Menu
▾
▴
[sbgn-svn-commit] SF.net SVN: sbgn:[803] ProcessDiagram/trunk
|
From: <stu...@us...> - 2011-09-03 10:40:06
|
Revision: 803
http://sbgn.svn.sourceforge.net/sbgn/?rev=803&view=rev
Author: stumoodie
Date: 2011-09-03 10:39:59 +0000 (Sat, 03 Sep 2011)
Log Message:
-----------
Fixed heading levels so correct and also ajusted formating so subparagraph easier to distinguish
Modified Paths:
--------------
ProcessDiagram/trunk/sbgn_PD-level1.pdf
ProcessDiagram/trunk/sources/catalysis.tex
ProcessDiagram/trunk/sources/consumption.tex
ProcessDiagram/trunk/sources/equivalenceArc.tex
ProcessDiagram/trunk/sources/glyphs.tex
ProcessDiagram/trunk/sources/inhibition.tex
ProcessDiagram/trunk/sources/latex-style.tex
ProcessDiagram/trunk/sources/logicArc.tex
ProcessDiagram/trunk/sources/modulation.tex
ProcessDiagram/trunk/sources/necessary_stim.tex
ProcessDiagram/trunk/sources/production.tex
ProcessDiagram/trunk/sources/simpleChemical.tex
ProcessDiagram/trunk/sources/stimulation.tex
Modified: ProcessDiagram/trunk/sbgn_PD-level1.pdf
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/sources/catalysis.tex
===================================================================
--- ProcessDiagram/trunk/sources/catalysis.tex 2011-09-01 18:11:54 UTC (rev 802)
+++ ProcessDiagram/trunk/sources/catalysis.tex 2011-09-03 10:39:59 UTC (rev 803)
@@ -2,7 +2,7 @@
%% Catalysis
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%\color{blue}
-\subsection{Glyph: \glyph{Catalysis}}\label{sec:catalysis}
+\paragraph{Glyph: \glyph{Catalysis}}\label{sec:catalysis}
A catalysis is a particular case of stimulation, where the effector affects
positively the flux of a process represented by the target process. The positive effect on the process is due to the lowering of the activation energy of a reaction.
Modified: ProcessDiagram/trunk/sources/consumption.tex
===================================================================
--- ProcessDiagram/trunk/sources/consumption.tex 2011-09-01 18:11:54 UTC (rev 802)
+++ ProcessDiagram/trunk/sources/consumption.tex 2011-09-03 10:39:59 UTC (rev 803)
@@ -4,7 +4,7 @@
%% Consumption
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\subsection{Glyph: \glyph{Consumption}}
+\paragraph{Glyph: \glyph{Consumption}}
\label{sec:consumption}
\glyph{Consumption} is the arc used to represent the fact that an entity pool is consumed by a process,
Modified: ProcessDiagram/trunk/sources/equivalenceArc.tex
===================================================================
--- ProcessDiagram/trunk/sources/equivalenceArc.tex 2011-09-01 18:11:54 UTC (rev 802)
+++ ProcessDiagram/trunk/sources/equivalenceArc.tex 2011-09-03 10:39:59 UTC (rev 803)
@@ -2,7 +2,7 @@
%% Equivalence Arc
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%\color{blue}
-\subsection{Glyph: \glyph{Equivalence arc} }\label{sec:equivalenceArc}
+\paragraph{Glyph: \glyph{Equivalence arc} }\label{sec:equivalenceArc}
\glyph{Equivalence arc} is the arc used to represent the fact that all entities
marked by a \glyph{tag} are equivalent.
Modified: ProcessDiagram/trunk/sources/glyphs.tex
===================================================================
--- ProcessDiagram/trunk/sources/glyphs.tex 2011-09-01 18:11:54 UTC (rev 802)
+++ ProcessDiagram/trunk/sources/glyphs.tex 2011-09-03 10:39:59 UTC (rev 803)
@@ -302,7 +302,7 @@
\input{sources/cloneMarker.tex}
-\section{Controlled vocabularies used in \SBGNPDLone}\label{sec:CVs}
+\section{Controlled vocabularies}\label{sec:CVs}
\input{sources/CVs.tex}
Modified: ProcessDiagram/trunk/sources/inhibition.tex
===================================================================
--- ProcessDiagram/trunk/sources/inhibition.tex 2011-09-01 18:11:54 UTC (rev 802)
+++ ProcessDiagram/trunk/sources/inhibition.tex 2011-09-03 10:39:59 UTC (rev 803)
@@ -2,7 +2,7 @@
%% Inhibition
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\subsection{Glyph: \glyph{Inhibition}}\label{sec:inhibition}
+\paragraph{Glyph: \glyph{Inhibition}}\label{sec:inhibition}
%\color{blue}
An inhibition \textbf{negatively} affects the flux of a process represented by the target process. This inhibition can be for instance a competitive inhibition or an allosteric inhibition.
