporware...
  

Practical chemistry visualization at ETH Zurich

Next week I will teach the short tutorial Practical introduction to chemistry visualization at ETH Zurich.

The idea is to transmit usable knowledge on visualization that could help chemists research work and help them consider more visualization in their research work.

I will appreciate if you can leave here some detail on your visualization experience and, after the course, comments/suggestions/critiques on it.

See you Monday!

Second Life for science

Yesterday we had also an extensive demo of Second Life, the virtual world. Karl Harrison from Oxford University had built the "Oxford island" inside the Second Life world, to test how this concept could help science teaching. I do not understand how this concept could help, but surely the world has an interesting interaction model.

Similar experience a grandmother participant to the conference that meets her grandchild in a virtual world park.

Run, run, GRC conference!

Two conference days passed so fast!

Scientific sessions and the poster area are full of interesting themes: from brain studies of perception to what chemistry students have in their minds. I like this interdisciplinarity. I like to mix ideas not only from the scientific visualization area. Maybe some new idea spark in the mind, maybe not. In any case it is enriching me.

One nice idea is to start the question time with five minutes of (forced? suggested? encouraged?) discussion with your seat neighbors. Yesterday the discussion continued also after the session in front of a beer.

But there are also 'undercover' activities: Monday an introduction to Flash; yesterday a Jmol tutorial and a GeoWall presentation.

• Flash: I do not know if could be of interest to us, but it is really simple to create and animated 2D application. Various professors use it to explain concepts or to make interactive demonstrations.

• Jmol: with the principal developer teaching, nothing less! Latest version rivals standard chem viz tools.

• GeoWall: cheap alternative for stereo projection screens. It uses polarized glasses to separate L and R info.

Conference starts

Seems the first day at the college: old friends reunions, laughs, ...

Before the two after-dinner sessions, an official from the GRC organization remembered (strongly remembered) the rules: no public relation of conference content.

Interesting rule: the rationale is to remove every possible block that could hinder the free discussion of advanced topics or new research lines. I agree, but this means here I can only post my sensations and the (public) titles of the talks.

So the two first sessions:

1. On visual perception: half known phenomenas, half a new effect that elicited a general "Wow!" from the audience.
2. On quaternions. Known mathematics, but some nice applications. Same of them were like an illusionist show.

Was hard to remain awake. But an interesting experiment was attempted: before questions, five minutes the people were forced to discuss together on the talk content. Nice method to make connections.

Design workshop ended

Last half day for the Visualization Design Workshop at the Gordon Research Conference. The good things always finish...

The final exercise of the workshop presented four ideas on how to redesign a visualization. Here are some comments on mine. But the best visualization was the animation of a protein docking made for illustration, not exploration. Amazing!

Then Barbara Tversky spoke on External Representations and especially on Animation usage.

Interesting:

• Animation is hard to perceive
• Animations are conceived as discrete steps
• It is showing, not explaining

That means, that I should reconsider how molecular animations are made. Currently they are simply the translation into images of the data received. Why I'm not able to extract important points? Why the sequence is never segmented into "worth note" and "transition" parts.

As usual the available time is the main constrain together with the difficulty to understand what the user want to demonstrate with the movie.

After dinner, the real Gordon Research Conference begins. Nice for the ones of us that are still not synchronized with the time zone...

GRC - The campus

The conference is in the Bryant University campus. For someone not used at the American campuses, it is really impressive: it is new and it is rich. The university has only financial and economic faculties. And that explains everything...

The student dormitory instead are quite poor. An educational method or what?

But the seminary room, has incredibly comfortable chairs and big desks. It helps a lot the attention.

Not to say, wireless everywhere. In the afternoon I want to try under the trees.

As a student, would I want to stay here? I don't know. It is far from everywhere. Seems to me you are forced to study a lot.

The Design Workshop

Before the Gordon Research Conference start I'm attending the pre-conference workshop on Design Principles for Creating Effective Visualizations.

It is short lectures and group work. A lot of group work!

Here are some sparse notes:

• Visualization is the use of graphical techniques to convey info and support reasoning
• Representation: The Mike Hann's "Ceci n'est pas une molecule". We are showing something that highlight some aspect of the original data, but it is not the original data. I have to read the handout form a Donald Norman book (Things that make us smart).
• The enormous power of representation that can change significantly the cost of the insight.
• Distributed cognition: it is the internal representation plus the external cognition artifacts that play together
• Visualization challenge: Design a representation that uses graphical techniques effectively. Design needs three interlocked disciplines: psychology, domain knowledge and art&design. The last is always forgotten.
• Then divided in 4 groups we selected good/bad visualizations. I presented the Ute Roehrig Alzhaimer proteins aggregation and the Davide Branduardi energy landscape (see my workshop materials page)
• Constructive criticisms: Do the audience knows what they are going to see? Challenge of conventions. The landscape is good because matches everyday experience (valleys, things going down).
• From another work (movement of lipids in a cellular membrane): use of highlight to direct attention. Animation of H atoms confusing, need same form of traces to be understandable. Good idea the use of zoom to attract attention.
• Unfortunately not open, but on flashchem.nelson.com there are nice examples of interactive Flash usage for concept explanation.
• Barbara presented idea on cognitive design principles. The viz designer must uncover the mental model of the viz user. Use the context to disambiguate the message.
  
