Biplab Bose
@biplabbose.bsky.social
Biologist | Bookworm | Cycloholic | Birder | Trying to understand the design principles of Life using Mathematics and Physics |
https://youtube.com/@sysbio
https://fac.iitg.ac.in/biplabbose
https://youtube.com/@sysbio
https://fac.iitg.ac.in/biplabbose
When science books cost a fortune, only publishers win. Open sharing—GitHub, arXiv—helps every learner. Isn’t it time to free ourselves from the 'medieval' prestige of being ‘published by a reputed publisher’? #scicom #edu #doingsciencd
November 15, 2025 at 7:18 AM
When science books cost a fortune, only publishers win. Open sharing—GitHub, arXiv—helps every learner. Isn’t it time to free ourselves from the 'medieval' prestige of being ‘published by a reputed publisher’? #scicom #edu #doingsciencd
Wet lab? Dry lab? I prefer the Symbolic lab.
Math-Bio isn't just HPC runs— derivations & proofs matter too. As always, Julia helps.
using Symbolics
@variables x y a b c d m n
f = [a/(1+y^n)-b*x, c/(1+x^m)-d*y]
J = Symbolics.jacobian(f,[x,y])
#Julialang #mathbio #computaionalbiology #sysbio
Math-Bio isn't just HPC runs— derivations & proofs matter too. As always, Julia helps.
using Symbolics
@variables x y a b c d m n
f = [a/(1+y^n)-b*x, c/(1+x^m)-d*y]
J = Symbolics.jacobian(f,[x,y])
#Julialang #mathbio #computaionalbiology #sysbio
November 14, 2025 at 6:03 AM
Wet lab? Dry lab? I prefer the Symbolic lab.
Math-Bio isn't just HPC runs— derivations & proofs matter too. As always, Julia helps.
using Symbolics
@variables x y a b c d m n
f = [a/(1+y^n)-b*x, c/(1+x^m)-d*y]
J = Symbolics.jacobian(f,[x,y])
#Julialang #mathbio #computaionalbiology #sysbio
Math-Bio isn't just HPC runs— derivations & proofs matter too. As always, Julia helps.
using Symbolics
@variables x y a b c d m n
f = [a/(1+y^n)-b*x, c/(1+x^m)-d*y]
J = Symbolics.jacobian(f,[x,y])
#Julialang #mathbio #computaionalbiology #sysbio
Calling any large, well-organised dataset "Systems Biology" is a bit like calling a census "social theory." Essential, powerful, and impressive — yes. But the explanations, through generalised theories/models, still have to be earned. #systemsbiology #sysbio #physicsoflife
November 13, 2025 at 4:21 AM
Calling any large, well-organised dataset "Systems Biology" is a bit like calling a census "social theory." Essential, powerful, and impressive — yes. But the explanations, through generalised theories/models, still have to be earned. #systemsbiology #sysbio #physicsoflife
PhD defense (Dramatized based on real events):
You (examiner): That statistics & conclusion are wrong. Needs correction for repeated tests.
Candidate: 🤔 (flustered).
Supervisor: No issues! 😡 This work is already published.
How often do you face such a situation?
#worldofbiologists #bio
You (examiner): That statistics & conclusion are wrong. Needs correction for repeated tests.
Candidate: 🤔 (flustered).
Supervisor: No issues! 😡 This work is already published.
How often do you face such a situation?
#worldofbiologists #bio
November 12, 2025 at 6:06 AM
PhD defense (Dramatized based on real events):
You (examiner): That statistics & conclusion are wrong. Needs correction for repeated tests.
Candidate: 🤔 (flustered).
Supervisor: No issues! 😡 This work is already published.
How often do you face such a situation?
#worldofbiologists #bio
You (examiner): That statistics & conclusion are wrong. Needs correction for repeated tests.
Candidate: 🤔 (flustered).
Supervisor: No issues! 😡 This work is already published.
How often do you face such a situation?