Modified: ProcessDiagram/trunk/sources/latex-style.tex
===================================================================
--- ProcessDiagram/trunk/sources/latex-style.tex 2011-09-01 18:11:54 UTC (rev 802)
+++ ProcessDiagram/trunk/sources/latex-style.tex 2011-09-03 10:39:59 UTC (rev 803)
@@ -202,9 +202,14 @@
{0.8ex}{\slshape\normalsize\bfseries\sffamily}}
\renewcommand{\paragraph}{\@startsection%
- {paragraph}{4}{0pt}{-1.25ex \@plus -1ex \@minus -.2ex}%
- {0.5ex}{\slshape\normalsize\sffamily}}
+ {paragraph}{4}{0pt}{-1.5ex \@plus -1ex \@minus -.2ex}%
+ {0.5ex}{\slshape\normalsize\bfseries\sffamily}}
+\renewcommand{\subparagraph}{\@startsection%
+ {subparagraph}{5}{-0.75cm}{-1.5ex \@plus -1ex \@minus -.2ex}%
+ {0.5ex}{\slshape\normalsize\bfseries\sffamily}}
+
+
% Below, we take out the heading embedded by the \tableofcontents
% command so that we can control where it's put.
Modified: ProcessDiagram/trunk/sources/logicArc.tex
===================================================================
--- ProcessDiagram/trunk/sources/logicArc.tex 2011-09-01 18:11:54 UTC (rev 802)
+++ ProcessDiagram/trunk/sources/logicArc.tex 2011-09-03 10:39:59 UTC (rev 803)
@@ -2,7 +2,7 @@
%% Logic arc
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%\color{blue}
-\subsection{Glyph: \glyph{Logic arc} }\label{sec:logicArc}
+\paragraph{Glyph: \glyph{Logic arc} }\label{sec:logicArc}
\glyph{Logic arc} is used to represent the fact that an entity influences
the outcome of a logic operator.
Modified: ProcessDiagram/trunk/sources/modulation.tex
===================================================================
--- ProcessDiagram/trunk/sources/modulation.tex 2011-09-01 18:11:54 UTC (rev 802)
+++ ProcessDiagram/trunk/sources/modulation.tex 2011-09-03 10:39:59 UTC (rev 803)
@@ -2,7 +2,7 @@
%% Modulation
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%\color{blue}
-\subsection{Glyph: \glyph{Modulation}}\label{sec:modulation}
+\paragraph{Glyph: \glyph{Modulation}}\label{sec:modulation}
A modulation affects the flux of a process
represented by the target process. Such a modulation can affect the
Modified: ProcessDiagram/trunk/sources/necessary_stim.tex
===================================================================
--- ProcessDiagram/trunk/sources/necessary_stim.tex 2011-09-01 18:11:54 UTC (rev 802)
+++ ProcessDiagram/trunk/sources/necessary_stim.tex 2011-09-03 10:39:59 UTC (rev 803)
@@ -4,7 +4,7 @@
%% Necessary_Stim
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\subsection{Glyph: \glyph{Necessary stimulation}}\label{sec:necessary_stim}
+\paragraph{Glyph: \glyph{Necessary stimulation}}\label{sec:necessary_stim}
A necessary stimulation, is one that is necessary for a process to take place. A process modulated by a necessary stimulation can only occur when this necessary stimulation is active.
Modified: ProcessDiagram/trunk/sources/production.tex
===================================================================
--- ProcessDiagram/trunk/sources/production.tex 2011-09-01 18:11:54 UTC (rev 802)
+++ ProcessDiagram/trunk/sources/production.tex 2011-09-03 10:39:59 UTC (rev 803)
@@ -4,7 +4,7 @@
%% Production
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\subsection{Glyph: \glyph{Production}}\label{sec:production}
+\paragraph{Glyph: \glyph{Production}}\label{sec:production}
\glyph{Production} is the arc used to represent the fact that an entity pool is
produced by a process. In the case of a reversible process, the
Modified: ProcessDiagram/trunk/sources/simpleChemical.tex
===================================================================
--- ProcessDiagram/trunk/sources/simpleChemical.tex 2011-09-01 18:11:54 UTC (rev 802)
+++ ProcessDiagram/trunk/sources/simpleChemical.tex 2011-09-03 10:39:59 UTC (rev 803)
@@ -53,7 +53,7 @@
\label{fig:simpleChemical}
\end{figure}
-\subparagraph{Glyph: \glyph{Simple chemical monomer}}
+\subparagraph{Glyph: \glyph{Simple chemical multimer}}
This glyph is used to represent a simple chemical with a cardinality
of one.
Modified: ProcessDiagram/trunk/sources/stimulation.tex
===================================================================
--- ProcessDiagram/trunk/sources/stimulation.tex 2011-09-01 18:11:54 UTC (rev 802)
+++ ProcessDiagram/trunk/sources/stimulation.tex 2011-09-03 10:39:59 UTC (rev 803)
@@ -2,7 +2,7 @@
%% Stimulation
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\subsection{Glyph: \glyph{Stimulation}}\label{sec:stimulation}
+\paragraph{Glyph: \glyph{Stimulation}}\label{sec:stimulation}
%\color{blue}
A stimulation affects \textbf{positively} the flux of a process represented by the target process. This stimulation can be for instance a catalysis or a positive allosteric regulation. Note that \glyph{catalysis} exists independently in SBGN, see \sect{catalysis}.
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
