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
To what extent can the foundations of thermodynamics & stat physics be built purely from combinatorics and probability—without relying on the usual concepts like work, heat, and energy? Are there any textbooks that develop the theory primarily from a probabilistic perspective only?
December 5, 2025 at 7:39 AM
To what extent can the foundations of thermodynamics & stat physics be built purely from combinatorics and probability—without relying on the usual concepts like work, heat, and energy? Are there any textbooks that develop the theory primarily from a probabilistic perspective only?
Don't be clueless! Better, understand how Julia thinks:
@code_lowered 2 + 3
@code_lowered 2 + 3.0
@code_lowered 2.0 + 3.0
Code better. Code smarter.
#JuliaLang #computing #sysbio #systemsbiology #qbio
@code_lowered 2 + 3
@code_lowered 2 + 3.0
@code_lowered 2.0 + 3.0
Code better. Code smarter.
#JuliaLang #computing #sysbio #systemsbiology #qbio
December 4, 2025 at 9:26 AM
Don't be clueless! Better, understand how Julia thinks:
@code_lowered 2 + 3
@code_lowered 2 + 3.0
@code_lowered 2.0 + 3.0
Code better. Code smarter.
#JuliaLang #computing #sysbio #systemsbiology #qbio
@code_lowered 2 + 3
@code_lowered 2 + 3.0
@code_lowered 2.0 + 3.0
Code better. Code smarter.
#JuliaLang #computing #sysbio #systemsbiology #qbio
High-throughput omics studies > lots of data transformations > 5,000 correlations to be tested through experiments.
Toy models with few parameters > the design principles behind the complexity of Life.
True Systems Biology: fewer spreadsheets, more ‘Aha!’ moments. #sysbio #mathbio #physicsoflife
Toy models with few parameters > the design principles behind the complexity of Life.
True Systems Biology: fewer spreadsheets, more ‘Aha!’ moments. #sysbio #mathbio #physicsoflife
December 3, 2025 at 10:56 AM
High-throughput omics studies > lots of data transformations > 5,000 correlations to be tested through experiments.
Toy models with few parameters > the design principles behind the complexity of Life.
True Systems Biology: fewer spreadsheets, more ‘Aha!’ moments. #sysbio #mathbio #physicsoflife
Toy models with few parameters > the design principles behind the complexity of Life.
True Systems Biology: fewer spreadsheets, more ‘Aha!’ moments. #sysbio #mathbio #physicsoflife
Why burden memory? Take a sneaky peek and get the job done!
A = rand(5,5)
W = @view A[2:4,2:4] # take a peek, no copying
@views W[1:2, 1:2] .= 0 # sneakily mutate
A # check the mutation
#julialang #computing
A = rand(5,5)
W = @view A[2:4,2:4] # take a peek, no copying
@views W[1:2, 1:2] .= 0 # sneakily mutate
A # check the mutation
#julialang #computing
December 2, 2025 at 5:27 AM
Why burden memory? Take a sneaky peek and get the job done!
A = rand(5,5)
W = @view A[2:4,2:4] # take a peek, no copying
@views W[1:2, 1:2] .= 0 # sneakily mutate
A # check the mutation
#julialang #computing
A = rand(5,5)
W = @view A[2:4,2:4] # take a peek, no copying
@views W[1:2, 1:2] .= 0 # sneakily mutate
A # check the mutation
#julialang #computing
Explaining non-equilibrium systems to students: ‘Imagine a system that refuses to relax.' Students: ‘Like us?’
#justforfun #teaching #physicsoflife #physicsoflivingmatter
#justforfun #teaching #physicsoflife #physicsoflivingmatter
December 1, 2025 at 6:58 AM
Explaining non-equilibrium systems to students: ‘Imagine a system that refuses to relax.' Students: ‘Like us?’
#justforfun #teaching #physicsoflife #physicsoflivingmatter
#justforfun #teaching #physicsoflife #physicsoflivingmatter
Schrödinger’s cat called. It is live and it wants a break. It didn’t sign up to explain superposition to every social media users. Enough!
