This directory contains MATLAB files with the Hoffmann et al. 2002 model featuring the paper

"A plausible identifiable model of the canonical NF-kappaB signaling pathway" 

by Joanna Jaruszewicz-Blonska, Ilona Kosiuk, Wiktor Prus, and Tomasz Lipniacki

PLOS One (2023)


This is a modified version of the encoded model "Hoffmann2002_WT_IkBNFkB_Signaling", see:

http://identifiers.org/biomodels.db/MODEL7158174175
http://identifiers.org/biomodels.db/BIOMD0000000140
described by http://identifiers.org/pubmed/12424381

and S1 Text (see supplementary materials).

====================
File list:

f.m
f_off.m
program_Hoffmann_continuous.m
program_Hoffman_5min_60min.m
program_Hoffman_5min_100min.m
program_Hoffman_5min_200min.m
program_Hoffman_22_5min_45min.m
program_Hoffman_45min_90min.m
=====================

Description:

- - - 1 - - - f.m

This MATLAB function characterizes a system of ODEs describing the
Hoffmann et al. 2002 model, when the signal is on.
The parameter values are taken from S2 Supplementary Text (Table 3),
but can be changed in order to obtain different types of behavior. 


- - - 2 - - - f_off.m

This MATLAB function characterizes a system of ODEs describing the
Hoffmann et al. 2002 model, when the signal is off.
The parameter values are taken from S2 Supplementary Text (Table 3),
but can be changed in order to obtain different types of behavior.

 
The files f.m and f_off differ by the value of the parameter k02.

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In each program file one can change values of three parameters t0, tw, te
that define a TNF stimulation protocol, i.e.,

t0 - time when signal is being introduced into the system [min] 
tw - length of signal stimulation                         [min]
te - length of simulation from introducing the signal     [min]

Here protocols are defined as in S1 Table (for WT cells). 

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- - - 3 - - - program_Hoffmann_continuous.m

This is a master program (calling f.m and f_off.m) for the Hoffmann et al.
2002 model for the protocol 'continuous' described in S1 Table. Running th
 program one can reproduce the results presented in S1 Fig (first row),
i.e., numerical (normalized) trajectories of wild type cells of the
3 variables (free nuclear NF-kappaB, mRNA IkappaBalpha, and free cytoplasmic
IkappaBalpha), generated by the Hoffman et al. 2002 model (full model,
shown in red).  

The version of the model for KO IkBb and IkBe is obtained by setting tr2b=0
and tr2e=0, in both f.m and f_off.m files. For these files, running the
program reproduces the results presented in S1 Fig (first row), i.e.,
numerical (normalized) trajectories of the 3 variables (free nuclear NF-kappaB,
mRNA IkappaBalpha, and free cytoplasmic IkappaBalpha) shown in blue.


- - - 4 - - - program_Hoffmann_5min_60min.m

This is a master program (calling f.m and f_off.m) for the Hoffmann et al.
2002 model for the protocol 'pulse 5-60' described in S1 Table.

Running the program one can reproduce the results presented in S1 Fig
(second row), i.e., numerical (normalized) trajectories of wild type (WT)
cells of the 3 variables (free nuclear NF-kappaB, mRNA IkappaBalpha, and free
cytoplasmic IkappaBalpha), generated by the Hoffman et al. 2002 model 
(full model shown in red).

The version of the model for KO IkBb and IkBe is obtained by setting tr2b=0
and tr2e=0, in both f.m and f_off.m files. For these files, running the
program reproduces the results presented in S6_Fig (second row), i.e.,
numerical (normalized) trajectories of the 3 variables (free nuclear NF-kappaB,
mRNA IkappaBalpha, and free cytoplasmic IkappaBalpha) shown in blue.


- - - 5 - - - program_Hoffmann_5min_100min.m

This is a master program (calling f.m and f_off.m) for the Hoffmann et al.
2002 model for the protocol 'pulse 5-100' described in S1 Table.

