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*.pyc | ||
build/ | ||
dist/ | ||
validation_data/ | ||
stocal.egg-info/ |
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include README.md | ||
include doc/* | ||
include stocal/examples/dsmts/*.csv |
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* stocal.algorithms.AndersonMethod.update_state is broken | ||
* stocal.experimental.samplers do not chain as claimed | ||
+ support for proper delay events (-> feature/events) | ||
= release/1.3 | ||
- remove dict support in MassAction.reactions and TransitionRule.infer_transitions | ||
- remove invalid-name arguments | ||
- remove AndersonNRM | ||
- remove TrajectorySampler | ||
- remove ReactionRule | ||
- remove Process.trajectory | ||
- allow species equals 0 in initial state? | ||
- regroup tests into specifications, unittests and bugs | ||
- move stocal.experimental.CaoMethod into stocal.algorithms | ||
= release/2.0 | ||
- utilities to simplify scipy/matplotlib interaction | ||
- persistency support (save and resume simulations) | ||
- arithmetic operations for Process | ||
- string rewrite rule support | ||
- support for proper delay events | ||
- other kinetic laws, e.g. Hill function | ||
- libSBML integration | ||
- statistical verification tests | ||
- every/until filters and other stop criteria | ||
- curried reactions (determine products only upon application) | ||
- other kinetic laws, e.g. Hill function | ||
- SSA profiling and algorithm variations | ||
- C/C++/D implementation | ||
= version 1.2+ | ||
- deprecate dict support in MassAction.reactions and ReactionRule.infer_transitions | ||
- deprecate invalid-name arguments | ||
= version 2 | ||
= version 2.1+ | ||
= version 3 |
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\documentclass[notitlepage]{revtex4-1} | ||
\usepackage{graphicx} | ||
\graphicspath{{validation_data/1.1.2-64-g0d0fc6f/}} | ||
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\begin{document} | ||
\title{DSMTS Validation results for \textit{stocal} samplers} | ||
\author{version: \VAR{version}} | ||
\maketitle{} | ||
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For each algorithm and model, figures show: | ||
\begin{itemize} | ||
\item on the left averaged trajectories of all system species over time | ||
obtained by simulation (green) versus reported values from the DSMTS | ||
repository (blue); | ||
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\item in the center the absolute standard error of sample averages | ||
($\bar X_{t}$) from the reported mean ($\mu_{t}$) as a function of | ||
sample size $N$: | ||
\[ | ||
\left|\frac{\bar X_{t}-\mu_{t}}{\sigma_{t}^{2}}\right| \sim \mathcal{N}\left(0, \frac{1}{\sqrt{N}}\right), | ||
\] | ||
where $\sigma_{t}$ is the reported standard deviation. | ||
The red line ($3/\sqrt{N}$) is an upper bound for the error scaling | ||
at three times the reported standard deviation and should be only | ||
occasionally exceeded; | ||
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\item on the right the relative standard error between sampled | ||
($\bar S_{t}^{2}$) and reported standard deviation ($\sigma_{t}^{2}$) | ||
as a function of sample size: | ||
\[ | ||
\left|\frac{\bar S_{t}^{2}}{\sigma_{t}^{2}} - 1\right| \sim \mathcal{N}\left(0, \frac{2}{N}\right) . | ||
\] | ||
The red line ($5/\sqrt{N/2}$) is an upper bound for the error scaling | ||
at five times the reported standard deviation and should be only | ||
occasionally exceeded. | ||
\end{itemize} | ||
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||
\BLOCK{ for method_name, figures in methods.items() } | ||
\section{\VAR{method_name}} | ||
\BLOCK{ for figure in figures } | ||
\includegraphics[width=\textwidth]{\VAR{figure}} | ||
\BLOCK{ endfor } | ||
\BLOCK{ endfor } | ||
\end{document} |
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@@ -8,7 +8,7 @@ def readme(): | |
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setup(name = "stocal", | ||
version = "1.1.2", | ||
version = "1.2", | ||
description = "simple rule-based stochastic simulation", | ||
long_description = readme(), | ||
classifiers=[ | ||
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@@ -24,7 +24,8 @@ def readme(): | |
author = "Harold Fellermann", | ||
author_email = "[email protected]", | ||
license='MIT', | ||
packages = ["stocal", "stocal.examples", "stocal.tests"], | ||
packages = ["stocal", "stocal.examples", "stocal.experimental", "stocal.tests"], | ||
include_package_data=True, | ||
zip_safe = True, | ||
test_suite = 'stocal.tests') | ||
test_suite = 'stocal.tests', | ||
install_requires=['pqdict']) |
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