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# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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"from base_classes import Measurement as _Measurement",
"from actin_dynamics import logger",
"_log = logger.getLogger(__file__)",
"class Length(_Measurement):\n def __init__(self, **kwargs):\n _Measurement.__init__(self, **kwargs)\n\n def perform(self, time, filaments):\n for filament in f... |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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"from registry import measurement_registry as registry",
"from filaments import *"
] |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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"filament_factory_registry = {}"
] |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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... | [
"import itertools",
"import random",
"from base_classes import FilamentFactory as _FilamentFactory",
"from actin_dynamics.state.single_strand_filaments import Filament",
"class SingleStateFixedLength(_FilamentFactory):\n def __init__(self, state=None, length=None, number=None, label=None):\n self.... |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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"from ..meta_classes import Registration",
"from registry import filament_factory_registry",
"class FilamentFactory(object):\n __metaclass__ = Registration\n registry = filament_factory_registry\n skip_registration = True\n\n def __init__(self, label=None):\n self.label = label",
" __met... |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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"from registry import filament_factory_registry as registry",
"from single_state import *",
"from inert_filaments import *"
] |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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"from base_classes import FilamentFactory as _FilamentFactory",
"from actin_dynamics.state.single_strand_filaments import Filament",
"class InertFilament(_FilamentFactory):\n def __init__(self, state=None, label=None):\n self.state = state\n _FilamentFactory.__init__(self, label=label)\n\n d... |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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"concentration_registry = {}"
] |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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"from base_classes import Concentration as _Concentration",
"class FixedConcentration(_Concentration):\n __slots__ = ['value', 'data']\n def __init__(self, concentration=-1, **kwargs):\n if concentration < 0:\n raise ValueError('Negative concentrations not allowed.')\n self.value = ... |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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"from ..meta_classes import Registration",
"from registry import concentration_registry",
"class Concentration(object):\n __metaclass__ = Registration\n registry = concentration_registry\n skip_registration = True\n\n __slots__ = ['label', 'sample_period', 'data']\n def __init__(self, sample_peri... |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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"from base_classes import Concentration as _Concentration",
"class FixedReagent(_Concentration):\n __slots__ = ['value', 'monomer_count', 'concentration_per_monomer']\n def __init__(self, initial_concentration=-1,\n filament_tip_concentration=-1,\n number=None, label=None):\n... |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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"from registry import concentration_registry as registry",
"from fixed_concentration import *",
"from fixed_reagent import *"
] |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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"objective_registry = {}"
] |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
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... | [
"from .base_classes import Objective as _Objective",
"from actin_dynamics.numerical import measurements",
"class ElongationRate(_Objective):\n def __init__(self, sample_period=None, label=None):\n self.sample_period = sample_period\n\n _Objective.__init__(self, label=label)\n\n def perform(s... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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0.322,
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"from .base_classes import Objective as _Objective",
"from actin_dynamics.numerical import residuals as _residuals",
"from actin_dynamics.numerical import interpolation as _interpolation",
"from actin_dynamics.numerical import measurements as _measurements",
"import itertools as _itertools",
"from actin_d... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
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... | [
"from ..meta_classes import Registration",
"from registry import objective_registry",
"class Objective(object):\n __metaclass__ = Registration\n registry = objective_registry\n skip_registration = True\n\n __slots__ = ['label']\n def __init__(self, label=None):\n self.label = label",
" ... |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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0.... | [
"from registry import objective_registry as registry",
"from simple_data_fit import *",
"from pyrene_fit import *",
"from diffusion_coefficient import *",
"from elongation_rate import *"
] |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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[
1,
0,
0.2676,
0.0141,
0,
0.... | [
"from .base_classes import Objective as _Objective",
"from actin_dynamics.numerical import residuals as _residuals",
"from actin_dynamics.numerical import measurements as _measurements",
"class PyreneFit(_Objective):\n def __init__(self, label=None, residual_type=None, **weights):\n self.residual_fu... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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[
