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From: <mh...@us...> - 2008-06-09 22:47:55
|
Revision: 305
http://sbgn.svn.sourceforge.net/sbgn/?rev=305&view=rev
Author: mhucka
Date: 2008-06-09 15:47:54 -0700 (Mon, 09 Jun 2008)
Log Message:
-----------
New MAPK diagram used in pd-overview.tex.
Added Paths:
-----------
trunk/documents/specifications/ProcessDiagram/Level1/examples/MAPK-only.ai
trunk/documents/specifications/ProcessDiagram/Level1/examples/MAPK-only.eps
trunk/documents/specifications/ProcessDiagram/Level1/examples/MAPK-only.pdf
trunk/documents/specifications/ProcessDiagram/Level1/examples/MAPK-only.svg
Added: trunk/documents/specifications/ProcessDiagram/Level1/examples/MAPK-only.ai
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/examples/MAPK-only.ai (rev 0)
+++ trunk/documents/specifications/ProcessDiagram/Level1/examples/MAPK-only.ai 2008-06-09 22:47:54 UTC (rev 305)
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|
From: <mh...@us...> - 2008-06-09 22:38:14
|
Revision: 304
http://sbgn.svn.sourceforge.net/sbgn/?rev=304&view=rev
Author: mhucka
Date: 2008-06-09 15:38:12 -0700 (Mon, 09 Jun 2008)
Log Message:
-----------
Renamed config.tex to the more appropriate name latex-macros.tex.
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.tex
Added Paths:
-----------
trunk/documents/specifications/ProcessDiagram/Level1/sources/latex-macros.tex
Removed Paths:
-------------
trunk/documents/specifications/ProcessDiagram/Level1/sources/config.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.tex 2008-06-09 22:36:26 UTC (rev 303)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.tex 2008-06-09 22:38:12 UTC (rev 304)
@@ -223,12 +223,86 @@
}
\makeatother
+% The following was ripped out of caption.sty, version 1.4b.
+% Copyright (C) 1994-95 Harald Axel Sommerfeldt
+% The first few lines set up the parameters for the layout created
+% by this style file.
+\newcommand{\captionsize}{\small}
+\newcommand{\captionfont}{\captionsize\itshape}
+\newcommand{\captionlabelfont}{\captionsize\sffamily\bfseries\upshape}
+\newlength{\captionmargin}
+\setlength{\captionmargin}{6ex}
+
+\makeatletter
+\newsavebox{\as@captionbox}
+\newlength{\as@captionwidth}
+\newcommand{\as@normalcaption}[2]{%
+ #1 #2\par}
+\let\as@caption\as@normalcaption
+\newcommand{\as@centercaption}[2]{%
+ \parbox[t]{\as@captionwidth}{{\centering#1 #2\par}}}
+\let\as@shortcaption\as@centercaption
+\newcommand{\as@makecaption}[2]{%
+ \setlength{\leftskip}{\captionmargin}%
+ \setlength{\rightskip}{\captionmargin}%
+ \addtolength{\as@captionwidth}{-2\captionmargin}%
+ \renewcommand{\baselinestretch}{0.9}
+ \captionfont%
+ \sbox{\as@captionbox}{{\captionlabelfont #1:} #2}%
+ \ifdim \wd\as@captionbox >\as@captionwidth
+ \as@caption{{\captionlabelfont #1:}}{#2}%
+ \else%
+ \as@shortcaption{{\captionlabelfont #1:}}{#2}%
+ \fi}
+\renewcommand{\@makecaption}[2]{%
+ \vskip\abovecaptionskip%
+ \setlength{\as@captionwidth}{\linewidth}%
+ \as@makecaption{#1}{#2}%
+ \vskip\belowcaptionskip}
+\ifx\@makerotcaption\undefined
+\else
+ \typeout{\space\space\space\space\space\space\space\space\space
+ `rotating' package detected}
+ \renewcommand{\@makerotcaption}[2]{%
+ \renewcommand{\baselinestretch}{0.9}
+ \captionfont%
+ \sbox{\as@captionbox}{{\captionlabelfont #1:} #2}%
+ \ifdim \wd\as@captionbox > .8\vsize
+ \rotatebox{90}{%
+ \setlength{\as@captionwidth}{.8\textheight}%
+ \begin{minipage}{\as@captionwidth}%
+ \as@caption{{\captionlabelfont #1:}}{#2}%
+ \end{minipage}}\par
+ \else%
+ \rotatebox{90}{\usebox{\as@captionbox}}%
+ \fi
+ \hspace{12pt}}
+\fi
+\ifx\floatc@plain\undefined
+\else
+ \typeout{\space\space\space\space\space\space\space\space\space
+ `float' package detected}
+ \renewcommand\floatc@plain[2]{%
+ \setlength{\as@captionwidth}{\linewidth}%
+ \as@makecaption{#1}{#2}}
+ \ifx\as@ruled\undefined
+ \else
+ \renewcommand\floatc@ruled[2]{%
+ \setlength{\as@captionwidth}{\linewidth}%
+ \renewcommand{\baselinestretch}{0.9}
+ \captionfont%
+ \as@caption{{\captionlabelfont #1:}}{#2}}
+ \fi
+\fi
+\makeatother
+
+
%% ---------------------------------------------------------------
%% Macro definitions for commonly-used commands.
