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BioBlender: Blender for Biologists

bioblender.eu

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Re: BioBlender: Blender for Biologists

#21

Post by Evgeny »

clarle wrote: post #8
goldfeld wrote: post #7

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 (g…

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 com…

Rosalind [1] (previously posted on HN) is pretty good for something like a Project Euler for bioinformatics

I think I have a new hobby!

Re: BioBlender: Blender for Biologists

#22

Post by 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

Re: BioBlender: Blender for Biologists

#25

Post by jamessb »

archgoon wrote: post #11
car wrote: post #4

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

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…

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.

Re: BioBlender: Blender for Biologists

#26

Post by pvaldes »

jostmey wrote: post #19

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.

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.

Re: BioBlender: Blender for Biologists

#27

Post by car »

archgoon wrote: post #11
car wrote: post #4

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

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…

Thanks for the reply, but of course this question was in the context of the parent.

Just fyi, mammalian genes are usually expressed in mammalian cells, not bacteria, because of posttranslational modification.

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