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Morpheus user forum
User forum for questions and answers on the use of the
Morpheus modeling environment
.
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How-to
questions
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Practical questions on usage, ideally with
example model.
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Implementation questions
:
Questions on how a feature is implemented.
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Bug reports
: Please include sufficient detail to reproduce the error.
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Feature requests
: Discussion of new features.
Developers may want to use the
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Osman Abhimata Nugraha
,
Lutz Brusch
4
12/23/24
More than one Neighborhood + DistanceTransform Plugin
Hi Osman, to extend the spatial range of the NeighborhoodReporter to around 20 lattice nodes would be
unread,
More than one Neighborhood + DistanceTransform Plugin
Hi Osman, to extend the spatial range of the NeighborhoodReporter to around 20 lattice nodes would be
12/23/24
Jessica Chen
,
Lutz Brusch
4
12/18/24
Cell area compression
Hi Jessica, yes, this can be done by a Variable and a Mapper with mapping="sum" in Global,
unread,
Cell area compression
Hi Jessica, yes, this can be done by a Variable and a Mapper with mapping="sum" in Global,
12/18/24
Эрвин Визард (Earvin Wizard)
,
Lutz Brusch
4
12/5/24
Save the results of several calculations into the single output file.
Yes, It is really easy in R Statistics: library(tidyverse) ##########################################
unread,
Save the results of several calculations into the single output file.
Yes, It is really easy in R Statistics: library(tidyverse) ##########################################
12/5/24
David Dolgitzer
,
Lutz Brusch
2
11/12/24
Distance from medium
Hi David, thank you for this question. 1. One (distributed cell-based) solution would be to
unread,
Distance from medium
Hi David, thank you for this question. 1. One (distributed cell-based) solution would be to
11/12/24
reily...@gmail.com
, …
Эрвин Визард (Earvin Wizard)
3
10/21/24
Q&A
Param Sweep Data Analysis
Thanks, ParamSweep tutorial is very helpful. пятница, 31 января 2020 г. в 16:31:59 UTC+3, Walter de
unread,
Q&A
Param Sweep Data Analysis
Thanks, ParamSweep tutorial is very helpful. пятница, 31 января 2020 г. в 16:31:59 UTC+3, Walter de
10/21/24
Madhav Binuraj Nair
,
Lutz Brusch
6
10/21/24
2D Cell Communication Model
Hi Madhav, the lateral signaling example had used a minimal cell representation of just one (
unread,
2D Cell Communication Model
Hi Madhav, the lateral signaling example had used a minimal cell representation of just one (
10/21/24
Эрвин Визард (Earvin Wizard)
,
Jörn Starruß
2
10/16/24
How to pin cells mass center?
Use DirectedMotion together with tracking of the cell displacement cell.center - cell.center.initial
unread,
How to pin cells mass center?
Use DirectedMotion together with tracking of the cell displacement cell.center - cell.center.initial
10/16/24
Эрвин Визард (Earvin Wizard)
,
Lutz Brusch
5
10/16/24
Running Morpheus through R Statistics
Ok, question is solved: Parameter sweep was presented in manual. понедельник, 14 октября 2024 г. в 13
unread,
Running Morpheus through R Statistics
Ok, question is solved: Parameter sweep was presented in manual. понедельник, 14 октября 2024 г. в 13
10/16/24
Randy Heiland
,
Lutz Brusch
2
7/12/24
Executing a Python script during a simulation
Hi Randy, yes, the Analysis/External plugin can start a Python script repeatedly *during* a
unread,
Executing a Python script during a simulation
Hi Randy, yes, the Analysis/External plugin can start a Python script repeatedly *during* a
7/12/24
Mavis Odonkor
,
Lutz Brusch
3
6/15/24
Balance between Differentiation and Proliferation
Hi Mavis, thank you for your question which refers to a common regulatory process in stem cell niches
unread,
Balance between Differentiation and Proliferation
Hi Mavis, thank you for your question which refers to a common regulatory process in stem cell niches
6/15/24
Эрвин Визард
,
Jörn Starruß
3
2/1/24
Modeling elongated objects.
Dear Earvin, unfortunately this model dates back to a pre-Morpheus-era and cell composed out of sub-
unread,
Modeling elongated objects.
Dear Earvin, unfortunately this model dates back to a pre-Morpheus-era and cell composed out of sub-
2/1/24
Elaine
,
Diego Jahn
2
1/19/24
2d Cell sorting model
Hi Elaine, you're right about the left plot, which shows cell type 'ct1' in red and '
unread,
2d Cell sorting model
Hi Elaine, you're right about the left plot, which shows cell type 'ct1' in red and '
1/19/24
suman Gare
,
Lutz Brusch
4
11/13/23
Reaction diffusion model
Hello, the diffusion solver allows for heterogeneous diffusion coefficients as expressions of any
unread,
Reaction diffusion model
Hello, the diffusion solver allows for heterogeneous diffusion coefficients as expressions of any
11/13/23
Randy Heiland
,
Diego Jahn
7
11/7/23
installing on macOS 13.5
Let me follow-up with some happier news. Only a different Mac M1 (arm64) where I updated to Sonoma
unread,
installing on macOS 13.5
Let me follow-up with some happier news. Only a different Mac M1 (arm64) where I updated to Sonoma
11/7/23
Randy Heiland
,
Lutz Brusch
5
11/7/23
specifying initial conditions for cells
Awesome - thank you! (and fwiw, I think you have a typo, "ragular", in the 2nd Population
unread,
specifying initial conditions for cells
Awesome - thank you! (and fwiw, I think you have a typo, "ragular", in the 2nd Population
11/7/23
Lieke van Woerden
,
Lutz Brusch
3
10/28/23
Specified RandomSeed yields different results
Hi Lutz, Thank you so much for taking the time to respond! I have followed your instructions and the
unread,
Specified RandomSeed yields different results
Hi Lutz, Thank you so much for taking the time to respond! I have followed your instructions and the
10/28/23
Эрвин Визард (Earvin Wizard)
,
Jörn Starruss
3
8/7/23
Active motion model using actine polimerization
Thank you very much! вторник, 27 июня 2023 г. в 09:47:32 UTC+3, Jörn Starruss: Dear Эрвин, the
unread,
Active motion model using actine polimerization
Thank you very much! вторник, 27 июня 2023 г. в 09:47:32 UTC+3, Jörn Starruss: Dear Эрвин, the
8/7/23
dewei “Djobi” ́
,
Jörn Starboerg
2
6/12/23
Can't launch Morpheus-gui
Dear Djobi, all binaries we provide are build for 64bit systems and depend on at least AVX support,
unread,
Can't launch Morpheus-gui
Dear Djobi, all binaries we provide are build for 64bit systems and depend on at least AVX support,
6/12/23
Schumer Clarisse
,
Lutz Brusch
2
4/17/23
Change from Morpheus:2.2.6 to 2.3.3
Hi Clarisse, true, such initial mismatch between versions may occur when a model uses a sequence of
unread,
Change from Morpheus:2.2.6 to 2.3.3
Hi Clarisse, true, such initial mismatch between versions may occur when a model uses a sequence of
4/17/23
Maya Kaul
,
Diego Jahn
5
1/19/23
installation difficulty on Ventura 13
resolved! (I think?) Fix: ran "brew doctor" again while trying to diff morpheus-functional
unread,
installation difficulty on Ventura 13
resolved! (I think?) Fix: ran "brew doctor" again while trying to diff morpheus-functional
1/19/23
Ian Wong
, …
Lutz Brusch
3
1/15/23
lack of cell motion in persistence2D example
Dear Ian, good questions, thank you. Yes, regarding motion initialization, the attached model file
unread,
lack of cell motion in persistence2D example
Dear Ian, good questions, thank you. Yes, regarding motion initialization, the attached model file
1/15/23
Megan Schupp
,
Lutz Brusch
2
5/15/22
Rho-RAC-ECM paper
Hi Megan, yes, Morpheus offers various Plugins like Mappers to do what you propose. To answer all the
unread,
Rho-RAC-ECM paper
Hi Megan, yes, Morpheus offers various Plugins like Mappers to do what you propose. To answer all the
5/15/22
Megan Schupp
,
Lutz Brusch
3
5/13/22
ECM-RHO-RAC PDE TO ODE
Hi Dr. Lutz, Thank you so much for the fast reply! I am still very new with Morpheus and I really
unread,
ECM-RHO-RAC PDE TO ODE
Hi Dr. Lutz, Thank you so much for the fast reply! I am still very new with Morpheus and I really
5/13/22
Ilya
,
Эрвин Визард
2
3/14/22
Comparison of Systems biology tools
Hello, Ilya! I'm not a part of Morpheus team, but I would note, that parameters fitting in
unread,
Comparison of Systems biology tools
Hello, Ilya! I'm not a part of Morpheus team, but I would note, that parameters fitting in
3/14/22
Lucie Plazen
, …
francois el-daher
4
2/15/22
Membrane elasticity
Hi, I face a similar limtation when trying to reproduce realistic protrusions of macrophages. I am
unread,
Membrane elasticity
Hi, I face a similar limtation when trying to reproduce realistic protrusions of macrophages. I am
2/15/22
Bob van Dijk
,
Jörn Starruss
3
2/14/22
3D TIFF Domain
Hi Jörn, Thank you for your quick response, I'll take a look into it! Best, Bob Op vrijdag 11
unread,
3D TIFF Domain
Hi Jörn, Thank you for your quick response, I'll take a look into it! Best, Bob Op vrijdag 11
2/14/22
Deepa
,
Lutz Brusch
24
2/7/22
Modeling cell to cell communication
Dear Deepa, true and same for me, the OME header data seems to interfere with that single slice.
unread,
Modeling cell to cell communication
Dear Deepa, true and same for me, the OME header data seems to interfere with that single slice.
2/7/22
Эрвин Визард
,
Lutz Brusch
4
1/10/22
Visualization pictures with the output of the current MCS.
Dear Эрвин, these rendering options can only be partially adjusted through the GUI. Time stamp and
unread,
Visualization pictures with the output of the current MCS.
Dear Эрвин, these rendering options can only be partially adjusted through the GUI. Time stamp and
1/10/22
Эрвин Визард
,
Lutz Brusch
3
12/28/21
Your opinion about FitMultiCell.
Dear Lutz, Thank you for your detailed answer! I hope in the near future I will be able to adapt my
unread,
Your opinion about FitMultiCell.
Dear Lutz, Thank you for your detailed answer! I hope in the near future I will be able to adapt my
12/28/21
Эрвин Визард
,
Lutz Brusch
8
11/23/21
Constant influx of immune cells into the computational domain.
Hi, Lutz! Thank you for your detailed answer! Now I can see the problem more clear than earlier. Very
unread,
Constant influx of immune cells into the computational domain.
Hi, Lutz! Thank you for your detailed answer! Now I can see the problem more clear than earlier. Very
11/23/21