%% ---------------------------------------------------------------
-\input{sources/config}
+\input{sources/latex-macros}
%% ---------------------------------------------------------------
Deleted: trunk/documents/specifications/ProcessDiagram/Level1/sources/config.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/config.tex 2008-06-09 22:36:26 UTC (rev 303)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/config.tex 2008-06-09 22:38:12 UTC (rev 304)
@@ -1,80 +0,0 @@
-% $HeadURL$
-
-% ----------------------------------------------------------------
-% Definitions that change with releases of the document.
-% ----------------------------------------------------------------
-
-\newcommand{\sbgndate}{\today}
-
-% ----------------------------------------------------------------
-% Common commands when writing.
-% ----------------------------------------------------------------
-
-\newcommand{\SBGNPDLone}{SBGN \PD Level~1\xspace}
-
-\newcommand{\PD}{Process Diagram\xspace}
-\newcommand{\PDs}{Process Diagrams\xspace}
-\newcommand{\ER}{Entity Relationship\xspace}
-\newcommand{\ERs}{Entity Relationship diagrams\xspace}
-\newcommand{\AF}{Activity Flow\xspace}
-\newcommand{\AFs}{Activity Flow diagrams\xspace}
-
-% The name of a glyph is emphasized. Note that this is only the
-% case when we talk about the glyph, not the biological concept
-% represented by the glyph.
-
-\newcommand{\glyph}[1] {\emph{#1}}
-\newcommand{\vglyph}[1] {\begin{sideways}\emph{#1}\end{sideways}}
-
-\newcommand{\ERonly} {\shabox{\textbf{ER only}}}
-\newcommand{\STonly} {\shabox{\textbf{ST only}}}
-\newcommand{\AFonly} {\shabox{\textbf{AF only}}}
-\newcommand{\NotER} {\shabox{\textbf{Not ER. AF and ST only}}}
-\newcommand{\NotAF} {\shabox{\textbf{Not AF. ST and ER only}}}
-
-\newcommand{\lenov} {Le~Nov\`{e}re\xspace}
-\newcommand{\D} {\displaystyle}
-\newcommand{\tm} {\textsuperscript{\tiny{\texttrademark}}}
-
-\newcommand{\literalFont}[1]{\textup{\texttt{#1}}}
-\newcommand{\figureFont}[1]{\textsf{\textbf{#1}}}
-
-\newcommand{\link}[2] {\literalFont{\href{#1}{#2}}}
-\newcommand{\mailto}[1] {\link{mailto:#1}{#1}}
-
-\newcommand{\chap}[1] {Chapter~\protect\ref{chp:#1}\xspace}
-\newcommand{\sect}[1] {Section~\protect\ref{sec:#1}\xspace}
-\newcommand{\fig}[1] {Figure~\protect\vref{fig:#1}\xspace}
-\newcommand{\tab}[1] {Table~\protect\vref{tab:#1}\xspace}
-\newcommand{\eg} {e.g.,\xspace}
-\newcommand{\ie} {i.e.,\xspace}
-
-
-% ----------------------------------------------------------------
-% SBGN logo.
-% ----------------------------------------------------------------
-
-\newcommand{\logofilebasename}{sbgn-logo-rgb}
-
-\ifpdf
- % When creating PDFs, request the JPG format specifically,
- % because the resulting quality in the PDF final output is best
- % that way.
- \newcommand{\SBGNLogoFile}{\logofilebasename.jpg}
-\else
- \newcommand{\SBGNLogoFile}{\logofilebasename.eps}
-\fi
-
-% Graphics path adjustments to get the logo. The path setup is so
-% that the \includegraphics can find the logo file no matter where
-% the document is located (but obviously, it only works for
-% certain path combinations -- it's a total hack).
-
-\graphicspath{{.}{./images/}{../images/}}
-
-
-
-% The following is for [X]Emacs users. Please leave in place.
-% Local Variables:
-% TeX-master: "../sbgn_PD-level1"
-% End:
Copied: trunk/documents/specifications/ProcessDiagram/Level1/sources/latex-macros.tex (from rev 296, trunk/documents/specifications/ProcessDiagram/Level1/sources/config.tex)
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/latex-macros.tex (rev 0)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/latex-macros.tex 2008-06-09 22:38:12 UTC (rev 304)
@@ -0,0 +1,80 @@
+% $HeadURL$
+
+% ----------------------------------------------------------------
+% Definitions that change with releases of the document.
+% ----------------------------------------------------------------
+
+\newcommand{\sbgndate}{\today}
+
+% ----------------------------------------------------------------
+% Common commands when writing.
+% ----------------------------------------------------------------
+
+\newcommand{\SBGNPDLone}{SBGN \PD Level~1\xspace}
+
+\newcommand{\PD}{Process Diagram\xspace}
+\newcommand{\PDs}{Process Diagrams\xspace}
+\newcommand{\ER}{Entity Relationship\xspace}
+\newcommand{\ERs}{Entity Relationship diagrams\xspace}
+\newcommand{\AF}{Activity Flow\xspace}
+\newcommand{\AFs}{Activity Flow diagrams\xspace}
+
+% The name of a glyph is emphasized. Note that this is only the
+% case when we talk about the glyph, not the biological concept
+% represented by the glyph.
