Activity for pybrn

  • Henning Lindhorst Henning Lindhorst committed [e71ff5]

    added reversibility for reactions, changes to n...

  • Steffen Waldherr committed [6f074d]

    Added test for sundials compilation with tempor...

  • Henning Lindhorst Henning Lindhorst committed [3d10e3]

    reworked rba as with ipopt solver, used linopt ...

  • Henning Lindhorst Henning Lindhorst committed [70ac77]

    added deFBA algorithm, warning rba is broken. S...

  • Henning Lindhorst Henning Lindhorst committed [b4dba1]

    working version of RBA

  • Henning Lindhorst Henning Lindhorst committed [196584]

    added basic RBA method implemented in gurobi

  • Henning Lindhorst Henning Lindhorst committed [5e50d7]

    corrected error in sorting stoich, species, and...

  • Henning Lindhorst Henning Lindhorst committed [a3de50]

    added catalytic constants for biomass productio...

  • Henning Lindhorst Henning Lindhorst committed [1b3083]

    added function to construct HC matrix

  • Henning Lindhorst Henning Lindhorst committed [450c6c]

    added calculation of biomass vector via fasta data

  • Henning Lindhorst Henning Lindhorst committed [51ddab]

    added molecular weight search and fixed some co...

  • Henning Lindhorst Henning Lindhorst committed [306ed0]

    added ribosomes to model; added energy cost to ...

  • Henning Lindhorst Henning Lindhorst committed [695c72]

    added a function to create the configuration fi...

  • Henning Lindhorst Henning Lindhorst committed [3fa213]

    added config file parser to the code for user, ...

  • Henning Lindhorst Henning Lindhorst committed [dfd0b7]

    added functions to sort the species to [x_ext, ...

  • Henning Lindhorst Henning Lindhorst committed [a98776]

    added function to add protein producing reactio...

  • Henning Lindhorst Henning Lindhorst committed [9ea40a]

    added function to add new reactions from OR ter...

  • Henning Lindhorst Henning Lindhorst committed [02f526]

    added interfaces to KEGG, BRENDA, YeastGenome t...

  • Steffen Waldherr committed [852c82]

    Added outer parenthesis around SBML function su...

  • Steffen Waldherr committed [4b9d9e]

    Partially fixed a bug with parentheses in SBML ...

  • Steffen Waldherr committed [f1e217]

    Fixed an error with output computation from sim...

  • Steffen Waldherr committed [1ce1e6]

    Changed output code format for jacobian string ...

  • Steffen Waldherr committed [9ad3c6]

    Importing C's M_PI as Python's pi in .pyx files...

  • Steffen Waldherr committed [473530]

    Generalized return value handling in Brn.simulate.

  • Steffen Waldherr committed [3a95ee]

    Made SBML import test run in standalone.

  • Steffen Waldherr committed [b253c5]

    Improved SBML import with boundary species.

  • Steffen Waldherr committed [dac54c]

    Revised import of boundary species.

  • Henning Lindhorst Henning Lindhorst committed [3008eb]

    cleared code and deleted unnecessary variables/...

  • Henning Lindhorst Henning Lindhorst committed [426948]

    added documentation

  • Henning Lindhorst Henning Lindhorst committed [aadd07]

    added additional methods for ode_rhs and rate e...

  • Steffen Waldherr committed [c63545]

    Removed the nojacobian unittest for casadi.

  • Steffen Waldherr committed [d56e7e]

    Fixed return arguments for CasadiSimulator.inte...

  • Steffen Waldherr committed [4a4c37]

    Revised interface for consistency with base cla...

  • Steffen Waldherr committed [6c478e]

    Revised CasadiSimulator's constructor.

  • Steffen Waldherr committed [ed6b57]

    Added unittests for casadi simulation.

  • Henning Lindhorst Henning Lindhorst committed [8dc704]

    working casadi integrator with variables support

  • Henning Lindhorst Henning Lindhorst committed [30a4bc]

    trying to include brn.variables as DAE to the c...

  • Henning Lindhorst Henning Lindhorst committed [669993]

    added CasadiSimulator class

  • Steffen Waldherr committed [1d50b5]

    Merged latest develop changes into casadi.

  • Steffen Waldherr committed [094eb8]

    Removed Jacobian computation fron SundialsSimul...

  • Steffen Waldherr committed [6b658c]

    Moved BrnNumerics and Simulator to __init__ mod...

  • Steffen Waldherr committed [e72dc0]

    Added scipy simulators to numerics __init__ file.

  • Steffen Waldherr committed [a68ab4]

    Added SundialsSimulatorStop to numerics subpack...

  • Steffen Waldherr committed [5b37a7]

    Added the ode_rhs method to SundialsSimulator.

  • Steffen Waldherr committed [d6e954]

    Started implementing separate numerics subpackage.

  • Steffen Waldherr committed [b54532]

    Added first implementation of SundialsSimulator.

  • Steffen Waldherr committed [b41a00]

    Fixed smaller interface and documentation issues.

  • Steffen Waldherr committed [fdc463]

    Added sympy import error message.

