
Formal Systems in Biology - tablet
https://github.com/prathyvsh/formal-systems-in-biology
======
ulrikrasmussen
The first entry on this list is McCulloch-Pitts nerve nets whose expressive
power were analysed by S.C. Kleene [1]. In his article he coined the term
"regular events" for the class of languages that could be expressed by nerve
nets/finite automata, and this is where regular expressions got their name
from. If you have ever thought the name was strange, rest assured that Kleene
didn't actually like it either, he just couldn't think of something better at
the time:

    
    
      > We shall presently describe a class of events which we will call "regular events" (We would welcome any suggestions as to a more descriptive term.*)
      > [...]
      > * McCulloch and Pitts use the term "prehensible," introduced rather differently; but since we did not understand their definition, we did not adopt the term.
    

So, had McCulloch and Pitts been a bit clearer in their seminal paper, then
maybe it would have been called "prehensible expressions" :).

[1]
[https://www.rand.org/content/dam/rand/pubs/research_memorand...](https://www.rand.org/content/dam/rand/pubs/research_memoranda/2008/RM704.pdf)

~~~
jchrisa
This stuff got me thinking, if RegExp comes from graphs, why not use it to
process graph databases. This paper is about a year old
[https://arxiv.org/pdf/1904.11653.pdf](https://arxiv.org/pdf/1904.11653.pdf)
Can anyone point to open source implementations?

~~~
JadeNB
Reminder: please link to arXiv abstract pages, not directly to PDF.

Wang, Han, Shao, and Li - Regular expression matching on billion-node graphs;
[https://arxiv.org/abs/1904.11653](https://arxiv.org/abs/1904.11653)

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ChefboyOG
This maybe a rudimentary question, but if someone was going to study this at a
university level, what would they study?

I ask because I'm starting my masters in CS, but I've also been going to
workshops/events at a local citizen bio lab and really enjoying it. I'd really
like to go deeper into the cross-section of CS and Bio, specifically the kinds
of things listed in this repo (modeling biological phenomenon as formal
systems, using computation to simulate those systems, etc.)

But when I look at potential programs to pursue after my CS course, I get a
bit lost in all the different titles—bioinformatics, systems biology,
computational biology, etc. It's hard for an outsider in the field to discern
any meaningful delineation. Does anyone with experience in the field know what
category of study these resources would fall under, from a university
perspective?

~~~
GregarianChild
I recommend looking at Luca Cardelli's work [1]. He's probably the leading
researcher in the intersection of CS and biology, in the sense of modelling
biological phenomenon as formal systems. Some of his lectures are online [2].
He's extremely approachable in my experience, so don't hesitate to contact him
if you want to educate yourself more in this field.

[1] [http://lucacardelli.name/](http://lucacardelli.name/)

[2]
[https://www.youtube.com/watch?v=o8q7kFeGUTM](https://www.youtube.com/watch?v=o8q7kFeGUTM)

~~~
nextos
His paper Abstract Machines of Systems Biology [1] is a wonderful, only
slightly outdated, of what the field might be able to achieve in the future.

I think and hope program analysis, abstract interpretation and friends will
make a comeback to biology. Definitely topics covered in CS not in
bioinformatics, which IMHO tends to be too applied for a first or second
degree. I'd rather stick to the basics.

[1]
[http://lucacardelli.name/Papers/Abstract%20Machines%20of%20S...](http://lucacardelli.name/Papers/Abstract%20Machines%20of%20Systems%20Biology%20%28Draft%29.pdf)

~~~
GregarianChild
Probabilistic model checking of (models of) biological systems is definite
done by Luca's group:

\- Design and Analysis of DNA Strand Displacement Devices using Probabilistic
Model Checking
[http://lucacardelli.name/Papers/Design%20and%20Analysis%20of...](http://lucacardelli.name/Papers/Design%20and%20Analysis%20of%20DNA%20Circuits.pdf)

\- Central Limit Model Checking
[http://lucacardelli.name/Papers/Central%20Limit%20Model%20Ch...](http://lucacardelli.name/Papers/Central%20Limit%20Model%20Checking.pdf)

------
fsiefken
I was wondering if there was any work in the field of evolving 'creatures'
moving in a virtual space, beyond what Karl Sims did 23 years ago.
[https://www.karlsims.com/evolved-virtual-
creatures.html](https://www.karlsims.com/evolved-virtual-creatures.html)
[https://www.karlsims.com/galapagos/index.html](https://www.karlsims.com/galapagos/index.html)

It would be nice if Karl Sims could open source it as it is really inspiring
visual example in the field of Artificial Life, next to seeing the generations
of metuselahs unfolding in Conway's game of life

Another interesting article in the field of Artificial Life:
[https://arxiv.org/pdf/1803.03453.pdf](https://arxiv.org/pdf/1803.03453.pdf)