#worldofbiologists #bio
My physicist friends love universality — until the system starts voting, reproducing, or trading stocks 🤪
#complexsystem #physicsoflife #physicsoflivingmatter #systemsbiology
#complexsystem #physicsoflife #physicsoflivingmatter #systemsbiology
November 11, 2025 at 7:47 AM
My physicist friends love universality — until the system starts voting, reproducing, or trading stocks 🤪
#complexsystem #physicsoflife #physicsoflivingmatter #systemsbiology
#complexsystem #physicsoflife #physicsoflivingmatter #systemsbiology
A = [1, 2, 3]
B = [3, 4, 5]
x = 9
x ∈ A ∪ B # -> false
Writing code using symbols in Julia feels like scribbling in a math notebook — except this one actually runs. It takes some time to get habituated, but then you get hooked.
#julialang #computing
B = [3, 4, 5]
x = 9
x ∈ A ∪ B # -> false
Writing code using symbols in Julia feels like scribbling in a math notebook — except this one actually runs. It takes some time to get habituated, but then you get hooked.
#julialang #computing
November 10, 2025 at 4:58 AM
A = [1, 2, 3]
B = [3, 4, 5]
x = 9
x ∈ A ∪ B # -> false
Writing code using symbols in Julia feels like scribbling in a math notebook — except this one actually runs. It takes some time to get habituated, but then you get hooked.
#julialang #computing
B = [3, 4, 5]
x = 9
x ∈ A ∪ B # -> false
Writing code using symbols in Julia feels like scribbling in a math notebook — except this one actually runs. It takes some time to get habituated, but then you get hooked.
#julialang #computing
In the age of AlphaFold, should we still teach homology modeling, threading, and other classical structure prediction algorithms? In the era of generative AI, the hardest question in teaching isn’t what to include—it’s what to leave out. #teaching #education #computationalbiology #AI
November 8, 2025 at 9:05 AM
In the age of AlphaFold, should we still teach homology modeling, threading, and other classical structure prediction algorithms? In the era of generative AI, the hardest question in teaching isn’t what to include—it’s what to leave out. #teaching #education #computationalbiology #AI
With a channel capacity of one bit, cells have ruled the world for millions of years. Maybe we need a different information theory to understand them. #complexity #systemsbiology #complexsystems
November 7, 2025 at 3:27 AM
With a channel capacity of one bit, cells have ruled the world for millions of years. Maybe we need a different information theory to understand them. #complexity #systemsbiology #complexsystems
PS Dodds cheekily reimagines the entire history of science as a three-volume saga. Beneath the wit lies a serious claim: complex systems aren't a fad but the long-awaited finale of scientific understanding. arxiv.org/abs/2511.00368 #complexity #systemsbiology
The Three Books of Science
We venture that the long evolution of science may be viewed as unfolding over three blurred epochs. The first epoch spans the slow, haphazard, error-ridden realization of scientific truths along with ...
arxiv.org
November 6, 2025 at 9:00 AM
PS Dodds cheekily reimagines the entire history of science as a three-volume saga. Beneath the wit lies a serious claim: complex systems aren't a fad but the long-awaited finale of scientific understanding. arxiv.org/abs/2511.00368 #complexity #systemsbiology
Robotic Experiment > Data > AI-driven [Model > Hypothesis > Experimental Design] > Robotic Experiment: This "closed-loop science" is set to become a reality soon, cutting costs & increasing efficiency. But data is not the limiting factor in Science; Our limited abstraction & generalization are.
November 5, 2025 at 8:24 AM
Robotic Experiment > Data > AI-driven [Model > Hypothesis > Experimental Design] > Robotic Experiment: This "closed-loop science" is set to become a reality soon, cutting costs & increasing efficiency. But data is not the limiting factor in Science; Our limited abstraction & generalization are.
Yes, current LLMs hallucinate and fail in many silly tasks. Current AI is surely not the same as human 'intelligence.' But why do we get hyperactive on social media with glee every time we find an error by an AI agent, LLM, or robot? Our existential crisis?
November 4, 2025 at 5:16 AM
Yes, current LLMs hallucinate and fail in many silly tasks. Current AI is surely not the same as human 'intelligence.' But why do we get hyperactive on social media with glee every time we find an error by an AI agent, LLM, or robot? Our existential crisis?
Julia keeps it rational.
1//3 + 1//6 == 1//2
Exact math. No floating-point drama.