  • Steffen Waldherr committed [2df6fe]

    Merging new numerics package.

  • Steffen Waldherr committed [6ab18b]

    Added new Simulator abstract class based on Brn...

  • Steffen Waldherr committed [8bc664]

    Fixed bug in Simulator.compute_outputs.

  • Steffen Waldherr committed [1b05db]

    Added new VodeSimulator class.

  • Steffen Waldherr committed [6acde6]

    Added the VodeSimulatorStop class to the numeri...

  • Henning Lindhorst Henning Lindhorst committed [f76010]

    added method to set rates as mass-action law ra...

  • Henning Lindhorst Henning Lindhorst committed [f30818]

    added import function from Brn to BrnCas

  • Henning Lindhorst Henning Lindhorst committed [12073f]

    added import function from Brn to BrnCas

  • Henning Lindhorst Henning Lindhorst committed [f93d13]

    added simulator method to brncas class and suit...

  • Henning Lindhorst Henning Lindhorst committed [fb1faa]

    corrected copy & paste error

  • Henning Lindhorst Henning Lindhorst committed [a1f61d]

    initial part for casadi class

  • Steffen Waldherr committed [b6de75]

    Fixed future warning due to None comparison in ...

  • Steffen Waldherr committed [6ebd36]

    Merged simulation of time-variant networks with...

  • Steffen Waldherr committed [882166]

    Updated documenation for simulation of time-var...

  • Christian Schlauch Christian Schlauch committed [b12ea6]

    adjusted unittest (3 instead of 4 places)

  • Christian Schlauch Christian Schlauch committed [ff7b36]

    Added passing of time-argument to ratefun

  • Christian Schlauch Christian Schlauch committed [17a615]

    Fix: time argument as optional parameter

  • Linda Eßmann Linda Eßmann committed [834b85]

    OC switch simulation with implemented cell comm...

  • Linda Eßmann Linda Eßmann committed [ddc0dc]

    OC switch simulation with implemented cell comm...

  • Steffen Waldherr committed [ff3a3a]

    Added unit test for simulation of time variant ...

  • Steffen Waldherr committed [4d9999]

    Added 'approximation' option in mathutils.rank ...

  • Linda Eßmann Linda Eßmann committed [2c3c88]

    Startwerte für Zeitpunkte und Trajektorie der Z...

  • Steffen Waldherr committed [2239e4]

    Now removing cells repeatedly until list length...

  • Steffen Waldherr committed [5f457e]

    Now actually removing removed cells from popula...

  • Steffen Waldherr committed [3934e4]

    Fixed bug when using params in sym2fun.

  • Steffen Waldherr committed [b61d2b]

    Improved brn.mathutils.sym2fun method.

  • Steffen Waldherr committed [980192]

    Added the mathutils.sym2fun method.

  • Steffen Waldherr committed [4fa3d3]

    Simulating ocs population without Jacobian.

  • Steffen Waldherr committed [b4dcd7]

    Discover SBML files with 'time' variable, issue...

  • Steffen Waldherr committed [076375]

    Added option to simulate without Jacobian.

  • Steffen Waldherr committed [8c32f3]

    Fixed Jacobian usage in brn.simulation.VodeSimu...

  • Steffen Waldherr committed [7b2cf4]

    Fixed a problem in VodeSimulator when sympy not...

  • Steffen Waldherr committed [fab6e5]

    Fixed a problem with Cell.evaluate for cells wh...

  • Steffen Waldherr committed [28974a]

    Added previous sundials simulation example as o...

  • Steffen Waldherr committed [efd3d6]

    Changed simulator in ocswitch population example.

  • Steffen Waldherr committed [84e0f2]

    Added example for population simulation.

  • Steffen Waldherr committed [121f36]

    Updated change history to include new populatio...

  • Steffen Waldherr committed [c8a1ff]

    Pulled new version number in CHANGES.txt from m...

  • Steffen Waldherr committed [04ce6c]

    Added files from project with Timm Strecker and...

  • Steffen Waldherr committed [297a6b]

    Started testing framework for cellpopsim.

  • Steffen Waldherr committed [d8a413]

    Passing time_points as optional kwarg in Popula...

  • Steffen Waldherr committed [81cbf5]

    Added check of internal division state to simul...

  • Steffen Waldherr committed [494aea]

    Division now generates two daughter cells inste...

  • Steffen Waldherr committed [8f9b6b]

    Added CellSimulator class and adjusted Cell con...

  • Steffen Waldherr committed [cd02f5]

    Fixed selection of time points in trajectory st...

  • Steffen Waldherr committed [491028]

    Removed unneeded old code.

  • Steffen Waldherr committed [c63717]

    Added methods to evaluate population size.

  • Steffen Waldherr committed [96e0a1]

    Changed default growth mechanism to network sim...

  • Steffen Waldherr committed [218e77]

    Fixed errors in population simulation.

  • Steffen Waldherr committed [bc77d4]

    Added trajectory time points to population simu...

  • Steffen Waldherr committed [824cb7]

    Added test with network-based growth.

  • Steffen Waldherr committed [dd3a62]

    Removed unneeded scipy import.

1 >