+
+\newcommand{\glyph}[1] {\emph{#1}}
+\newcommand{\vglyph}[1] {\begin{sideways}\emph{#1}\end{sideways}}
+
+\newcommand{\ERonly} {\shabox{\textbf{ER only}}}
+\newcommand{\STonly} {\shabox{\textbf{ST only}}}
+\newcommand{\AFonly} {\shabox{\textbf{AF only}}}
+\newcommand{\NotER} {\shabox{\textbf{Not ER. AF and ST only}}}
+\newcommand{\NotAF} {\shabox{\textbf{Not AF. ST and ER only}}}
+
+\newcommand{\lenov} {Le~Nov\`{e}re\xspace}
+\newcommand{\D} {\displaystyle}
+\newcommand{\tm} {\textsuperscript{\tiny{\texttrademark}}}
+
+\newcommand{\literalFont}[1]{\textup{\texttt{#1}}}
+\newcommand{\figureFont}[1]{\textsf{\textbf{#1}}}
+
+\newcommand{\link}[2] {\literalFont{\href{#1}{#2}}}
+\newcommand{\mailto}[1] {\link{mailto:#1}{#1}}
+
+\newcommand{\chap}[1] {Chapter~\protect\ref{chp:#1}\xspace}
+\newcommand{\sect}[1] {Section~\protect\ref{sec:#1}\xspace}
+\newcommand{\fig}[1] {Figure~\protect\vref{fig:#1}\xspace}
+\newcommand{\tab}[1] {Table~\protect\vref{tab:#1}\xspace}
+\newcommand{\eg} {e.g.,\xspace}
+\newcommand{\ie} {i.e.,\xspace}
+
+
+% ----------------------------------------------------------------
+% SBGN logo.
+% ----------------------------------------------------------------
+
+\newcommand{\logofilebasename}{sbgn-logo-rgb}
+
+\ifpdf
+ % When creating PDFs, request the JPG format specifically,
+ % because the resulting quality in the PDF final output is best
+ % that way.
+ \newcommand{\SBGNLogoFile}{\logofilebasename.jpg}
+\else
+ \newcommand{\SBGNLogoFile}{\logofilebasename.eps}
+\fi
+
+% Graphics path adjustments to get the logo. The path setup is so
+% that the \includegraphics can find the logo file no matter where
+% the document is located (but obviously, it only works for
+% certain path combinations -- it's a total hack).
+
+\graphicspath{{.}{./images/}{../images/}}
+
+
+
+% The following is for [X]Emacs users. Please leave in place.
+% Local Variables:
+% TeX-master: "../sbgn_PD-level1"
+% End:
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mh...@us...> - 2008-06-09 22:36:31
|
Revision: 303
http://sbgn.svn.sourceforge.net/sbgn/?rev=303&view=rev
Author: mhucka
Date: 2008-06-09 15:36:26 -0700 (Mon, 09 Jun 2008)
Log Message:
-----------
Refilled paragraphs.
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/sources/pd-overview.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/pd-overview.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/pd-overview.tex 2008-06-09 11:27:04 UTC (rev 302)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/pd-overview.tex 2008-06-09 22:36:26 UTC (rev 303)
@@ -1,8 +1,6 @@
% $HeadURL$
-To set the stage for what follows in this chapter, we first give a brief
-overview of some of the concepts in the \PD notation with the help of an
-example shown in \fig{eg1}.
+To set the stage for what follows in this chapter, we first give a brief overview of some of the concepts in the \PD notation with the help of an example shown in \fig{eg1}.
\begin{figure}[htb]
\centering
@@ -20,44 +18,11 @@
\label{fig:eg1}
\end{figure}
-The diagram in \fig{eg1} is a simple diagram for part of a
-mitogen-activated protein kinase (MAPK) cascade. The larger nodes in
-\fig{eg1} (some of which are in the shape of rounded rectangles and others
-in the shape of circles) represent biological materials---things like
-macromolecules and simple chemicals. The biological materials are altered
-via processes, which are indicated in SBGN by lines with arrows and other
-decorations. In this particular diagram, all of the processes happen to be
-the same: transitions catalyzed by biochemical entities. The directions of
-the arrows indicate the direction of the transitions; for example,
-unphosphorylated RAF kinase transitions to phosphorylated RAF kinase via a
-process catalyzed by RAS. ATP and ADP are also involved in the same
-process, but the focus of the diagram is on what happens to RAF, so ATP and
-ADP are shown as incidental to the main transition. The small circles on
-the nodes for RAF and other entity pools represent units of information (in
-this case, phosphorylation sites), while the other small circles touching
-small squares indicate a specific kind of process. The details of this and
-other aspects of \PD are explained in the rest of this chapter.
+The diagram in \fig{eg1} is a simple diagram for part of a mitogen-activated protein kinase (MAPK) cascade. The larger nodes in \fig{eg1} (some of which are in the shape of rounded rectangles and others in the shape of circles) represent biological materials---things like macromolecules and simple chemicals. The biological materials are altered via processes, which are indicated in SBGN by lines with arrows and other decorations. In this particular diagram, all of the processes happen to be the same: transitions catalyzed by biochemical entities. The directions of the arrows indicate the direction of the transitions; for example, unphosphorylated RAF kinase transitions to phosphorylated RAF kinase via a process catalyzed by RAS. ATP and ADP are also involved in the same process, but the focus of the diagram is on what happens to RAF, so ATP and ADP are shown as incidental to the main transition. The small circles on the nodes for RAF and other entity pools represent units of information (in this case, phosphorylation sites), while the other small circles touching small squares indicate a specific kind of process. The details of this and other aspects of \PD are explained in the rest of this chapter.
