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#LyX 2.2 created this file. For more info see http://www.lyx.org/
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\begin_body
\begin_layout Title
Plotting and Analysis for Neural Database-Oriented Research Applications
(PANDORA) Toolbox —
\begin_inset Newline newline
\end_inset
User's and Programmer's Manual
\end_layout
\begin_layout Author
Cengiz G
\begin_inset ERT
status collapsed
\begin_layout Plain Layout
\backslash
"
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unay
\end_layout
\begin_layout Date
Document Revision
\begin_inset ERT
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CVSRevision{}
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,
\begin_inset ERT
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today
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status collapsed
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\begin_layout Standard
\begin_inset CommandInset toc
LatexCommand tableofcontents
\end_inset
\end_layout
\begin_layout Standard
\begin_inset Note Comment
status collapsed
\begin_layout Plain Layout
\begin_inset FloatList figure
\end_inset
\end_layout
\end_inset
\end_layout
\begin_layout Standard
\begin_inset Note Note
status collapsed
\begin_layout Plain Layout
TODO:
\end_layout
\begin_layout Plain Layout
- make a tutorial section that explains usage bottom-up.
start from trace, profile, and dataset to database.
\end_layout
\begin_layout Plain Layout
- more visualization.
look at paper figures and do similar examples.
weed out obsolete methods, put examples into funcref of current usage.
\end_layout
\begin_layout Plain Layout
- add section on extensibility.
maybe at end of software part.
\end_layout
\begin_layout Plain Layout
- put download info in install section.
before that include all external functions, choose a license, and make
an ant file to create binary and documentation packages.
\end_layout
\begin_layout Plain Layout
- separate document into two? user's and admin manuals? [no...]
\end_layout
\end_inset
\end_layout
\begin_layout Section
Introduction
\end_layout
\begin_layout Subsection
What is the
\begin_inset ERT
status collapsed
\begin_layout Plain Layout
\backslash
appname{}
\end_layout
\end_inset
?
\end_layout
\begin_layout Standard
The
\begin_inset ERT
status collapsed
\begin_layout Plain Layout
\backslash
appname{}
\end_layout
\end_inset
is a software package which consists of a collection of
\noun on
Matlab
\noun default
object-oriented classes and script functions for creating, analyzing and
visualizing databases based on data from electrophysiological neuron simulation
s and recordings.
\end_layout
\begin_layout Subsection
Why did you make it?
\end_layout
\begin_layout Standard
Motivations to create this software were:
\end_layout
\begin_layout Itemize
Analyze data generated by brute-force and other parameter search methods.
\end_layout
\begin_layout Itemize
Analyze subsets of parameter spaces and special cases.
\end_layout
\begin_layout Itemize
Evaluate robustness of model neurons.
\end_layout
\begin_layout Itemize
Find functional roles of specific conductances.
\end_layout
\begin_layout Subsection
How is it implemented?
\end_layout
\begin_layout Standard
A custom database management system (DBMS) is written from scratch in the
\noun on
Matlab
\noun default
language.
The toolbox design follows object-oriented programming principles.
It uses functions from the statistics and signal processing toolboxes of
\noun on
Matlab
\noun default
, but they are not strictly necessary.
It does not use
\noun on
Matlab
\noun default
's database (DB) toolbox.
\begin_inset Foot
status collapsed
\begin_layout Plain Layout
At the time of initial design, the author did not have access to the DB
toolbox.
Future versions may support the DB toolbox.
\end_layout
\end_inset
\end_layout
\begin_layout Subsection
How can I use it?
\end_layout
\begin_layout Standard
The
\begin_inset ERT
status collapsed
\begin_layout Plain Layout
\backslash
appname{}
\end_layout
\end_inset
uses an object-oriented approach to provide maximal flexibility for interactive
use on the
\noun on
Matlab
\noun default
command-line.
\begin_inset Foot
status collapsed
\begin_layout Plain Layout
This version of the toolbox does not yet have a general graphical user interface
(GUI).
The author prefers to have a flexible command-line interface than to maintain
a limited GUI.
However, once commonly used functions can be conveniently placed within
a GUI, it will be added to the toolbox.
\end_layout
\end_inset
Objects can be created, modified, analyzed, and visualized interactively
in few steps.
It is straightforward to save and load binary representations of these
objects into files.
Scripts can be made to programmatically repeat these procedures.
Existing object classes are designed with the prospect of future extension,
to accommodate new types of data and analyses.
\end_layout
\begin_layout Subsection
Who is it made for?
