Changeset 321

Timestamp:

06/04/08 15:17:28 (6 months ago)

Author:

apdavison

Message:

Started filling out lectures - mostly a copy and paste from users guide, so far

Files:

• doc/Freiburg2008/backends.tex (modified) (1 diff)
• doc/Freiburg2008/contributing.tex (modified) (1 diff)
• doc/Freiburg2008/freiburg_PyNN_lectures.tex (modified) (1 diff)
• doc/Freiburg2008/installation.tex (modified) (1 diff)
• doc/Freiburg2008/larger_networks.tex (modified) (1 diff)
• doc/Freiburg2008/native_celltypes.tex (modified) (1 diff)
• doc/Freiburg2008/plasticity.tex (modified) (1 diff)
• doc/Freiburg2008/porting.tex (modified) (1 diff)
• doc/Freiburg2008/small_networks.tex (modified) (1 diff)
• doc/Freiburg2008/standard_celltypes.tex (modified) (1 diff)

doc/Freiburg2008/backends.tex

@@ -1 @@
-
+==============
-\section{PyNN backends}
-
+% ..................................................................................
+\subsection{NEST} 
+
-\begin{frame} % --------------------------------------------------------------------
-
+{NEST}
-
-\end{frame}
+
+
+\begin{frame} % --------------------------------------------------------------------
+\frametitle{NEST}
+\framesubtitle{Installation}
+
+\end{frame}
+
+\begin{frame} % --------------------------------------------------------------------
+\frametitle{NEST}
+\framesubtitle{Documentation and resources}
+
+\end{frame}
+
+\begin{frame} % --------------------------------------------------------------------
+\frametitle{NEST}
+\framesubtitle{PyNEST}
+
+\end{frame}
+
+% ..................................................................................
+\subsection{NEURON}
+
+\begin{frame} % --------------------------------------------------------------------
+\frametitle{NEURON}
+
+\end{frame}
+
+
+\begin{frame} % --------------------------------------------------------------------
+\frametitle{NEURON}
+\framesubtitle{Installation}
+
+\end{frame}
+
+\begin{frame} % --------------------------------------------------------------------
+\frametitle{NEURON}
+\framesubtitle{Documentation and resources}
+
+\end{frame}
+
+\begin{frame} % --------------------------------------------------------------------
+\frametitle{NEURON}
+\framesubtitle{nrnpython}
+
+\end{frame}
+
+
+% ..................................................................................
+\subsection{PCSIM}
+
+\begin{frame} % --------------------------------------------------------------------
+\frametitle{PCSIM}
+
+\end{frame}
+
+
+\begin{frame} % --------------------------------------------------------------------
+\frametitle{PCSIM}
+\framesubtitle{Installation}
+
+\end{frame}
+
+\begin{frame} % --------------------------------------------------------------------
+\frametitle{PCSIM}
+\framesubtitle{Documentation and resources}
+
+\end{frame}
+
+\begin{frame} % --------------------------------------------------------------------
+\frametitle{PCSIM}
+\framesubtitle{PyPCSIM}
+
+\end{frame}
+
+
+% ..................................................................................
+\subsection{Brian}
+
+
+\begin{frame} % --------------------------------------------------------------------
+\frametitle{Brian}
+
+\end{frame}
+
+
+\begin{frame} % --------------------------------------------------------------------
+\frametitle{Brian}
+\framesubtitle{Installation}
+
+\end{frame}
+
+\begin{frame} % --------------------------------------------------------------------
+\frametitle{Brian}
+\framesubtitle{Documentation and resources}
+
+\end{frame}
+
+\begin{frame} % --------------------------------------------------------------------
+\frametitle{Brian}
+\framesubtitle{Examples}
+
+\end{frame}
+

