Stochastic simulations of biological filaments, especially actin.
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mark-burnett/filament-dynamics
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------------------------------------------------------------------------ - License - ------------------------------------------------------------------------ This software package is licensed under the GNU GPL (version 3). See the LICENSE file for more details. ------------------------------------------------------------------------ - NOTICE - ------------------------------------------------------------------------ This readme is (unfortunately) out of date. I will clean it up over the summer, as I refactor the project to a global fit paradigm. ------------------------------------------------------------------------ - Requirements - ------------------------------------------------------------------------ CPython version 2.6 or later (Not 3.x ready yet.) The Boost c++ library, and build system (bjam). The Google Test c++ library (libgtest). mysql you can just use sqlite for testing, but for the real deal, use mysql (postgresql should also work) IPython (used for analysis shell) Python Packages: argparse (if using python 2.6) configobj dateutil discover mysqldb sqlalchemy yaml dulwich numpy scipy matplotlib ------------------------------------------------------------------------ - Setup - ------------------------------------------------------------------------ First, you must compile the C++ component of this package. This may require some editing of the cpp_stochastic/Jamroot file so that boost build can find your system libraries. To build, type: cd cpp_stochastic bjam -q install cd .. Before you bother running any simulations, I highly recommend that you perform all the unit tests and integration tests: ./run_tests.sh -a If they do not all pass, you should make sure that all required packages are installed, then start hunting for the problem. This package requires a (mysql) database server to interact with. The mysql username and password can be edited in the config.ini file (if you aren't using the defaults, you may want to edit the bin/create_db_user.sh and bin/reset_db.sh files). To just run with the defaults: bin/create_db_user.sh bin/reset_db.sh The reset command will give you an error saying it couldn't drop the database, because it doesn't exist. That's no problem. If you are going to have worker process running on machines other than the one hosting your database, make sure the database server is setup to accept outside connections. You also may need to change the maximum number of connections. ------------------------------------------------------------------------ - Running - ------------------------------------------------------------------------ ------------------------------------------------------------------------ - Adding Simulations - ------------------------------------------------------------------------
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