7 ms·

BioBlender: Blender for Biologists

109 points by rocco 14y ago

anigbrowl 14y ago
(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.
epenn 14y ago
This looks interesting but doesn't appear to have been updated in a year and a half unfortunately.
- cing 14y ago
  It's my understanding that this project has been superseded by ePMV (http://epmv.scripps.edu/ http://epmv.scripps.edu/).
car 14y ago
Does anyone know how to 3D-print protein structures?
- jamesmcbennett 14y ago
  I can connect you to http://www.deskgen.com/ http://www.deskgen.com/ who might be able to help?
- kanzure 14y ago
  > Does anyone know how to 3D-print protein structures? Use pdb2stl. It's part of mayavi.
  - car 14y ago
    Thanks for your reply, most helpful!
- archgoon 14y ago
  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 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 http://www.genscript.com/gene_synthesis.html
  - michaelbuddy 14y ago
    "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 14y ago
      Not trolling! Honest! http://en.wikipedia.org/wiki/Plasmid#Vectors http://en.wikipedia.org/wiki/Plasmid#Vectors
  - jamessb 14y ago
    Depending on what exactly you want, you may be able to use a cell free translation system rather than transfecting a bacterial host (or yeast, or whatevever else). 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.
- whyenot 14y ago
  Most people use ribosomes to do this.
  - car 14y ago
    Who makes these, and where can I order one?
clarle 14y ago
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/ http://pymol.org/
- kayhi 14y ago
  Great to see some other crystallographers in the crowd, also worth checking out is Discovery Studio Visualizer.
- thundara 14y ago
  What worth would the 3d simulations produced by Blender's physics engine be? I'd imagine that they wouldn't even compare to those produced by full MD simulations, which are already of debatable correctness depending on the size of the system, force field + parameters, time step, solvent, etc...
- pedrobeltrao 14y ago
  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.
goldfeld 14y ago
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 14y ago
  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/ http://rosalind.info/
  - Evgeny 14y ago
    Rosalind [1] (previously posted on HN) is pretty good for something like a Project Euler for bioinformatics I think I have a new hobby!
  - archgoon 14y ago
    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!
  - daniel-levin 14y ago
    +1 for this. 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.
- 14y ago
jostmey 14y ago
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 14y ago
  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.
shiven 14y ago
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 http://pymolwiki.org/index.php/Blender
_ZeD_ 14y ago
Cool! how is this comparable with avogadro? http://avogadro.openmolecules.net/wiki/Main_Page http://avogadro.openmolecules.net/wiki/Main_Page

109 points by rocco 14y ago

(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.

epenn 14y ago

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

cing 14y ago
It's my understanding that this project has been superseded by ePMV (http://epmv.scripps.edu/ http://epmv.scripps.edu/).

car 14y ago

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

jamesmcbennett 14y ago
I can connect you to http://www.deskgen.com/ http://www.deskgen.com/ who might be able to help?
kanzure 14y ago
> Does anyone know how to 3D-print protein structures? Use pdb2stl. It's part of mayavi.
- car 14y ago
  Thanks for your reply, most helpful!
archgoon 14y ago
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 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 http://www.genscript.com/gene_synthesis.html
- michaelbuddy 14y ago
  "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 14y ago
    Not trolling! Honest! http://en.wikipedia.org/wiki/Plasmid#Vectors http://en.wikipedia.org/wiki/Plasmid#Vectors
- jamessb 14y ago
  Depending on what exactly you want, you may be able to use a cell free translation system rather than transfecting a bacterial host (or yeast, or whatevever else). 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.
whyenot 14y ago
Most people use ribosomes to do this.
- car 14y ago
  Who makes these, and where can I order one?

clarle 14y ago

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/ http://pymol.org/

kayhi 14y ago
Great to see some other crystallographers in the crowd, also worth checking out is Discovery Studio Visualizer.
thundara 14y ago
What worth would the 3d simulations produced by Blender's physics engine be? I'd imagine that they wouldn't even compare to those produced by full MD simulations, which are already of debatable correctness depending on the size of the system, force field + parameters, time step, solvent, etc...
pedrobeltrao 14y ago
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.

goldfeld 14y ago

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 14y ago
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/ http://rosalind.info/
- Evgeny 14y ago
  Rosalind [1] (previously posted on HN) is pretty good for something like a Project Euler for bioinformatics I think I have a new hobby!
- archgoon 14y ago
  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!
- daniel-levin 14y ago
  +1 for this. 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.
14y ago

jostmey 14y ago

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 14y ago
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.

shiven 14y ago

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 http://pymolwiki.org/index.php/Blender

_ZeD_ 14y ago

Cool! how is this comparable with avogadro? http://avogadro.openmolecules.net/wiki/Main_Page http://avogadro.openmolecules.net/wiki/Main_Page