Sciencemotionology: Could you tell us a little bit about your background?

 

Monica: I studied biology at the University of Milano, in the '80s; then I moved to several other labs in Italy and abroad, always doing molecular research, and finally obtained a permanent position at the CNR in Pisa, in 2001.

 

Sciencemotionology: What drove you from your animal cell technology research group to create your own scientific visualization group?

 

Monica: It was actually because of a major problem in the lab. So i ended up in front of a computer, and I thought that the technology could be mature enough to do experiments in a virtual world, rather than in the actual lab. Of course I was completely wrong, but when I found out, it was already late; in the meantime I had acquired some experience and defined the project in better detail.

 

Sciencemotionology: Could you describe us the context in which SciVis group was created?

 

Monica: After my initial effort with Maya,  I realized that what I needed to really bring biology into a 3D system was a major effort that could bring together people with different expertise, that's when I finally got funding for making 3D biology, and could hire a group of people that made up the SciVis group.

 

Sciencemotionology: Previously you told me about the multidisciplinary group of people that made part of the Scivis team. Could you tell us more about the life inside Scivis?

 

Monica: We started big: it was a group of 6 or 7 people  with very different backgrounds: math, physics, computer science, computer graphics, artist, biologist, chemist. The first two months were spent doing reciprocal education in the different fields: in the morning we would have two sessions of two hours each, kept by one of us, and in the afternoon we would start doing things, trying to practice what we had learnt in the morning. It was a very intense time, but I consider it time very well spent. When we really started doing protein animations, we knew each other, what each one of us could do, and we knew how to talk, we had a common vocabulary. In the following years, we always had a good understanding of what other people were doing, and I think that this helped a lot to the quality of the results.

 

Sciencemotionology: How would you describe the work you do at SciVis? Do you think your animations have a higher scientific accuracy than other scientific animators since your work is done inside a research institute?

 

Monica: When we start a new work, we first set out, all together, to decide how much time and effort we can dedicated, considering the audience, the budget and all other 'technical' details. Next, we do some research: in structural biology, but also in genetics, biochemistry, and cellular biology. We have to decide what to show, how to deliver the message, and which aspects we can make the center of the animation. At this point we sit again all together, and make a plan with storyboard, decide on the accompanying text or music, and assign the task to the group components. During all the production time there is constant exchange of files, of comments, ideas and questions: it is very normal that every day we meet with new problems, and discuss how to solve them.

 

I think that our work has a good scientific accuracy. And I have seen also many other animations that seem highly accurate. I would not say that it is the fact of being inside a research institute to make our work accurate: the root of such accuracy is, for me, in the many years of work in the laboratory, where precision and accuracy is extremely important for reproducibility of results, and in the fact that  I have always tried to imagine in my mind what happened inside the cells, also during my years at the bench. I think that my vision matured during those years, and when I finally started to make it visible also to others, with the animation project, i had a good mental view of how the inside of a cell would look like. Of course, nobody has really seen it, so there is a major element of imagination and artistic liberty in the way each animator produces their work. But this is true also for 'human size' cinema: the choice of the camera, the lens, the lights, the speed  of motion... these are all elements that are not right or wrong: but they help the viewer, making it more or less easy to build an internal image of objects that were never seen in real life. For this reason we put a strong emphasis in photo-realism. This is also the reason why we have not yet introduced colors in our animation.


Sciencemotionology: What motivated you to launch BioBlender? Which are the main features of BioBlender?

 

Monica: You mean: with the good packages already out there dedicated to molecular visualization, what was the need to build yet another one? BioBlender was initially considered a necessary instrument for making the movies. I had no idea of how complex it would become: just import the pdb file, make the surface and paint on the surface the chemical and physical features associated to the protein. Also, since proteins move (and Blender is an animation tool, right?), the 'simple' idea was to interpolate between different conformations: just make sure that atoms behave sensibly! The good part of being ignorant, sometimes, is that one engages in projects that are so much bigger than what they seem! But I can claim some indulgence, since it was not all my fault: CG people make such amazing works that one is justified in believing that everything is possible! In the end, yes! BioBlender is yet another biomolecular visualization tool but, because of the way it was conceived, it contains features that are different from all others, such as the unique concept of showing the lipophilic and electrostatic potential in the environment, and not using colors.

 

Sciencemotionology: I heard you recently participated in the production of a short scientific animation for The Dark Gene movie. Could you describe to us how that project was developed?

 

Monica: That was nice:  the Directors of the film contacted us asking for some animations that could reproduce the inner workings of depression. They had seen some of our previous work, and liked the atmosphere, they thought it had an artistic and imaginative content that was not present in other molecular animations. We were very happy, of course, so we considered the idea and proposed the Serotonin cycle in the synapse, the communication junction between neurons in the brain.  Initially we were prepared to do a big animation, but the budget was quite limited (The Dark Gene is an independent production), so we limited the work to less than 5 minutes. I think we did a nice animation anyway. The directors were happy with the work, and for us it has been a good opportunity to go beyond the traditional 'molecular animation' audience. We are looking forward to see what  the public will say about it.

 

Sciencemotionology: Which were your biggest challenges during the production of The Dark Gene animation?

 

Monica: Probably the handling of many thousand particles in the panoramic view of the synapse. When the vesicle releases the serotonin, there are more than 50 thousands objects in the scene, and they all have to behave properly!

 

Sciencemotionology: How would you describe the actual market for scientific animations in Europe?

 

Monica: Why, is there a market? If you find it, please let us know!

 

Sciencemotionology: Do you have any advice for young researchers now starting their work in scientific visualization?

 

Monica: The world of scientific visualization is still quite young, it seems to me that everyone is moving in small steps, with no clear direction. My vision was developed with a very long term, but I am not sure if our colleagues have the same vision, or if they have a long term vision at all. For young researchers this can be good: because it means that they can bring new ideas and concepts, but it can also be difficult, because at the same time there is quite some confusion.With time, some kind of visualization will eventually become a standard and most people will take up that kind of visualization as the only possible one. It is to be seen which forces will determine the standard: if the most effective, the most easy to produce, the one with the most 'push' (i.e. those adopted by big groups, or even by commercial enterprise) ...

 

Sciencemotionology: Where can we see The Dark Gene?

 

Monica: We are waiting to the official release in the cinema. Any news will be released on the production website: http://www.filmtank.de/p/the-dark-gene/

Monica Zoppè 

Group Leader

www.scivis.it

Interviewing...

Monica started the Scientific Visualization group in Pisa, Italy. The idea that there could be a virtual lab running experiments lead to the creation of Scivis. 

 

THE DARK GENE

DOCUMENTARY FILM, FILM
D/CH 2015 – 99 MIN

HIV virions approaching a white blood cell © Scivis

BioBlender © Scivis

"...how to deliver the message..."

"...to do experiments

in a virtual world..."

"...I have always tried to imagine in my mind what happened inside the cells"

"...'human size' cinema: the choice of the camera, the lens, the lights..."

"...to go beyond the traditional 'molecular animation' audience."

"...there are more than 50 thousand objects in the scene, and they all have to behave..."