Package for the lattice-based simulation of active polymer microemulsions, such as dense DNA suspensions.
active-microemulsion depends on the boost-program-options, boost-system and boost-filesystem libraries (tested on version 1.62). See https://www.boost.org/ for further information on the libraries and on how to install them.
On Ubuntu these can easily be installed via the official repositories using the apt package manager:
- Either by installing the
libboost-program-options-dev,libboost-system-devandlibboost-filesystem-devpackages. - Or by installing the entire
libboost-all-devmetapackage.
On macOS (Sierra Version 10.12.6) we installed the follwing libraries using Homebrew:
brew install gcc
brew install boost
The utils/sequenceFigureBuilder.sh script depends on the ImageMagick suite for producing figures, specifically on the convert and montage commands.
These can be obtained on Ubuntu from the official repositories by installing the imagemagick package.
Full documentation for how to build, configure and run can be found at the documentation page of the repository.
You can also find a tutorial for building and scheduling on BwUniCluster (work in progress...).
Basic usage:
./active-microemulsion
Getting the help:
./active-microemulsion --help
Supported options:
-h [ --help ] Show this help and exit
-d [ --debug ] Enable the debug logging level
--coarse-debug Enable the coarse_debug logging level
-q [ --quiet ] Restrict logging to PRODUCTION,WARNING,
ERROR levels
-Q [ --Quiet ] Restrict logging to WARNING,ERROR
levels
-m [ --minutes ] Time variables are expressed in minutes
instead of seconds
--no-chain-integrity Do not enforce chain integrity
--no-sticky-boundary Do not make boundary sticky to
chromatin
--flavopiridol arg Apply Flavopiridol at cutoff time(s).
Cutoff time(s) can be specified as
parameter
--actinomycin-D arg Apply Actinomycin D at cutoff time.
Cutoff time(s) can be specified as
parameter
--activate arg Activate transcription at cutoff time.
Cutoff time(s) can be specified as
parameter
--txn-spike arg Set a transcription spike at cutoff
time. Cutoff time(s) can be specified
as parameter
-o [ --output-dir ] arg (=./Out) Specify the folder to use for output
(log and data)
-i [ --input-image ] arg Specify the image to be used as initial
value for grid configuration
-P [ --chains-config ] arg (=testConfig.chains)
Specify the chains config file to be
used for grid configuration
-T [ --end-time ] arg (=1000) End time for the simulation
-C [ --cutoff-time ] arg (=-1) Time at which the chemical reaction
cutoff takes place
-c [ --cutoff-time-fraction ] arg (=1)
Fraction of endTime at which the
chemical reaction cutoff takes place
-t [ --snapshot-interval ] arg (=-1) Time interval (in seconds) between
visualization snapshots. A negative
time lets the '-S' flag take over
-S [ --number-snapshots ] arg (=100) Number of visualization snapshots to
take. Only applied if '-t' is negative
or not set
-e [ --extra-snapshot ] arg (=-1) Time interval (in seconds) between
cutoff events and their respective
extra snapshot. A negative time
disables the extra snapshot.
-E [ --extra-snapshot-abs ] arg (=-1) Time (in seconds) when the extra
snapshot should be taken. A negative
time disables this setting. This
overrides -e.
--additional-snapshots arg Explicitly add additional snapshot
time(s). Snapshot time(s) can be
specified as parameter
(space-separated)
-W [ --width ] arg (=50) Width of the simulation grid
-H [ --height ] arg (=50) Height of the simulation grid
--threads arg (=-1) Number of threads to use for
parallelization. A negative value lets
OMP_NUM_THREADS take precedence
-w [ --omega ] arg (=0.25) Energy cost for contiguity of
non-affine species (omega model
parameter)
-s [ --sppps ] arg (=3000) Number of average swap attempts per
pixel per second
--kOn arg (=0.00125) Reaction rate - Chromatin from
non-transcribable to transcribable
state
--kOff arg (=0.0025000000000000001) Reaction rate - Chromatin from
transcribable to non-transcribable
state
--kChromPlus arg (=0.0044444000000000003)
Reaction rate - Transcription turned ON
--kChromMinus arg (=0.0011111000000000001)
Reaction rate - Transcription turned
OFF
--kRnaPlus arg (=0.041666599999999998)
Reaction rate - RBP from free to bound
state
--kRnaMinusRbp arg (=0.000416666) Reaction rate - RBP from bound to free
state
--kRnaTransfer arg (=0.016666666659999999)
Reaction rate - RNA migrating from
transcription site to an RBP site