November 30, 2025 at 9:54 AM
Schrödinger’s cat called. It is live and it wants a break. It didn’t sign up to explain superposition to every social media users. Enough!
Using ± in Julia code? Yes, because real models don’t come with exact parameters.
using DifferentialEquations, MonteCarloMeasurements
k = 1.0 ± 0.1
u0 = 1.0 ± 0
prob = ODEProblem((u,p,t)->-k*u, u0, (0,5))
sol = solve(prob)
mean(sol[end])
#JuliaLang #computing
using DifferentialEquations, MonteCarloMeasurements
k = 1.0 ± 0.1
u0 = 1.0 ± 0
prob = ODEProblem((u,p,t)->-k*u, u0, (0,5))
sol = solve(prob)
mean(sol[end])
#JuliaLang #computing
November 29, 2025 at 7:07 AM
Using ± in Julia code? Yes, because real models don’t come with exact parameters.
using DifferentialEquations, MonteCarloMeasurements
k = 1.0 ± 0.1
u0 = 1.0 ± 0
prob = ODEProblem((u,p,t)->-k*u, u0, (0,5))
sol = solve(prob)
mean(sol[end])
#JuliaLang #computing
using DifferentialEquations, MonteCarloMeasurements
k = 1.0 ± 0.1
u0 = 1.0 ± 0
prob = ODEProblem((u,p,t)->-k*u, u0, (0,5))
sol = solve(prob)
mean(sol[end])
#JuliaLang #computing
Temperature is not just a thermometer thing. Physicists, chemists, biologists, economists, and data analysts all use it differently. Maybe one day we'll find a single rule that links them all. Until then, temp keeps its cool by being complicated.
November 27, 2025 at 4:51 AM
Temperature is not just a thermometer thing. Physicists, chemists, biologists, economists, and data analysts all use it differently. Maybe one day we'll find a single rule that links them all. Until then, temp keeps its cool by being complicated.
Another review article worth bookmarking: Signed Networks: theory, methods, and applications."
arxiv.org/abs/2511.17247
Perfect for my Systems Biology course.
#sysbio #complexsystem #graph #network #compbio #mathbio
arxiv.org/abs/2511.17247
Perfect for my Systems Biology course.
#sysbio #complexsystem #graph #network #compbio #mathbio
Signed Networks: theory, methods, and applications
Signed networks provide a principled framework for representing systems in which interactions are not merely present or absent but qualitatively distinct: friendly or antagonistic, supportive or confl...
arxiv.org
November 25, 2025 at 5:03 AM
Another review article worth bookmarking: Signed Networks: theory, methods, and applications."
arxiv.org/abs/2511.17247
Perfect for my Systems Biology course.
#sysbio #complexsystem #graph #network #compbio #mathbio
arxiv.org/abs/2511.17247
Perfect for my Systems Biology course.
#sysbio #complexsystem #graph #network #compbio #mathbio
Many bugs don't scream. They whisper in wrong units. Using units in your code can save you. Again, Julia helps in that.
using Unitful
D = 0.01u"mm^2/s" # 0.01 mm^2 s^-1
t = 100u"s" # 100 s
√(2D*t) # 1.4142 mm
#julialang #computing #sysbio #systemsbiology
using Unitful
D = 0.01u"mm^2/s" # 0.01 mm^2 s^-1
t = 100u"s" # 100 s
√(2D*t) # 1.4142 mm
#julialang #computing #sysbio #systemsbiology
November 24, 2025 at 7:20 AM
Many bugs don't scream. They whisper in wrong units. Using units in your code can save you. Again, Julia helps in that.
using Unitful
D = 0.01u"mm^2/s" # 0.01 mm^2 s^-1
t = 100u"s" # 100 s
√(2D*t) # 1.4142 mm
#julialang #computing #sysbio #systemsbiology
using Unitful
D = 0.01u"mm^2/s" # 0.01 mm^2 s^-1
t = 100u"s" # 100 s
√(2D*t) # 1.4142 mm
#julialang #computing #sysbio #systemsbiology
Identical genome. Same environment. Totally different life choices. Turns out even cells have an identity crisis. #sysbio #physicsoflife
November 23, 2025 at 12:28 PM
Identical genome. Same environment. Totally different life choices. Turns out even cells have an identity crisis. #sysbio #physicsoflife
I get confused when philosophers and scientists debate “reality.”