1,
0,
0.2159,
0.0114,
0,
... | [
"from .base_classes import Objective as _Objective",
"from actin_dynamics.numerical import residuals as _residuals",
"from actin_dynamics.numerical import regression",
"class DiffusionCoefficient(_Objective):\n def __init__(self, analysis_prefix=None, label=None):\n self.analysis_prefix = analysis... |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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] | [
"analysis_registry = {}"
] |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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"import math",
"import operator",
"from . import base_classes as _base_classes",
"from . import utils",
"from actin_dynamics.numerical import interpolation, workalike",
"from actin_dynamics import logger as _logger",
"_log = _logger.getLogger(__file__)",
"class StandardErrorMean(_base_classes.Analysis... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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[
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0.1887,
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"import numpy",
"from . import base_classes as _base_classes",
"from . import utils",
"from actin_dynamics.numerical import interpolation, workalike, measurements, histograms, regression, residuals",
"from actin_dynamics import logger as _logger",
"_log = _logger.getLogger(__file__)",
"class TipDiffusio... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
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0,
0.5333,
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[
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0,
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... | [
"from ..meta_classes import Registration",
"from registry import analysis_registry",
"class Analysis(object):\n __metaclass__ = Registration\n registry = analysis_registry\n skip_registration = True\n\n __slots__ = ['label']\n def __init__(self, label=None, **kwargs):\n self.label = label"... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
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0,
0,
71,
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],
[
2,
0,
0.6711,
0.3158,
0,
0... | [
"from actin_dynamics import logger as _logger",
"_log = _logger.getLogger(__file__)",
"def get_measurement(simulation_results, name, measurement_type):\n if 'filament' == measurement_type:\n iterator = iter_filaments(simulation_results)\n measurement_key = 'measurements'\n else:\n ite... |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
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0,
0,
216,
0,
0
],
[
1,
0,
0.9048,
0.0476,
0,
0.6... | [
"from registry import analysis_registry as registry",
"from standard_error_of_mean import *",
"from tip_diffusion import *"
] |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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[
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0.... | [
"import analyses",
"import concentrations",
"import end_conditions",
"import measurements",
"import filaments",
"import file_readers",
"import objectives",
"import transitions"
] |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
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"class Registration(type):\n def __init__(cls, class_name, base_classes, class_dict):\n # This allows exluding base classes from registration.\n if not class_dict.get('skip_registration', False):\n cls.registry[class_name] = cls",
" def __init__(cls, class_name, base_classes, class_... |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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"end_condition_registry = {}"
] |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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"from ..meta_classes import Registration",
"from registry import end_condition_registry",
"class EndCondition(object):\n __metaclass__ = Registration\n registry = end_condition_registry\n skip_registration = True\n \n def __init__(self, label=None):\n self.label = label",
" __metaclas... |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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0,
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] | [
"from registry import end_condition_registry as registry",
"from duration import *"
] |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
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... | [
"\"\"\"\n This module contains various end conditions for the simulations.\n\"\"\"",
"from base_classes import EndCondition as _EndCondition",
"import random",
"class Duration(_EndCondition):\n 'End simulation after duration seconds.'\n\n __slots__ = ['duration']\n def __init__(self, duration=None... |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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[
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"\"\"\"\n This module contains a general Kinetic Monte Carlo simulation.\n\"\"\"",
"import bisect",
"import math",
"import random",
"import traceback",
"from .numerical import utils",
"from . import logger",
"log = logger.getLogger(__file__)",
"class Simulation(object):\n \"\"\"\n Kinetic M... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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[
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... | [
"import time",
"import datetime",
"import socket",
"import os",
"import contextlib",
"import sqlalchemy.exceptions",
"from . import database",
"from . import version",
"from . import logger",
"log = logger.getLogger(__file__)",
"PID = None",
"def process(process_type, db_session):\n '''\n ... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
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0,
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0,
0,
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[