-The essence of the \PD is \emph{change}: it shows how different entities in
-the system transition from one form to another. The entities themselves
-can be many different things. In the example of \fig{eg1}, they are either
-pools of macromolecules or pools of simple chemicals, but as will become
-clear later in this chapter, they can be other material and conceptual
-constructs as well. Note also that we speak of \emph{entity pools} rather
-than individuals; this is because in biochemical network models, one does
-not focus on single molecules, but rather collections of molecules of the
-same kind. The molecules in a given pool are considered indistinguishable
-from each other. The way in which a type of entity is transformed into
-another is conveyed by \emph{process nodes}, and links between entity pool
-nodes and process nodes indicate an influence by the entities on the
-processes. In the case of \fig{eg1}, they happen all to be catalysis,
-\sect{catalysis}, but others are possible. Finally, nodes in \PDs are not
-usually repeated; if they do need to be repeated, they are marked with
-\emph{clone markers}---specific modifications to the appearance of the node
-(\sect{cloneMarker}).
+The essence of the \PD is \emph{change}: it shows how different entities in the system transition from one form to another. The entities themselves can be many different things. In the example of \fig{eg1}, they are either pools of macromolecules or pools of simple chemicals, but as will become clear later in this chapter, they can be other material and conceptual constructs as well. Note also that we speak of \emph{entity pools} rather than individuals; this is because in biochemical network models, one does not focus on single molecules, but rather collections of molecules of the same kind. The molecules in a given pool are considered indistinguishable from each other. The way in which a type of entity is transformed into another is conveyed by \emph{process nodes}, and links between entity pool nodes and process nodes indicate an influence by the entities on the processes. In the case of \fig{eg1}, they happen all to be catalysis, \sect{catalysis}, but others are possible. Finally, nodes in \PDs are not usually repeated; if they do need to be repeated, they are marked with \emph{clone markers}---specific modifications to the appearance of the node (\sect{cloneMarker}).
-\tab{component-summary} summarizes the different SBGN abstractions
-described in this chapter.
+\tab{component-summary} summarizes the different SBGN abstractions described in this chapter.
\newcolumntype{P}[1]{>{\raggedright\hspace{0pt}\arraybackslash}p{#1}}
@@ -71,7 +36,7 @@
Entity pool node
& EPN
& A population of entities that cannot be distinguished from each other
- & Ions, macromolecules, multimer, other unspecified entity\\[0.5em]
+ & Specific macromolecules or other chemical species \\[0.5em]
Container node
& CN
@@ -80,7 +45,7 @@
Process node
& PN
- & A process that transforms one or more EPN into one or more other EPNs
+ & A process that transforms one or more EPNs into one or more other EPNs
& Transition, association, dissociation \\[0.5em]
Connecting arc
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|
From: <mh...@us...> - 2008-06-09 11:27:09
|
Revision: 302
http://sbgn.svn.sourceforge.net/sbgn/?rev=302&view=rev
Author: mhucka
Date: 2008-06-09 04:27:04 -0700 (Mon, 09 Jun 2008)
Log Message:
-----------
Slight reorganization of author list.
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/sources/front-page.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/front-page.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/front-page.tex 2008-06-09 11:20:18 UTC (rev 301)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/front-page.tex 2008-06-09 11:27:04 UTC (rev 302)
@@ -35,12 +35,13 @@
Nicolas \lenov & \emph{EMBL European Bioinformatics Institute, UK}\\
Stuart Moodie & \emph{University of Edinburgh, UK}\\
Anatoly Sorokin & \emph{University of Edinburgh, UK}\\
+Michael Hucka & \emph{California Institute of Technology, USA}\\
Falk Schreiber & \emph{Leibniz Institute IPK, Germany}\\
Emek Demir & \emph{MSKCC Computational Biology Center, USA}\\
-Katja Wegner & \emph{University of Hertfordshire, UK}\\
-Michael Hucka & \emph{California Institute of Technology, USA}\\
Huaiyu Mi & \emph{SRI International, USA}\\
Yukiko Matsuoka & \emph{The Systems Biology Institute, Japan}\\
+Katja Wegner & \emph{University of Hertfordshire, UK}\\
+\multicolumn{2}{l}{\emph{and}}\\
Hiroaki Kitano & \emph{The Systems Biology Institute, Japan}\\
\end{tabular}
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From: <mh...@us...> - 2008-06-09 11:20:20
|
Revision: 301
http://sbgn.svn.sourceforge.net/sbgn/?rev=301&view=rev
Author: mhucka
Date: 2008-06-09 04:20:18 -0700 (Mon, 09 Jun 2008)
Log Message:
-----------
New overview section for chapter 2.
Added Paths:
-----------
trunk/documents/specifications/ProcessDiagram/Level1/sources/pd-overview.tex
Added: trunk/documents/specifications/ProcessDiagram/Level1/sources/pd-overview.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/pd-overview.tex (rev 0)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/pd-overview.tex 2008-06-09 11:20:18 UTC (rev 301)
@@ -0,0 +1,109 @@
+% $HeadURL$
+
+To set the stage for what follows in this chapter, we first give a brief
+overview of some of the concepts in the \PD notation with the help of an
+example shown in \fig{eg1}.
+
+\begin{figure}[htb]
+ \centering
+ \includegraphics[width = 2.5in, trim = 1.5in 2.5in 3.15in 2.65in]{examples/MAPK-only}
+ \caption{This example of a \PD uses two kinds of entity pool nodes: one
+ for pools of different macromolecules (\sect{macromolecule}) and
+ another for pools of simple chemicals (\sect{simpleChemical}). Most
+ macromolecule nodes in this diagram are adorned with units of
+ information (\sect{unitInfo}) representing phosphorylation states.