#JuliaLang #lovingJulia #sillyposts
1//3 + 1//6 == 1//2
Exact math. No floating-point drama.
#JuliaLang #lovingJulia #sillyposts
November 3, 2025 at 7:47 AM
Julia keeps it rational.
1//3 + 1//6 == 1//2
Exact math. No floating-point drama.
#JuliaLang #lovingJulia #sillyposts
1//3 + 1//6 == 1//2
Exact math. No floating-point drama.
#JuliaLang #lovingJulia #sillyposts
Statistical physics was built to understand gases.
Now we use it to understand flocks, tissues, and tumors. Same mathematics, new meanings—order out of interaction. Perhaps we should develop new thermodynamic variables beyond V, P, and T that are more suitable for living systems. #complexsystems
Now we use it to understand flocks, tissues, and tumors. Same mathematics, new meanings—order out of interaction. Perhaps we should develop new thermodynamic variables beyond V, P, and T that are more suitable for living systems. #complexsystems
November 2, 2025 at 4:36 AM
Statistical physics was built to understand gases.
Now we use it to understand flocks, tissues, and tumors. Same mathematics, new meanings—order out of interaction. Perhaps we should develop new thermodynamic variables beyond V, P, and T that are more suitable for living systems. #complexsystems
Now we use it to understand flocks, tissues, and tumors. Same mathematics, new meanings—order out of interaction. Perhaps we should develop new thermodynamic variables beyond V, P, and T that are more suitable for living systems. #complexsystems
Between the animate and the inanimate lies a missing theory — not of matter, but of matter becoming intention. Or the concept of teleonomy is just another trap? Possibly! #complexity #physicsoflife
November 1, 2025 at 12:29 AM
Between the animate and the inanimate lies a missing theory — not of matter, but of matter becoming intention. Or the concept of teleonomy is just another trap? Possibly! #complexity #physicsoflife
Physicists see the forest, mathematicians see the pattern, & biologists... name every tree, catalog leaf shapes, & write three papers on bark texture before asking why forests exist. Wish my friends from the Biology community would read and re-read the old classic: sciencedirect.com/science/arti...
Can a biologist fix a radio?—Or, what I learned while studying apoptosis
sciencedirect.com
October 31, 2025 at 8:01 AM
Physicists see the forest, mathematicians see the pattern, & biologists... name every tree, catalog leaf shapes, & write three papers on bark texture before asking why forests exist. Wish my friends from the Biology community would read and re-read the old classic: sciencedirect.com/science/arti...
If I want to teach undergraduate students about driven non-equilibrium systems, which two toy models should I choose? The mathematics must be intuitive, and the simulations must be easy. What do you suggest? #statmech #physics #complexsystem #systemsbiology
October 30, 2025 at 4:57 AM
If I want to teach undergraduate students about driven non-equilibrium systems, which two toy models should I choose? The mathematics must be intuitive, and the simulations must be easy. What do you suggest? #statmech #physics #complexsystem #systemsbiology
In #Julia, even the script evolves with time (without mutation) 😃
julia> @time sum(rand(10^7))
[0.086688 seconds, 57.81% gc time]
julia> @time sum(rand(10^7))
[0.026221 seconds, 29.82% gc time]
.
.
julia> @time sum(rand(10^7))
[0.017704 seconds, 2.34% gc time]
#Julialang #computing
julia> @time sum(rand(10^7))
[0.086688 seconds, 57.81% gc time]
julia> @time sum(rand(10^7))
[0.026221 seconds, 29.82% gc time]
.
.
julia> @time sum(rand(10^7))
[0.017704 seconds, 2.34% gc time]
#Julialang #computing
October 29, 2025 at 10:03 AM
In #Julia, even the script evolves with time (without mutation) 😃
julia> @time sum(rand(10^7))
[0.086688 seconds, 57.81% gc time]
julia> @time sum(rand(10^7))
[0.026221 seconds, 29.82% gc time]
.
.
julia> @time sum(rand(10^7))
[0.017704 seconds, 2.34% gc time]
#Julialang #computing
julia> @time sum(rand(10^7))
[0.086688 seconds, 57.81% gc time]
julia> @time sum(rand(10^7))
[0.026221 seconds, 29.82% gc time]
.
