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From: <stu...@us...> - 2013-03-16 16:01:05
|
Revision: 858
http://sbgn.svn.sourceforge.net/sbgn/?rev=858&view=rev
Author: stumoodie
Date: 2013-03-16 16:00:58 +0000 (Sat, 16 Mar 2013)
Log Message:
-----------
Renamed to be consistent with naming conventions of other tags
Added Paths:
-----------
ProcessDiagram/tags/L1V1.3Manual/
Removed Paths:
-------------
ProcessDiagram/tags/Level1V1.3Manual/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <stu...@us...> - 2013-03-16 15:56:19
|
Revision: 857
http://sbgn.svn.sourceforge.net/sbgn/?rev=857&view=rev
Author: stumoodie
Date: 2013-03-16 15:56:10 +0000 (Sat, 16 Mar 2013)
Log Message:
-----------
The V1.3 manual
Added Paths:
-----------
ProcessDiagram/tags/Level1V1.3Manual/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <stu...@us...> - 2013-03-16 11:10:52
|
Revision: 856
http://sbgn.svn.sourceforge.net/sbgn/?rev=856&view=rev
Author: stumoodie
Date: 2013-03-16 11:10:41 +0000 (Sat, 16 Mar 2013)
Log Message:
-----------
Removed tmp files and sbgn logo file.
Added Paths:
-----------
ProcessDiagram/trunk/UserManual/images/sbgn-logo-rgb.jpg
Removed Paths:
-------------
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.aux
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.blg
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.out
ProcessDiagram/trunk/UserManual/sources/build.aux
ProcessDiagram/trunk/UserManual/sources/interpret.aux
ProcessDiagram/trunk/UserManual/sources/introduction.aux
ProcessDiagram/trunk/UserManual/sources/refcard.aux
ProcessDiagram/trunk/UserManual/sources/symbols.aux
Added: ProcessDiagram/trunk/UserManual/images/sbgn-logo-rgb.jpg
===================================================================
(Binary files differ)
Property changes on: ProcessDiagram/trunk/UserManual/images/sbgn-logo-rgb.jpg
___________________________________________________________________
Added: svn:mime-type
+ image/jpeg
Deleted: ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.aux
===================================================================
--- ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.aux 2012-11-29 23:36:40 UTC (rev 855)
+++ ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.aux 2013-03-16 11:10:41 UTC (rev 856)
@@ -1,16 +0,0 @@
-\relax
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Deleted: ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.blg
===================================================================
--- ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.blg 2012-11-29 23:36:40 UTC (rev 855)
+++ ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.blg 2013-03-16 11:10:41 UTC (rev 856)
@@ -1,7 +0,0 @@
-This is BibTeX, Version 0.99dThe top-level auxiliary file: sbgn_PD-level1-user.aux
-A level-1 auxiliary file: sources/introduction.aux
-A level-1 auxiliary file: sources/symbols.aux
-A level-1 auxiliary file: sources/build.aux
-A level-1 auxiliary file: sources/refcard.aux
-The style file: unsrt.bst
-Database file #1: sbgn_PD-level1-user.bib
Deleted: ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log
===================================================================
--- ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log 2012-11-29 23:36:40 UTC (rev 855)
+++ ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log 2013-03-16 11:10:41 UTC (rev 856)
@@ -1,1313 +0,0 @@
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===================================================================
--- ProcessDiagram/trunk/UserManual/sources/build.aux 2012-11-29 2...
[truncated message content] |
|
From: <le...@us...> - 2012-11-29 23:36:47
|
Revision: 855
http://sbgn.svn.sourceforge.net/sbgn/?rev=855&view=rev
Author: lenov
Date: 2012-11-29 23:36:40 +0000 (Thu, 29 Nov 2012)
Log Message:
-----------
Modified Paths:
--------------
EntityRelationship/trunk/sbgn_ER-level1.pdf
EntityRelationship/trunk/sources/er-overview.tex
EntityRelationship/trunk/sources/front-page.tex
EntityRelationship/trunk/sources/glyphs.tex
EntityRelationship/trunk/sources/introduction.tex
Added Paths:
-----------
EntityRelationship/trunk/examples/HelloWorld.pdf
EntityRelationship/trunk/sources/community.tex
EntityRelationship/trunk/sources/typography.tex
EntityRelationship/trunk/sources/versioning.tex
Added: EntityRelationship/trunk/examples/HelloWorld.pdf
===================================================================
(Binary files differ)
Property changes on: EntityRelationship/trunk/examples/HelloWorld.pdf
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Modified: EntityRelationship/trunk/sbgn_ER-level1.pdf
===================================================================
(Binary files differ)
Added: EntityRelationship/trunk/sources/community.tex
===================================================================
--- EntityRelationship/trunk/sources/community.tex (rev 0)
+++ EntityRelationship/trunk/sources/community.tex 2012-11-29 23:36:40 UTC (rev 855)
@@ -0,0 +1,12 @@
+% =============================================================================
+% community
+% =============================================================================
+
+\section{Developments, discussions, and notifications of updates}
+\label{sec:discussions}
+
+The SBGN website (\url{http://sbgn.org/}) is a portal for all things related to SBGN. It provides a web forum interface to the SBGN discussion list (\mailto{sbg...@ca...}) and information about how anyone may subscribe to it. The easiest and best way to get involved in SBGN discussions is to join the mailing list and participate.
+
+Face-to-face meetings of the SBGN community are announced on the website as well as the mailing list. Although no set schedule currently exists for workshops and other meetings, we envision holding at least one public workshop per year. As with other similar efforts, the workshops are likely to be held as satellite workshops of larger conferences, enabling attendees to use their international travel time and money more efficiently.
+
+Notifications of updates to the SBGN specification are also broadcast on the mailing list and announced on the SBGN website.
Modified: EntityRelationship/trunk/sources/er-overview.tex
===================================================================
--- EntityRelationship/trunk/sources/er-overview.tex 2012-11-29 12:34:32 UTC (rev 854)
+++ EntityRelationship/trunk/sources/er-overview.tex 2012-11-29 23:36:40 UTC (rev 855)
@@ -2,20 +2,41 @@
% overview
% =============================================================================
-\section{Overview}\label{sec:overview}
+\section{Overview of the Entity Relationship language}\label{sec:overview}
-To set the stage for what follows in this chapter, we first give a brief overview of some of the concepts in the \ER notation with the help of an example shown in \fig{eg1}. This example will be re-used throughout the description of the graphical symbols (glyphs) used by \SBGNERLone (with a few additions when the concepts are missing in the example)
+To set the stage for what follows in this chapter, we first give a brief overview of some of the concepts in the \ER notation with the help of an example shown in \fig{eg1}.
\begin{figure}[H]
\centering
\vspace*{-0.75em}
+ \includegraphics[scale=0.45]{examples/HelloWorld}
+ \caption{This example of an \ERm represent an entity 1 interacting with another entity 2. The assignment of value 1 to the state variable of the entity 1 stimulates the interaction.}
+ \label{fig:eg1}
+\end{figure}
+
+The essence of the \ERs is to depict the influences of entities upon the behaviour of others. The entities are things that exist, either on their own, or when statements become true. For instance, an entity can exist (such as ``entity 1'' in \fig{eg1}), different entities can interact (such as ``entity 1'' and ``entity 2'' in \fig{eg1}), or a value can be assigned to an entity's property (such as ``value 1'' to property ``var'' of ``entity 1'' in \fig{eg1}). The influences can therefore be understood as logical consequences of this existence. The stimulation of the interaction between ``entity 1'' and ``entity 2'' in \fig{eg1} takes place if `value 1'' is really assigned to property ``var'' of ``entity 1''. The existence of the assignment is represented by the black dot (called \glyph{outcome}). On the contrary to the \PDl, where the different processes affect each other in a way that the behaviour of the depicted system can only be understood taking into account the whole system, the relationships are essentially independent. On can imagine that each of the relationships represents a specific conclusion of a scientific experience reported in an article. Their addition on a map represents the knowledge we have of the effects of the entities represented upon each other. In \fig{eg1}, we have three statements:
+
+\begin{itemize}
+ \item ``entity 1'' can interact with ``entity 2''.
+ \item property ``var'' of ``entity 1'' can take the value ``value 1''.
+ \item if ``var'' is set to ``value 1'', the interaction between ``entity 1'' and ``entity 2'' is stimulated.
+\end{itemize}
+
+
+The independence of relationships in \ERs is the key to avoid the combinatorial explosions inherent to \PDs.
+
+A more complex and realistic example of \ERm is shown in \fig{eg2}. This example will be re-used throughout the description of the graphical symbols (glyphs) used by \SBGNERLone (with a few additions when the concepts are missing in the example)
+
+\begin{figure}[H]
+ \centering
+ \vspace*{-0.75em}
\includegraphics[scale=0.45]{examples/CaMKII-intro}
\caption{This example of an \ERm depicts the effect of a depolarisation (dV) on the intracellular calcium, that binds to calmodulin, that itself binds to the calcium/calmoduline kinase II (CaMKII). The binding of calmodulin inhibits the folding of CaMKII monomer on itself, thus relieving the inhibition on the kinase activity. The phosphorylation of the glutamate receptors finally leads to the Long Term Potentiation (LTP) of the synapses. In addition, the map shows the effect of trans-phosphorylation on threonine 286, that makes the enzyme constitutively active, and on threonine 306, that renders the kinase insensitive to calmodulin, as well as the dimerisation of the kinase.}
- \label{fig:eg1}
+ \label{fig:eg2}
\end{figure}
-The essence of the \ERs is to depict the influences of entities upon the behaviour of others. The entities are things that exist, either on their own or when statements become true. For instance, an entity can exist, different entities can interact, or a value can be assigned to an entity's property. The influences can therefore be understood as logical consequences of this existence. Contrary to the \PDl, where the different processes affect each other in a way that the behaviour of the depicted system can only be understood taking into account the whole system, the relationships are essentially independent. On can imagine that each of the relationships represents a specific conclusion of a scientific experience reported in an article. Their addition on a map represents the knowledge we have of the effects of the entities represented upon each other. The independence of relationships in \ERs is the key to avoid the combinatorial explosions inherent to \PDs.
+
\tab{component-summary} summarizes the different SBGN abstractions described in this chapter.
\newcolumntype{P}[1]{>{\raggedright\hspace{0pt}\arraybackslash}p{#1}}
Modified: EntityRelationship/trunk/sources/front-page.tex
===================================================================
--- EntityRelationship/trunk/sources/front-page.tex 2012-11-29 12:34:32 UTC (rev 854)
+++ EntityRelationship/trunk/sources/front-page.tex 2012-11-29 23:36:40 UTC (rev 855)
@@ -34,7 +34,7 @@
Huaiyu Mi & \emph{University of Southern California, USA}\\
Stuart Moodie & \emph{EMBL-EBI, UK}\\
Anatoly Sorokin & \emph{Institute of Cell Biophysics RAS, RU}\\
-Alice Vill\'{e}ger & \emph{Current affiliation, UK}
+Alice Vill\'{e}ger & \emph{Freelance IT Consultant, UK}
\end{tabular}
\vfill
Modified: EntityRelationship/trunk/sources/glyphs.tex
===================================================================
--- EntityRelationship/trunk/sources/glyphs.tex 2012-11-29 12:34:32 UTC (rev 854)
+++ EntityRelationship/trunk/sources/glyphs.tex 2012-11-29 23:36:40 UTC (rev 855)
@@ -9,7 +9,6 @@
In \chap{grammar} beginning on page~\pageref{chp:grammar}, we describe the rules for combining these glyphs into legal SBGN \ERs, and in \chap{layout} beginning on page~\pageref{chp:layout}, we describe requirements and guidelines for the way that maps are visually organized.
-\input{sources/er-overview.tex}
\input{sources/ENs.tex}
\input{sources/relationships.tex}
\input{sources/auxiliary.tex}
Modified: EntityRelationship/trunk/sources/introduction.tex
===================================================================
--- EntityRelationship/trunk/sources/introduction.tex 2012-11-29 12:34:32 UTC (rev 854)
+++ EntityRelationship/trunk/sources/introduction.tex 2012-11-29 23:36:40 UTC (rev 855)
@@ -12,21 +12,7 @@
This document defines the \emph{\ER{}} visual language of SBGN. \ERs are one of three views of a biological process offered by SBGN, the others being \PDs and \AFs. SBGN \ERl{} allows to see all the relationships in which a given entity participates, regardless of the temporal aspects. Entities are defined here in a broad sense as something that exists. Relationships can be seen as rules describing the influences of entities nodes on other relationships. An overview of \ERs is given in \sect{overview}.
-\section{SBGN levels and versions}
-\label{sec:sbgn-levels}
-
-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 the development of other standards, i.e. stratify language development into levels.
-
-A \emph{level} of one of the SBGN languages 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. Within \emph{levels}, \emph{versions} represent small evolution of a language, that may involve new glyphs, refined semantics, but no fundamental change of the way maps are to be generated and interpreted. 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 or version. In this way, the development of SBGN languages is envisioned to proceed in stages, with each higher levels adding richness compared to the levels below it.
-
-\section{Developments, discussions, and notifications of updates}
-\label{sec:discussions}
-
-The SBGN website (\url{http://sbgn.org/}) is a portal for all things related to SBGN. It provides a web forum interface to the SBGN discussion list (\mailto{sbg...@ca...}) and information about how anyone may subscribe to it. The easiest and best way to get involved in SBGN discussions is to join the mailing list and participate.
-
-Face-to-face meetings of the SBGN community are announced on the website as well as the mailing list. Although no set schedule currently exists for workshops and other meetings, we envision holding at least one public workshop per year. As with other similar efforts, the workshops are likely to be held as satellite workshops of larger conferences, enabling attendees to use their international travel time and money more efficiently.
-
-Notifications of updates to the SBGN specification are also broadcast on the mailing list and announced on the SBGN website.
-
-\section{Note on typographical convention}
-The concept represented by a glyph is written using a normal font, while a \glyph{glyph} means the SBGN visual representation of the concept. For instance ``a biological entity is encoded by the SBGN ER \glyph{entity}''.
+\input{sources/er-overview.tex}
+\input{sources/versioning.tex}
+\input{sources/community.tex}
+\input{sources/typography.tex}
Added: EntityRelationship/trunk/sources/typography.tex
===================================================================
--- EntityRelationship/trunk/sources/typography.tex (rev 0)
+++ EntityRelationship/trunk/sources/typography.tex 2012-11-29 23:36:40 UTC (rev 855)
@@ -0,0 +1,7 @@
+% =============================================================================
+% typographical conventions
+% =============================================================================
+
+\section{Note on typographical convention}
+
+The concept represented by a glyph is written using a normal font, while a \glyph{glyph} means the SBGN visual representation of the concept. For instance ``a biological entity is encoded by the SBGN ER \glyph{entity}''.
Added: EntityRelationship/trunk/sources/versioning.tex
===================================================================
--- EntityRelationship/trunk/sources/versioning.tex (rev 0)
+++ EntityRelationship/trunk/sources/versioning.tex 2012-11-29 23:36:40 UTC (rev 855)
@@ -0,0 +1,10 @@
+% =============================================================================
+% SBGN versioning
+% =============================================================================
+
+\section{SBGN levels and versions}
+\label{sec:sbgn-levels}
+
+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 the development of other standards, i.e. stratify language development into levels.
+
+A \emph{level} of one of the SBGN languages 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. Within \emph{levels}, \emph{versions} represent small evolution of a language, that may involve new glyphs, refined semantics, but no fundamental change of the way maps are to be generated and interpreted. 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 or version. In this way, the development of SBGN languages is envisioned to proceed in stages, with each higher levels adding richness compared to the levels below it.
\ No newline at end of file
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ali...@us...> - 2012-11-29 12:34:44
|
Revision: 854
http://sbgn.svn.sourceforge.net/sbgn/?rev=854&view=rev
Author: alice_villeger
Date: 2012-11-29 12:34:32 +0000 (Thu, 29 Nov 2012)
Log Message:
-----------
Added first figure and legend to primer
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/sources/front-page.tex
ProcessDiagram/trunk/Specification/sources/primer.tex
Added Paths:
-----------
ProcessDiagram/trunk/Specification/images/keyconcepts.svg
Added: ProcessDiagram/trunk/Specification/images/keyconcepts.svg
===================================================================
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+ style="fill:#ffffff;stroke:#ffffff;stroke-width:2;stroke-linecap:round;stroke-linejoin:round;font-family:sans-serif"
+ id="g78"
+ image-rendering="optimizeQuality"
+ text-rendering="optimizeLegibility"
+ transform="translate(192,86)">
+ <path
+ style="stroke:none"
+ inkscape:connector-curvature="0"
+ id="path80"
+ clip-path="url(#clipPath2)"
+ d="M 109,31 C 109,47.5685 84.8234,61 55,61 25.1766,61 1,47.5685 1,31 1,14.4315 25.1766,1 55,1 c 29.8234,0 54,13.4315 54,30 z" />
+ <path
+ style="fill:none;stroke:#000000"
+ inkscape:connector-curvature="0"
+ id="path82"
+ clip-path="url(#clipPath2)"
+ d="M 109,31 C 109,47.5685 84.8234,61 55,61 25.1766,61 1,47.5685 1,31 1,14.4315 25.1766,1 55,1 c 29.8234,0 54,13.4315 54,30 z" />
+ </g>
+ <g
+ style="font-size:14px;font-family:Arial"
+ id="g84"
+ image-rendering="optimizeQuality"
+ transform="translate(238,108)"
+ font-size="14"
+ text-rendering="geometricPrecision">
+ <text
+ style="stroke:none"
+ id="text86"
+ clip-path="url(#clipPath4)"
+ y="14"
+ x="5"
+ xml:space="preserve">E</text>
+ </g>
+ </g>
+ <g
+ transform="translate(234,204)"
+ text-rendering="optimizeLegibility"
+ image-rendering="optimizeQuality"
+ id="g88"
+ style="fill:#ffffff;stroke:#ffffff;stroke-width:2;stroke-linecap:round;stroke-linejoin:round;font-family:sans-serif">
+ <path
+ d="M 1,1 25,1 25,25 1,25 1,1 z"
+ clip-path="url(#clipPath7)"
+ id="path90"
+ inkscape:connector-curvature="0"
+ style="stroke:none" />
+ <path
+ d="M 1,1 25,1 25,25 1,25 1,1 z"
+ clip-path="url(#clipPath7)"
+ id="path92"
+ inkscape:connector-curvature="0"
+ style="fill:none;stroke:#000000" />
+ </g>
+ <g
+ transform="translate(239.5,147)"
+ text-rendering="optimizeLegibility"
+ image-rendering="optimizeQuality"
+ id="g114"
+ style="stroke-width:1.5;stroke-linecap:butt;stroke-linejoin:round;font-family:sans-serif">
+ <path
+ d="m 7.5,0.75 0,38.125"
+ clip-path="url(#clipPath10)"
+ id="path116"
+ inkscape:connector-curvature="0"
+ style="fill:none" />
+ <path
+ d="m 0.75,45.625 6.75,-6.75 6.75,6.75 -6.75,6.75 z"
+ clip-path="url(#clipPath10)"
+ id="path118"
+ inkscape:connector-curvature="0"
+ style="fill:#ffffff;stroke:none" />
+ <path
+ d="m 0.75,45.625 6.75,-6.75 6.75,6.75 -6.75,6.75 z"
+ clip-path="url(#clipPath10)"
+ id="path120"
+ inkscape:connector-curvature="0"
+ style="fill:none" />
+ </g>
+ </g>
+</svg>
Modified: ProcessDiagram/trunk/Specification/sources/front-page.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/front-page.tex 2012-11-29 09:15:19 UTC (rev 853)
+++ ProcessDiagram/trunk/Specification/sources/front-page.tex 2012-11-29 12:34:32 UTC (rev 854)
@@ -37,7 +37,7 @@
Nicolas \lenov & \emph{EMBL European Bioinformatics Institute, UK}\\
Emek Demir & \emph{Sloan-Kettering Institute, USA}\\
Huaiyu Mi & \emph{University of Southern California, USA}\\
-Alice Vil\'{e}ger & \emph{London, UK}\\
+Alice Vill\'{e}ger & \emph{Freelance IT Consultant, London, UK}\\
\end{tabular}
% \vspace*{1em}
Modified: ProcessDiagram/trunk/Specification/sources/primer.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/primer.tex 2012-11-29 09:15:19 UTC (rev 853)
+++ ProcessDiagram/trunk/Specification/sources/primer.tex 2012-11-29 12:34:32 UTC (rev 854)
@@ -4,6 +4,13 @@
The first thing to understand is the SBGN-PD does not describe biochemical reactions or gene expression --- at least not directly. Instead this language describes collections --- pools --- of entities that are manipulated by processes which can convert them from one type of entity to another. An entity pool that is the input to a process is said to consumed and that which is an output is produced. There is a third class of entity pool associated with a process: namely those that affect --- modulate --- the rate at which a process converts entity from one set of pools to another. The amount of entity in a modulating pools is not changed by the process. These very briefly are the key concepts of PD and are illustrated in figure \ref{fig:keyconcepts}.
+\begin{figure}[htb]
+\begin{center}
+\scalebox{0.5}{\includegraphics{images/keyconcepts}}
+\caption{A process consuming the entity pools A and B and producing the entity pools C and D. The entity pool E modulates the process. The process is represented as a square. Each (unspecified) entity pool is represented as an ellipsis identified by a label. The relationships between the process and each entity pool involved are represented by connecting lines called arcs. Depending on the type of relationship (consumption, production, modulation), these arcs are decorated with different symbols (respectively nothing, arrowhead, and diamond).}\label{fig:key concepts}
+\end{center}
+\end{figure}
+
So how do this enable us to describe biological processes? Very simply. Figure \ref{fig:biochem} illustrates a biochemical reaction and shows how the essential components of that reaction, substrate, product and enzyme catalyst are all conveniently described by the representation. Likewise in figure \ref{fig:genereg} we can see again the concept of entity pools and process flow can be applied to gene regulation. This approach gives us a lot of flexibility and enables one to summarise biological processes that may incorporate many biochemical reactions (figure \ref{fig:summarisingproc}).
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lp...@us...> - 2012-11-29 09:15:30
|
Revision: 853
http://sbgn.svn.sourceforge.net/sbgn/?rev=853&view=rev
Author: lptolik
Date: 2012-11-29 09:15:19 +0000 (Thu, 29 Nov 2012)
Log Message:
-----------
minor fixes
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
ProcessDiagram/trunk/Specification/sources/glyphs.tex
Modified: ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/Specification/sources/glyphs.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/glyphs.tex 2012-11-29 00:50:59 UTC (rev 852)
+++ ProcessDiagram/trunk/Specification/sources/glyphs.tex 2012-11-29 09:15:19 UTC (rev 853)
@@ -2374,7 +2374,7 @@
\sbgnclass{EntityPoolNode}s contained by this compartment.
\end{attributes}
-\subsection{Logical Identity}
+\subsubsection{Logical Identity}
\begin{logicalkey}
\item \attrib{owning\_map}
@@ -2385,7 +2385,7 @@
\begin{itemize}
\item \attrib{name} must not be used by another instance of
- \sbgnclass{Container} contained by the same instance of
+ \sbgnclass{Compartment} contained by the same instance of
\sbgnclass{Map}.
\item \attrib{epns} must contain a unique set of
\sbgnclass{EntityPoolNodes}. See section \ref{sec:epnuniqueness} for
@@ -3694,8 +3694,8 @@
\subsubsection{Rules and Constraints}
\begin{itemize}
-\item Only subclasses of \classref{StatefulEPN} can contain
-labelled clone markers.
+\item Only subclasses of \classref{StatelessEPN} can contain
+\sbgnclass{SimpleCloneMarker}s.
\end{itemize}
\subsubsection{Notation}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <le...@us...> - 2012-11-29 00:51:06
|
Revision: 852
http://sbgn.svn.sourceforge.net/sbgn/?rev=852&view=rev
Author: lenov
Date: 2012-11-29 00:50:59 +0000 (Thu, 29 Nov 2012)
Log Message:
-----------
Modified Paths:
--------------
EntityRelationship/trunk/sbgn_ER-level1.pdf
EntityRelationship/trunk/sources/ENs.tex
EntityRelationship/trunk/sources/domain.tex
EntityRelationship/trunk/sources/entity.tex
EntityRelationship/trunk/sources/front-page.tex
EntityRelationship/trunk/sources/glyphs.tex
EntityRelationship/trunk/sources/latex-style.tex
EntityRelationship/trunk/sources/stateVariable.tex
ProcessDiagram/tags/L1V1.3Full/images/dissociation.pdf
ProcessDiagram/tags/L1V1.3Full/images/dissociation.svg
ProcessDiagram/tags/L1V1.3Full/images/phenotype.pdf
Modified: EntityRelationship/trunk/sbgn_ER-level1.pdf
===================================================================
(Binary files differ)
Modified: EntityRelationship/trunk/sources/ENs.tex
===================================================================
--- EntityRelationship/trunk/sources/ENs.tex 2012-11-28 23:30:22 UTC (rev 851)
+++ EntityRelationship/trunk/sources/ENs.tex 2012-11-29 00:50:59 UTC (rev 852)
@@ -8,7 +8,7 @@
\glyph{Entity nodes} (ENs) represent element of truth, things that exist.
%In ontology parlance, they would be ``continuants''.
-Entity nodes are the source of influences. \SBGNERLone{} provides three different types of \glyph{entity nodes}, the \glyph{interactors}, the \glyph{logical operators} and the \glyph{perturbing agent}.
+Entity nodes are the source of \glyph{influences} (\sect{influences}). \SBGNERLone{} provides three different types of \glyph{entity nodes}, the \glyph{interactors}, the \glyph{logical operators} and the \glyph{perturbing agent}.
\subsection{Interactors}\label{sec:interactors}
Modified: EntityRelationship/trunk/sources/domain.tex
===================================================================
--- EntityRelationship/trunk/sources/domain.tex 2012-11-28 23:30:22 UTC (rev 851)
+++ EntityRelationship/trunk/sources/domain.tex 2012-11-29 00:50:59 UTC (rev 852)
@@ -2,7 +2,7 @@
%% Domain
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\subsection{\glyph{Entity} nesting }
+\section{\glyph{Entity} nesting }
\label{sec:domain}
\SBGNERLone Version 2 allows \glyph{entities} to be nested. The relationships between the enclosed \glyph{entity} and the enclosing \glyph{entity} is partship. Note that this relation between \glyph{entities} of different levels does not imply anything about \glyph{entities} of the same level. In the \fig{domain}, A is part of X and B is part of X. However, nothing is said about A and B. A and B could be of different nature (transmembrane domain and transduction domain) or could be overlapping (binding domain and catalytic domain sharing some amino-acids).
@@ -14,13 +14,13 @@
\label{fig:domain}
\end{figure}
-As any other \glyph{entity}, a nested \glyph{entity} can carry \glyph{state variables} and \glyph{units of information}. The contour of the containing \glyph{entity} must surround the totality of all contained \glyph{entities} including their \glyph{state variables} and \glyph{units of information}. This does not include the \glyph{assignments} and the \glyph{variable values}. A nested \glyph{entity} can participate to \glyph{interactions}, and generate \glyph{influences}. For more information about the use and interpretation of domains, see \sect{semanticsDomain}
+As any other \glyph{entity}, a nested \glyph{entity} can carry \glyph{state variables} and \glyph{units of information}. The contour of the containing \glyph{entity} must surround the totality of all contained \glyph{entities} including their \glyph{state variables} and \glyph{units of information}. This does not include the \glyph{assignments} and the \glyph{variable values}. A nested \glyph{entity} can participate to \glyph{interactions}, with ``sibling'' \glyph{entities} (part of the same containing \glyph{entity}), or others. They can also generate \glyph{influences}. For more information about the use and interpretation of domains, see \sect{semanticsDomain}
+[FIXME: put a figure showing two domains of the same protein interacting within the enclosing entity, and an outcome affecting something outside (an assignment on the container?)]
+
\begin{figure}[H]
\centering
\includegraphics[scale = 0.5]{examples/ex-domain}
\caption{Illustration of the use of \glyph{domains}. This map contains five \glyph{entities}. Three are top-level, while the \glyph{entities} ``res10-180'' and ``auto-inhibitory'' are domains of the \glyph{entity} ``CaMKII''. The controlled terms carried by the \glyph{units of information} tell us that those \glyph{domains} are a catalytic domain and a binding site respectively. As far as the relationships with the \glyph{entities} ``calmoduline'' and ``target'' are concerned, the interpretation does not differ from the one we would derive from a map where all the \glyph{entities} would be entirely separated. However the regulation of localisation of ``CaMKII'' to the post-synaptic densite (PSD) by phosphorylation of threonine 286 also causes the localisation of ``res10-180'' and ``auto-inhibitory'', even if none carry the \glyph{state variables} involved.}
\label{fig:ex-domain}
\end{figure}
-
-\normalcolor
\ No newline at end of file
Modified: EntityRelationship/trunk/sources/entity.tex
===================================================================
--- EntityRelationship/trunk/sources/entity.tex 2012-11-28 23:30:22 UTC (rev 851)
+++ EntityRelationship/trunk/sources/entity.tex 2012-11-29 00:50:59 UTC (rev 852)
@@ -14,13 +14,11 @@
\glyphContainer An \glyph{entity} is represented by a rectangular container with rounded corners, as illustrated in \fig{entity}.
-\glyphLabel An \glyph{entity} is identified by a label placed in an unbordered box containing a string of characters. The characters can be distributed on several lines to improve readability, although this is not mandatory. The label box must be attached to the center of the container. The label may spill outside of the container.
+\glyphLabel An \glyph{entity} is identified by a label placed in an unbordered box containing a string of characters. The characters can be distributed on several lines to improve readability, although this is not mandatory. The center of the label box must be located in the container. The label may spill outside of the container.
\glyphAux An \glyph{entity} might carry state variables that can add information about its state (\sect{stateVariable}). A state variable is represented by a ``stadium'', that is a rectangle capped with two hemi-circles, with the long axis of this stadium placed on the border of the \glyph{entity}'s container, as illustrated in \fig{entity}. The label of the state variable (which can precise the type of characteristic represented by the state variable, residue type, residue number etc.) is written within the state variable's container. Particular \glyph{state variables} are the existence (\sect{existence}) and the location (\sect{location}).
An \glyph{entity} can carry one or several \glyph{units of information} (\sect{unitInformation}). Particular \glyph{units of information} are available for describing the material type (\sect{material-types-cv}) and the conceptual type (\sect{conceptual-types-cv}) of a macromolecule. The center of the bounding box of a \glyph{unit of information} is located on the mid-line of the border of the macromolecule.
-%
-% An \glyph{entity} can carry one of several \glyph{domains}. \glyph{Domains} are represented by labelled subsections of the \glyph{entity}. The leftward section represents the whole entity.
\end{glyphDescription}
@@ -38,4 +36,8 @@
\label{fig:ex-entity}
\end{figure}
+The granularity of the representation, that is what a given \glyph{entity} actually represents, is let to the person generating the map. For instance, one could choose to represent phosphorylated and non-phosphorylated forms of a protein using a single \glyph{entity}, carrying a \glyph{state variable} representing the phosphorylation. The phosphorylated form would be represented by the \glyph{outcome} located on the \glyph{assignment}. Alternatively one could use two separate entities, carrying the \glyph{existence} \glyph{state variable}. The phosphorylated form would be represented by the \glyph{entity}.
+
+[FIXME: Put an example showing the alternative above, plus a kinase phosphorylating the entities, and an influence coming from the phosphorylated forms]
+
%\normalcolor
Modified: EntityRelationship/trunk/sources/front-page.tex
===================================================================
--- EntityRelationship/trunk/sources/front-page.tex 2012-11-28 23:30:22 UTC (rev 851)
+++ EntityRelationship/trunk/sources/front-page.tex 2012-11-29 00:50:59 UTC (rev 852)
@@ -29,11 +29,12 @@
\textbf{\sffamily Editors}:\\[7pt]
\begin{tabular}{l>{\hspace*{15pt}}r}
-Nicolas \lenov & \emph{EMBL European Bioinformatics Institute, UK}\\
+Nicolas \lenov & \emph{Babraham Institute, UK}\\
Emek Demir & \emph{Memorial Sloan-Kettering Institute, USA}\\
Huaiyu Mi & \emph{University of Southern California, USA}\\
-Stuart Moodie & \emph{School of Informatics, University of Edinburgh, UK}\\
-Alive Vill\'{e}ger & \emph{Manchester Centre for Integrative Systems Biology, UK}
+Stuart Moodie & \emph{EMBL-EBI, UK}\\
+Anatoly Sorokin & \emph{Institute of Cell Biophysics RAS, RU}\\
+Alice Vill\'{e}ger & \emph{Current affiliation, UK}
\end{tabular}
\vfill
Modified: EntityRelationship/trunk/sources/glyphs.tex
===================================================================
--- EntityRelationship/trunk/sources/glyphs.tex 2012-11-28 23:30:22 UTC (rev 851)
+++ EntityRelationship/trunk/sources/glyphs.tex 2012-11-29 00:50:59 UTC (rev 852)
@@ -10,10 +10,9 @@
In \chap{grammar} beginning on page~\pageref{chp:grammar}, we describe the rules for combining these glyphs into legal SBGN \ERs, and in \chap{layout} beginning on page~\pageref{chp:layout}, we describe requirements and guidelines for the way that maps are visually organized.
\input{sources/er-overview.tex}
-\input{sources/CVs.tex}
\input{sources/ENs.tex}
\input{sources/relationships.tex}
-\input{sources/annotation.tex}
\input{sources/auxiliary.tex}
-\input{sources/domain.tex}
+\input{sources/CVs.tex}
\input{sources/annotation.tex}
+\input{sources/domain.tex}
Modified: EntityRelationship/trunk/sources/latex-style.tex
===================================================================
--- EntityRelationship/trunk/sources/latex-style.tex 2012-11-28 23:30:22 UTC (rev 851)
+++ EntityRelationship/trunk/sources/latex-style.tex 2012-11-29 00:50:59 UTC (rev 852)
@@ -5,29 +5,8 @@
%% ----------------------------------------------------------------------------
% Warning: more \usepackage commands are used later in this file.
-
-\usepackage[a4paper,centering,margin=1in,marginparwidth=0.75in]{geometry}
-\usepackage[utf8]{inputenc} % unicode support
-\usepackage{shadow}
-\usepackage{supertabular}
-\usepackage{multirow}
-\usepackage{multicol}
-\usepackage{enumitem}
-\usepackage{lscape}
-\usepackage{layout}
-\usepackage{array}
-\usepackage{fancybox}
-\usepackage{xspace}
\usepackage{ifpdf}
-\usepackage{float}
-\usepackage[american]{varioref}
-\usepackage[normalem]{ulem}
-\usepackage{eso-pic}
-% Hyperref, xcolor, graphicx and possibly others have a flag "pdftex"
-% that needs to be used if pdflatex is being used. The following puts
-% these inside a conditional for that situation.
-
\ifpdf
% Case: using pdflatex
@@ -42,7 +21,7 @@
\usepackage[pdftex,breaklinks=true,colorlinks=true,plainpages=false,
pdfpagelabels,bookmarks=true,bookmarksopen=true,bookmarksopenlevel=2,
pdfhighlight=/O,linkcolor={RoyalBlue},citecolor={RoyalBlue},
- pagecolor={RoyalBlue},urlcolor={RoyalBlue}]{hyperref}
+ urlcolor={RoyalBlue}]{hyperref}
\usepackage[pdftex,rgb,dvipsnames,svgnames,hyperref,table]{xcolor}
@@ -57,6 +36,30 @@
\fi
+
+\usepackage[a4paper,centering,margin=1in,marginparwidth=0.75in]{geometry}
+\usepackage[utf8]{inputenc} % unicode support
+\usepackage{shadow}
+\usepackage{supertabular}
+\usepackage{multirow}
+\usepackage{multicol}
+\usepackage{enumitem}
+\usepackage{lscape}
+\usepackage{layout}
+\usepackage{array}
+\usepackage{fancybox}
+\usepackage{xspace}
+\usepackage{float}
+\usepackage[american]{varioref}
+\usepackage[normalem]{ulem}
+\usepackage{eso-pic}
+
+% Hyperref, xcolor, graphicx and possibly others have a flag "pdftex"
+% that needs to be used if pdflatex is being used. The following puts
+% these inside a conditional for that situation.
+
+
+
% Package 'rotating' needs to come after the others.
\usepackage{rotating}
Modified: EntityRelationship/trunk/sources/stateVariable.tex
===================================================================
--- EntityRelationship/trunk/sources/stateVariable.tex 2012-11-28 23:30:22 UTC (rev 851)
+++ EntityRelationship/trunk/sources/stateVariable.tex 2012-11-29 00:50:59 UTC (rev 852)
@@ -16,7 +16,7 @@
\glyphSboTerm Not applicable.
-\glyphContainer A \glyph{state variable} is represented by a ''stadium'' container, that is two hemicercles of same radius joined by parallel segments, as shown in \fig{state-var}. The parallel segment axis should be tangent to the border of the glyph of the \glyph{EN} being modified by the \glyph{state variable}. The center of the bounding box of a \glyph{state variable} should be located on the mid-line of the border of the \glyph{EN}.
+\glyphContainer A \glyph{state variable} is represented by a ''stadium'' container, that is two semicircles of same radius joined by parallel segments, as shown in \fig{state-var}. The parallel segment axis should be tangent to the border of the glyph of the \glyph{EN} being modified by the \glyph{state variable}. The center of the bounding box of a \glyph{state variable} should be located on the mid-line of the border of the \glyph{EN}.
\glyphLabel A \glyph{state variable} is identified by a label placed in an unbordered box containing a string of characters. The characters can be distributed on several lines to improve readability, although this is not mandatory. The label box must be attached to the center of the container. The label may spill outside of the container.
Modified: ProcessDiagram/tags/L1V1.3Full/images/dissociation.pdf
===================================================================
(Binary files differ)
Modified: ProcessDiagram/tags/L1V1.3Full/images/dissociation.svg
===================================================================
--- ProcessDiagram/tags/L1V1.3Full/images/dissociation.svg 2012-11-28 23:30:22 UTC (rev 851)
+++ ProcessDiagram/tags/L1V1.3Full/images/dissociation.svg 2012-11-29 00:50:59 UTC (rev 852)
@@ -1,5 +1,6 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
<svg
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:cc="http://creativecommons.org/ns#"
@@ -12,12 +13,11 @@
height="744.09448"
id="svg2"
sodipodi:version="0.32"
- inkscape:version="0.46"
+ inkscape:version="0.48.3.1 r9886"
version="1.0"
- sodipodi:docbase="/home/lenov/SBGN/svn/sbgn/trunk/documents/specifications/ProcessDiagram/Level1/images"
sodipodi:docname="dissociation.svg"
inkscape:output_extension="org.inkscape.output.svg.inkscape"
- inkscape:export-filename="/home/lenov/SBGN/svn/sbgn/trunk/documents/specifications/ProcessDiagram/Level1/images/dissociation.png"
+ inkscape:export-filename="/home/lenov/SBGN/svn/sbgn/ProcessDiagram/trunk/UserManual/images/dissociation.png"
inkscape:export-xdpi="150"
inkscape:export-ydpi="150">
<defs
@@ -67,19 +67,20 @@
inkscape:pageopacity="0.0"
inkscape:pageshadow="2"
inkscape:zoom="1.979899"
- inkscape:cx="470.0513"
+ inkscape:cx="380.14772"
inkscape:cy="454.09424"
inkscape:document-units="px"
inkscape:current-layer="layer2"
width="1052.3622px"
height="744.09448px"
- inkscape:window-width="1392"
- inkscape:window-height="1022"
+ inkscape:window-width="1272"
+ inkscape:window-height="771"
inkscape:window-x="0"
inkscape:window-y="0"
showguides="true"
inkscape:guide-bbox="true"
- showgrid="false">
+ showgrid="false"
+ inkscape:window-maximized="0">
<sodipodi:guide
orientation="vertical"
position="476.42857"
@@ -93,6 +94,7 @@
<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>
@@ -122,7 +124,7 @@
id="path2839" />
<path
sodipodi:type="arc"
- style="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="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"
id="path3090"
sodipodi:cx="418.57144"
sodipodi:cy="290.52304"
@@ -138,7 +140,7 @@
sodipodi:cy="290.52304"
sodipodi:cx="418.57144"
id="path3114"
- style="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="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"
sodipodi:type="arc" />
</g>
</svg>
Modified: ProcessDiagram/tags/L1V1.3Full/images/phenotype.pdf
===================================================================
(Binary files differ)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <stu...@us...> - 2012-11-28 23:30:28
|
Revision: 851
http://sbgn.svn.sourceforge.net/sbgn/?rev=851&view=rev
Author: stumoodie
Date: 2012-11-28 23:30:22 +0000 (Wed, 28 Nov 2012)
Log Message:
-----------
Added a very draft primer section
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex
Added Paths:
-----------
ProcessDiagram/trunk/Specification/sources/primer.tex
Modified: ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
===================================================================
(Binary files differ)
Modified: ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex 2012-11-28 21:29:17 UTC (rev 850)
+++ ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex 2012-11-28 23:30:22 UTC (rev 851)
@@ -30,6 +30,8 @@
\include{sources/introduction}
\include{sources/concepts}
+\include{sources/primer}
+
\include{sources/glyphs}
\include{sources/layout}
Added: ProcessDiagram/trunk/Specification/sources/primer.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/primer.tex (rev 0)
+++ ProcessDiagram/trunk/Specification/sources/primer.tex 2012-11-28 23:30:22 UTC (rev 851)
@@ -0,0 +1,25 @@
+\chapter{A \PD Primer}
+
+\SBGNPDLone is a visual language. Like any language like English it has a vocabulary, which in the case of SBGN is represented by the symbols that we call glyphs. Again like English our language has grammar, which are the underlying rules and concepts of the language that define its meaning. This specification aims to provide a detailed description of both the vocabulary and grammar rules of the language as a reference. However, to understand this it is essential to grasp what an \PDm describes.
+
+The first thing to understand is the SBGN-PD does not describe biochemical reactions or gene expression --- at least not directly. Instead this language describes collections --- pools --- of entities that are manipulated by processes which can convert them from one type of entity to another. An entity pool that is the input to a process is said to consumed and that which is an output is produced. There is a third class of entity pool associated with a process: namely those that affect --- modulate --- the rate at which a process converts entity from one set of pools to another. The amount of entity in a modulating pools is not changed by the process. These very briefly are the key concepts of PD and are illustrated in figure \ref{fig:keyconcepts}.
+
+So how do this enable us to describe biological processes? Very simply. Figure \ref{fig:biochem} illustrates a biochemical reaction and shows how the essential components of that reaction, substrate, product and enzyme catalyst are all conveniently described by the representation. Likewise in figure \ref{fig:genereg} we can see again the concept of entity pools and process flow can be applied to gene regulation. This approach gives us a lot of flexibility and enables one to summarise biological processes that may incorporate many biochemical reactions (figure \ref{fig:summarisingproc}).
+
+
+%%% Diff EPN & Process types here.
+
+In the above examples of biological processes a number of different glyphs where used to illustrate different biological entities: the macromolecule, the simple chemical and the gene.
+
+
+%%% Compartments.
+
+
+%%% Clone markers and identity
+
+%%% Logic gates
+
+%%% Maps & Submaps
+
+
+%%%Overview of the UML/Class specification.
\ No newline at end of file
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <fal...@us...> - 2012-11-28 21:29:29
|
Revision: 850
http://sbgn.svn.sourceforge.net/sbgn/?rev=850&view=rev
Author: falkschreiber
Date: 2012-11-28 21:29:17 +0000 (Wed, 28 Nov 2012)
Log Message:
-----------
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/sources/glyphs.tex
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.aux
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.bbl
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.bib
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.blg
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.out
ProcessDiagram/trunk/UserManual/sources/introduction.aux
ProcessDiagram/trunk/UserManual/sources/introduction.tex
ProcessDiagram/trunk/UserManual/sources/refcard.aux
ProcessDiagram/trunk/UserManual/sources/symbols.aux
ProcessDiagram/trunk/UserManual/sources/symbols.tex
Modified: ProcessDiagram/trunk/Specification/sources/glyphs.tex
===================================================================
--- ProcessDiagram/trunk/Specification/sources/glyphs.tex 2012-11-28 18:21:05 UTC (rev 849)
+++ ProcessDiagram/trunk/Specification/sources/glyphs.tex 2012-11-28 21:29:17 UTC (rev 850)
@@ -1,3 +1,6 @@
+% WinEdt modes
+% -*- TeX -*- -*- EN -*- -*- UK -*-
+
% $HeadURL$
\chapter{Language Elements}
@@ -314,7 +317,7 @@
\subsubsection{Associations}
\begin{attributes}
-\associtem{elements}{SBGNGlyph}{*} The collection of glyphs held by the map.
+\associtem{elements}{SBGNGlyph}{*} The collection of glyphs held by the map.
\end{attributes}
\subsubsection{Rules and Constraints}
@@ -422,7 +425,7 @@
\sbgnclass{SBGNArc} classes.}
\label{fig:sbgnnodearcuml}
\end{figure}
-
+
The \sbgnclass{SBGNNode} (figure \ref{fig:sbgnnodearcuml}) represents
the nodes in the graph structure that is the core representation
within the \PDl. The nodes are connected to glyphs descended from
@@ -444,14 +447,14 @@
\associtem{out\_arcs}{SBGNArc}{*} The arcs that are leaving this node.
\associtem{in\_arcs}{SBGNArc}{*} The arcs that are entering this node.
\end{attributes}
-
+
\subsubsection{Rules and Constraints}
\begin{itemize}
\item The set of \sbgnclass{SBGNNode}s linked to this node via a
\sbgnclass{SBGNArc} (its adjacent nodes) must be all belong to
different entity pools (as defined by \sbgnclass{EntityPoolNode})
- and cannot include more than one clone of the same entity pool.
+ and cannot include more than one clone of the same entity pool.
\end{itemize}
\subsubsection{Changes from Previous Version}
@@ -508,7 +511,7 @@
\sbgnclass{EntityPoolNode} logical identity.}
\label{fig:entitytypeuml}
\end{figure}
-
+
The \sbgnclass{EntityType}\query{The concept of an entity pool's type
has been there implicitly in previous versions and comes up in
discussions. This class aims to formalise that concept and the rules
@@ -637,7 +640,7 @@
\caption{UML definition of the entity pool node and its descendant glyphs.}
\label{fig:epnuml}
\end{figure}
-
+
The \sbgnclass{EntityPoolNode} (figure \ref{fig:epnuml}) is the
definition of the entity pool and it shares an \sbgnclass{EntityType}
with other identical entities\query{Although this concept is discussed
@@ -1004,7 +1007,7 @@
\paragraph{Glyph: \glyph{Unspecified entity}}
\begin{glyphDescription}
-\glyphSboTerm SBO:0000285 ! material entity of unspecified nature
+\glyphSboTerm SBO:0000285 ! material entity of unspecified nature
\glyphContainer An \glyph{unspecified entity} is represented by an
elliptic container, as shown in \ref{fig:unspecified}. Note that this
must remain an ellipse to avoid confusion with the Simple Chemical
@@ -1129,7 +1132,7 @@
two or more state variables with the same name are permitted.
\item The \sbgnclass{LabelledCloneMarker} must be used to indicate
cloning for instances of \sbgnclass{StatefulEPN} and its subclasses,
- with a must use the same
+ with a must use the same
\end{itemize}
\subsubsection{Changes from Previous Version}
@@ -1179,7 +1182,7 @@
\paragraph{Glyph: \glyph{Macromolecule monomer}}
\begin{glyphDescription}
-\glyphSboTerm SBO:0000245 ! macromolecule
+\glyphSboTerm SBO:0000245 ! macromolecule
\glyphContainer A macromolecule is represented by a rectangular container with rounded
corners, as illustrated in \fig{macromolecule}.
\glyphLabel A \glyph{macromolecule} is identified by a label placed in an unbordered box containing a string of characters. The characters can be distributed on several lines to improve readability, although this is not mandatory. The label box must be attached to the center of the container. The label may spill outside of the container.
@@ -1214,7 +1217,7 @@
\paragraph{Usage Examples}
\label{sec:CplxEPNs}
-In this section, we provide examples of Entity Pool Node representations drawn using the \SBGNPDLone glyphs described above.
+In this section, we provide examples of Entity Pool Node representations drawn using the \SBGNPDLone glyphs described above.
\fig{example-camkii} represents calcium/calmodulin kinase II, with phosphorylation on the sites threonine 286 and 306, as well as catalytic and autoinhibitory domains. Note the use of \emph{units of information} and \emph{state variables}.
@@ -1289,7 +1292,7 @@
\includegraphics[width = 3.5in]{images/genetic}
\caption{The \PD glyph for \glyph{nucleic acid feature monomer}, shown plain and
unadorned on the left and with an additional state variable and a
- unit of information in the middle and the cloned form on the right.}
+ unit of information in the middle and the cloned form on the right.}
\label{fig:genetic}
\end{figure}
@@ -1299,7 +1302,7 @@
\begin{glyphDescription}
-\glyphSboTerm SBO:0000419 ! multimer of informational molecule segments
+\glyphSboTerm SBO:0000419 ! multimer of informational molecule segments
\glyphContainer A \glyph{Nucleic acid feature multimer} is represented by two identical containers shifted horizontally and vertically and stacked one on top of the other. \fig{genetic-multimer} illustrates the glyph.
@@ -1312,7 +1315,7 @@
\includegraphics[width = 3.5in]{images/geneticMultimer}
\caption{The \PD glyph for \glyph{nucleic acid feature multimer}, shown plain and
unadorned on the left and with an additional state variable and a
- unit of information in the middle and the cloned form on the right.}
+ unit of information in the middle and the cloned form on the right.}
\label{fig:genetic-multimer}
\end{figure}
@@ -1349,12 +1352,12 @@
\subsubsection{Generalisations}
\begin{itemize}
-\item \classref{EntityPoolNode}
+\item \classref{EntityPoolNode}
\end{itemize}
\subsubsection{Attributes}
-No additional attributes
+No additional attributes
\subsubsection{Associations}
@@ -1461,7 +1464,7 @@
\subsubsection{Generalisation}
\begin{itemize}
-\item \classref{EntityPoolNode}
+\item \classref{EntityPoolNode}
\end{itemize}
\subsubsection{Attributes}
@@ -1719,7 +1722,7 @@
mandatory. The label box must be attached to the center of the
\glyph{phenotype} container. The label may spill outside of the container.
\end{glyphDescription}
-
+
\begin{figure}[H]
\centering
\includegraphics[scale = 0.3]{images/phenotype}
@@ -1959,7 +1962,7 @@
subclasses of \sbgnclass{FluxArc} and \sbgnclass{ModulationArc}.}
\label{fig:stoichprocessuml}
\end{figure}
-
+
A stoichiometric process\query{New concept, but discussed in previous
meetings. The semantics of the process being stoichiometrically
balanced has not been discussed in detail for the stoichiometric
@@ -2042,7 +2045,7 @@
\caption{A valid reversible process. A process is reversible if its LHS and RHS contain only \glyph{production} arcs.}
\label{fig:process-reversibility}
\end{figure}
-
+
\subsubsection{Generalisation}
\begin{itemize}
@@ -2163,7 +2166,7 @@
\label{fig:trans-phos}
\end{figure}
-The example in \fig{trans-react} illustrates the use of a \glyph{process} node to represent a reaction between two reactants that generates three products.
+The example in \fig{trans-react} illustrates the use of a \glyph{process} node to represent a reaction between two reactants that generates three products.
\begin{figure}[H]
\centering
@@ -2258,7 +2261,7 @@
\begin{glyphDescription}
\glyphSboTerm SBO:0000177 ! non-covalent binding.
- \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.
+ \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]
@@ -2327,7 +2330,7 @@
Although the \sbgnclass{NonStoichiometricProcess} was not explicitly defined in
the previous version the semantics and glyphs are unchanged.