+ This diagram uses one type of process node, the transition node
+ (\sect{transition}), and one kind of connecting arc, catalysis
+ (\sect{catalysis}). Finally, some entity pool nodes have dark bands
+ along their bottoms; these are clone markers indicating that the same
+ pool nodes appear multiple times in the diagram.}
+ \label{fig:eg1}
+\end{figure}
+
+The diagram in \fig{eg1} is a simple diagram for part of a
+mitogen-activated protein kinase (MAPK) cascade. The larger nodes in
+\fig{eg1} (some of which are in the shape of rounded rectangles and others
+in the shape of circles) represent biological materials---things like
+macromolecules and simple chemicals. The biological materials are altered
+via processes, which are indicated in SBGN by lines with arrows and other
+decorations. In this particular diagram, all of the processes happen to be
+the same: transitions catalyzed by biochemical entities. The directions of
+the arrows indicate the direction of the transitions; for example,
+unphosphorylated RAF kinase transitions to phosphorylated RAF kinase via a
+process catalyzed by RAS. ATP and ADP are also involved in the same
+process, but the focus of the diagram is on what happens to RAF, so ATP and
+ADP are shown as incidental to the main transition. The small circles on
+the nodes for RAF and other entity pools represent units of information (in
+this case, phosphorylation sites), while the other small circles touching
+small squares indicate a specific kind of process. The details of this and
+other aspects of \PD are explained in the rest of this chapter.
+
+The essence of the \PD is \emph{change}: it shows how different entities in
+the system transition from one form to another. The entities themselves
+can be many different things. In the example of \fig{eg1}, they are either
+pools of macromolecules or pools of simple chemicals, but as will become
+clear later in this chapter, they can be other material and conceptual
+constructs as well. Note also that we speak of \emph{entity pools} rather
+than individuals; this is because in biochemical network models, one does
+not focus on single molecules, but rather collections of molecules of the
+same kind. The molecules in a given pool are considered indistinguishable
+from each other. The way in which a type of entity is transformed into
+another is conveyed by \emph{process nodes}, and links between entity pool
+nodes and process nodes indicate an influence by the entities on the
+processes. In the case of \fig{eg1}, they happen all to be catalysis,
+\sect{catalysis}, but others are possible. Finally, nodes in \PDs are not
+usually repeated; if they do need to be repeated, they are marked with
+\emph{clone markers}---specific modifications to the appearance of the node
+(\sect{cloneMarker}).
+
+\tab{component-summary} summarizes the different SBGN abstractions
+described in this chapter.
+
+\newcolumntype{P}[1]{>{\raggedright\hspace{0pt}\arraybackslash}p{#1}}
+
+\begin{table}[bh]
+ \centering
+ \small
+ \begin{tabular}{@{}llP{2.4in}P{1.6in}@{}}
+ \toprule
+ \textbf{Component} & \textbf{Abbrev.} & \textbf{Role} & \textbf{Examples}\\
+ \midrule
+ Entity pool node
+ & EPN
+ & A population of entities that cannot be distinguished from each other
+ & Ions, macromolecules, multimer, other unspecified entity\\[0.5em]
+
+ Container node
+ & CN
+ & An encapsulation of one or more other SBGN constructs
+ & Complexes, compartments \\[1.6em]
+
+ Process node
+ & PN
+ & A process that transforms one or more EPN into one or more other EPNs
+ & Transition, association, dissociation \\[0.5em]
+
+ Connecting arc
+ & ---
+ & Links from EPNs to PNs to indicate influence by the EPNs on the PNs
+ & Stimulation, modulation, catalysis, inhibition \\[0.5em]
+
+ Logical operators
+ & ---
+ & Combines multiple inputs into one output
+ & Boolean \emph{and}, \emph{or}, \emph{not} \\
+ \bottomrule
+ \end{tabular}
+ \caption{Summary of \PD components and their roles.}
+ \label{tab:component-summary}
+\end{table}
+
+
+
+
+
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: "../sbgn_PD-level1"
+%%% End:
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From: <mh...@us...> - 2008-06-09 11:18:00
|
Revision: 300
http://sbgn.svn.sourceforge.net/sbgn/?rev=300&view=rev
Author: mhucka
Date: 2008-06-09 04:17:59 -0700 (Mon, 09 Jun 2008)
Log Message:
-----------
Trivial edit done in passing.
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/sources/introduction.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/introduction.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/introduction.tex 2008-06-09 11:17:19 UTC (rev 299)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/introduction.tex 2008-06-09 11:17:59 UTC (rev 300)
@@ -91,7 +91,7 @@
It was clear at the outset of SBGN development that it would be impossible to design a perfect and complete notation right from the beginning. Apart from the prescience this would require (which, sadly, none of the authors possess), it also would likely require a vast language that most newcomers would shun as being too complex. Thus, the SBGN community followed an idea used in SBML development~\cite{Hucka:2003}: stratify language development into levels.
-A \emph{level} of SBGN represents a set of features deemed to fit together cohesively, constituting a usable set of functionality that the user community agrees is sufficient for a reasonable set of tasks and goals. Capabilities and features that cannot be agreed upon and are judged insufficiently critical to require inclusion in a given level, are postponed to a higher level. Thus, SBGN development is envisioned to proceed in stages, with each higher SBGN level adding richness compared to the levels below it.
+A \emph{level} of SBGN represents a set of features deemed to fit together cohesively, constituting a usable set of functionality that the user community agrees is sufficient for a reasonable set of tasks and goals. Capabilities and features that cannot be agreed upon and are judged insufficiently critical to require inclusion in a given level, are postponed to a higher level. In this way, SBGN development is envisioned to proceed in stages, with each higher SBGN level adding richness compared to the levels below it.