• Color usage ideas: known guidelines. But a new ideas: hue for periodic data. Hue is circular, so can convey ideas on things like phase (that it is circular). It also show very clearly discontinuities.
• Space usage: look at cartography. To show one thing better, the cartographer must absolutely distort something else.
• The viz scientists learn by observing. Learn by examples.
• Design a visualization. Do not lock into a solution too early!

Today we must present a design to make more effective one presented visualization. More on this later. But seems we are not able to select one visualization...

The Gordon Research Conference

I'm near Providence RI for the Gordon Research Conference on Visualization in Science and Education.

Do you know what are those conferences? They are not usual conferences with publications, proceedings and so on. The main idea is to join people from diverse fields but with a common interest to freely discuss and exchange ideas. For this reason it is strictly prohibited to make any reference to work presented at the conference.

To quote from the home page:

The Gordon Research Conferences promote discussions and the free exchange of ideas at the research frontiers of the biological, chemical and physical sciences. Scientists with common professional interests come together for a full week of intense discussion and examination of the most advanced aspects of their field. These Conferences provide a valuable means of disseminating information and ideas in a way that cannot be achieved through the usual channels of communication - publications and presentations at large scientific meetings.

My impressions till now:

• The atmosphere is the one of a college or school, not of a conference. No one seems urged to demonstrate anything
• Multidisciplinarity at the top! Psychologists, chemistry professors, educators, a documentary maker, biologists...
• Real interest for each other work
• Close contact with famous names in the visualization area: Pat Hanrahan, Barbara Tversky
  

Now I'm in the middle of a pre-conference workshop on Design Principles for Creating Effective Visualizations. More on this later.

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

Ideas and questions from the audience:

1. 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.
2. Is there any universal data file format? Yes! It is called CML (Chemystry Markup Language) but unfortunately no one care about it.
3. 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.
4. 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.
5. 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.
6. An image is worth 10.000 words, but should be the right 10.000 words!

Molecular Visualization Day - talks

Stefano Leoni, Max-Planck Institute for Chemical Physics of Solids
Thinking with the Eyes: Productive Visualization in Natural Sciences

Real life examples of visualizations from his own research. A lot of images were done with my STM4, but he added an interesting creative touch. Notable highlights:

• Illuminated streamlines to show atom movements
• Translucent polyhedra to draw attention to the important parts of the scene
• Busy ball-and-stick structure where, due to the crossing of bonds, the formation of a phase transition seed was highligthed

Matt Cooper, Department of Science and Technology (ITN), University of Linköping
Evaluating the Effectiveness of Haptics for Biomolecular Education

Interesting study on the effectiveness of haptic interfaces for a protein docking problem. He made a distinction between been used to an interface method and having help from the interface. At the end the conclusion was thatreally haptic does not help much for understanding of data. Another consideration worth noting is that the haptic force feedback device needed was not a simple 3D one, but a 6D one (position plus rotations). That means higher cost and computation requirements.

He also defined visualization as a process with an image at the end. Later someone corrected the definition to: visualization is a process with an image in the middle. Quite true, also if compared to the James Watson discovery loop I show in my talks.

I envy the T-shirt Matt was wearing: the capsicine structural formula on the front and hot peppers on the back!

Jens Thomas, Computational Chemistry Group, Daresbury Laboratory
CCP1GUI Visualization System

A GUI for the Gamess-UK computational code. Besides the usual structure viewer, it featured an interesting Grid interface for the computational code. The idea was to create and unified, simple interface for computationale chemists so they have a single entry point for all their works. Interesting. The code is written in Python and is available.

Ganga Periyasamy, School of Chemistry, University of Manchester
Visualization to understand magnetically induced currents in transition metal complexes

This talk was interesting because visualization were disappointing...

She spoke on her research about the electronic currents in various compounds. The computations were done with Matlab that produced the 2D contour charts (1 a.u. below, on the molecule plane and 1 a.u. above). Due to the scarcity of points, Matlab produced horrible artefacts instead of smooth contours of the modulus of the vector currents).

This problem has been already solved (see the work of Daniel Sebastiani here at CSCS), but in my opinion the interest of this talk derived from a study of the problems a non-specialized tool could create for visualization.

Manchester Molecular Visualization Day

Last April 20 the University of Manchester organized a Molecular Visualization Day to advertise what visualization could do to help chemistry researchers.

I was the star of the show with two talks (here are the abstracts and slides). I tried to cover my research on chemistry representations and visualization tools. The questions were stimulating (and the hospitality splendid too!).

Next posts I will cover ideas from the other speakers and comments and ideas from my own talks.