.
julia> @time sum(rand(10^7))
[0.017704 seconds, 2.34% gc time]
#Julialang #computing
Gradient systems give you landscapes. Non-gradient systems give you the weather. That's why cellular fate feels more like climate chaos than a downhill stroll on Waddington's landscape. #systemsbiology #dynamicalsystems #complexsystems
October 28, 2025 at 5:31 AM
Gradient systems give you landscapes. Non-gradient systems give you the weather. That's why cellular fate feels more like climate chaos than a downhill stroll on Waddington's landscape. #systemsbiology #dynamicalsystems #complexsystems
Reposted by Biplab Bose
How can we design complex computational systems using synthetic biology? Check our paper, where we use space as a computational element, dramatically reducing communication requirements while allowing modularity, reusability, scalability & minimal cell engineering.
journals.plos.org/ploscompbiol...
journals.plos.org/ploscompbiol...
October 26, 2025 at 8:08 PM
How can we design complex computational systems using synthetic biology? Check our paper, where we use space as a computational element, dramatically reducing communication requirements while allowing modularity, reusability, scalability & minimal cell engineering.
journals.plos.org/ploscompbiol...
journals.plos.org/ploscompbiol...
Embryonic development is robust but fluctuations and variations are inevitable. Nature smartly sells those variations as features not bug.
#systemsbiology #complexsystems
#systemsbiology #complexsystems
October 27, 2025 at 3:19 AM
Embryonic development is robust but fluctuations and variations are inevitable. Nature smartly sells those variations as features not bug.
#systemsbiology #complexsystems
#systemsbiology #complexsystems
LLMs don’t live—yet they learn, adapt, and hallucinate. Strange! Is not it? Biologists need to rethink the key ideas of Life. #physicsoflife #mathbio #complexity #systemsbiology
October 26, 2025 at 4:36 AM
LLMs don’t live—yet they learn, adapt, and hallucinate. Strange! Is not it? Biologists need to rethink the key ideas of Life. #physicsoflife #mathbio #complexity #systemsbiology
Does a cell have a 'mind' - say a proto-mind or basal cognition? Although it was once a fringe idea, recent experimental and mathematical works are accumulating in its support. Here is an interesting recent work: www.biorxiv.org/content/10.1... #complexsystem #systemsbiology #sysbio
Engineering Basal Cognition: Minimal Genetic Circuits for Habituation, Sensitization, and Massed–Spaced Learning
Cognition is often associated with complex brains, yet many forms of learning—such as habituation, sensitization, and even spacing effects—have been observed in single cells and aneural organisms. The...
www.biorxiv.org
October 25, 2025 at 9:45 AM
Does a cell have a 'mind' - say a proto-mind or basal cognition? Although it was once a fringe idea, recent experimental and mathematical works are accumulating in its support. Here is an interesting recent work: www.biorxiv.org/content/10.1... #complexsystem #systemsbiology #sysbio
Reposted by Biplab Bose
Data-driven modeling of complex biological systems
Thank you for joining us at today's NITMB Seminar with Cody FitzGerald, James S. McDonnell Foundation Postdoctoral Fellow at Northwestern University!
📽️ Watch the seminar recording - www.youtube.com/watch?v=B2Y9...
Thank you for joining us at today's NITMB Seminar with Cody FitzGerald, James S. McDonnell Foundation Postdoctoral Fellow at Northwestern University!
📽️ Watch the seminar recording - www.youtube.com/watch?v=B2Y9...
October 24, 2025 at 9:27 PM
Data-driven modeling of complex biological systems
Thank you for joining us at today's NITMB Seminar with Cody FitzGerald, James S. McDonnell Foundation Postdoctoral Fellow at Northwestern University!
📽️ Watch the seminar recording - www.youtube.com/watch?v=B2Y9...
Thank you for joining us at today's NITMB Seminar with Cody FitzGerald, James S. McDonnell Foundation Postdoctoral Fellow at Northwestern University!
📽️ Watch the seminar recording - www.youtube.com/watch?v=B2Y9...