3,
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0.4608,
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0.66... | [
"from sqlalchemy import orm as _orm",
"from . import tables as _tables",
"class Parameter(object):\n def __init__(self, name, value):\n self.name = name\n self.value = value\n\n def __repr__(self):\n return \"%s(id=%s, name='%s', value=%s)\" % (\n self.__class__.__name... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
1,
0,
0.2208,
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835,
0,
1,
0,
0,
835,
0,
0
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[
1,
0,
0.2468,
0.013,
0,
0.66,
0.1667,
0,
0,
1,
0,
0,
0,
0,
0
],
[
1,
0,
0.2597,
0.013,
0,
0.66,
... | [
"from sqlalchemy import orm as _orm",
"from . import tables as _tables",
"from . import runs as _runs",
"class Process(object):\n def __init__(self, type=None, code_revision=None, code_changeset=None,\n hostname=None, uname=None):\n if type:\n self.type = type\n if ... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
1,
0,
0.1828,
0.0108,
0,
0.66,
0,
835,
0,
1,
0,
0,
835,
0,
0
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[
1,
0,
0.1935,
0.0108,
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0.66,
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0,
0,
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[
1,
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0.... | [
"from sqlalchemy import orm as _orm",
"from sqlalchemy.ext.associationproxy import association_proxy as _ap",
"from . import tables as _tables",
"from . import parameters as _parameters",
"from . import analyses as _analyses",
"from . import objectives as _objectives",
"from . import models as _models",... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
1,
0,
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0,
835,
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1,
0,
0,
835,
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[
1,
0,
0.4419,
0.0233,
0,
0.66,
0.25,
0,
0,
1,
0,
0,
0,
0,
0
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[
1,
0,
0.4651,
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0.66,
... | [
"from sqlalchemy import orm as _orm",
"from . import tables as _tables",
"from . import binds as _binds",
"class Model(object):\n def __init__(self, name=None, session=None, concentrations=None,\n transitions=None):\n if name:\n self.name = name\n if session:\n ... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
1,
0,
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1,
0,
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0,
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[
1,
0,
0.3091,
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0,
0.66,
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87,
0,
1,
0,
0,
87,
0,
0
],
[
1,
0,
0.3455,
0.0182,
0,
0.... | [
"from sqlalchemy import orm as _orm",
"from sqlalchemy.ext.associationproxy import association_proxy as _ap",
"from . import tables as _tables",
"from . import experiments as _experiments",
"from . import parameters as _parameters",
"from . import models as _models",
"class Session(object):\n def __i... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
1,
0,
0.3148,
0.0185,
0,
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0,
835,
0,
1,
0,
0,
835,
0,
0
],
[
1,
0,
0.3333,
0.0185,
0,
0.66,
0.1667,
87,
0,
1,
0,
0,
87,
0,
0
],
[
1,
0,
0.3704,
0.0185,
0,
0.... | [
"from sqlalchemy import orm as _orm",
"from sqlalchemy.ext.associationproxy import association_proxy as _ap",
"from . import tables as _tables",
"from . import binds as _binds",
"from . import parameters as _parameters",
"class Objective(object):\n def __init__(self, run=None, bind=None, value=None, pa... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
1,
0,
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808,
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1,
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1,
0,
0,
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[
1,
0,
0.3065,
0.0161,
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0... | [
"import itertools",
"from sqlalchemy import orm as _orm",
"from sqlalchemy.ext.associationproxy import association_proxy as _ap",
"from . import tables as _tables",
"from . import binds as _binds",
"from . import experiments as _experiments",
"from . import results as _results",
"class Analysis(object... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
1,
0,
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0,
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0,
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[
3,
0,
0.413,
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0,
0.66,... | [
"from sqlalchemy import orm as _orm",
"from . import tables as _tables",
"class Argument(object): pass",
"_orm.mapper(Argument, _tables.argument_table,\n polymorphic_on=_tables.argument_table.c.type)",
"class FixedArgument(Argument):\n def __init__(self, name, value):\n self.name = nam... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
1,
0,
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0,
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0,
0,
0,
0,
0
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[
3,
0,
0.6585,
0.3171,
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0.66... | [
"from sqlalchemy import orm as _orm",
"from . import tables as _tables",
"class _Data(object):\n def __init__(self, abscissa=None, ordinate=None, error=None):\n if abscissa is not None:\n self.abscissa = abscissa\n if ordinate is not None:\n self.ordinate = ordinate\n ... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
1,
0,
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0,
0.66,
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933,
3,
0,
0,
0,
857,
10,
1
]
] | [
"import sqlalchemy as _sqlalchemy",
"metadata = _sqlalchemy.MetaData()"
] |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
1,
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0,
