

BioBlender: Blender for Biologists - rocco
http://bioblender.eu/

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clarle
Sounds really cool!

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/>

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pedrobeltrao
I agree with the need for better visualization tools in biology. There is an
interesting group/project started at UCSF and headed by Graham Johnson
(www.grahamjlab.org/). Some of these tools are still closer to art than
science but I think it is really worth the investment. It is clear that these
will help us think about biological objects.

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goldfeld
I have been wanting to get into bioinformatics, but there's something I miss
coming from webdev: the ability to create something over a few weeks. I don't
mean I want to discover something new, and I'm not sure I'd want to get into
research at all. I wanted to be able to experiment and __see __stuff show up
on a screen related to the structures and formulas I'm learning. Some fun and
practical, even if not very useful (games?), project I can tackle while
learning bioinformatics. Is there such a thing?

~~~
clarle
Rosalind [1] (previously posted on HN) is pretty good for something like a
Project Euler for bioinformatics. The problems are pretty similar to the
introductory computational biology course at my school for upper-year
undergrads and first-year grad students.

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!

[1]: <http://rosalind.info/>

~~~
archgoon
That is absolutely fantastic! Kudos to UCSD and Saint Petersburg Academic
University for creating such an awesome educational resource! And thank you
for pointing me to it!

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anigbrowl
(Applause)

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.

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shiven
Great to see so many structural biologists and crystallographers on HN!

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!

[0] <http://pymolwiki.org/index.php/Blender>

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epenn
This looks interesting but doesn't appear to have been updated in a year and a
half unfortunately.

~~~
cing
It's my understanding that this project has been superseded by ePMV
(<http://epmv.scripps.edu/>).

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_ZeD_
Cool!

how is this comparable with avogadro?

<http://avogadro.openmolecules.net/wiki/Main_Page>

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car
Does anyone know how to 3D-print protein structures?

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archgoon
You do not 3D-print protein structures (unless you mean 3D models of proteins
in which case ignore the rest of this post). Not in the sense of "here's an
arbitrary position of atoms, give me a molecule". There's a reason why
Folding@Home takes a lot of processing power. It's very hard to figure out how
chains of amino acids will interact with themselves.

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.

<http://www.genscript.com/gene_synthesis.html>

~~~
michaelbuddy
"will manufacture a specified gene, and send you back frozen plasmids, which
you can then inject into your favorite bacterial host."

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.

~~~
archgoon
Not trolling! Honest!

<http://en.wikipedia.org/wiki/Plasmid#Vectors>

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jostmey
It looks really cool, but I cannot figure out how to use the program to open
up crystal structures (PDB file format) on my desktop.

~~~
pvaldes
You can glue this with a python script probably. Then, call this script from
blender converting your data to a readable result. Untested, only an idea.