~~~
rzzzt
"Flexible Muscle-Based Locomotion for Bipedal Creatures":
[https://www.goatstream.com/research/papers/SA2013/](https://www.goatstream.com/research/papers/SA2013/)

------
carapace
"What Bodies Think About: Bioelectric Computation Outside the Nervous System"

[https://www.youtube.com/watch?v=RjD1aLm4Thg](https://www.youtube.com/watch?v=RjD1aLm4Thg)

[https://news.ycombinator.com/item?id=18736698](https://news.ycombinator.com/item?id=18736698)

and

"Team Builds the First Living Robots, Tiny 'xenobots' assembled from cells..."

[https://www.uvm.edu/uvmnews/news/team-builds-first-living-
ro...](https://www.uvm.edu/uvmnews/news/team-builds-first-living-robots)

[https://news.ycombinator.com/item?id=22040150](https://news.ycombinator.com/item?id=22040150)

~~~
Eugeleo
I LOVE the first talk, I think I discovered it on HN. I study bioinformatics
and had no idea something like that existed.

~~~
carapace
I'd wager it's the most important and most obscure research being done today.
Can you imagine being able to regrow a limb!? :-D

------
ArtWomb
A-Life 2020 is virtual this summer (Jul 13-18). For all interested in lifting
the veil between its and bits ;)

[https://vermontcomplexsystems.org/events/ALIFE-2020/](https://vermontcomplexsystems.org/events/ALIFE-2020/)

------
Jhsto
Do you think that software should be architected as autonomous agents for it
to scale infinitely? I watched an Alan Kay video [1] some time back. In the
video, he had an argument about how software systems cannot scale unless the
basis is the most complex "computation" system that we know -- that system
being our own biological system.

[1]:
[https://www.youtube.com/watch?v=NdSD07U5uBs](https://www.youtube.com/watch?v=NdSD07U5uBs)

~~~
uoaei
To limit complexity in complex systems design, you need to be able to create
agents which perform simple functions based on well-defined inputs. You can
have a few different types of those agents interacting, and each should be
discrete and be able to "survive" in an adequate "environment". Then the
system, if designed correctly, can become much greater than the sum of its
parts but you retain the relative simplicity to monkey around with the
internals of the agents as well as the reservoirs to which they're attached,
etc. Nature has seemed to become a system where iterative improvement is
performed by virtue of the finite life cycle and sexual reproduction
(including all the ways that DNA shuttles around the necessary source code).

------
ImaCake
I love the neuron simulator linked under McCulloch and Pitts [0]. Very fun to
play around with and build your own networks. Reminds me of Conway's Game of
Life and Minecraft redstone.

0\. [https://github.com/prathyvsh/formal-systems-in-
biology](https://github.com/prathyvsh/formal-systems-in-biology)

------
twic
At the end it just says:

> Prior Art

> Ramón y Cayal

> Golgi

Those guys did a hell of a lot of stuff, so sure!

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steve_gh
Wow - takes me back to my PhD - I think I must have read everything on that
list that was published before 2000.

Wonderful stuff!

Steve

~~~
qnsi
hey Steve,

What was your thesis about?

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PaulDavisThe1st
I'm not sure why, but I feel certain that Ilya Prigogine's work on non-
equilibrium systems deserves to be on this list.

~~~
prathyvsh
Thanks for the note! I have added this to research section.

------
bingerman
Looks interesting, gotta take a closer look in the summer.

I think it's Stanislaw (Ulam) not Stainslaw.

~~~
qnsi
it should be Stanisław Ulam if we want to be hyper precise :)