0,
87,
0,
0
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[
1,
0,
0.2151,
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0.... | [
"from sqlalchemy import orm as _orm",
"from sqlalchemy.ext.associationproxy import association_proxy as _ap",
"from . import tables as _tables",
"from . import binds as _binds",
"from . import parameters as _parameters",
"from . import objectives as _objectives",
"class Experiment(object):\n def __in... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
1,
0,
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951,
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0,
0,
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[
1,
0,
0.4348,
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0.66... | [
"import global_state",
"from . import tables",
"from .analyses import *",
"from .arguments import *",
"from .binds import *",
"from .experiments import *",
"from .jobs import *",
"from .logs import *",
"from .models import *",
"from .objectives import *",
"from .parameters import *",
"from .re... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
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[
1,
0,
0.0538,
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0... | [
"import datetime",
"from sqlalchemy import schema",
"from . import global_state",
"MAX_NAME_LENGTH = 128",
"MAX_POLY_LENGTH = 16",
"MAX_TABLE_NAME_LENGTH = 30",
"MAX_COLUMN_NAME_LENGTH = 30",
"MAX_LOG_MESSAGE_SIZE = 1024",
"slice_definition_table = schema.Table('slice_definition', global_state.meta... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
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423,
0,
0
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[
1,
0,
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0.0078,
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0.66... | [
"import datetime as _datetime",
"import traceback as _traceback",
"from sqlalchemy import orm as _orm",
"from . import jobs as _jobs",
"from . import tables as _tables",
"class DBTraceback(object):\n def __init__(self, filename=None, lineno=None, module=None, line=None):\n if filename:\n ... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
1,
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[
1,
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0.2676,
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0.66,... | [
"from sqlalchemy import orm as _orm",
"from . import tables as _tables",
"from . import binds as _binds",
"class SliceMesh(object):\n def __init__(self, parameter=None, value=None):\n if parameter:\n self.parameter = parameter\n if value is not None:\n self.value = value... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
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"import itertools as _itertools",
"from sqlalchemy import orm as _orm",
"from sqlalchemy.ext.associationproxy import association_proxy as _ap",
"from . import tables as _tables",
"from . import arguments as _arguments",
"from . import results as _results",
"def _create_bind(key, value):\n value.label... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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"import logging",
"from actin_dynamics import database",
"from actin_dynamics import job_control",
"class SQLAlachemyHandler(logging.Handler):\n def __init__(self, *args, **kwargs):\n self.db_session = database.DBSession()\n logging.Handler.__init__(self, *args, **kwargs)\n\n def emit(self... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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"WHITE = None",
"BLACK = 30",
"RED = 31",
"GREEN = 32",
"YELLOW = 33",
"BLUE = 34",
"PURPLE = 35",
"CYAN = 36",
"GREY = 37",
"ESCAPE_SEQUENCE = '\\033['",
"def make_sequence(foreground=WHITE, background=BLACK, bold=False):\n if foreground:\n if bold:\n fg_identif... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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[
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"import logging",
"import os.path",
"def getLogger(filename):\n long_name, junk = os.path.splitext(filename)\n begining, end = os.path.split(long_name)\n logger_name = ''\n while not ('actin_dynamics' == end):\n logger_name = '.' + end + logger_name\n begining, end = os.path.split(beg... |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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"import mercurial.hg",
"import mercurial.ui",
"def source_revision():\n repo = mercurial.hg.repository(mercurial.ui.ui(), '.')\n parent = repo.parents()[0]\n return parent.rev(), parent.hex()",
" repo = mercurial.hg.repository(mercurial.ui.ui(), '.')",
" parent = repo.parents()[0]",
" re... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
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... | [
"import operator",
"from . import database",
"from .numerical import meshes",
"from . import logger",
"log = logger.getLogger(__file__)",
"class Controller(object):\n def __init__(self, session, parameter_specifications={}):\n self.session = session\n self.parameter_specifications = param... |
# Copyright (C) 2010-2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This prog... | [
[
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"from sqlalchemy import schema",
"from . import factories",
"from . import logger",
"from . import database",
"from . import logger",
"log = logger.getLogger(__file__)",
"def run_job(job, db_session):\n run = job.run\n num_sims = int(run.all_parameters['number_of_simulations'])\n log.info('Star... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
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[
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0... | [
"import argparse",
"import datetime",
"def _config(parser):\n parser.add_argument('-c', '--config', default='config.ini',\n help='Configuration file name')\n return parser",
" parser.add_argument('-c', '--config', default='config.ini',\n help='Configurati... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
