Methodology to find Initial Concentration and Forward-Backward Reaction Kinetics of Molecular Species using Western Blot images

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Vijeth Ullal

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Jun 6, 2023, 12:58:34 AM6/6/23
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Hello everyone!!

I'm currently working on a Systems biology project on Angiogenesis…

I wanted to extract Initial Concentration and Kinetic parameters I.e., Forward and Backward reaction kinetics of Molecular species.

In the Literature review, I came across papers which said I can get them by analyzing Western Blot images. 

I followed these steps
1) ImageJ: To analyze Western Blot images and get plots of the band
2) Grabit function on MATLAB: Calibrate the plots and grab the point
3) Excel: Determine the concentration and find the initial and final rates

I’m getting stuck at finding the concentration as the points on the plot appear as a Line Chart and are difficult to analyze.

Can Somebody please help meet out with this?

Scampicchio Matteo Mario

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Jun 6, 2023, 1:11:01 AM6/6/23
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This is a copasi-user-forum. Please, pose a question related to the use of Copasi. 


Da: copasi-u...@googlegroups.com <copasi-u...@googlegroups.com> per conto di Vijeth Ullal <vijethu...@gmail.com>
Inviato: martedì 6 giugno 2023 06:58
A: COPASI User Forum <copasi-u...@googlegroups.com>
Oggetto: [copasi-user-forum] Methodology to find Initial Concentration and Forward-Backward Reaction Kinetics of Molecular Species using Western Blot images
 
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Pedro Mendes

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Jun 6, 2023, 7:42:49 AM6/6/23
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> I’m getting stuck at finding the concentration as the points on the
> plot appear as a Line Chart and are difficult to analyze.

While this is indeed rather separate from COPASI, if you want to
digitize a line plot, you can use something like this;

https://automeris.io/WebPlotDigitizer/
or
http://markummitchell.github.io/engauge-digitizer/

Pedro

--
Pedro Mendes, PhD
Professor and Director
Richard D. Berlin Center for Cell Analysis and Modeling
University of Connecticut School of Medicine
group website: http://www.comp-sys-bio.org

ICSB2023: https://icsb2023.bioscience-ct.net/


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