Systems Biology Graphical Notation

Revision: 822
          http://sbgn.svn.sourceforge.net/sbgn/?rev=822&view=rev
Author:   lenov
Date:     2012-05-20 11:59:35 +0000 (Sun, 20 May 2012)
Log Message:
-----------


Modified Paths:
--------------
    ProcessDiagram/trunk/UserManual/images/uncertain.eps
    ProcessDiagram/trunk/UserManual/images/uncertain.pdf
    ProcessDiagram/trunk/UserManual/images/uncertain.png
    ProcessDiagram/trunk/UserManual/images/uncertain.svg
    ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log
    ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.pdf
    ProcessDiagram/trunk/UserManual/sources/CVs.tex
    ProcessDiagram/trunk/UserManual/sources/front-page.tex
    ProcessDiagram/trunk/UserManual/sources/multimer.tex
    ProcessDiagram/trunk/UserManual/sources/symbols.aux
    ProcessDiagram/trunk/UserManual/sources/symbols.tex
    ProcessDiagram/trunk/UserManual/sources/symbols.tex.backup

Modified: ProcessDiagram/trunk/UserManual/images/uncertain.eps
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Modified: ProcessDiagram/trunk/UserManual/images/uncertain.pdf
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Modified: ProcessDiagram/trunk/UserManual/images/uncertain.png
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Modified: ProcessDiagram/trunk/UserManual/images/uncertain.svg
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+     inkscape:window-y="36"
      showguides="true"
-     inkscape:guide-bbox="true">
+     inkscape:guide-bbox="true"
+     showgrid="false"
+     inkscape:window-maximized="0">
     <sodipodi:guide
        orientation="vertical"
        position="301.42857"
@@ -82,6 +87,7 @@
         <dc:format>image/svg+xml</dc:format>
         <dc:type
            rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
+        <dc:title></dc:title>
       </cc:Work>
     </rdf:RDF>
   </metadata>
@@ -125,7 +131,7 @@
        height="41.42857"
        width="44.285713"
        id="rect2829"
-       style="opacity:1;fill:white;fill-opacity:1;fill-rule:nonzero;stroke:black;stroke-width:5;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1" />
+       style="opacity:1;fill:#ffffc8;fill-opacity:1;fill-rule:nonzero;stroke:black;stroke-width:5;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1" />
     <text
        xml:space="preserve"
        style="font-size:12px;font-style:normal;font-weight:normal;fill:black;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;font-family:Bitstream Vera Sans"

Modified: ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log
===================================================================
--- ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log	2012-05-20 05:28:21 UTC (rev 821)
+++ ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log	2012-05-20 11:59:35 UTC (rev 822)
@@ -1,4 +1,4 @@
-This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) (format=pdflatex 2012.5.4)  4 MAY 2012 18:21
+This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) (format=pdflatex 2012.5.4)  20 MAY 2012 08:09
 entering extended mode
  %&-line parsing enabled.
 **sbgn_PD-level1-user.tex
@@ -1062,9 +1062,6 @@
 (Font)              Font shape `T1/futs/b/n' tried instead on input line 24.
 
 
-LaTeX Warning: Reference `sec:process' on page 1 undefined on input line 24.
-
-
 LaTeX Warning: Reference `sec:consumption' on page 1 undefined on input line 24
 .
 
@@ -1076,9 +1073,6 @@
 LaTeX Warning: Reference `sec:catalysis' on page 1 undefined on input line 24.
 
 
-LaTeX Warning: Reference `sec:process' on page 1 undefined on input line 24.
-
-
 LaTeX Warning: Reference `sec:consumption' on page 1 undefined on input line 24
 .
 
@@ -1188,53 +1182,104 @@
 <images/perturbing_agent.pdf, id=83, 265.99374pt x 110.4125pt>
 File: images/perturbing_agent.pdf Graphic file (type pdf)
 
-<use images/perturbing_agent.pdf>) (./sources/unitInformation.tex
-
-LaTeX Warning: Reference `sec:CVs' on page 7 undefined on input line 8.
-
-<images/unitInformation.pdf, id=84, 263.98625pt x 109.40875pt>
+<use images/perturbing_agent.pdf>) (./sources/multimer.tex
+<images/multimer.pdf, id=84, 329.23pt x 217.81375pt>
+File: images/multimer.pdf Graphic file (type pdf)
+ <use images/multimer.pdf>) (./sources/unitInformation.tex [7 <./images/sourceS
+ink.pdf> <./images/perturbing_agent.pdf> <./images/multimer.pdf>]
+<images/unitInformation.pdf, id=113, 263.98625pt x 109.40875pt>
 File: images/unitInformation.pdf Graphic file (type pdf)
 
-<use images/unitInformation.pdf>) (./sources/stateVariable.tex [7 <./images/sou
-rceSink.pdf> <./images/perturbing_agent.pdf> <./images/unitInformation.pdf>]
-<images/stateVariable.pdf, id=109, 263.98625pt x 111.41624pt>
+<use images/unitInformation.pdf>) (./sources/stateVariable.tex
+<images/stateVariable.pdf, id=114, 263.98625pt x 111.41624pt>
 File: images/stateVariable.pdf Graphic file (type pdf)
 
 <use images/stateVariable.pdf>) (./sources/cloneMarker.tex
 
 LaTeX Warning: Reference `sec:submap' on page 8 undefined on input line 5.
 
-<images/simpleCloneMarker.pdf, id=110, 170.6375pt x 171.64125pt>
+[8 <./images/unitInformation.pdf> <./images/stateVariable.pdf>]
+<images/simpleCloneMarker.pdf, id=130, 170.6375pt x 171.64125pt>
 File: images/simpleCloneMarker.pdf Graphic file (type pdf)
 
-<use images/simpleCloneMarker.pdf> [8 <./images/stateVariable.pdf>]
+<use images/simpleCloneMarker.pdf>
 Overfull \hbox (0.13669pt too wide) in paragraph at lines 16--17
 []\T1/futs/m/n/10.95 Unlike the \T1/futs/m/it/10.95 sim-ple clone marker\T1/fut
 s/m/n/10.95 , the \T1/futs/m/it/10.95 la-beled clone marker \T1/futs/m/n/10.95 
 in-cludes (un-sur-pris-ingly, given its name)
  []
 
-<images/labeledCloneMarker.pdf, id=120, 323.2075pt x 215.80624pt>
+<images/labeledCloneMarker.pdf, id=131, 323.2075pt x 215.80624pt>
 File: images/labeledCloneMarker.pdf Graphic file (type pdf)
 
-<use images/labeledCloneMarker.pdf>)) [9 <./images/simpleCloneMarker.pdf> <./im
-ages/labeledCloneMarker.pdf>]
+<use images/labeledCloneMarker.pdf>) (./sources/CVs.tex [9 <./images/simpleClon
+eMarker.pdf> <./images/labeledCloneMarker.pdf>] [10]
+
+LaTeX Warning: Reference `sec:phenotype' on page 11 undefined on input line 99.
+
+
+LaTeX Font Info:    Font shape `T1/txtt/m/it' in size <10> not available
+(Font)              Font shape `T1/txtt/m/sl' tried instead on input line 135.
+
+LaTeX Warning: `h' float specifier changed to `ht'.
+
+)
+
+LaTeX Warning: Reference `sec:association' on page 11 undefined on input line 4
+4.
+
+
+LaTeX Warning: Reference `sec:dissociation' on page 11 undefined on input line 
+44.
+
+
+LaTeX Warning: Reference `sec:phenotype' on page 11 undefined on input line 44.
+
+
+[11] (./sources/process.tex
+
+LaTeX Warning: Reference `sec:consumption' on page 12 undefined on input line 8
+.
+
+
+LaTeX Warning: Reference `sec:production' on page 12 undefined on input line 8.
+
+
+
+LaTeX Warning: Reference `sec:arcs' on page 12 undefined on input line 8.
+
+<images/process.pdf, id=157, 244.915pt x 84.315pt>
+File: images/process.pdf Graphic file (type pdf)
+ <use images/process.pdf>)
+(./sources/omitted.tex
+
+LaTeX Warning: Reference `sec:submap' on page 12 undefined on input line 7.
+
+<images/omitted.pdf, id=158, 244.915pt x 84.315pt>
+File: images/omitted.pdf Graphic file (type pdf)
+ <use images/omitted.pdf>)
+(./sources/uncertain.tex [12 <./images/process.pdf> <./images/omitted.pdf>]
+<images/uncertain.pdf, id=168, 244.915pt x 84.315pt>
+File: images/uncertain.pdf Graphic file (type pdf)
+
+<use images/uncertain.pdf>)) [13 <./images/uncertain.pdf>]
 \openout2 = `sources/refcard.aux'.
 
