[Bf-committers] BioBlender AddOn

Monica Zoppè mzoppe at ifc.cnr.it
Fri Nov 28 14:22:45 CET 2014

Dear Blender Developers,

I am writing following the Blender Conference in which, some of you 
may remember, I made an appeal for help with BioBlender, since 
unfortunately our group has dissolved, due to end of funding. 
However, I constantly receive requests from people attempting to use 
it, meaning that the program is welcome in the community of biologists.

Having more or less understood what means 'open repository', I am 
prepared to perform the necessary steps.
However, I am a total newcomer, and I would greatly appreciate any suggestion.

To frame the request, please read the following.

BioBlender was initially developed by our group (SciVis), with the 
contribution of Mike Pan, as a special version of Blender capable of 
dealing with molecules, which are complex object, composed of many 
(up to thousands) atoms, each one connected in a specific way to some 
others. This was a branch of Blender 2.5 (patched, called BioBlender 
V0.6, available <http://www.bioblender.eu/download/>here)
A couple of years ago, we decided to make an AddOn, and developed 
BioBlender 1.0 (can download <http://www.bioblender.eu/download/>here)

That's where the problems are:
1. Proteins with more than few hundreds atoms take forever to build, 
due to the updating of the dependency graph each time an atom is added.
2. MLP (Molecular lipopohilic potential) cannot be mapped to the 
mesh, because the vertices are not listed (this I am not sure I 
perfectly understand).

In the meantime, we wanted to add some more features to BioBlender, 
first of all the capability of  importing and handling two molecular 
objects in  an independent way in the same scene. This led to 
BioBlender 2.0 which does provide some additional features, but still 
has the same problems of BB 1.

We (myself and Davide) are willing to do whatever it takes, as long 
as my interventions are likely to solve problems, rather than creating ones :)
Given my background and preparation, I am not sure how much that will 
be, but rest assured that i will do my best.
Thanks in advance

Monica and Davide

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