We usually just use PyMOL [1] in our lab, but it looks like BioBlender takes PyMOL, Blender, and a few other structural biology and builds on top of both of them.
It looks like the biggest contribution from BioBlender is that it takes properties such as electrostatic potential and combines it with Blender's physics engine to better simulate movement when creating molecular animations. Most of our work usually involves just examining the 3D structure of a protein, so I don't usually create animations, but this is definitely a really useful tool to do so if any lab might ever need to do something like that.
We really do need more people dedicated to just purely better visualization software in the biological community. A lot of interesting hypotheses often start from just rotating around 3D structures, and making it easier to do so can only help.
[1]: http://pymol.org/
It's a really good way to get a good overview of the field, and what some of the problems have been already solved in bioinformatics. It's definitely best to combine it with a more traditional textbook such as "Introduction to Computational Biology" (Haubold and Wiehe) or "Biological Sequence Analysis" (Mitchison, Krogh, Durbin, and Eddy).
Hope that helps!
Rosalind is a great way of improving your knowledge of biology and CS. It is quite cool to see computer science and mathematics problems and techniques applied to bioinformatics.
I think I have a new hobby!
But here's the rub: if you want to learn "bioinformatics", you're going to have to accept that most of the work is inherently not visual. I worked in about the most shiny, graphical part of biology possible (protein structure), and maybe only 20% of the work involved spinning molecules on a screen.
The real work of bioinformatics involves thinking very hard about problems that are deeply mathematical. The visualization part is strictly secondary -- though it gets the most attention, for obvious reasons.
I have always admired Blender in general, and interfacing it it to load molecular structures like this is genius. I hope it's the first of many such explorations. Although I'm not a biologist this is cool enough that I would install blender again just to have fun with making neat images.
PyMOL has been progressing leaps and bounds over the last few years under Jason Vertrees guidance at Schrodinger LLC. So do give it a look if you are excited about this stuff. The development model is also quite nice, in that the most avant-garde features are released in the 'incentive' version (costs money) but then are released into the open source version after the next version update, sometimes even earlier.
It has been a personal interest of mine to use Blender and PyMOL together for visualization and graphics[0].
Good luck to BioBlender and thanks for sharing on HN!
how is this comparable with avogadro?
The best you can do is do gene synthesis using a method called Oligonucleotide Synthesis
http://en.wikipedia.org/wiki/Oligonucleotide_synthesis
Using this technique, you can take an arbitrary gene sequence (ATGC sequence) and get a plasmid out of it. This will specify a sequence of amino acids that will fold into a protein. Then you just have to get a bacterial host to take it up into it's DNA and then make sure the chemical conditions of the host are right to generate your protein (you can't synthesize a protein if there aren't the right types of Amino Acids floating around, for example).
Companies like Genscript (which I found by randomly googling) will manufacture a specified gene, and send you back frozen plasmids, which you can then inject into your favorite bacterial host.
Short peptides can also be produced by solid-phase synthesis: there are automated machines (peptide synthesisers) that produce a peptide with any arbitrary sequence from the constituent amino acids.
Just fyi, mammalian genes are usually expressed in mammalian cells, not bacteria, because of posttranslational modification.
As a fan of the Bioshock series, I wasn't sure if you were trolling here or I'm just completely unaware of the current state of real biology.
Use pdb2stl. It's part of mayavi.