- (./sources/refcard.tex
+
+(./sources/refcard.tex
 Appendix A.
-<images/refcard.pdf, id=140, 798.985pt x 575.14874pt>
+<images/refcard.pdf, id=178, 798.985pt x 575.14874pt>
 File: images/refcard.pdf Graphic file (type pdf)
  <use images/refcard.pdf>)
 Overfull \hbox (7.15172pt too wide) in paragraph at lines 4--29
 [] 
  []
 
-[10
+[14
 
 
 
-] [11 <./images/refcard.pdf>] (./sbgn_PD-level1-user.bbl) [12
+] [15 <./images/refcard.pdf>] (./sbgn_PD-level1-user.bbl) [16
 
 
 
@@ -1247,24 +1292,24 @@
 
  ) 
 Here is how much of TeX's memory you used:
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- 62052 string characters out of 1152824
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+ 4720 strings out of 493848
+ 63167 string characters out of 1152824
+ 142739 words of memory out of 3000000
+ 7759 multiletter control sequences out of 15000+50000
+ 112722 words of font info for 88 fonts, out of 3000000 for 9000
  714 hyphenation exceptions out of 8191
- 32i,7n,32p,1530b,290s stack positions out of 5000i,500n,10000p,200000b,50000s
+ 32i,8n,32p,1530b,290s stack positions out of 5000i,500n,10000p,200000b,50000s
 {/usr/share/texmf-texlive/fonts/enc/dvips/base/8r.enc}</usr/share/texmf-texli
 ve/fonts/type1/public/fourier/fourier-ms.pfb></usr/share/texmf-texlive/fonts/ty
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 putr8a.pfb></usr/share/texmf-texlive/fonts/type1/adobe/utopia/putr8a.pfb></usr/
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-urw/helvetic/uhvb8a.pfb></usr/share/texmf-texlive/fonts/type1/urw/helvetic/uhvb
-o8a.pfb>
-Output written on sbgn_PD-level1-user.pdf (13 pages, 888985 bytes).
+public/txfonts/t1xtt.pfb></usr/share/texmf-texlive/fonts/type1/urw/helvetic/uhv
+b8a.pfb></usr/share/texmf-texlive/fonts/type1/urw/helvetic/uhvbo8a.pfb>
+Output written on sbgn_PD-level1-user.pdf (17 pages, 926607 bytes).
 PDF statistics:
- 189 PDF objects out of 1000 (max. 8388607)
+ 229 PDF objects out of 1000 (max. 8388607)
  0 named destinations out of 1000 (max. 500000)
- 71 words of extra memory for PDF output out of 10000 (max. 10000000)
+ 91 words of extra memory for PDF output out of 10000 (max. 10000000)
 

Modified: ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.pdf
===================================================================
(Binary files differ)

Modified: ProcessDiagram/trunk/UserManual/sources/CVs.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/CVs.tex	2012-05-20 05:28:21 UTC (rev 821)
+++ ProcessDiagram/trunk/UserManual/sources/CVs.tex	2012-05-20 11:59:35 UTC (rev 822)
@@ -118,7 +118,7 @@
 \subsubsection{Cardinality}
 \label{sec:cardinality-cv}
 
-\SBGNPDLone defines a special unit of information usable on multimers for describing the number of monomers composing the multimer.  \tab{cardinality-cv} shows the way in which the values must be written.  Note that the value is an positive non-zero integer, and not (for example) a range.  There is no provision in \SBGNPDLone for specifying a range in this context because it leads to problems of entity identifiability.
+\SBGNPDLone defines a special unit of information usable on multimers for describing the number of monomers composing the multimer.  \tab{cardinality-cv} shows the way in which the values must be written.  Note that the value is an positive non-zero integer, and not (for example) a range.  There is at present no provision in \SBGNPDLone for specifying a range in this context because it leads to problems of entity identifiability.
 
 \begin{table}[h]
   \centering

Modified: ProcessDiagram/trunk/UserManual/sources/front-page.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/front-page.tex	2012-05-20 05:28:21 UTC (rev 821)
+++ ProcessDiagram/trunk/UserManual/sources/front-page.tex	2012-05-20 11:59:35 UTC (rev 822)
@@ -11,7 +11,7 @@
 \vspace*{0.5in}
 
 \Large
-\textbf{Version 2.0}\\[0.1in]
+\textbf{Version 1.3}\\[0.1in]
 \large
 % Date: \sbgndate\\[0.25in]
 Date: \today\\[0.25in]

Modified: ProcessDiagram/trunk/UserManual/sources/multimer.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/multimer.tex	2012-05-20 05:28:21 UTC (rev 821)
+++ ProcessDiagram/trunk/UserManual/sources/multimer.tex	2012-05-20 11:59:35 UTC (rev 822)
@@ -1,7 +1,7 @@
 \subsection{Glyph: \glyph{Multimer}}
 \label{sec:multimer}
 
-As its name implies, a multimer is an aggregation of multiple identical or pseudo-identical entities held together by non-covalent bonds. Thus, they are distinguished from polymers by the fact that the latter involve covalent bonds, and should be represented by \glyphs{macromolecules}. Here \emph{pseudo-identical} refers to the possibility that the entities differ chemically but retain some common global characteristic, such as a structure or function, and so can be considered identical within the context of the SBGN \PD.  An example of this are the homologous subunits in a hetero-oligomeric receptor. SBGN \PD accepts multimers of \glyph{simple chemical} (\sect{simpleChemical}), \glyph{macromolecule} (\sect{macromolecule}), \glyph{nucleic acid feature} (\sect{genetic}) or \glyph{complex} (\sect{complex}). A \glyph{multimer} is represented by two identical containers shifted horizontally and vertically and stacked one on top of the other as illustrated in \fig{multimer}.
+As its name implies, a multimer is an aggregation of multiple identical or pseudo-identical entities held together by non-covalent bonds. Thus, they are distinguished from polymers by the fact that the latter involve covalent bonds, and should be represented by \glyph{macromolecules}. Here \emph{pseudo-identical} refers to the possibility that the entities differ chemically but retain some common global characteristic, such as a structure or function, and so can be considered identical within the context of the SBGN \PD.  An example of this are the homologous subunits in a hetero-oligomeric receptor. SBGN \PD accepts multimers of \glyph{simple chemical} (\sect{simpleChemical}), \glyph{macromolecule} (\sect{macromolecule}), \glyph{nucleic acid feature} (\sect{genetic}) or \glyph{complex} (\sect{complex}). A \glyph{multimer} is represented by two identical containers shifted horizontally and vertically and stacked one on top of the other as illustrated in \fig{multimer}.
 
