This has been out for a while. Would be interesting to see the next steps.
Yeah, I haven't updated the site in a while. (This really wasn't the best time for a Hacker News blitz. I was just telling my friend that Nemaload hadn't been on HN yet, as far as I knew, and he simply decided to fix that pronto.) But there have been plenty of developments since November (when I think I last updated the site). I have access to a few candidate strains for pan-neuronal calcium imaging (though the genet…
Show HN: My friend's project to simulate an entire C. Elegans
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Re: Show HN: My friend's project to simulate an entire C. Elegans
#12Earlier quoted context omitted.
Doesn't seem to be same thing. OpenWorm is computer simulation, while the OP plans to build a model based on observing an actual living individual [1]. [1] http://nemaload.davidad.org/about
That's about right. My end product is also a computer simulation, as far as that goes, but I'm taking an obsessively data-driven approach, motivated by the advent of new technologies for single-neuron measurement and perturbation in living, behaving animals. Meanwhile, OpenWorm is taking a bottom-up approach, driven by physics and other first principles. We'll meet in the middle eventually.
BTW, what you're attempting blew my mind away. That's a nice hack involving many different disciplines, it will be amazing if you can pull this off.
Re: Show HN: My friend's project to simulate an entire C. Elegans
#13Earlier quoted context omitted.
Doesn't seem to be same thing. OpenWorm is computer simulation, while the OP plans to build a model based on observing an actual living individual [1]. [1] http://nemaload.davidad.org/about
That's about right. My end product is also a computer simulation, as far as that goes, but I'm taking an obsessively data-driven approach, motivated by the advent of new technologies for single-neuron measurement and perturbation in living, behaving animals. Meanwhile, OpenWorm is taking a bottom-up approach, driven by physics and other first principles. We'll meet in the middle eventually.
yo david, long time no talk.. did you ever get a chance to make use of this data set?
ftp://anonymous@ftp.mrc-lmb.cam.ac.uk/pub/tjucikas/wormdatabase/results-12-06-08/Laura%20Grundy
It's a few thousand hours of videos of the worms under different stimulation conditions for observing/identifying common behaviors.
We miss you in IRC.
Re: Show HN: My friend's project to simulate an entire C. Elegans
#14The about page [1] is very interesting. "3. Providing a foundation for uploading research .... If it can be done for a worm, the next steps are to attempt a zebrafish, then a fruit fly, then a honeybee, then a mouse, then a dog, then a macaque monkey, then a chimpanzee, and, ultimately, a human. " -- that really fascinate me.
Isn't that awesome? But ... "the philosophical assumptions fail, and human immortality through uploading is fundamentally impossible".
Could anybody explain this a little bit?
Re: Show HN: My friend's project to simulate an entire C. Elegans
#15The about page [1] is very interesting. "3. Providing a foundation for uploading research .... If it can be done for a worm, the next steps are to attempt a zebrafish, then a fruit fly, then a honeybee, then a mouse, then a dog, then a macaque monkey, then a chimpanzee, and, ultimately, a human. " -- that really fascinate me. Isn't that awesome? But ... "the philosophical assumptions fail, and human immortality throu…
The link in the sidebar offers a reasonable elaboration: http://nemaload.davidad.org/about/philosophy
Re: Show HN: My friend's project to simulate an entire C. Elegans
#16Sounds really interesting. You could try to secure additional funding for this project via Microryza ( http://www.microryza.com/ ), which is a kickstarter for scientific research.
I do not think funding is David's problem :-).
Re: Show HN: My friend's project to simulate an entire C. Elegans
#17[deleted]
Re: Show HN: My friend's project to simulate an entire C. Elegans
#18Earlier quoted context omitted.
Yeah, I haven't updated the site in a while. (This really wasn't the best time for a Hacker News blitz. I was just telling my friend that Nemaload hadn't been on HN yet, as far as I knew, and he simply decided to fix that pronto.) But there have been plenty of developments since November (when I think I last updated the site). I have access to a few candidate strains for pan-neuronal calcium imaging (though the genet…
$ !! > http://nemaload.davidad.org/news
OK, I can't argue with that. https://nemaload.davidad.org/news/2013-developments
Re: Show HN: My friend's project to simulate an entire C. Elegans
#19The about page [1] is very interesting. "3. Providing a foundation for uploading research .... If it can be done for a worm, the next steps are to attempt a zebrafish, then a fruit fly, then a honeybee, then a mouse, then a dog, then a macaque monkey, then a chimpanzee, and, ultimately, a human. " -- that really fascinate me. Isn't that awesome? But ... "the philosophical assumptions fail, and human immortality throu…
The jump from honeybee to mouse is enormous - much larger than any of the other jumps except chimpanzee to human.
Maybe try lizard in between them.
Re: Show HN: My friend's project to simulate an entire C. Elegans
#20Sounds really interesting. You could try to secure additional funding for this project via Microryza ( http://www.microryza.com/ ), which is a kickstarter for scientific research.
Side note, I used to do work with CAD systems for simulating/building gene circuits. I can't wait until we move from open tools (Tinkercell, Biobricks, Genome Compiler, etc) to fully-modeled open platforms for organisms. Imagine having the latest build for E.Coli or C.Elegans, or a package manager to organize them, at your fingertips so that you can hack away at new designs.
It makes you wonder, with so many people independently studying and creating observed and simulated data, are there centralized places to aggregate and share these?