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Formal Systems in Biology

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Re: Formal Systems in Biology

#21

Post by Amygaz »

ChefboyOG wrote: post #15

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 form…

Lots of statistic. Especially anything to do with clustering, and how to analyze and compare gene and protein expression networks from various species, or tissues. Those are particularly important in this COVID-19 era.

In term of general network analysis and visualization, I think logic, symbolism, Petri net, are underutilized. Probably because they require more CS and Math type of trained people to work on those than your typical biologist becoming bioinformatician learned to handle.

Re: Formal Systems in Biology

#22

Post by jchrisa »

ulrikrasmussen wrote: post #13

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…

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 Can anyone point to open source implementations?

Re: Formal Systems in Biology

#23

Post by JadeNB »

jchrisa wrote: post #22
ulrikrasmussen wrote: post #13

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…

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 Can anyone point to open source implementations?

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

Re: Formal Systems in Biology

#24

Post by GregarianChild »

ChefboyOG wrote: post #15

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 form…

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/

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

Re: Formal Systems in Biology

#25

Post by __roland__ »

GregarianChild wrote: post #24
ChefboyOG wrote: post #15

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 form…

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/ [2] https://www.youtube.com/wa…

Totally agree. I think his paper "Can a Systems Biologist Fix a Tamagotchi?" is really nice, shows some of the fundamental conceptional issues and very fun reading nonetheless: http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.131...

Re: Formal Systems in Biology

#26

Post by nextos »

GregarianChild wrote: post #24
ChefboyOG wrote: post #15

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 form…

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/ [2] https://www.youtube.com/wa…

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...

Re: Formal Systems in Biology

#27

Post by GregarianChild »

nextos wrote: post #26
GregarianChild wrote: post #24

Earlier quoted context omitted.

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/ [2] https://www.youtube.com/wa…

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://luca…

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...

- Central Limit Model Checking http://lucacardelli.name/Papers/Central%20Limit%20Model%20Ch...

Re: Formal Systems in Biology

#28

Post by uoaei »

jchrisa wrote: post #22
ulrikrasmussen wrote: post #13

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…

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 Can anyone point to open source implementations?

Is this not how SPARQL or other graph query languages work?

Re: Formal Systems in Biology

#29

Post by uoaei »

Jhsto wrote: post #5

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

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).

Re: Formal Systems in Biology

#30

Post by bglazer »

twic wrote: post #20
ChefboyOG wrote: post #15

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 form…

A lot of the stuff in the repo is pretty marginal, from the point of view of mainstream molecular/cell/developmental biology, so i don't think there is a reliable systematic way to find it. In particular, that repo collects what are basically discrete maths approaches to biology: representing living things as systems of symbols rather than differential equations. I have always found that approach intuitively appealin…

I'm curious about your thoughts (if you have any) on the boolean modeling formalism. Basically, you represent bio-molecules as having two states: active and inactive. Their states change according to boolean logic update rules that are determined by the state of other molecules in the system. You end up with a very simple dynamical system. Theoretical biologists have been working with Boolean models for >15 years [1]. Boolean circuits also have some pretty deep connections to theoretical computer science [2]. The goal of this very simple formalism is to get the structure of a system, while retaining much of the quantitative behavior. How productive this is depends on your perspective, I guess.

Also, that's a pretty uncharitable view of systems biology. It seems clear to me that understanding even moderately complex phenotypes practically requires models of biology that include many molecules, with significant feedback loops. Further we see emergent biological behavior across multiple scales of time and space, from milli-second long protein-protein interactions to multi-year developmental processes. Systems biology is basically just studying biology while taking all of that into account. That seems worth studying to me, especially given the ineffectiveness of our current therapies in managing most diseases.

So, I'm interested in what parts of systems biology you would describe as "smoke and mirrors".

[1] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6388622/pdf/nih... [2] https://www.quantamagazine.org/mathematician-solves-computer...

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