 \begin{figure}[H]
   \centering

Modified: ProcessDiagram/trunk/UserManual/sources/symbols.aux
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/symbols.aux	2012-05-20 05:28:21 UTC (rev 821)
+++ ProcessDiagram/trunk/UserManual/sources/symbols.aux	2012-05-20 11:59:35 UTC (rev 822)
@@ -33,24 +33,64 @@
 \newlabel{sec:perturbing agent}{{2.1.7}{7}}
 \@writefile{lof}{\contentsline {figure}{\numberline {2.7}{\ignorespaces The Process Description\xspace  glyph for \emph  {perturbing agent}.}}{7}}
 \newlabel{fig:perturbing agent}{{2.7}{7}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.1.8}Glyph: \emph  {Multimer}}{7}}
+\newlabel{sec:multimer}{{2.1.8}{7}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.8}{\ignorespaces The Process Description\xspace  glyph for \emph  {multimer}. }}{7}}
+\newlabel{fig:multimer}{{2.8}{7}}
 \@writefile{toc}{\contentsline {section}{\numberline {2.2}Decorations of the entity pool nodes}{7}}
 \newlabel{sec:decorations}{{2.2}{7}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {2.2.1}Glyph: \emph  {Unit of information}}{7}}
-\newlabel{sec:unitInfo}{{2.2.1}{7}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.8}{\ignorespaces The Process Description\xspace  glyph for \emph  {unit of information}.}}{7}}
-\newlabel{fig:unitInfo}{{2.8}{7}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.2.1}Glyph: \emph  {Unit of information}}{8}}
+\newlabel{sec:unitInfo}{{2.2.1}{8}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.9}{\ignorespaces The Process Description\xspace  glyph for \emph  {unit of information}.}}{8}}
+\newlabel{fig:unitInfo}{{2.9}{8}}
 \@writefile{toc}{\contentsline {subsection}{\numberline {2.2.2}Glyph: \emph  {State variable}}{8}}
 \newlabel{sec:stateVariable}{{2.2.2}{8}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.9}{\ignorespaces The Process Description\xspace  glyph for \emph  {state variable}.}}{8}}
-\newlabel{fig:state-var}{{2.9}{8}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {2.2.3}Glyph: \emph  {Clone marker}}{8}}
-\newlabel{sec:cloneMarker}{{2.2.3}{8}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.10}{\ignorespaces The Process Description\xspace  glyph for \emph  {simple clone marker} applied to a \emph  {simple chemical}}}{9}}
-\newlabel{fig:simpleCloneMarker}{{2.10}{9}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.11}{\ignorespaces The Process Description\xspace  glyph for \emph  {labeled clone marker} applied to a \emph  {multimer} of \emph  {macromolecules}.}}{9}}
-\newlabel{fig:labeledCloneMarker}{{2.11}{9}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.10}{\ignorespaces The Process Description\xspace  glyph for \emph  {state variable}.}}{8}}
+\newlabel{fig:state-var}{{2.10}{8}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.2.3}Glyph: \emph  {Clone marker}}{9}}
+\newlabel{sec:cloneMarker}{{2.2.3}{9}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.11}{\ignorespaces The Process Description\xspace  glyph for \emph  {simple clone marker} applied to a \emph  {simple chemical}}}{9}}
+\newlabel{fig:simpleCloneMarker}{{2.11}{9}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.12}{\ignorespaces The Process Description\xspace  glyph for \emph  {labeled clone marker} applied to a \emph  {multimer} of \emph  {macromolecules}.}}{9}}
+\newlabel{fig:labeledCloneMarker}{{2.12}{9}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.2.4}Controlled vocabularies used in SBGN Process Description\xspace  Level\nobreakspace  {}1\xspace  }{9}}
+\newlabel{sec:CVs}{{2.2.4}{9}}
+\@writefile{toc}{\contentsline {subsubsection}{Entity pool node material types}{10}}
+\newlabel{sec:material-types-cv}{{2.2.4}{10}}
+\@writefile{lot}{\contentsline {table}{\numberline {2.1}{\ignorespaces A sample of values from the \emph  {material types} controlled vocabulary (Section\nobreakspace  {}\ref {sec:material-types-cv}\xspace  ).}}{10}}
+\newlabel{tab:material-types-cv}{{2.1}{10}}
+\@writefile{toc}{\contentsline {subsubsection}{Entity pool node conceptual types}{10}}
+\newlabel{sec:conceptual-types-cv}{{2.2.4}{10}}
+\@writefile{lot}{\contentsline {table}{\numberline {2.2}{\ignorespaces A sample of values from the \emph  {conceptual types} vocabulary (Section\nobreakspace  {}\ref {sec:conceptual-types-cv}\xspace  ).}}{10}}
+\newlabel{tab:conceptual-types-cv}{{2.2}{10}}
+\@writefile{toc}{\contentsline {subsubsection}{Macromolecule covalent modifications}{10}}
+\newlabel{sec:covalent-mod-cv}{{2.2.4}{10}}
+\@writefile{lot}{\contentsline {table}{\numberline {2.3}{\ignorespaces A sample of values from the \emph  {covalent modifications} vocabulary (Section\nobreakspace  {}\ref {sec:covalent-mod-cv}\xspace  ).}}{11}}
+\newlabel{tab:covalent-mod-cv}{{2.3}{11}}
+\@writefile{toc}{\contentsline {subsubsection}{Physical characteristics}{11}}
+\newlabel{sec:physical-characteristics-cv}{{2.2.4}{11}}
+\@writefile{lot}{\contentsline {table}{\numberline {2.4}{\ignorespaces A sample of values from the \emph  {physical characteristics} vocabulary (Section\nobreakspace  {}\ref {sec:physical-characteristics-cv}\xspace  ).}}{11}}
+\newlabel{tab:physical-characteristics-cv}{{2.4}{11}}
+\@writefile{toc}{\contentsline {subsubsection}{Cardinality}{11}}
+\newlabel{sec:cardinality-cv}{{2.2.4}{11}}
+\@writefile{lot}{\contentsline {table}{\numberline {2.5}{\ignorespaces The format of the possible values for the \emph  {cardinality} unit of information (Section\nobreakspace  {}\ref {sec:cardinality-cv}\xspace  ). Here, \texttt  {\#} stands for the number; for example, ``\texttt  {N:5}''.}}{12}}
+\newlabel{tab:cardinality-cv}{{2.5}{12}}
+\@writefile{toc}{\contentsline {section}{\numberline {2.3}Process nodes}{12}}
+\newlabel{sec:PNs}{{2.3}{12}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.3.1}Glyph: \emph  {Process}}{12}}
+\newlabel{sec:process}{{2.3.1}{12}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.13}{\ignorespaces The Process Description\xspace  glyph for \emph  {process}.}}{12}}
+\newlabel{fig:process}{{2.13}{12}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.3.2}Glyph: \emph  {Omitted process}}{12}}
+\newlabel{sec:omitted}{{2.3.2}{12}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.14}{\ignorespaces The Process Description\xspace  glyph for \emph  {omitted process}.}}{12}}
+\newlabel{fig:omitted}{{2.14}{12}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.3.3}Glyph: \emph  {Uncertain process}}{13}}
+\newlabel{sec:uncertain}{{2.3.3}{13}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.15}{\ignorespaces The Process Description\xspace  glyph for an \emph  {uncertain process}.}}{13}}
+\newlabel{fig:uncertain}{{2.15}{13}}
 \@setckpt{sources/symbols}{
-\setcounter{page}{10}
+\setcounter{page}{14}
 \setcounter{equation}{0}
 \setcounter{enumi}{0}
 \setcounter{enumii}{0}
@@ -60,13 +100,13 @@
 \setcounter{mpfootnote}{0}
 \setcounter{part}{0}
 \setcounter{chapter}{2}
-\setcounter{section}{2}
+\setcounter{section}{3}
 \setcounter{subsection}{3}
 \setcounter{subsubsection}{0}
 \setcounter{paragraph}{0}
 \setcounter{subparagraph}{0}
-\setcounter{figure}{11}
-\setcounter{table}{0}
+\setcounter{figure}{15}
+\setcounter{table}{5}
 \setcounter{float@...}
 \setcounter{r@...}
 }

