
Show HN: My friend's project to simulate an entire C. Elegans - SlyShy
http://nemaload.davidad.org/
======
apl
While interesting (especially from a funding perspective!), most of these
approaches aren't quite as ground-breaking as one might think. Neuroscientists
in academia _are_ doing most of these things. For optogenetics, see
Deisseroth's work; for in vivo Ca2+ imaging in nematodes, refer to the work of
Bargmann as well as the various Witesides collaborations involving
microfluidics; pan-neuronal in vivo imaging is currently being pioneered by
Engert at Harvard and a couple of Janelia Farm labs.

These are massive efforts, and involve horrendous heaps of diligent busywork.
This makes me the boring naysayer, but please don't be distracted by the
startup-like appearance and the peculiar financing situation. It's possible
but unlikely that the major obstacle here is simply the combination of
available techniques!

Honestly, what I'm most curious about are his thoughts on model-driven
interrogation of an in vivo system -- biologists, and even computational
neuroscientists, are a bit too hesitant when it comes to letting computers
find and test hypotheses. In the age of highly advanced genetic techniques
(e.g., binary expression systems in Drosophila or zebrafish) and 2-photon
imaging, the process of actually evaluating hypotheses has become a bit old-
fashioned...

~~~
Hitchhiker
David's start is at 14 and not post 20 as most grad students. At minimum, he
will end up making something like Mathematica like Wolfram and at max, he will
change the world.

The Big and Little Oh of this story are both extreme events.

~~~
lmm
That's an awfully high "minimum". I knew several "geniuses" at that age (might
even qualify myself, though admittedly I was only three years ahead of par at
that age); most of them have gone on to fairly normal (though by no means
unsuccessful) careers, and a couple burned out quite spectacularly. I don't
think putting that weight of expectation on is helpful.

~~~
Hitchhiker
In deed, you remind me of Solon's warning. Perhaps the better way to put it is
he's attacking one heck of a problem - and with the right detachment to both
industry and academia - so the minimum is based more on the quality of
problems than the individual ( as unique as that is in this particular case ).

But yes, being an entrepreneur is an added layer, as you've to learn to
arrange people to attain a larger goal than just research.

And he shows signs of that even on the jobs page while avoiding the broken
method of interviewing that is oft practiced, he's almost defining a boundary
for relatively high signal from the applicants.

His fluid approach is reminiscent of the caper that the Google guys pulled at
Stanford.. and as it turns out, I think he also got funded by Larry.

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adventureloop
I love the internship application page <http://nemaload.davidad.org/jobs>. The
author does expect any candidate to be perfect before meeting, but sets out a
small set of criteria for any potential candidate to research.

Probably in the process of researching any of these topics a potential intern
would gain a good understanding of the upcoming internship.

Sometimes I wish job interviews were laid out like this.

------
netvarun
Sounds 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.

~~~
irollboozers
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?

~~~
kanzure
How is "Genome Compiler" an open tool? I hate those guys, it's not even an
actual compiler. or open. If they wanted to do something useful, then yeah I
would shoot for that package management concept.

~~~
irollboozers
Hmm - it seems those guys are not what I remembered/thought they were. I think
they were somehow tied to the open bio standards project which is what I was
thinking of.

~~~
kanzure
Oh definitely, they pump out lots of confusing/wrong marketing all the time. I
can see how they would get into that sort of list. Edit: you have a phd in
pirate science?

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dylangs1030
This isn't directly related, but he enrolled in an MIT graduate program at the
age of _14_? That's incredible.

I would love to see how this project progresses. It has fascinating
implications for artificial intelligence and singularity.

~~~
sweettea
...and was fired from it.

~~~
DaniFong
This is not actually true.

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songgao
The 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?

[1] <http://nemaload.davidad.org/about>

~~~
ars
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.

~~~
davidad_
I'm tempted to point out that reptiles are so distinct from either mammals or
insects that they wouldn't be a natural stepping stone. But some of my
esteemed colleagues advocate jumping from _zebrafish_ to mouse, and I just
realized they're probably thinking along similar lines: why try to figure out
insects along the way from fish to mammals?

Personally, though, I'm limiting my scope to the worm (at least for now!). The
particular path which is best to take beyond that is much less clear.

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soccerniru
Interesting .. although a similar project already exists
(<http://www.openworm.org/>), and is, from a cursory glance, much more
developed.

~~~
hcarvalhoalves
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>

~~~
davidad_
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.

~~~
kanzure
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.

~~~
bntlyb
The videos and statistics, as well as a description of the setup used for the
recordings can be found here:

<http://wormbehavior.mrc-lmb.cam.ac.uk/>

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codeulike
So its not just 'simulate', its more like 'virtualise'. They want to examine
neurons in a real worm in real time and then model that. You know all those
sci-fi books where people upload their minds into software? This worm is going
to get there first. Hope they give it somewhere nice to virtually live.

------
vitno
Oooh Exciting stuff! I've been following openworm off and on for a while now.
The projects should be extremely complementary. I hope they communicate.

(This projects is going to collect a totally new dataset)

~~~
davidad_
Yes, I know Stephen Larson and some of the other OpenWorm guys. In fact, I'm
even a member of their organization on GitHub
<[https://github.com/openworm?tab=members>](https://github.com/openworm?tab=members>).
Once both projects are a bit more developed, I expect ample opportunities for
substantive cooperation; but for now, I'm focusing on data collection
challenges, while they're focusing on simulations, visualizations, and data
management.

------
feniv
I like the "optional" hands-on challenges he listed for applicants in the jobs
page. It may end up filtering out some talented candidates (not wanting to put
in this much effort for one application), but it will certainly call out to
the tinkerers and hobbyists who would do those tasks for fun anyway.

~~~
ProblemFactory
The challenges are great because it's not just another meaningless programming
test. Instead it's "week 1" of the internship, where you learn the background
necessary to start work on the project. And even if you don't get the
position, all those tasks are useful for a grad student in neuroscience or
bioinformatics.

------
Hitchhiker
This has been out for a while. Would be interesting to see the next steps.

~~~
davidad_
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 genetic engineering is still an
ongoing optimization process) and have collected a couple of large datasets,
one on a light-sheet microscope and one on a light-field microscope. Much of
the data is useless, and we're still working on the algorithms to extract
signals from it, as well as the infrastructure for opening it up for
distribution. But there will certainly be more publicly visible activity soon
(June at the latest).

~~~
rmrfrmrf
$ !! > <http://nemaload.davidad.org/news>

~~~
davidad_
OK, I can't argue with that.
<https://nemaload.davidad.org/news/2013-developments>

~~~
davidad_
Oops, didn't mean to link to the HTTPS-restricted area.
<[http://nemaload.davidad.org/news/2013-developments>](http://nemaload.davidad.org/news/2013-developments>),
but it's basically just what I wrote above, as suggested (-:

