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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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Practical questions on usage, ideally with
example model.
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Implementation questions
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Questions on how a feature is implemented.
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Randy Heiland
,
Lutz Brusch
2
Jul 12
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
Jul 12
Mavis Odonkor
,
Lutz Brusch
3
Jun 15
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
Jun 15
Эрвин Визард
,
Jörn Starruß
3
Feb 1
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-
Feb 1
Elaine
,
Diego Jahn
2
Jan 19
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 '
Jan 19
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
Эрвин Визард
,
Jörn Starruss
3
11/22/21
How it works: Connectivity constraints?
Dear Erwin, probably Morpheus does not use exactly the logics Roeland Marks used. We just demand the
unread,
How it works: Connectivity constraints?
Dear Erwin, probably Morpheus does not use exactly the logics Roeland Marks used. We just demand the
11/22/21
Эрвин Визард
,
Lutz Brusch
4
11/20/21
How to get motion parameters?
Lutz, thank you! It works well! понедельник, 15 ноября 2021 г. в 15:35:55 UTC+3, Lutz Brusch: Hi
unread,
How to get motion parameters?
Lutz, thank you! It works well! понедельник, 15 ноября 2021 г. в 15:35:55 UTC+3, Lutz Brusch: Hi
11/20/21
Эрвин Визард
,
Lutz Brusch
3
11/1/21
ChangeCellType: several conditions
Hi, Lutz! Thank you very much for your helpful advice and the link! It was really valuable
unread,
ChangeCellType: several conditions
Hi, Lutz! Thank you very much for your helpful advice and the link! It was really valuable
11/1/21
Deepa
,
Jörn Starruss
6
10/25/21
Building a 3D model in Morpheus
Hello Jörn, I tried by checking just the `ignore medium` icon since in teh documentation it is
unread,
Building a 3D model in Morpheus
Hello Jörn, I tried by checking just the `ignore medium` icon since in teh documentation it is
10/25/21
Эрвин Визард
,
Jörn Starruss
4
10/25/21
Conditions for performing division
Dear Jörn, Thank you very much for your answer! I will check it. And for any time limit I used such
unread,
Conditions for performing division
Dear Jörn, Thank you very much for your answer! I will check it. And for any time limit I used such
10/25/21
Deepa
,
Lutz Brusch
2
10/15/21
initial cellular configuration via poisson disc sampling
Hi Deepa, an example model with the InitPoissonDisc initialization of the cell arrangement is
unread,
initial cellular configuration via poisson disc sampling
Hi Deepa, an example model with the InitPoissonDisc initialization of the cell arrangement is
10/15/21
Bob van Dijk
,
Jörn Starruss
7
9/29/21
Morpheus 2.2.5 crashes when starting multiple jobs
Dear Jörn, Thank you for the pre-release! This version allows me to sometimes start bigger sweeps
unread,
Morpheus 2.2.5 crashes when starting multiple jobs
Dear Jörn, Thank you for the pre-release! This version allows me to sometimes start bigger sweeps
9/29/21
Suhail Alsalehi
,
Jörn Starruss
4
9/28/21
Concurrent jobs and job multi-threading
1,2 - Indeed, CPM takes ~80% of teh job time so threading is not very helpful in this case. 3 - This
unread,
Concurrent jobs and job multi-threading
1,2 - Indeed, CPM takes ~80% of teh job time so threading is not very helpful in this case. 3 - This
9/28/21