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From: <mh...@us...> - 2008-06-09 11:17:20
|
Revision: 299
http://sbgn.svn.sourceforge.net/sbgn/?rev=299&view=rev
Author: mhucka
Date: 2008-06-09 04:17:19 -0700 (Mon, 09 Jun 2008)
Log Message:
-----------
Added latex label.
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/sources/layout.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/layout.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/layout.tex 2008-06-09 11:16:49 UTC (rev 298)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/layout.tex 2008-06-09 11:17:19 UTC (rev 299)
@@ -1,4 +1,5 @@
\chapter{General layout of a graph in SBGN}
+\label{chp:layout}
\section{Introduction}
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From: <mh...@us...> - 2008-06-09 11:16:51
|
Revision: 298
http://sbgn.svn.sourceforge.net/sbgn/?rev=298&view=rev
Author: mhucka
Date: 2008-06-09 04:16:49 -0700 (Mon, 09 Jun 2008)
Log Message:
-----------
Added intro paragraph + overview section.
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/sources/glyphs.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/glyphs.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/glyphs.tex 2008-06-09 11:16:08 UTC (rev 297)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/glyphs.tex 2008-06-09 11:16:49 UTC (rev 298)
@@ -4,6 +4,12 @@
%[Note on the color code: \textcolor{blue}{The glyphs that have been thorougly discussed, and are considered frozen, are represented in blue}. \textcolor{green}{The glyphs that have been thorougly discussed, but are still posing problems are represented in green}. \textcolor{red}{The glyphs that have been proposed but for which in-depth discussion is yet to come are represented in red}.]
+This chapter provides a catalog of the graphical symbols available for representing entities in \PDs. There are different classes of glyphs corresponding to different classes of material or conceptual entities, containers, processes, connecting arcs, and logical operators. In \chap{grammar} beginning on page~\pageref{chp:grammar}, we describe the rules for combining these glyphs into a legal SBGN \PD, and in \chap{layout} beginning on page~\pageref{chp:layout}, we describe requirements and guidelines for the way that diagrams are visually organized.
+
+\section{Overview}
+
+\input{sources/pd-overview.tex}
+
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%% State nodes
@@ -11,6 +17,7 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\input{sources/CVs.tex}
+
\section{Entity pool nodes}\label{sec:EPNs}
\SBGNPDLone{} contains five glyphs representing classes of material entities: \glyph{unspecified entity}, \glyph{simple chemical}, \glyph{macromolecule}, \glyph{genetic entity} and \glyph{multimer}. Specific types of macromolecules, such as protein, RNA, DNA, polysaccharide, or simple chemicals such as radical, ion, small molecule etc. may be part of future levels of SBGN. In addition to the material entities, \SBGNPDLone{} represents four conceptual entities: \glyph{tag}, \glyph{source/sink}, \glyph{perturbation}, and \glyph{observable}. Material and conceptual entities can optionally carry auxiliary units such as \glyph{clone markers}, \glyph{state variables} and \glyph{units of information}.
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From: <mh...@us...> - 2008-06-09 11:16:13
|
Revision: 297
http://sbgn.svn.sourceforge.net/sbgn/?rev=297&view=rev
Author: mhucka
Date: 2008-06-09 04:16:08 -0700 (Mon, 09 Jun 2008)
Log Message:
-----------
Minor editing done in passing.
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/sources/grammar.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/grammar.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/grammar.tex 2008-06-09 11:15:40 UTC (rev 296)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/grammar.tex 2008-06-09 11:16:08 UTC (rev 297)
@@ -1,8 +1,9 @@
\chapter{Process Diagram grammar}
+\label{chp:grammar}
\section{Overview}
-In this section we will describe how the glyphs of SBGN can be combined
+In this chapter, we describe how the glyphs of SBGN can be combined
to make a valid SBGN diagram. To do this, we must at the very least
define what glyphs can be connected to each other. This is called
syntax. Next, we must define rules over and above connection rules,
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|
From: <mh...@us...> - 2008-06-09 11:15:42
|
Revision: 296
http://sbgn.svn.sourceforge.net/sbgn/?rev=296&view=rev
Author: mhucka
Date: 2008-06-09 04:15:40 -0700 (Mon, 09 Jun 2008)
Log Message:
-----------
Added macros for references to figures, sections, etc.
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/sources/config.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/config.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/config.tex 2008-06-09 02:27:06 UTC (rev 295)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/config.tex 2008-06-09 11:15:40 UTC (rev 296)
@@ -33,8 +33,6 @@
\newcommand{\NotAF} {\shabox{\textbf{Not AF. ST and ER only}}}
\newcommand{\lenov} {Le~Nov\`{e}re\xspace}
-\newcommand{\eg} {e.g.,\xspace}
-\newcommand{\ie} {i.e.,\xspace}
\newcommand{\D} {\displaystyle}
\newcommand{\tm} {\textsuperscript{\tiny{\texttrademark}}}
@@ -44,6 +42,14 @@
\newcommand{\link}[2] {\literalFont{\href{#1}{#2}}}
\newcommand{\mailto}[1] {\link{mailto:#1}{#1}}
+\newcommand{\chap}[1] {Chapter~\protect\ref{chp:#1}\xspace}
+\newcommand{\sect}[1] {Section~\protect\ref{sec:#1}\xspace}
+\newcommand{\fig}[1] {Figure~\protect\vref{fig:#1}\xspace}
+\newcommand{\tab}[1] {Table~\protect\vref{tab:#1}\xspace}
+\newcommand{\eg} {e.g.,\xspace}
+\newcommand{\ie} {i.e.,\xspace}
+
+
% ----------------------------------------------------------------
% SBGN logo.