If I slap someone, they feel pain and may hit back. That’s real.
So clearly, I’m missing something much deeper. #justsaying
If I slap someone, they feel pain and may hit back. That’s real.
So clearly, I’m missing something much deeper. #justsaying
November 22, 2025 at 12:09 PM
I get confused when philosophers and scientists debate “reality.”
If I slap someone, they feel pain and may hit back. That’s real.
So clearly, I’m missing something much deeper. #justsaying
If I slap someone, they feel pain and may hit back. That’s real.
So clearly, I’m missing something much deeper. #justsaying
In biology, we’re still busy naming T cells and debating EMT or autophagy — a bit like arguing over bird names while the real wonder lies in understanding how they fly.
#complexsystem #PhysicsOfLife #sysbio
#complexsystem #PhysicsOfLife #sysbio
November 21, 2025 at 3:48 AM
In biology, we’re still busy naming T cells and debating EMT or autophagy — a bit like arguing over bird names while the real wonder lies in understanding how they fly.
#complexsystem #PhysicsOfLife #sysbio
#complexsystem #PhysicsOfLife #sysbio
Dear developmental biologists, Julia comes with a Zygote that auto-differentiates. 😀
using Zygote
f(x) = x^2 + 3x + sin(x)
f'(2.0) # returns 6.58385
#Julialang #mathbio #qBio #compbio #sysbio #systemsbiology
using Zygote
f(x) = x^2 + 3x + sin(x)
f'(2.0) # returns 6.58385
#Julialang #mathbio #qBio #compbio #sysbio #systemsbiology
November 20, 2025 at 4:42 AM
Dear developmental biologists, Julia comes with a Zygote that auto-differentiates. 😀
using Zygote
f(x) = x^2 + 3x + sin(x)
f'(2.0) # returns 6.58385
#Julialang #mathbio #qBio #compbio #sysbio #systemsbiology
using Zygote
f(x) = x^2 + 3x + sin(x)
f'(2.0) # returns 6.58385
#Julialang #mathbio #qBio #compbio #sysbio #systemsbiology
At the beginning of this year, Active Matter researchers published a 'review of reviews' — yes, a meta-meta study. When your field grows so fast, you need a map of the maps. Worth bookmarking.
link.springer.com/article/10.1... #activematter #physicsoflife #physicalbiology #complexity
link.springer.com/article/10.1... #activematter #physicsoflife #physicalbiology #complexity
Metareview: a survey of active matter reviews - The European Physical Journal E
Abstract In the past years, the amount of research on active matter has grown extremely rapidly, a fact that is reflected in particular by the existence of more than 1000 reviews on this topic. Moreov...
link.springer.com
November 19, 2025 at 7:56 AM
At the beginning of this year, Active Matter researchers published a 'review of reviews' — yes, a meta-meta study. When your field grows so fast, you need a map of the maps. Worth bookmarking.
link.springer.com/article/10.1... #activematter #physicsoflife #physicalbiology #complexity
link.springer.com/article/10.1... #activematter #physicsoflife #physicalbiology #complexity
Is it weird that I prefer old biology papers—the ones with two figures, zero rainbow plots, and actual ideas? Or am I just allergic to 100-page supplements that explain nothing?
November 17, 2025 at 8:17 AM
Is it weird that I prefer old biology papers—the ones with two figures, zero rainbow plots, and actual ideas? Or am I just allergic to 100-page supplements that explain nothing?
Every time I get overwhelmed, I remember- a lot of statistical physics is basically fancy bookkeeping for balls in boxes.
November 16, 2025 at 11:31 AM
Every time I get overwhelmed, I remember- a lot of statistical physics is basically fancy bookkeeping for balls in boxes.
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