doc/Freiburg2008/contributing.tex

@@ -3 +3 @@
-
-\begin{frame} % --------------------------------------------------------------------
-
+
+
+
-
-\end{frame}
+
+\begin{frame} % --------------------------------------------------------------------
+\frametitle{Reporting a bug}
+
+screenshot of New Ticket page
+
+\end{frame}
+
+\begin{frame} % --------------------------------------------------------------------
+\frametitle{Asking a question}
+
+screenshot of Google groups
+
+\end{frame}
+
+\begin{frame} % --------------------------------------------------------------------
+\frametitle{svn commit}
+
+STOP! First, run the test suite.
+
+Show how to do this.
+
+STOP! Now write an informative commit message (using Trac syntax if possible)
+
+
+\end{frame}

doc/Freiburg2008/freiburg_PyNN_lectures.tex

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-% $Id:  $
-
+[utf8]
-
-\mode<presentation>

doc/Freiburg2008/installation.tex

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-
-\begin{frame} % --------------------------------------------------------------------
-
+
+
-
-\end{frame}
+
+
+\begin{frame} % --------------------------------------------------------------------
+\frametitle{Running a PyNN simulation}
+
+% mention the sys.argv trick
+
+\end{frame}

doc/Freiburg2008/larger_networks.tex

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+==============
-\section{Larger networks}
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doc/Freiburg2008/native_celltypes.tex

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-
+==============
-\section{Native cell types}
-
-\begin{frame} % --------------------------------------------------------------------
-
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-\end{frame}

doc/Freiburg2008/plasticity.tex

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-\section{Plasticity}
-
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-
-\end{frame}
+
+\begin{frame}[fragile] % --------------------------------------------------------------------
+\frametitle{SynapseDynamics objects}
+
+To set the model of synapse dynamics to use for the connections of a given
+\verb|Projection|, we pass a \verb|SynapseDynamics| object as the \verb|synapse_dynamics|
+keyword argument to the \verb|Projection|constructor.
+
+The \verb|SynapseDynamics| object is simply a container that has attributes \verb|fast|,
+which, if set, is an instance of a subclass of the abstract class
+\verb|ShortTermPlasticityMechanism|, and \verb|slow|, which is an instance of a
+subclass of the abstract class \verb|STDPMechanism|.
+
+Only a single subclass of \verb|ShortTermPlasticityMechanism| is currently available in
+PyNN: \verb|TsodkysMarkramMechanism|.
+
+\verb|STDPMechanism| objects are further decomposed into components for the
+timing-dependence, weight-dependence and post-synaptic voltage-dependence of
+the mechanism.
+
+\end{frame}
+
+\begin{frame}[fragile] % --------------------------------------------------------------------
+\frametitle{Example}
+
+An example of defining a \verb|Projection| with facilitating/depressing synapses,
+but no long-term plasticity:
+        \begin{verbatim}
+    >>> depressing_syn = SynapseDynamics(fast=TsodyksMarkramMechanism(**params))
+    >>> prj = Projection(pre, post, AllToAllConnector(),
+    ...                  synapse_dynamics = depressing_syn)
+    \end{verbatim}                     
+and one with long-term plasticity, using a spike-pair rule and with additive
+weight updates (i.e. the weight change is independent of the current weight
+value):
+        \begin{verbatim}
+    >>> stdp_model = STDPMechanism(
+           timing_dependence=SpikePairRule(tau_plus=20.0, tau_minus=20.0),
+           weight_dependence=AdditiveWeightDependence(w_min=0, w_max=0.02,
+                                                      A_plus=0.01, A_minus=0.012)
+        )
+    >>> prj2 = Projection(pre, post, FixedProbabilityConnector(p=0.1),
+    ...                   synapse_dynamics=SynapseDynamics(slow=stdp_model))
+        \end{verbatim}
+
+\end{frame}

doc/Freiburg2008/porting.tex

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-
-\begin{frame} % --------------------------------------------------------------------
-
+{Example of porting a NEURON model to PyNN}
-
-\end{frame}
+
+\begin{frame} % --------------------------------------------------------------------
+\frametitle{Example of porting a NEST model to PyNN}
+
+\end{frame}

doc/Freiburg2008/small_networks.tex

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+==============
-\section{Small networks}
-
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