% ----------------------------------------------------------------
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|
|
From: <mh...@us...> - 2008-06-09 02:27:08
|
Revision: 295
http://sbgn.svn.sourceforge.net/sbgn/?rev=295&view=rev
Author: mhucka
Date: 2008-06-08 19:27:06 -0700 (Sun, 08 Jun 2008)
Log Message:
-----------
Tightened line spacing because it struck me as too wide.
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.tex 2008-06-09 02:18:55 UTC (rev 294)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.tex 2008-06-09 02:27:06 UTC (rev 295)
@@ -6,7 +6,7 @@
% =============================================================================
\documentclass[11pt,oneside]{book}
-\usepackage[a4paper,centering,top=1in,left=1in,right=1in,bottom=1in]{geometry}
+\usepackage[a4paper,centering,top=1in,left=1in,right=1in]{geometry}
\usepackage[utf8]{inputenc} % unicode support
\usepackage{shadow}
\usepackage{supertabular}
@@ -85,6 +85,7 @@
%% ---------------------------------------------------------------
\raggedbottom
+\renewcommand{\baselinestretch}{0.98}
% Numbers the paragraph, but does not lists them in the ToC
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From: <mh...@us...> - 2008-06-09 02:19:05
|
Revision: 294
http://sbgn.svn.sourceforge.net/sbgn/?rev=294&view=rev
Author: mhucka
Date: 2008-06-08 19:18:55 -0700 (Sun, 08 Jun 2008)
Log Message:
-----------
Fixed mailing list inconsistency, plus made logo smaller.
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/sources/front-page.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/front-page.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/front-page.tex 2008-06-08 06:30:35 UTC (rev 293)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/front-page.tex 2008-06-09 02:18:55 UTC (rev 294)
@@ -49,14 +49,14 @@
\normalsize
\begin{minipage}{5in}
\emph{To discuss any aspect of SBGN, please send your messages
- to the mailing list \texttt{sbg...@sb...}. To get
+ to the mailing list \mailto{sbg...@sb...}. To get
subscribed to the mailing list or to contact us directly,
please write to \mailto{sbg...@sb...}.}
\end{minipage}
\vfill
-\centerline{\includegraphics[width=1.5in]{\SBGNLogoFile}}
+\centerline{\includegraphics[width=1.25in]{\SBGNLogoFile}}
\end{center}
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From: <mh...@us...> - 2008-06-08 06:30:37
|
Revision: 293
http://sbgn.svn.sourceforge.net/sbgn/?rev=293&view=rev
Author: mhucka
Date: 2008-06-07 23:30:35 -0700 (Sat, 07 Jun 2008)
Log Message:
-----------
EPS version of the logo.
Added Paths:
-----------
trunk/documents/specifications/ProcessDiagram/Level1/images/sbgn-logo-rgb.eps
Added: trunk/documents/specifications/ProcessDiagram/Level1/images/sbgn-logo-rgb.eps
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/images/sbgn-logo-rgb.eps (rev 0)
+++ trunk/documents/specifications/ProcessDiagram/Level1/images/sbgn-logo-rgb.eps 2008-06-08 06:30:35 UTC (rev 293)
@@ -0,0 +1,9644 @@
@@ Diff output truncated at 100000 characters. @@
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|
From: <mh...@us...> - 2008-06-08 03:46:56
|
Revision: 292
http://sbgn.svn.sourceforge.net/sbgn/?rev=292&view=rev
Author: mhucka
Date: 2008-06-07 20:46:55 -0700 (Sat, 07 Jun 2008)
Log Message:
-----------
Fixed warning about duplicate page numbers.
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.tex 2008-06-08 03:46:28 UTC (rev 291)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.tex 2008-06-08 03:46:55 UTC (rev 292)
@@ -55,10 +55,10 @@
% Test whether we're being run from latex or latex2html.
\latexhtml{
% For latex.
- \usepackage[breaklinks]{hyperref}
+ \usepackage[breaklinks,plainpages=false,pdfpagelabels]{hyperref}
}{
% For latex2html.
- \usepackage[latex2html,breaklinks]{hyperref}
+ \usepackage[latex2html,breaklinks,plainpages=false,pdfpagelabels]{hyperref}
}
\usepackage[rgb,dvipsnames,svgnames,hyperref,table]{xcolor}
@@ -234,10 +234,9 @@
\begin{document}
%% ---------------------------------------------------------------
-\input{sources/front-page}
-
\frontmatter
+\input{sources/front-page}
\input{sources/preface}
\input{sources/toc}
@@ -254,10 +253,9 @@
\include{sources/refcard}
\include{sources/working}
-\clearpage
-
\backmatter
+\clearpage
\bibliographystyle{unsrt}
\bibliography{sbgn_PD-level1}
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From: <mh...@us...> - 2008-06-08 03:46:29
|
Revision: 291
http://sbgn.svn.sourceforge.net/sbgn/?rev=291&view=rev
Author: mhucka
Date: 2008-06-07 20:46:28 -0700 (Sat, 07 Jun 2008)
Log Message:
-----------
Fixed warning about duplicate page numbers.