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... | [
"import configobj",
"from . import database",
"from . import logger",
"def full_config(filename):\n co = configobj.ConfigObj(filename)\n database.setup_database_from_dict(co['database'])\n logger.setup_logging_from_dict(co['logging'])",
" co = configobj.ConfigObj(filename)",
" database.setu... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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808,
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[
2,
0,
0.8654,
0.3077,
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0.6... | [
"import logging",
"from actin_dynamics.logger import handlers",
"def setup_logging_from_dict(log_dict):\n root_logger = logging.getLogger()\n\n levelname = log_dict.get('level', 'WARN')\n level = getattr(logging, levelname)\n root_logger.setLevel(level)\n\n root_logger.addHandler(handlers.SQLAlac... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [] | [] |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
1,
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1,
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"import configobj",
"from sqlalchemy import orm, create_engine",
"from actin_dynamics import database",
"class DatabaseConfiguration(object):\n def __init__(self, server_type=None, username=None, password=None,\n host=None, database_name=None):\n self.server_type = server_type\n ... |
# Copyright (C) 2010 - 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This pr... | [
[
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1,
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"import logging",
"import logging.handlers",
"import primitives",
"try:\n nh = logging.handlers.NullHandler()\nexcept AttributeError:\n class NullHandler(logging.Handler):\n def emit(self, record):\n pass\n\n nh = NullHandler()",
" nh = logging.handlers.NullHandler()",
" c... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
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"_COLORS = [['#06246F', '#2A4380', '#123EAB', '#466FD5', '#6C8AD5'], # blue\n ['#3F046F', '#582781', '#640CAB', '#9240D5', '#A468D5'], # purple\n ['#00782D', '#238B49', '#00B945', '#37DC74', '#63DC90'], # green\n ['#A66F00', '#BF9030', '#FFAB00', '#FFC040', '#FFD173']] # orange",
... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
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0,
0.3478,
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735,
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... | [
"import pylab",
"from . import measurements",
"from . import slicing",
"from actin_dynamics.numerical.zero_crossings import zero_crossings",
"def elongation_rate_vs_conc(session, **kwargs):\n ob = session.get_experiment('critical_concentration').objectives['elongation_rate']\n\n s = slicing.Slicer.fro... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
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954,
0,
1,
0,
0,
954,
0,
0
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[
1,
0,
0.2394,
0.0141,
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735,
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0,
735,
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[
2,
0,
0.2958,
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... | [
"import numpy",
"import pylab",
"def bar(measurement, color='black', **kwargs):\n centers, values, errors = measurement\n\n pylab.bar(centers, values, width=width, align='center', color=color,\n **kwargs)",
" centers, values, errors = measurement",
" pylab.bar(centers, values, width... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
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0,
0,
772,
0,
0
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[
1,
0,
0.3276,
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0.66... | [
"from actin_dynamics import io",
"from actin_dynamics.analysis import accessors, utils, fluorescence",
"from .. import measurements",
"from .. import themes",
"def plot_run(run, final_pyrene_value=3, with_data=True,\n pyrene_color=None, adppi_color=None, length_color=None,\n pyrene_n... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
1,
0,
0.0602,
0.0038,
0,
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0,
735,
0,
1,
0,
0,
735,
0,
0
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1,
0,
0.0677,
0.0038,
0,
0.66,
0.125,
0,
0,
1,
0,
0,
0,
0,
0
],
[
1,
0,
0.0752,
0.0038,
0,
0.66,... | [
"import pylab",
"from .. import slicing",
"from .. import fit",
"def random_adppi(adppi_ob, pyrene_ob):\n adppi_slicer = slicing.Slicer.from_objective_bind(adppi_ob)\n pyrene_slicer = slicing.Slicer.from_objective_bind(pyrene_ob)\n# max_val = 14\n pylab.figure()\n\n blvd, best_pyrene_id = pyre... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
1,
0,
0.2353,
0.0147,
0,
0.66,
0,
57,
0,
1,
0,
0,
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0,
0
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[
1,
0,
0.25,
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0,
0,
772,
0,
0
],
[
1,
0,
0.2794,
0.0147,
0,
0.66,
... | [
"from actin_dynamics import io",
"from actin_dynamics.analysis import accessors",
"from .. import measurements",
"from .. import themes",
"def kinsim_comparison(run=None, pollard_simulations=False, theme=None):\n # Get color and style settings.\n if not theme:\n theme = themes.Polymerization()\... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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0,
0.6667,
0.0417,
0,
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0,
340,
0,
1,
0,
0,
340,
0,
0
]
] | [
"import talk"
] |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
1,
0,
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405,
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[
1,
0,
0.8261,
0.0435,
0,
0.6... | [
"import slicing",
"import pieper_wegner",
"import measurements",
"import fujiwara",
"import critical_concentration",