\end_layout
\begin_layout Standard
\begin_inset ERT
status collapsed
\begin_layout Plain Layout
\backslash
appname{}
\end_layout
\end_inset
is customized for neuroscientific research.
However, the concepts of a complex dataset, extraction of multiple observations
from each item of the dataset, and analysis of multi-dimensional parameter
spaces are universal.
In its current form the database and dataset classes can be used for data
other than electrophysiologic sources.
As this toolbox is designed for flexible extensibility, one can add extensions
that deal with different types of data and analyses.
\begin_inset Note Note
status collapsed
\begin_layout Plain Layout
link to extensibility section
\end_layout
\end_inset
\end_layout
\begin_layout Subsection
Finding your way around
\begin_inset CommandInset label
LatexCommand label
name "subsec:Finding-your-way-around"
\end_inset
\end_layout
\begin_layout Standard
The source code uses
\noun on
Matlab
\noun default
's documentation system, therefore all methods and classes are documented.
To get help about all classes, issue the
\end_layout
\begin_layout LyX-Code
>> help classes
\end_layout
\begin_layout Standard
at the
\noun on
Matlab
\noun default
prompt.
This should give you an overview of available classes.
Then, to learn about a specific class, ask for the documentation for the
constructor method.
For instance, for the
\family typewriter
trace
\family default
class, issuing
\end_layout
\begin_layout LyX-Code
>> help trace
\end_layout
\begin_layout Standard
gives you the documentation for the constructor together with an overview
for the class.
Sometimes, if there are multiple methods with the same name under different
classes, you may get the wrong documentation.
In that case, you can specify the class from which to take the method by
prepending the class name to the method, such as in
\end_layout
\begin_layout LyX-Code
>> help trace/spikes
\end_layout
\begin_layout Standard
In order to learn all methods available for a class, you can use
\noun on
Matlab
\noun default
's
\family typewriter
methods
\family default
command.
For the
\family typewriter
trace
\family default
class, do
\end_layout
\begin_layout LyX-Code
>> methods(trace)
\end_layout
\begin_layout Standard
However, some documentation may be outdated or simply wrong.
Please report these to the author via e-mail to
\family typewriter
cgunay AT emory.edu
\family default
.
\end_layout
\begin_layout Subsection
Overview of this document
\end_layout
\begin_layout Standard
\begin_inset Note Note
status collapsed
\begin_layout Plain Layout
put this in the preface?
\end_layout
\end_inset
Next, Section
\begin_inset CommandInset ref
LatexCommand ref
reference "sec:Installation"
\end_inset
guides the reader through the installation of the package and other dependencie
s.
You can skip this section if you already have a running software environment.
Section
\begin_inset CommandInset ref
LatexCommand ref
reference "sec:Class-hierarchies"
\end_inset
introduces the essential components of the software and talks about their
design decisions.
You can also skip this part if you're not interested in the guts of the
system and you are in favor of a quick start.
The recipes in Section
\begin_inset CommandInset ref
LatexCommand ref
reference "sec:Recipes"
\end_inset
provide a tutorial for some common tasks.
It may be easier for some readers to follow these recipes to jump-start
using the software.
However, it is recommended that you familiarize yourself with the basic
organization of the classes before proceeding into more complex tasks.
Section
\begin_inset CommandInset ref
LatexCommand ref
reference "sec:Visualization"
\end_inset
takes the tutorial approach to describe common visualization tasks.
Finally, Section
\begin_inset CommandInset ref
LatexCommand ref
reference "sec:Function-Reference"
\end_inset
points to the list of individual methods provided by the software.
These methods are documented in detail using the
\noun on
Matlab
\noun default
online help system.
\end_layout
\begin_layout Section
Installation
\begin_inset CommandInset label
LatexCommand label
name "sec:Installation"
\end_inset
\begin_inset Note Note
status collapsed
\begin_layout Plain Layout
move everything from alf and cengiz directories into the toolbox, and make
the installation automatic.
make package available on ftp/http site.
\end_layout
\end_inset
\end_layout
\begin_layout Standard
Download the latest package file from:
\end_layout
\begin_layout Standard
\begin_inset Flex URL
status collapsed
\begin_layout Plain Layout
http://userwww.service.emory.edu/~cgunay/pandora
\end_layout
\end_inset
.
\end_layout
\begin_layout Standard
Unpack the archive anywhere in your system, using
\end_layout
\begin_layout LyX-Code
$ tar xzf pandora-xyz.tar.gz
\end_layout
\begin_layout Standard
and follow the instructions in the README file.
