A newbie question on Julia:

Converted a large MC code set in Julia from C. It is a one-to-one mapping from my previous C code, except few vectorizations.

It uses only one library- Random, for rand().

The Julia code is terribly slower than the C code.

Can someone please throw some pointers on this problem?

#Julia #JuliaLanguage #programming #mathbio #computationalbiology
#dynamicalsystems
#statisticalPhysics

A newbie question on Julia:

Converted a large MC code set in Julia from C. It is a one-to-one mapping from my previous C code, except few vectorizations.

It uses only one library- Random, for rand().

The Julia code is terribly slower than the C code.

Can someone please throw some pointers on this problem?

#Julia #JuliaLanguage #programming #mathbio #computationalbiology
#dynamicalsystems
#statisticalPhysics

@gvdr

Heard the same about Julia from many. I explored it a bit superficially. Looks very rich.

I have used Matlab for most of my academic life. I am now thinking of migrating to Julia. But it is not easy.

I am looking for resources showing Matlab and Julia syntax/rule comparisons. One-to-one correspondences. That will make learning easy.

Do you know any such resources?

#Julia #matlab #dynamicalsystems #scientificComputing

Self-organization happens due to local interactions (local cues). In certain biological systems, the organization of cells involves both local and global cues.
A. What are the advantages of using local interaction over global cues?
B. Do we need both local and global cues?
C. Can't a global cue, like a diffusible morphogen, achieve the same without a local cue?
Looking forward to suggestions and cues on these questions.

#dynamicalsystems #complexity
#selforganization
#statisticalPhysics

Self-organization happens due to local interactions (local cues). In certain biological systems, the organization of cells involves both local and global cues.
A. What are the advantages of using local interaction over global cues?
B. Do we need both local and global cues?
C. Can't a global cue, like a diffusible morphogen, achieve the same without a local cue?
Looking forward to suggestions and cues on these questions.

#dynamicalsystems #complexity
#selforganization
#statisticalPhysics

Question for computational/mathematical biologists working on dynamical systems:

What is your favorite language for simulation/analysis of ODE and PDE-based problems currently?

#dynamicalsystems #matlab #julia #python

Can someone point me to any literature on the use of Proper Orthogonal Decomposition (POD) /SVD in any dynamical problem other than fluid dynamics? Also excluding the uses in image processing/analysis. Thanks in advance!

#machinelearning #dynamicalsystem
#dynamicalsystems
#modeling
#reducedordermodel
#fluiddynamics

Discussion meeting on "Patterns Dynamics Computation" on 5 Dec. The Institute of Mathematical Sciences. Chennai. Live stream on YouTube.

https://pbs.twimg.com/media/FiFQTBWVIAA4uri?format=jpg&name=large

#dynamicalsystems #nonlineardynamics
#statisticalPhysics
#complexity

#Galactica from #Meta is creating a ripple. Here is what I got when I asked Galactica to write on "Bifurcation theory in epithelial to mesenchymal transition." As you see, it has done a reasonable job.

https://galactica.org/?prompt=Bifurcation+theory+in+epithelial+to+mesenchymal+transition+&max_new_tokens=1600

But be careful! Galactica is just a science-specific language model and as the page warns - "Outputs may be unreliable! Language Models are prone to hallucinate text."

#machinelearning #nlp #AI #systemsbiology #EMT #dynamicalsystems

I am writing a textbook on Computational Systems Biology.

Nine chapters of the book, along with video lectures, are now on my page:

https://www.iitg.ac.in/biplabbose/files/sysbio/

You can use these book chapters and videos to learn/teach mathematical biology and systems biology.

Please do share your suggestions/observations.

I will keep updating the page with new chapters and videos.

#book #teaching #openscience #openaccess #mathbio #systemsbiology #ScienceMastodon #youtube #qbio #dynamicalsystems #biology

> René Lozi. "Can we trust in numerical computations of chaotic solutions of dynamical systems?". World Scientific Series on Nonlinear Science, World Scientific, 2013, Topology and Dynamics of Chaos
In Celebration of Robert Gilmore’s 70th Birthday, 84, pp.63-98. 10.1142/9789814434867_0004 . hal-
00682818 HAL Id: hal-00682818 https://hal.archives-ouvertes.fr/hal-00682818

#AmReading slowly as it's quite long (42 pages)

#Chaos #DynamicalSystems #NumericalComputation #Math #Maths