"import new_pollard"
] |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
1,
0,
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325,
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1,
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0.1064,
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"import bisect",
"import numpy",
"from sqlalchemy import func, schema, sql",
"from actin_dynamics import database",
"class Slicer(object):\n def __init__(self, table, meshes, column_map):\n self.table = table\n self.meshes = meshes\n self.column_map = column_map\n\n @clas... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
1,
0,
0.1006,
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735,
0,
1,
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735,
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[
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276,
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[
1,
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... | [
"import pylab",
"import pprint",
"from actin_dynamics import database",
"from actin_dynamics import numerical",
"import actin_dynamics.numerical.measurements",
"from actin_dynamics.factories import bindings",
"from . import slicing",
"from . import fit",
"from . import measurements",
"from . impor... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
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0,
0.0643,
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954,
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1,
0,
0,
954,
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[
1,
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0,
735,
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[
1,
0,
0.0723,
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"import numpy",
"import pylab",
"import matplotlib.ticker",
"import itertools",
"import operator",
"import actin_dynamics.numerical.measurements",
"from actin_dynamics import numerical",
"from . import measurements",
"from . import themes",
"import pprint",
"def plot_slice(slicer, abscissae_name... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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"import pylab",
"import numpy",
"from . import measurements",
"from . import slicing",
"from actin_dynamics import database",
"from actin_dynamics.numerical.zero_crossings import zero_crossings",
"def D_vs_concentration(session, cc_scale=False, **kwargs):\n e = session.get_experiment('fujiwara_2002')... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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[
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... | [
"import itertools",
"import numpy",
"from scipy import polyfit",
"from scipy.optimize import fmin",
"from . import residuals",
"from actin_dynamics import logger",
"log = logger.getLogger(__file__)",
"def fit_gaussian(x_mesh, y_mesh):\n total_y = sum(y_mesh)\n mean = sum(x * y for x, y in iterto... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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[
1,
0,
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"import math",
"import bisect",
"from . import workalike",
"from actin_dynamics import logger",
"log = logger.getLogger(__file__)",
"def make_histogram(values, bin_size):\n bin_size = float(bin_size)\n smallest_relative_index = - get_bin_distance(min(values), bin_size)\n largest_relative_index =... |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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0,
526,
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[
1,
0,
0.3065,
0.0161,
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"import itertools",
"import math",
"from . import workalike",
"class ParameterMeshIterator(object):\n def __init__(self, names, parameter_sets):\n self.names = names\n self.parameter_sets = itertools.product(*parameter_sets)\n \n def __iter__(self):\n return self",
" def __i... |
# Copyright (C) 2010-2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This prog... | [
[
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1,
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"import copy",
"import math",
"import bisect",
"import itertools",
"import numpy",
"from actin_dynamics.numerical import workalike",
"def time_slice(measurement, start_time=None, stop_time=None):\n start_index = 0\n stop_index = len(measurement[0])\n if start_time is not None:\n start_i... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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[
2,
0,
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... | [
"import numpy",
"from . import interpolation",
"def zero_crossings(x, y, interpolate=True):\n zero_crossings = numpy.where(numpy.diff(numpy.sign(y)))[0]\n\n if not interpolate:\n return [x[i] for i in zero_crossings]\n\n results = []\n for i in zero_crossings:",
" zero_crossings = numpy.... |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
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[
1,
0,
0.2235,
0.0118,
0,
0.6... | [
"import itertools",
"import math",
"from . import workalike",
"def chi_squared(a, b, minimum_error=0.001):\n at, av = a[:2]\n bt, bv = b[:2]\n\n errors = [0 for x in av]\n if 3 == len(a):\n ae = a[2]\n errors = workalike.add(errors, [ax**2 for ax in ae])",
" at, av = a[:2]",
"... |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
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0,
0,
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],
[
14,
1,
0.8696,
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1,
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... | [
"def running_total(values):\n \"\"\"\n Generator that calculates a running total of a sequence.\n \"\"\"\n total = 0\n for v in values:\n total += v\n yield total",
" \"\"\"\n Generator that calculates a running total of a sequence.\n \"\"\"",
" total = 0",
" for v ... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
