Comments for COMPUTE CANCER

Comment on Visualization of 3D tumor using isosurfaces and simple blur by jpoleszczuk

jpoleszczuk — Sat, 22 May 2021 10:01:24 +0000

In reply to LBN.

You have the code that generates the input to the visualization function in the first part of the code, but in general the input variable” L” is a 3D logical matrix that have true values only in places occupied by cells + on the boundary and “cells” is an accompanying vector with positions of cells using linear indexing. Of course you can construct “cells” from “L” and vice versa if you want to reduce number of input parameters.

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Comment on Visualization of 3D tumor using isosurfaces and simple blur by LBN

LBN — Sat, 08 May 2021 12:04:55 +0000

Hey can you please give me an example for the inputs to visualize the data

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Comment on Agent-Based Modeling (ABM) of Tumors in Java by Lisa

Lisa — Fri, 04 Oct 2019 09:14:48 +0000

Amazing work! So each image is like after 2hrs, 4hrs, 6hrs… and so on?

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Comment on Cancer stem cell driven tumor growth model in less than 70 lines of code by Amir Behjat

Amir Behjat — Fri, 11 Jan 2019 14:39:25 +0000

In reply to jpoleszczuk.

Thanks. I finally used the C code you had which was so fast. Thanks again.

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Comment on Cancer stem cell driven tumor growth model in less than 70 lines of code by jpoleszczuk

jpoleszczuk — Fri, 11 Jan 2019 10:51:26 +0000

In reply to Amir Behjat.

I’m glad that you are considering to use the model. You can either cite the blog post directly (follow standard guidelines) or cite one of my papers with Heiko Enderling (e.g. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004025 ).

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Comment on Cancer stem cell driven tumor growth model in less than 70 lines of code by Amir Behjat

Amir Behjat — Wed, 09 Jan 2019 03:24:52 +0000

Hi How can I cite your work if I want to use it?

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Comment on Cancer stem cell driven tumor growth model in C++ by jpoleszczuk

jpoleszczuk — Tue, 31 Jul 2018 15:38:08 +0000

In reply to Margriet Palm.

I’m glad that you found the code useful. And you are right – the cell without any empty spot in the surrounding can’t die and cancer stem cells are immortal. Both of the above are modeling assumptions that you can easily modify. The rationale behind the former is that the cell death occurs because of unsuccessful division.

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Comment on Cancer stem cell driven tumor growth model in C++ by Margriet Palm

Margriet Palm — Tue, 31 Jul 2018 15:14:30 +0000

Thanks for this code! Maybe I’m misreading the code, but it seems to me that a cell that can’t find a spot for proliferation or migration also can’t die:

} else {//no free spot
cellsTmp.push_back(currCell);
}

also, stem cells seem to be immortal. Is there a reason behind this?

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Comment on Some ideas about how to efficently store simulation data by jpoleszczuk

jpoleszczuk — Mon, 16 Apr 2018 17:02:03 +0000

In reply to Myroslav Zapukhlyak.

I think that it would be overkill in this case…

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Comment on Some ideas about how to efficently store simulation data by Myroslav Zapukhlyak

Myroslav Zapukhlyak — Mon, 16 Apr 2018 13:42:18 +0000

hdf5, netcdf etc ?

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