\end_layout
\begin_layout Standard
Basically it involves pointing your
\noun on
Matlab
\noun default
installation to look at the
\family typewriter
pandora/
\family default
subdirectory for loading the PANDORA files.
This can be achieved
\begin_inset Note Comment
status collapsed
\begin_layout Plain Layout
either by copying the
\family typewriter
pandora/
\family default
directory under the
\family typewriter
toolbox/
\family default
directory in your
\noun on
Matlab
\noun default
installation, or [this doesn't work!]
\end_layout
\end_inset
by adding this directory to your
\noun on
Matlab
\noun default
search path using the
\family typewriter
addpath
\family default
Matlab command.
To avoid its repeated application for each new session, you can have a
startup script,
\family typewriter
startup.m
\family default
, in the directory that you run
\noun on
Matlab
\noun default
with the following commands:
\end_layout
\begin_layout LyX-Code
%--- startup.m for matlab
\end_layout
\begin_layout LyX-Code
addpath
\family typewriter
/my/download/directory/pandora-1.0b/pandora
\end_layout
\begin_layout LyX-Code
%--- end startup.m
\end_layout
\begin_layout Standard
This will be loaded everytime you run
\noun on
Matlab
\noun default
from this directory.
in UN*X systems, this can be improved further by placing the command in
the file
\family typewriter
$HOME/matlab/startup.m, which
\family default
is executed no matter from where
\noun on
Matlab
\noun default
is called, especially if you are running Matlab from different or unknown
places each time.
In Windows, place the file under
\family typewriter
My Documents/MATLAB
\family default
, or add the directory to the search path using the
\emph on
File->Set Path
\emph default
menu option.
\end_layout
\begin_layout Part
Software Architecture
\end_layout
\begin_layout Section
Toolbox Components
\begin_inset CommandInset label
LatexCommand label
name "sec:Class-hierarchies"
\end_inset
\end_layout
\begin_layout Standard
\begin_inset Float figure
wide false
sideways false
status collapsed
\begin_layout Plain Layout
\align center
\begin_inset ERT
status collapsed
\begin_layout Plain Layout
\backslash
makebox[0pt]{
\end_layout
\end_inset
\begin_inset Graphics
filename db-overview.eps
lyxscale 50
width 80page%
\end_inset
\begin_inset ERT
status collapsed
\begin_layout Plain Layout
}
\end_layout
\end_inset
\end_layout
\begin_layout Plain Layout
\begin_inset Caption Standard
\begin_layout Plain Layout
\begin_inset CommandInset label
LatexCommand label
name "figcap:Database-overview"
\end_inset
Schematic overview of the database software.
\end_layout
\end_inset
\end_layout
\end_inset
An overview of the toolbox functionality is shown in Figure
\begin_inset CommandInset ref
LatexCommand ref
reference "figcap:Database-overview"
\end_inset
.
In the figure, boxes represent objects that can be created with the toolbox.
Flow starts from the dataset object on the top left which represents the
collection of raw data files.
The raw data is loaded using information in the dataset to create intermediate
objects that, for instance, contain data traces.
These objects define electrophysiological measurements to be entered into
the data matrix of the database object on the top right.
The database object allows filtering and querying to refine its contents.
From the database object, one can always go back to the dataset and find
the raw data that results from a query.
The arrows going to bottom objects and corresponding plots show the types
of possible analyses that can be done on a database object.
These analyses are typically for displaying statistical information.
The red arrow is a speacial analysis for searching and matching rows between
different databases.
The match is done by taking a row from a database created with data from
real neurons and finding best matching model neurons from a simulation
database.
\end_layout
\begin_layout Standard
The objects in the figure are instances of classes that define their properties
in the object-oriented framework.
Each class comes with a hierarchy of of subclasses that specialize to specific
functions.
Subsequent sections describe each of these class hierarchies that make
up the main components of the toolbox.
\end_layout
\begin_layout Subsection
Databases hold all the information
\end_layout
\begin_layout Standard
The database object is at the center of this toolbox (see Figure
\begin_inset CommandInset ref
LatexCommand ref
reference "figcap:Database-overview"
\end_inset
).
It holds a data matrix with rows as observations and columns as attributes.
The rows would normally correspond to results from individual data traces,
or simply neurons.
The columns hold values of separate measurements, statistical data, or
parameter values.
\end_layout
\begin_layout Standard
\begin_inset Float figure
wide false
sideways false
status collapsed
\begin_layout Plain Layout
\align center
\begin_inset ERT
status collapsed
\begin_layout Plain Layout