Running the program one can reproduce the results presented in S1 Fig
(third row), i.e., numerical (normalized) trajectories of wild type (WT)
cells of the 3 variables (free nuclear NF-kappaB, mRNA IkappaBalpha, and free
cytoplasmic IkappaBalpha), generated by the Hoffman et al. 2002  model
(full model shown in red).

The version of the model for KO IkBb and IkBe is obtained by setting tr2b=0
and tr2e=0, in both f.m and f_off.m files. For these files, running the
program reproduces the results presented in S1 Fig (third row), i.e.,
numerical (normalized) trajectories of the 3 variables (free nuclear NF-kappaB,
mRNA IkappaBalpha, and free cytoplasmic IkappaBalpha) shown in blue.


- - - 6 - - - program_Hoffmann_5min_200min.m

This is a master program (calling f.m and f_off.m) for the Hoffmann et al.
2002 model for the protocol 'pulse 5-200' described in S1 Table.

Running the program one can reproduce the results presented in S1 Fig
(fourth row), i.e., numerical (normalized) trajectories of wild type (WT)
cells of the 3 variables (free nuclear NF-kappaB, mRNA IkappaBalpha, and
free cytoplasmic IkappaBalpha), generated by the Hoffman et al. 2002  model
(full model shown in red).

The version of the model for KO IkBb and IkBe is obtained by setting tr2b=0
and tr2e=0, in both f.m and f_off.m files. For these files, running the
program reproduces the results presented in S1 Fig (fourth row), i.e.,
numerical (normalized) trajectories of the 3 variables (free nuclear NF-kappaB,
mRNA IkappaBalpha, and free cytoplasmic IkappaBalpha) shown in blue.


- - - 7 - - - program_Hoffmann_22_5min_45min.m

This is a master program (calling f.m and f_off.m) for the Hoffmann et al.
2002 model for the protocol 'pulse 22.5-45' described in S1 Table.

Running the program one can reproduce the results presented in S1 Fig
(fifth row), i.e., numerical (normalized) trajectories of wild type (WT)
cells of the 3 variables (free nuclear NF-kappaB, mRNA IkappaBalpha, and free
cytoplasmic IkappaBalpha), generated by the Hoffman et al. 2002  model
(full model shown in red).

The version of the model for KO IkBb and IkBe is obtained by setting tr2b=0
and tr2e=0, in both f.m and f_off.m files. For these files, running the
program reproduces the results presented in S1 Fig (fifth row), i.e.,
numerical (normalized) trajectories of the 3 variables (free nuclear NF-kappaB,
mRNA IkappaBalpha, and free cytoplasmic IkappaBalpha) shown in blue.


- - - 8 - - - program_Hoffmann_45min_90min.m

This is a master program (calling f.m and f_off.m) for the Hoffmann et al.
2002 model for the protocol 'pulse 45-90' described in S1 Table.

Running the program one can reproduce the results presented in S1 Fig
(sixth row), i.e., numerical (normalized) trajectories of wild type (WT)
cells of the 3 variables (free nuclear NF-kappaB, mRNA IkappaBalpha, and free
cytoplasmic IkappaBalpha), generated by the Hoffman et al. 2002  model
(full model shown in red).

The version of the model for KO IkBb and IkBe is obtained by setting tr2b=0
and tr2e=0, in both f.m and f_off.m files. For these files, running the
program reproduces the results presented in S1 Fig (sixth row), i.e.,
numerical (normalized) trajectories of the 3 variables (free nuclear NF-kappaB,
mRNA IkappaBalpha, and free cytoplasmic IkappaBalpha) shown in blue.

============================

How to:

 0. Unzip the archive MATLAB_codes.zip (a directory MATLAB_codes_Hoffmann is generated).
 1. Start MATLAB.
 2. Run one of the files: 
       program_Hoffmann_continuous.m, program_Hoffmann_5min_60min.m, or program_Hoffmann_5min_100min.m, etc.
 3. New parameters can be specified in the 'f.m' and 'f_off.m' files.
       New stimulation protocols can be specified in each of the program files by changing t0, tw, te.