1,
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[
2,
0,
0.47,
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0,
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0.... | [
"import itertools",
"import math",
"def add(a, b):\n result = []\n for ax, bx in itertools.izip(a, b):\n result.append(ax + bx)\n\n return result",
" result = []",
" for ax, bx in itertools.izip(a, b):\n result.append(ax + bx)",
" result.append(ax + bx)",
" return ... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [] | [] |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
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[
2,
1,
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"import bisect",
"def interp1d(x_data, y_data):\n def inner(x):\n left = bisect.bisect_left(x_data, x)\n if left > 0:\n result = linear_project(x_data[left - 1], y_data[left - 1],\n x_data[left], y_data[left],\n x... |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
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0,
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],
[
2,
0,
0.119,
0.0179,
0,
0.6... | [
"import itertools",
"import collections",
"def _ddict_factory():\n # XXX Consider making these (ordered) sets instead of lists (performance).\n return collections.defaultdict(list)",
" return collections.defaultdict(list)",
"class Filament(object):\n __slots__ = ['states', 'relative_state_indice... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
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[
2,
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"import itertools",
"import collections",
"def iterate_pairs(lst):\n i = iter(lst)\n prev = i.next()\n for item in i:\n yield prev, item\n prev = item",
" i = iter(lst)",
" prev = i.next()",
" for item in i:\n yield prev, item\n prev = item",
" yield ... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [] | [] |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
1,
0,
0.381,
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0,
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],
[
3,
0,
0.5476,
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0,
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... | [
"import csv",
"from . import comments",
"class DataThiefDialect(csv.Dialect):\n delimiter = ' '\n quotechar = '\"'\n doublequote = True\n skipinitialspace = True\n lineterminator = '\\r\\n'\n quoting = csv.QUOTE_NONNUMERIC",
" delimiter = ' '",
" quotechar = '\"'",
" doublequote... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
1,
0,
0.2909,
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0,
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960,
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0,
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79,
0,
0
],
[
1,
0,
0.3273,
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0,
0.... | [
"import yaml",
"import os.path",
"import sys",
"from .. import logger",
"log = logger.getLogger(__file__)",
"def load_definition(filename):\n results = None\n log.debug(\"Loading definition from '%s'.\", filename)\n try:\n with open(filename) as f:\n results = yaml.load(f)\n ... |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
1,
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],
[
13,
1,
1,
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0.4,
0,... | [
"import yaml",
"def parse_object_graph_file(obj_file):\n return yaml.load(obj_file)",
" return yaml.load(obj_file)"
] |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
3,
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0,
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],
[
14,
2,
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0.0256,
2,
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... | [
"class CommentFilter(object):\n def __init__(self, stream, ownership=False):\n self.stream = stream\n self._ownership = ownership\n\n @classmethod\n def from_filename(cls, filename):\n return cls(open(filename), ownership=True)",
" def __init__(self, stream, ownership=False):\n ... |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [] | [] |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [] | [] |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [] | [] |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [] | [] |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [] | [] |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [] | [] |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
1,
0,
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[
1,
0,
0.6452,
0.0323,
0,
0.... | [
"import unittest",
"from sqlalchemy import create_engine, orm",
"from actin_dynamics import database",
"class DBTestCase(unittest.TestCase):\n def setUp(self):\n self.engine = create_engine('sqlite:///:memory:')\n self.DBSession = orm.sessionmaker(bind=self.engine)\n self.db_session = ... |
# Copyright (C) 2011 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [] | [] |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
1,
0,
0.5,
0.0312,
0,
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0,
0,
193,
0,
0
],
[
3,
0,
0.7969,
0.4375,
0,
0.66,
... | [
"import itertools",
"import collections",
"class MockTransition(object):\n def __init__(self, add_value, rate):\n self.add_value = add_value\n self.rate = rate\n self.measurements = collections.defaultdict(list)\n\n def R(self, filaments, concentrations):\n return list(itertool... |
# Copyright (C) 2010 Mark Burnett
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program i... | [
[
3,
0,
0.8478,
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0,
0,
0,
0,
0
],
[
14,
2,
0.7826,
0.0435,
2,
0.61,
... | [
"class MockMeasurement(object):\n def __init__(self, label=None, index=0):\n self.index = index\n self.label = label\n\n def perform(self, time, filaments):\n for i, filament in enumerate(filaments):\n filament.measurements[self.label].append((time, filament[-1]))",
" def ... |
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