Modified: ProcessDiagram/trunk/UserManual/sources/symbols.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/symbols.tex	2012-05-20 05:28:21 UTC (rev 821)
+++ ProcessDiagram/trunk/UserManual/sources/symbols.tex	2012-05-20 11:59:35 UTC (rev 822)
@@ -1,10 +1,14 @@
 \chapter{Symbols used in SBGN Process Descriptions}
 \label{chp:symbols}
 
-% Refactor the structure of this chapter. We need less sections and a simpler structure. For instance, auxiliary units must be defined in the EPN section. 
-
 An SBGN \PDm is mainly is bipartite graph, i.e. it is made up of two types of nodes that connect in an alternate way (some exceptions are described below, e.g. when \glyph{logical operators} or \glyph{tag} are used). The two types of nodes are the \glyph{process nodes} and the \glyph{entity pools nodes}, representing the things that are modified by processes. These nodes are connected by arcs. In addition, the \glyph{entity pools nodes} can be contained in \glyph{compartments}. 
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%                   Entity pool nodes
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
 \section{Entity pool nodes}\label{sec:EPNs}
 
 An entity pool is a population of entities that cannot be distinguished from each other, when it comes to the \SBGNPDLone map. For instance all the molecular entities that fulfill the same role in a given process form an entity pool. As a result, an entity pool can represent different granularity levels, such as all the proteins, all the instances of a given protein, only certain forms of a given protein. It really depends on what we want to represent. To belong to different compartments is sufficient to belong to different entity pools. Calcium ions in the endoplasmic reticulum and calcium ions in the cytosol belong to different entity pools when it comes to representing calcium release from the endoplasmic reticulum.
@@ -27,52 +31,21 @@
 \input{sources/unitInformation.tex}
 \input{sources/stateVariable.tex}
 \input{sources/cloneMarker.tex}
+\input{sources/CVs.tex}
 
-% \input{sources/CVs.tex}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%                   Process nodes
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-
-
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%                   Containers
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% 
-% %\section{Container nodes}\label{sec:CNs}
-% \section{Representing compartments}
-% 
-% \input{sources/compartment.tex}
-% 
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%                   Submap
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% 
-% \section{Submaps}
-% \input{sources/submap.tex}
-
-% \section{Referring to other Nodes}
-% 
-% Reference nodes handle links or relationships between elements of a map and sub-map. At present there is only one reference glyph, \glyph{tag}, which can be used in a map refered to by a \glyph{submap} (\sect{submap}) or as an auxilary unit on the \glyph{submap}. The \glyph{clone marker} can also provide additional reference mechanisms and is discussed below (\sect{cloneMarker}).
-% 
-% \input{sources/tag.tex}
-% 
-% 
-% 
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%                   Process nodes
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% 
-% \section{Process nodes}\label{sec:PNs}
-% 
-% Process nodes represent processes that transform one or several entity pools into one or several entity pools, identical or different.  \SBGNPDLone defines a generic \glyph{process} (\sect{process}), as well as five more specific ones: the \glyph{omitted process} (\sect{omitted}), the \glyph{uncertain process} (\sect{uncertain}), the \glyph{association} (\sect{association}), the \glyph{dissociation} (\sect{dissociation}), and the \glyph{phenotype} (\sect{phenotype}).  In future levels of the SBGN \PDl, more processes may be defined.  (One can even envision the development of a controlled vocabulary of processes, as is done now for \glyph{EPNs}; see \sect{CVs}.)
-% 
-% \input{sources/process.tex}
-% \input{sources/omitted.tex}
-% \input{sources/uncertain.tex}
+\section{Process nodes}\label{sec:PNs}
+ 
+Process nodes represent processes that transform one or several entity pools into one or several entity pools, identical or different.  \SBGNPDLone defines a generic \glyph{process} (\sect{process}), as well as five more specific ones: the \glyph{omitted process} (\sect{omitted}), the \glyph{uncertain process} (\sect{uncertain}), the \glyph{association} (\sect{association}), the \glyph{dissociation} (\sect{dissociation}), and the \glyph{phenotype} (\sect{phenotype}). 
+ 
+\input{sources/process.tex}
+\input{sources/omitted.tex}
+\input{sources/uncertain.tex}
 % \input{sources/association.tex}
 % \input{sources/dissociation.tex}
 % \input{sources/phenotype.tex}
@@ -109,3 +82,33 @@
 % \input{sources/and.tex}
 % \input{sources/or.tex}
 % \input{sources/not.tex}
+
+
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%                   Containers
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% 
+% %\section{Container nodes}\label{sec:CNs}
+%\section{Representing compartments}
+%
+%\input{sources/compartment.tex}
+% 
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%                   Submap
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% 
+% \section{Submaps}
+% \input{sources/submap.tex}
+
+% \section{Referring to other Nodes}
+% 
+% Reference nodes handle links or relationships between elements of a map and sub-map. At present there is only one reference glyph, \glyph{tag}, which can be used in a map refered to by a \glyph{submap} (\sect{submap}) or as an auxilary unit on the \glyph{submap}. The \glyph{clone marker} can also provide additional reference mechanisms and is discussed below (\sect{cloneMarker}).
+% 
+% \input{sources/tag.tex}
+% 
+% 
+% 

Modified: ProcessDiagram/trunk/UserManual/sources/symbols.tex.backup
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/symbols.tex.backup	2012-05-20 05:28:21 UTC (rev 821)
+++ ProcessDiagram/trunk/UserManual/sources/symbols.tex.backup	2012-05-20 11:59:35 UTC (rev 822)
@@ -1,10 +1,14 @@
 \chapter{Symbols used in SBGN Process Descriptions}
 \label{chp:symbols}
 
-% Refactor the structure of this chapter. We need less sections and a simpler structure. For instance, auxiliary units must be defined in the EPN section. 
-
 An SBGN \PDm is mainly is bipartite graph, i.e. it is made up of two types of nodes that connect in an alternate way (some exceptions are described below, e.g. when \glyph{logical operators} or \glyph{tag} are used). The two types of nodes are the \glyph{process nodes} and the \glyph{entity pools nodes}, representing the things that are modified by processes. These nodes are connected by arcs. In addition, the \glyph{entity pools nodes} can be contained in \glyph{compartments}. 
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%                   Entity pool nodes
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
 \section{Entity pool nodes}\label{sec:EPNs}
 
 An entity pool is a population of entities that cannot be distinguished from each other, when it comes to the \SBGNPDLone map. For instance all the molecular entities that fulfill the same role in a given process form an entity pool. As a result, an entity pool can represent different granularity levels, such as all the proteins, all the instances of a given protein, only certain forms of a given protein. It really depends on what we want to represent. To belong to different compartments is sufficient to belong to different entity pools. Calcium ions in the endoplasmic reticulum and calcium ions in the cytosol belong to different entity pools when it comes to representing calcium release from the endoplasmic reticulum.
@@ -12,67 +16,34 @@
 The \PDl contains six glyphs representing classes of material entities: \glyph{unspecified entity} (\sect{unspecifiedEntity}), \glyph{simple chemical} (\sect{simpleChemical}), \glyph{macromolecule} (\sect{macromolecule}), \glyph{nucleic acid feature} (\sect{genetic}), and \glyph{complex} (\sect{complex}).  (Specific types of macromolecules, such as protein, RNA, DNA, polysaccharide, and specific simple chemicals are not defined by \PD but may be part of future levels of SBGN). In addition to the material entities, the \PDl represents two conceptual entities: An absorbing pool, called \glyph{source and sink} (\sect{sourceSink}), and a \glyph{perturbing agent} (\sect{perturbing agent}).  Material and conceptual entities can optionally carry auxiliary units such as \glyph{units of information} (\sect{unitInfo}), \glyph{state variables}  (\sect{stateVariable}) and \glyph{clone markers} (\sect{cloneMarker}).
 