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/sources/front-page.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sources/front-page.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sources/front-page.tex 2008-06-07 18:06:47 UTC (rev 290)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sources/front-page.tex 2008-06-08 03:46:28 UTC (rev 291)
@@ -62,7 +62,20 @@
\end{titlepage}
+% The title page is considered unnumbered and the next page after this
+% starts with the page number 1 (actually, i), but the duplication of page
+% number 1 confuses hyperref and leads to the following latex warning:
+%
+% "pdfTeX warning (ext4): destination with the same identifier
+% (name{page.1}) has been already used, duplicate ignored"
+%
+% The following change makes the title page have page number 1 and the next
+% page after that it becomes page ii. This is unorthodox, but seems not
+% completely unreasonable, and it avoids the confusing warning above.
+\setcounter{page}{2}
+
+
% The following is for [X]Emacs users. Please leave in place.
% Local Variables:
% TeX-master: "../sbgn_PD-level1"
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From: <mh...@us...> - 2008-06-07 18:06:48
|
Revision: 290
http://sbgn.svn.sourceforge.net/sbgn/?rev=290&view=rev
Author: mhucka
Date: 2008-06-07 11:06:47 -0700 (Sat, 07 Jun 2008)
Log Message:
-----------
Still fiddling with organization of file header.
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.tex
Modified: trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.tex
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.tex 2008-06-07 18:06:20 UTC (rev 289)
+++ trunk/documents/specifications/ProcessDiagram/Level1/sbgn_PD-level1.tex 2008-06-07 18:06:47 UTC (rev 290)
@@ -1,4 +1,9 @@
+% =============================================================================
+% $Id$
+% Top-level latex file for the SBGN Process Diagram specification document.
+%
% $HeadURL$
+% =============================================================================
\documentclass[11pt,oneside]{book}
\usepackage[a4paper,centering,top=1in,left=1in,right=1in,bottom=1in]{geometry}
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From: <mh...@us...> - 2008-06-07 18:06:24
|
Revision: 289
http://sbgn.svn.sourceforge.net/sbgn/?rev=289&view=rev
Author: mhucka
Date: 2008-06-07 11:06:20 -0700 (Sat, 07 Jun 2008)
Log Message:
-----------
Still fiddling with organization of file header.
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/Makefile
Modified: trunk/documents/specifications/ProcessDiagram/Level1/Makefile
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/Makefile 2008-06-07 17:59:31 UTC (rev 288)
+++ trunk/documents/specifications/ProcessDiagram/Level1/Makefile 2008-06-07 18:06:20 UTC (rev 289)
@@ -1,9 +1,9 @@
+# =============================================================================
+# $Id$
+# Top-level Makefile for the SBGN Process Diagram specification.
+#
# $HeadURL$
-#
-# Description: Top-level Makefile for the SBGN Process Diagram specification.
-# Last modified by: $Author$
-# $Id$
-# -----------------------------------------------------------------------------
+# =============================================================================
MAIN = sbgn_PD-level1
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From: <mh...@us...> - 2008-06-07 17:59:32
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Revision: 288
http://sbgn.svn.sourceforge.net/sbgn/?rev=288&view=rev
Author: mhucka
Date: 2008-06-07 10:59:31 -0700 (Sat, 07 Jun 2008)
Log Message:
-----------
Trying to use pdflatex by default.
Modified Paths:
--------------
trunk/documents/specifications/ProcessDiagram/Level1/Makefile
Modified: trunk/documents/specifications/ProcessDiagram/Level1/Makefile
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/Makefile 2008-06-07 17:47:49 UTC (rev 287)
+++ trunk/documents/specifications/ProcessDiagram/Level1/Makefile 2008-06-07 17:59:31 UTC (rev 288)
@@ -1,11 +1,17 @@
-MAIN = sbgn_PD-level1
+# $HeadURL$
+#
+# Description: Top-level Makefile for the SBGN Process Diagram specification.
+# Last modified by: $Author$
+# $Id$
+# -----------------------------------------------------------------------------
+MAIN = sbgn_PD-level1
+LATEX = pdflatex
+BIBTEX = bibtex
+
all default:
- latex $(MAIN).tex
- latex $(MAIN).tex
- bibtex $(MAIN)
- latex $(MAIN).tex
- dvipdf $(MAIN)
-
-
+ $(LATEX) $(MAIN).tex
+ $(LATEX) $(MAIN).tex
+ $(BIBTEX) $(MAIN)
+ $(LATEX) $(MAIN).tex
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From: <mh...@us...> - 2008-06-07 17:47:54
|
Revision: 287
http://sbgn.svn.sourceforge.net/sbgn/?rev=287&view=rev
Author: mhucka
Date: 2008-06-07 10:47:49 -0700 (Sat, 07 Jun 2008)
Log Message:
-----------
Added a brief intro file.
Added Paths:
-----------
trunk/documents/specifications/ProcessDiagram/Level1/README.txt
Added: trunk/documents/specifications/ProcessDiagram/Level1/README.txt
===================================================================
--- trunk/documents/specifications/ProcessDiagram/Level1/README.txt (rev 0)
+++ trunk/documents/specifications/ProcessDiagram/Level1/README.txt 2008-06-07 17:47:49 UTC (rev 287)
@@ -0,0 +1,13 @@
+
+ Specification for the
+
+ ----------------------------------------
+ Systems Biology Graphical Notation (SBGN)
+ Process Diagrams Level 1
+ ----------------------------------------
+
+ For more information about SBGN, visit:
+ http://sbgn.org
+
+ Please join the sbgn-discuss mailing list by visiting
+ http://www.sbgn.org/Forums
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