 \input{sources/unspecified.tex}
- \input{sources/macromolecule.tex}
+\input{sources/macromolecule.tex}
 \input{sources/simpleChemical.tex}
-% \input{sources/genetic.tex}
-% \input{sources/complex.tex}
-% \input{sources/sourceSink.tex}
-% \input{sources/perturbing_agent.tex}
-% 
-% \section{Modification of the entity pool nodes}
+\input{sources/genetic.tex}
+\input{sources/complex.tex}
+\input{sources/sourceSink.tex}
+\input{sources/perturbing_agent.tex}
+\input{sources/multimer.tex}
 
-% \subsection{Auxiliary Units}
-% 
-% Auxiliary units are glyphs that decorate other glyphs, providing additional information that may be useful to the reader. These can provide annotation (\glyph{unit of information}), state information (\glyph{state variable}) or indicate duplication of entity pool nodes (\glyph{clone marker}).
-% 
-% \input{sources/unitInformation.tex}
-% \input{sources/stateVariable.tex}
-% \input{sources/cloneMarker.tex}
+\section{Decorations of the entity pool nodes}\label{sec:decorations}
 
-% \input{sources/CVs.tex}
+SBGN \PD provides glyphs that decorate other glyphs, providing additional information that may be useful to the reader. These can provide annotation (\glyph{unit of information}), state information (\glyph{state variable}) or indicate duplication of entity pool nodes (\glyph{clone marker}).
 
-% \input{sources/multimer.tex}
+\input{sources/unitInformation.tex}
+\input{sources/stateVariable.tex}
+\input{sources/cloneMarker.tex}
+\input{sources/CVs.tex}
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%                   Process nodes
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%                   Containers
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% 
-% %\section{Container nodes}\label{sec:CNs}
-% \section{Representing compartments}
-% 
-% \input{sources/compartment.tex}
-% 
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%                   Submap
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% 
-% \section{Submaps}
-% \input{sources/submap.tex}
-
-% \section{Referring to other Nodes}
-% 
-% Reference nodes handle links or relationships between elements of a map and sub-map. At present there is only one reference glyph, \glyph{tag}, which can be used in a map refered to by a \glyph{submap} (\sect{submap}) or as an auxilary unit on the \glyph{submap}. The \glyph{clone marker} can also provide additional reference mechanisms and is discussed below (\sect{cloneMarker}).
-% 
-% \input{sources/tag.tex}
-% 
-% 
-% 
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%                   Process nodes
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% 
-% \section{Process nodes}\label{sec:PNs}
-% 
-% Process nodes represent processes that transform one or several entity pools into one or several entity pools, identical or different.  \SBGNPDLone defines a generic \glyph{process} (\sect{process}), as well as five more specific ones: the \glyph{omitted process} (\sect{omitted}), the \glyph{uncertain process} (\sect{uncertain}), the \glyph{association} (\sect{association}), the \glyph{dissociation} (\sect{dissociation}), and the \glyph{phenotype} (\sect{phenotype}).  In future levels of the SBGN \PDl, more processes may be defined.  (One can even envision the development of a controlled vocabulary of processes, as is done now for \glyph{EPNs}; see \sect{CVs}.)
-% 
-% \input{sources/process.tex}
+\section{Process nodes}\label{sec:PNs}
+ 
+Process nodes represent processes that transform one or several entity pools into one or several entity pools, identical or different.  \SBGNPDLone defines a generic \glyph{process} (\sect{process}), as well as five more specific ones: the \glyph{omitted process} (\sect{omitted}), the \glyph{uncertain process} (\sect{uncertain}), the \glyph{association} (\sect{association}), the \glyph{dissociation} (\sect{dissociation}), and the \glyph{phenotype} (\sect{phenotype}). 
+ 
+\input{sources/process.tex}
 % \input{sources/omitted.tex}
 % \input{sources/uncertain.tex}
 % \input{sources/association.tex}
@@ -111,3 +82,33 @@
 % \input{sources/and.tex}
 % \input{sources/or.tex}
 % \input{sources/not.tex}
+
+
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%                   Containers
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% 
+% %\section{Container nodes}\label{sec:CNs}
+%\section{Representing compartments}
+%
+%\input{sources/compartment.tex}
+% 
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%                   Submap
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% 
+% \section{Submaps}
+% \input{sources/submap.tex}
+
+% \section{Referring to other Nodes}
+% 
+% Reference nodes handle links or relationships between elements of a map and sub-map. At present there is only one reference glyph, \glyph{tag}, which can be used in a map refered to by a \glyph{submap} (\sect{submap}) or as an auxilary unit on the \glyph{submap}. The \glyph{clone marker} can also provide additional reference mechanisms and is discussed below (\sect{cloneMarker}).
+% 
+% \input{sources/tag.tex}
+% 
+% 
+% 

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 823
          http://sbgn.svn.sourceforge.net/sbgn/?rev=823&view=rev
Author:   lenov
Date:     2012-05-20 12:02:30 +0000 (Sun, 20 May 2012)
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Added: ProcessDiagram/trunk/UserManual/sources/association.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/association.tex	                        (rev 0)
+++ ProcessDiagram/trunk/UserManual/sources/association.tex	2012-05-20 12:02:30 UTC (rev 823)
@@ -0,0 +1,57 @@
+% $HeadURL: https://sbgn.svn.sourceforge.net/svnroot/sbgn/ProcessDiagram/tags/L1V1.3Full/sources/association.tex $
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%                     Association
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\subsection{Glyph: \glyph{Association}}\label{sec:association}
+
+The association between one or more \glyph{EPNs} represents the non-covalent binding of the biological objects represented by those \glyph{EPNs} into a larger complex.
+
+\begin{glyphDescription}
+ \glyphSboTerm SBO:0000177 ! non-covalent binding.
+ \glyphOrigin One or more \glyph{consumption} arcs (\sect{consumption}).
+ \glyphTarget  One \glyph{production} arc (\sect{production}).
+ \glyphNode An \glyph{association} between several entities is represented by a filled disc linked to two connectors, small arcs attached on point separated by 180 degrees. The consumption (\sect{consumption}) and production (\sect{production}) arcs are linked to the extremities of those connectors. 
+ \end{glyphDescription}
+
+\begin{figure}[H]
+  \centering
+  \includegraphics[scale = 0.5]{images/association}
+  \caption{The \PD glyph for \glyph{association}.}
+  \label{fig:association}
+\end{figure}
+
+The example in \fig{assoc-cyclin} illustrates the association of cyclin and CDC2 kinase into the Maturation Promoting Factor.
+
+\begin{figure}[H]
+  \centering
+  \includegraphics[scale = 0.3]{examples/association-MPF}
+  \caption{Association of cyclin and CDC2 kinase into the Maturation Promoting Factor.}
+  \label{fig:assoc-cyclin}
+\end{figure}
+
+\fig{assoc-unamed} gives an example illustrating the association of a pentameric macromolecule (a nicotinic acetylcholine receptor) with a simple chemical (the local anesthetic chlorpromazin) in an unnamed complex.
+
+\begin{figure}[H]
+  \centering
+  \includegraphics[scale = 0.3]{examples/association-unamed}
+  \caption{The association of a pentameric macromolecule with a simple chemical in an unnamed complex.}
+  \label{fig:assoc-unamed}
+\end{figure}
+
+An association does not necessarily result in the formation of a \glyph{complex}; it can also produce a \glyph{multimer}, or a \glyph{macromolecule} (although the latter case is semantically borderline).  \fig{assoc-multi} gives an example of this, using the formation of hemoglobin.
+
+\begin{figure}[H]
+  \centering
+  \includegraphics[scale = 0.3]{examples/association-multimerisation}
+  \caption{Formation of hemoglobin.}
+  \label{fig:assoc-multi}
+\end{figure}
+
+
+
+% The following is for [X]Emacs users.  Please leave in place.
+% Local Variables:
+% TeX-master: "../sbgn_PD-level1"
+% End:

Added: ProcessDiagram/trunk/UserManual/sources/dissociation.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/dissociation.tex	                        (rev 0)
+++ ProcessDiagram/trunk/UserManual/sources/dissociation.tex	2012-05-20 12:02:30 UTC (rev 823)
@@ -0,0 +1,31 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%                     Dissociation
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%\color{blue}
+\subsection{Glyph: \glyph{Dissociation}}\label{sec:dissociation}
+
+The dissociation of an \glyph{EPN} into one or more \glyph{EPNs} represents the rupture of a non-covalent binding between the biological entities represented by those \glyph{EPNs}.
+
+\begin{glyphDescription}
+ \glyphSboTerm SBO:0000180 ! dissociation.
+ \glyphOrigin One \glyph{consumption} arc (\sect{consumption}).
+ \glyphTarget  One or more \glyph{production} arc (\sect{production}).
+ \glyphNode A \glyph{dissociation} between several entities is represented by two concentric circles. A simple empty disc could be, in some cases, confused with the \glyph{catalysis} (section \sect{catalysis}). Moreover, the existence of two circles reminds the dissociation, by contrast with the filled disc of the \glyph{association} (\sect{association}).
+ \end{glyphDescription}
+
+
+\begin{figure}[H]
+  \centering
+  \includegraphics[scale = 0.5]{images/dissociation}
+  \caption{The \PD glyph for \glyph{dissociation}.}
+  \label{fig:dissociation}
+\end{figure}
+
+The example in \fig{dissoc-ribo} illustrates the dissociation of the small and large ribosomal subunits from a messenger RNA.
+
+\begin{figure}[H]
+  \centering
+  \includegraphics[scale = 0.3]{examples/dissociation-ribosome}
+  \caption{Dissociation of the small and large ribosomal subunits from a messenger RNA.}
+  \label{fig:dissoc-ribo}
+\end{figure}

Added: ProcessDiagram/trunk/UserManual/sources/omitted.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/omitted.tex	                        (rev 0)
+++ ProcessDiagram/trunk/UserManual/sources/omitted.tex	2012-05-20 12:02:30 UTC (rev 823)
@@ -0,0 +1,17 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%                     Omitted Process
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%\color{blue}
+\subsection{Glyph: \glyph{Omitted process}}\label{sec:omitted}
+
+Omitted processes are processes that are known to exist, but are omitted from the map for the sake of clarity or parsimony. A single \glyph{omitted process} can represent any number of actual processes. For instance, one may want to represent a long chain of processes leading from one biochemical compound to another, without detailing all steps, but highlighting the fact that this is not a direct transformation.  The \glyph{omitted process} is different from a \glyph{submap} (\sect{submap}). While a \glyph{submap} references to an explicit content, that is hidden in the main map, the \glyph{omitted process} does not ``hide'' anything within the context of the map, and cannot be ``unfolded''. An \glyph{omitted process} is represented by a \glyph{process} in which the square box contains a two parallel slanted lines oriented northwest-to-southeast and separated by an empty space.
+
+\begin{figure}[H]
+  \centering
+  \includegraphics[scale = 0.5]{images/omitted}
+  \caption{The \PD glyph for \glyph{omitted process}.}
+  \label{fig:omitted}
+\end{figure}
+
+
+

Added: ProcessDiagram/trunk/UserManual/sources/process.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/process.tex	                        (rev 0)
+++ ProcessDiagram/trunk/UserManual/sources/process.tex	2012-05-20 12:02:30 UTC (rev 823)
@@ -0,0 +1,16 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%                     Process
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\subsection{Glyph: \glyph{Process}}
+\label{sec:process}
+
+A process is the basic process node in SBGN.  It describes a process that transforms a given set of biochemical entities---macromolecules, simple chemicals or unspecified entities---into another set of biochemical entities.  Such a transformation might imply modification of covalent bonds (conversion), modification of the relative position of constituents (conformational process) or movement from one compartment to another (translocation). A process transforms a set of entity pools (represented by \glyph{EPNs} in \SBGNPDLone) into another set of entity pools. A \glyph{process} is represented by a square box linked to two connectors, small arcs attached to the centers of opposite sides. The consumption (\sect{consumption}) and production (\sect{production}) arcs are linked to the extremities of those connectors. The modulatory arcs (\sect{arcs}) point to the other two sides of the box. A \glyph{process} connected to \glyph{production} arcs on opposite sides is a reversible process. 
+
+\begin{figure}[H]
+  \centering
+  \includegraphics[scale = 0.4]{images/process}
+  \caption{The \PD glyph for \glyph{process}.}
+  \label{fig:process}
+\end{figure}
+

Added: ProcessDiagram/trunk/UserManual/sources/refcard.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/refcard.tex	                        (rev 0)
+++ ProcessDiagram/trunk/UserManual/sources/refcard.tex	2012-05-20 12:02:30 UTC (rev 823)
@@ -0,0 +1,4 @@
+\chapter{Reference card}
+Print the summary of SBGN symbols on the next page for a quick reference.
+
+\noindent\rotatebox{-90}{\scalebox{0.8}{\includegraphics{images/refcard}}}

Added: ProcessDiagram/trunk/UserManual/sources/uncertain.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/uncertain.tex	                        (rev 0)
+++ ProcessDiagram/trunk/UserManual/sources/uncertain.tex	2012-05-20 12:02:30 UTC (rev 823)
@@ -0,0 +1,15 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%                     Uncertain Process
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%\color{blue}
+\subsection{Glyph: \glyph{Uncertain process}}\label{sec:uncertain}
+
+Uncertain processes are processes that may not exist. A single \glyph{uncertain process} can represent any number of actual processes. \glyph{Uncertain process} would be used to represent hypothesis, reactions which existence is supported by weak evidence etc. An \glyph{uncertain process} is represented by a \glyph{process} which square box contains a question mark.
+
+\begin{figure}[H]
+  \centering
+  \includegraphics[scale = 0.5]{images/uncertain}
+  \caption{The \PD glyph for an \glyph{uncertain process}.}
+  \label{fig:uncertain}
+\end{figure}
+

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 824
          http://sbgn.svn.sourceforge.net/sbgn/?rev=824&view=rev
Author:   lenov
Date:     2012-05-21 10:39:18 +0000 (Mon, 21 May 2012)
Log Message:
-----------


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This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 825
          http://sbgn.svn.sourceforge.net/sbgn/?rev=825&view=rev
Author:   lenov
Date:     2012-05-23 13:37:17 +0000 (Wed, 23 May 2012)
Log Message:
-----------


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+++ ProcessDiagram/trunk/UserManual/images/compartment.svg	2012-05-23 13:37:17 UTC (rev 825)
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Modified: ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log
===================================================================
--- ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log	2012-05-21 10:39:18 UTC (rev 824)
+++ ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log	2012-05-23 13:37:17 UTC (rev 825)
@@ -1,4 +1,4 @@
-This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) (format=pdflatex 2012.5.4)  21 MAY 2012 11:13
+This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) (format=pdflatex 2012.5.4)  23 MAY 2012 14:35
 entering extended mode
  %&-line parsing enabled.
 **sbgn_PD-level1-user.tex
@@ -1261,29 +1261,31 @@
 <images/not.pdf, id=252, 158.5925pt x 69.25874pt>
 File: images/not.pdf Graphic file (type pdf)
  <use images/not.pdf> [16 <./images/necessary_stim.pdf> <./images/logicArc.pdf>
- <./images/equivalence.pdf> <./images/and.pdf> <./images/or.pdf>])) [17 <./imag
-es/not.pdf>]
+ <./images/equivalence.pdf> <./images/and.pdf> <./images/or.pdf>]) (./sources/c
+ompartment.tex
+<images/compartment.pdf, id=286, 451.6875pt x 319.1925pt>
+File: images/compartment.pdf Graphic file (type pdf)
+
+<use images/compartment.pdf>)) [17 <./images/not.pdf> <./images/compartment.pdf
+>]
 \openout2 = `sources/refcard.aux'.
 
-
-(./sources/refcard.tex
-Appendix A.
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+ (./sources/refcard.tex
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+Overfull \hbox (7.15172pt too wide) in paragraph at lines 1--27
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+ <./images/refcard.pdf>] (./sbgn_PD-level1-user.bbl) [19
 
-] [19 <./images/refcard.pdf>] (./sbgn_PD-level1-user.bbl) [20
 
 
 
-
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Modified: ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.pdf
===================================================================
(Binary files differ)

Modified: ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.tex	2012-05-21 10:39:18 UTC (rev 824)
+++ ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.tex	2012-05-23 13:37:17 UTC (rev 825)
@@ -24,8 +24,6 @@
 %\include{sources/build}
 %\include{sources/interpret}
 
-\appendix
-
 \include{sources/refcard}
 
 \backmatter

Added: ProcessDiagram/trunk/UserManual/sources/compartment.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/compartment.tex	                        (rev 0)
+++ ProcessDiagram/trunk/UserManual/sources/compartment.tex	2012-05-23 13:37:17 UTC (rev 825)
@@ -0,0 +1,16 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%                   Compartment
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\subsection{Glyph: \glyph{Compartment}}\label{sec:compartment}
+
+A compartment is a logical or physical structure that contains entity pool nodes. An \glyph{EPN} can only belong to one compartment. Therefore, the ``same'' biochemical species located in two different compartments are in fact two different ``pools'' and should be represented by two \glyph{EPNs}.  A compartment is represented by a surface enclosed in a continuous border or located between continuous borders. These borders should be noticeably thicker than the borders of the \glyph{EPNs}. A compartment can take \textbf{any} geometry. A compartment must always be entirely enclosed.
+
+\begin{figure}[H]
+  \centering
+  \includegraphics[scale = 0.3]{images/compartment}
+  \caption{The \PD glyph for \glyph{compartment}.}
+  \label{fig:compartment}
+\end{figure}
+
+To allow more aesthetically pleasing and understandable maps, compartments are allowed to overlap each other visually, but it must be kept in mind that this does not mean the top compartment contains part of the bottom compartment. 
\ No newline at end of file

Modified: ProcessDiagram/trunk/UserManual/sources/refcard.aux
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/refcard.aux	2012-05-21 10:39:18 UTC (rev 824)
+++ ProcessDiagram/trunk/UserManual/sources/refcard.aux	2012-05-23 13:37:17 UTC (rev 825)
@@ -1,9 +1,6 @@
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-\@writefile{toc}{\contentsline {chapter}{\numberline {A}Reference card}{18}}
-\@writefile{lof}{\addvspace {10\p@ }}
-\@writefile{lot}{\addvspace {10\p@ }}
 \@setckpt{sources/refcard}{
-\setcounter{page}{20}
+\setcounter{page}{19}
 \setcounter{equation}{0}
 \setcounter{enumi}{0}
 \setcounter{enumii}{0}
@@ -12,14 +9,14 @@
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+\setcounter{figure}{31}
+\setcounter{table}{5}
 \setcounter{float@...}
 \setcounter{r@...}
 }

Modified: ProcessDiagram/trunk/UserManual/sources/refcard.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/refcard.tex	2012-05-21 10:39:18 UTC (rev 824)
+++ ProcessDiagram/trunk/UserManual/sources/refcard.tex	2012-05-23 13:37:17 UTC (rev 825)
@@ -1,4 +1 @@
-\chapter{Reference card}
-Print the summary of SBGN symbols on the next page for a quick reference.
-
 \noindent\rotatebox{-90}{\scalebox{0.8}{\includegraphics{images/refcard}}}

Added: ProcessDiagram/trunk/UserManual/sources/submap.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/submap.tex	                        (rev 0)
+++ ProcessDiagram/trunk/UserManual/sources/submap.tex	2012-05-23 13:37:17 UTC (rev 825)
@@ -0,0 +1,55 @@
+% $HeadURL: https://sbgn.svn.sourceforge.net/svnroot/sbgn/ProcessDiagram/tags/L1V1.3Full/sources/submap.tex $
+
+\subsection{Glyph: \glyph{Submap}}
+\label{sec:submap}
+
+A \glyph{submap} is used to encapsulate processes (including all types of nodes and edges) within one glyph.  The \glyph{submap} hides its content to the users, and display only input terminals (or ports), linked to \glyph{EPNs} (\sect{EPNs}). A \glyph{submap} is not equivalent to an \glyph{omitted process} (see \sect{omitted}).  In the case of an SBGN description that is made available through a software tool, the content of a \glyph{submap} may be available to the tool.  A user could then ask the tool to expand the \glyph{submap}, for instance by clicking on the icon representing the \glyph{submap}.  The tool might then expand and show the \glyph{submap} within the same map (on the same canvas), or it might open it in a different canvas. In the case of an SBGN description made available in a book or a website, the content of the \glyph{submap} may be available on another page, possibly accessible via an hyperlink on the \glyph{submap}.
+
+\begin{glyphDescription}
+
+\glyphSboTerm SBO:0000395 ! encapsulating process
+
+\glyphContainer The \glyph{submap} is represented as a square box to remind the viewer that it is fundamentally a process.
+
+\glyphLabel The identification of the \glyph{submap} is carried by an unbordered box containing a string of characters.  The characters may be distributed on several lines to improve readability, although this is not mandatory.  The label box has to be attached to the center of the container box.
+
+\glyphAux A \glyph{submap} carries labeled terminals.  When the \glyph{submap} is represented folded, those terminals are linked to external \glyph{EPNs} (\sect{EPNs}).  In the unfolded view, exposing the internal structure of the \glyph{submap}, a set of \glyph{tags} point to the corresponding internal \glyph{EPNs} \sect{EPNs}.
+
+\end{glyphDescription}
+
+
+\begin{figure}[H]
+  \centering
+  \includegraphics[scale = 0.22]{images/submap}
+  \caption{The \PD glyph for \glyph{submap}. (Upper part) folded submap. (Lower part) content of the submap.}
+  \label{fig:submap}
+\end{figure}
+
+\fig{submap-folded} represents a \glyph{submap} that transforms glucose into fructose-6-phosphate. The \glyph{submap} carries five terminals, four linked to EPNs and one linked to a \glyph{compartment}.  The latter is particularly important in the case of EPNs present only in a \glyph{compartment} enclosed in a \glyph{submap}, and that are not linked to terminals themselves.  Note that the terminals do not define a ``direction'', such as input or output.  The flux of the reactions is determined by the context.
+
+\begin{figure}[H]
+  \centering
+  \includegraphics[scale = 0.4]{examples/submap-folded}
+  \caption{Example of a submap with contents elided.}
+  \label{fig:submap-folded}
+\end{figure}
+
+The map in \fig{submap-unfolded} represents an unfolded version of a \glyph{submap}.  Here, anything outside the \glyph{submap} has disappeared, and the internal \glyph{tags} are not linked to the corresponding external \glyph{terminals}.  Note the tag 5, linking the compartment ``mito'' of the \glyph{submap} to the compartment ``mito'' outside the \glyph{submap}.  The compartment containing Glu6P is implicitly defined as the same as the compartment containing Glu and Fru6P.  There is no ambiguity because if Glu and Fru6P were in different compartments, one of them should have been defined within the \glyph{submap}.
+
+\begin{figure}[H]
+  \centering
+  \includegraphics[scale = 0.35]{examples/submap-dissociated}
+  \caption{Example of an unfolded submap. The unfolded submap corresponds to the folded submap of \fig{submap-folded}.}
+  \label{fig:submap-unfolded}
+\end{figure}
+
+
+
+
+
+
+% The following is for [X]Emacs users.  Please leave in place.
+% Local Variables:
+% TeX-master: "../sbgn_PD-level1"
+% End:
+

Modified: ProcessDiagram/trunk/UserManual/sources/symbols.aux
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/symbols.aux	2012-05-21 10:39:18 UTC (rev 824)
+++ ProcessDiagram/trunk/UserManual/sources/symbols.aux	2012-05-23 13:37:17 UTC (rev 825)
@@ -153,6 +153,11 @@
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 \@writefile{lof}{\contentsline {figure}{\numberline {2.30}{\ignorespaces The Process Description\xspace  glyph for \emph  {not}.}}{17}}
 \newlabel{fig:not}{{2.30}{17}}
+\@writefile{toc}{\contentsline {section}{\numberline {2.6}Representing compartments}{17}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.6.1}Glyph: \emph  {Compartment}}{17}}
+\newlabel{sec:compartment}{{2.6.1}{17}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.31}{\ignorespaces The Process Description\xspace  glyph for \emph  {compartment}.}}{17}}
+\newlabel{fig:compartment}{{2.31}{17}}
 \@setckpt{sources/symbols}{
 \setcounter{page}{18}
 \setcounter{equation}{0}
@@ -164,12 +169,12 @@
 \setcounter{mpfootnote}{0}
 \setcounter{part}{0}
 \setcounter{chapter}{2}
-\setcounter{section}{5}
-\setcounter{subsection}{3}
+\setcounter{section}{6}
+\setcounter{subsection}{1}
 \setcounter{subsubsection}{0}
 \setcounter{paragraph}{0}
 \setcounter{subparagraph}{0}
-\setcounter{figure}{30}
+\setcounter{figure}{31}
 \setcounter{table}{5}
 \setcounter{float@...}
 \setcounter{r@...}

Modified: ProcessDiagram/trunk/UserManual/sources/symbols.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/symbols.tex	2012-05-21 10:39:18 UTC (rev 824)
+++ ProcessDiagram/trunk/UserManual/sources/symbols.tex	2012-05-23 13:37:17 UTC (rev 825)
@@ -82,20 +82,19 @@
 \input{sources/or.tex}
 \input{sources/not.tex}
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%                   Compartments
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% %\section{Container nodes}\label{sec:CNs}
+\section{Representing compartments}
 
+\input{sources/compartment.tex}
+ 
 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%                   Containers
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% 
-% %\section{Container nodes}\label{sec:CNs}
-%\section{Representing compartments}
-%
-%\input{sources/compartment.tex}
-% 
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % %%%%                   Submap
 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Modified: ProcessDiagram/trunk/UserManual/sources/symbols.tex.backup
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/symbols.tex.backup	2012-05-21 10:39:18 UTC (rev 824)
+++ ProcessDiagram/trunk/UserManual/sources/symbols.tex.backup	2012-05-23 13:37:17 UTC (rev 825)
@@ -58,33 +58,31 @@
  
 \section{Arcs}\label{sec:arcs}
  
-Arcs are lines that link nodes of SBGN together. The symbols attached to their extremities indicate their meaning. \SBGNPDLone defines nine arcs. \glyph{consumption} (\sect{consumption}), \glyph{production} (\sect{production}), \glyph{modulation} (\sect{modulation}), \glyph{stimulation} (\sect{stimulation}), \glyph{catalysis} (\sect{catalysis}), \glyph{inhibition} (\sect{inhibition}), and \glyph{necessary stimulation} (\sect{necessary_stim}) connect \glyph{EPNs} to \glyph{PDs}. 
+Arcs are lines that link nodes of SBGN together. The symbols attached to their extremities indicate their meaning. \SBGNPDLone defines nine arcs. \glyph{consumption} (\sect{consumption}), \glyph{production} (\sect{production}), \glyph{modulation} (\sect{modulation}), \glyph{stimulation} (\sect{stimulation}), \glyph{catalysis} (\sect{catalysis}), \glyph{inhibition} (\sect{inhibition}), and \glyph{necessary stimulation} (\sect{necessary_stim}) connect \glyph{EPNs} to \glyph{PDs}. \glyph{LogicArc} (\sect{logicArc}) link \glyph{EPNs} and \glyph{logic arcs}.  \glyph{equivalenceArc} (\sect{equivalenceArc}) link nodes to \glyph{tag}. Arcs can take any shape, and are not restricted to segments of straight lines. 
+
+\input{sources/consumption.tex}
+\input{sources/production.tex}
+\input{sources/modulation.tex}
+\input{sources/stimulation.tex}
+\input{sources/catalysis.tex}
+\input{sources/inhibition.tex}
+\input{sources/necessary_stim.tex}
+\input{sources/logicArc.tex}
+\input{sources/equivalenceArc.tex}
  
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%                   Logical operators
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+ 
+\section{Logical operators}\label{sec:logic}
+ 
+\input{sources/and.tex}
+\input{sources/or.tex}
+\input{sources/not.tex}
 
-% \input{sources/consumption.tex}
-% \input{sources/production.tex}
-% \input{sources/modulation.tex}
-% \input{sources/stimulation.tex}
-% \input{sources/catalysis.tex}
-% \input{sources/inhibition.tex}
-% \input{sources/necessary_stim.tex}
-% \input{sources/logicArc.tex}
-% \input{sources/equivalenceArc.tex}
-% 
-% 
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%                   Logical operators
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% 
-% \section{Logical operators}\label{sec:logic}
-% 
-% \input{sources/and.tex}
-% \input{sources/or.tex}
-% \input{sources/not.tex}
 
-
 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % %%%%                   Containers

Modified: ProcessDiagram/trunk/UserManual/sources/symbols.tex~
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/symbols.tex~	2012-05-21 10:39:18 UTC (rev 824)
+++ ProcessDiagram/trunk/UserManual/sources/symbols.tex~	2012-05-23 13:37:17 UTC (rev 825)
@@ -69,34 +69,32 @@
 \input{sources/necessary_stim.tex}
 \input{sources/logicArc.tex}
 \input{sources/equivalenceArc.tex}
+ 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%                   Logical operators
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+ 
+\section{Logical operators}\label{sec:logic}
+ 
+\input{sources/and.tex}
+\input{sources/or.tex}
+\input{sources/not.tex}
 
-% 
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%                   Logical operators
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% 
-% \section{Logical operators}\label{sec:logic}
-% 
-% \input{sources/and.tex}
-% \input{sources/or.tex}
-% \input{sources/not.tex}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%                   Compartments
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% %\section{Container nodes}\label{sec:CNs}
+\section{Representing compartments}
 
-
+\input{sources/compartment.tex}
+ 
 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%                   Containers
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% 
-% %\section{Container nodes}\label{sec:CNs}
-%\section{Representing compartments}
-%
-%\input{sources/compartment.tex}
-% 
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % %%%%                   Submap
 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

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