-
+
\subsection{Compartment}
\label{defn:Compartment}
@@ -2395,7 +2398,7 @@
\begin{glyphDescription}
-\glyphSboTerm SBO:0000290 ! physical compartment
+\glyphSboTerm SBO:0000290 ! physical compartment
\glyphContainer 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 EPNs. A compartment can take \textbf{any} geometry. A compartment must always be entirely enclosed.
@@ -2756,7 +2759,7 @@
via a callout (see figure \ref{fig:ex-annotation}. The callout should
overlap with the object it is annotating.
-\glyphLabel An \glyph{annotation} contains information placed in an unbordered box containing a string of characters. The characters can be distributed on several lines to improve readability, although this is not mandatory. The label box must be attached to the center of the container. The label may spill outside of the container.
+\glyphLabel An \glyph{annotation} contains information placed in an unbordered box containing a string of characters. The characters can be distributed on several lines to improve readability, although this is not mandatory. The label box must be attached to the center of the container. The label may spill outside of the container.
\end{glyphDescription}
@@ -2871,7 +2874,7 @@
an empty arrowhead. The
flat edge opposite the arrowhead should be aligned to the edge of the
\glyph{Submap} glyph and the connecting should connect to the middle
-of this face (see figure \ref{fig:submapterminal}).
+of this face (see figure \ref{fig:submapterminal}).
\glyphLabel A \glyph{tag} is identified by a label placed in an
unbordered box containing a string of characters. The characters can
@@ -2957,7 +2960,7 @@
\caption{The UML definition of the \sbgnclass{FluxArc} and its subclasses.}
\label{fig:fluxarcuml}
\end{figure}
-
+
The \sbgnclass{FluxArc} permits a quantity of entities to flow through
the arc and in doing so connects a stoichiometric process
(\classref{StoichiometricProcess}) and an EPN
@@ -3239,8 +3242,8 @@
% \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
+% \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
% \glyph{production} arc also acts as a \glyph{consumption} arc.
% \begin{glyphDescription}
@@ -3273,7 +3276,7 @@
subclasses of \sbgnclass{StoichiometricProcess}.}
\label{fig:modulationarcuml}
\end{figure}
-
+
The \sbgnclass{ModulationArc} (figure \ref{fig:modulationarcuml})
affects the flux of a process represented by the target process. Such
a modulation can affect the process \textbf{positively or negatively},
@@ -3333,7 +3336,7 @@
would imply an implicit AND or OR operator. For clarity only
one \glyph{necessary stimulation} can be assigned to a \glyph{process}, and such combinations must be
explicitly expressed using \glyph{logical operators}\query{Taken
- from the grammar section of the previous specification.}.
+ from the grammar section of the previous specification.}.
\item At most one \glyph{catalysis} can be assigned to a
\glyph{process}. Modulation by a catalysis arc implies that the exact biochemical mechanism underlying
the process is known. In this context two \glyph{catalysis} cannot
@@ -3377,7 +3380,7 @@
\label{fig:modulation}
\end{figure}
-\fig{modul-nico} represents the effect of nicotine on the process between closed and open states of a nicotinic acetylcholine receptor. High concentrations of nicotine open the receptor while low concentrations can desensitize it without opening.
+\fig{modul-nico} represents the effect of nicotine on the process between closed and open states of a nicotinic acetylcholine receptor. High concentrations of nicotine open the receptor while low concentrations can desensitize it without opening.
\begin{figure}[H]
\centering
@@ -3536,7 +3539,7 @@
\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.
+the outcome of a logic operator.
\begin{glyphDescription}
\glyphSboTerm SBO:0000398 ! logical relationship.
@@ -3782,7 +3785,7 @@
\glyphSboTerm Not applicable.
-\glyphContainer The labeled \glyph{clone marker} is a portion of the surface of an \glyph{EPN} that has been modified visually through the use of a different shade, texture, or color. The \glyph{clone marker} occupies the lower part of the EPN glyph. The filled area must be smaller than the unfilled one, but the be large enough to have a height larger than the \glyph{clone marker}'s label (cf below).
+\glyphContainer The labeled \glyph{clone marker} is a portion of the surface of an \glyph{EPN} that has been modified visually through the use of a different shade, texture, or color. The \glyph{clone marker} occupies the lower part of the EPN glyph. The filled area must be smaller than the unfilled one, but the be large enough to have a height larger than the \glyph{clone marker}'s label (cf below).
\glyphLabel A \glyph{clone marker} is identified by a label placed in an unbordered box containing a string of characters. The characters can be distributed on several lines to improve readability, although this is not mandatory. The label box must be attached to the center of the container. The label may spill outside of the container (the portion of the surface of the EPN that has been modified visually). The font color of the label and the color of the clone marker should contrast with one another. The label on a \glyph{labeled clone marker} is mandatory.
@@ -4102,7 +4105,7 @@
The following rules apply to the use of the \sbgnclass{SubmapNode} and
submaps in the \PDl\query{These rules are taken from the previous
version of the spec, but rules about the depth of submap `recursion',
- the uniqueness of reference\_id values and cloning between maps are not}.
+ the uniqueness of reference\_id values and cloning between maps are not}.
\begin{itemize}
Modified: ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.aux
===================================================================
--- ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.aux 2012-11-28 18:21:05 UTC (rev 849)
+++ ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.aux 2012-11-28 21:29:17 UTC (rev 850)
@@ -1,23 +1,16 @@
-\relax
-\ifx\hyper@anchor\@undefined
-\global \let \oldcontentsline\contentsline
-\gdef \contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}}
-\global \let \oldnewlabel\newlabel
-\gdef \newlabel#1#2{\newlabelxx{#1}#2}
-\gdef \newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}}
-\AtEndDocument{\let \contentsline\oldcontentsline
-\let \newlabel\oldnewlabel}
-\else
-\global \let \hyper@last\relax
-\fi
-
-\@input{sources/introduction.aux}
-\@input{sources/symbols.aux}
-\@input{sources/build.aux}
-\@input{sources/refcard.aux}
-\bibstyle{unsrt}
-\bibdata{sbgn_PD-level1-user}
-\bibcite{LeNovere:2009p1}{1}
-\bibcite{Moodie:2011}{2}
-\bibcite{Courtot:2011}{3}
-\bibcite{Hucka:2003}{4}
+\relax
+\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument}
+\HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined
+\global\let\oldcontentsline\contentsline
+\gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}}
+\global\let\oldnewlabel\newlabel
+\gdef\newlabel#1#2{\newlabelxx{#1}#2}
+\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}}
+\AtEndDocument{\ifx\hyper@anchor\@undefined
+\let\contentsline\oldcontentsline
+\let\newlabel\oldnewlabel
+\fi}
+\fi}
+\global\let\hyper@last\relax
+\gdef\HyperFirstAtBeginDocument#1{#1}
+\providecommand\HyField@AuxAddToFields[1]{}
Modified: ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.bbl
===================================================================
--- ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.bbl 2012-11-28 18:21:05 UTC (rev 849)
+++ ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.bbl 2012-11-28 21:29:17 UTC (rev 850)
@@ -1,43 +1,50 @@
-\begin{thebibliography}{1}
-
-\bibitem{LeNovere:2009p1}
-N~Le~Nov\`{e}re, Michael Hucka, Huaiyu Mi, Stuart Moodie, Falk Schreiber,
- Anatoly Sorokin, Emek Demir, Katja Wegner, Mirit~I Aladjem, M~Sarala
- Wimalaratne, Frank~T Bergman, Ralph Gauges, Peter Ghazal, Hideya Kawaji,
- Lu~Li, Yukiko Matsuoka, Alice Villeger, Sarah~E Boyd, Laurence Calzone,
- M\'{e}lanie Courtot, Ugur Dogrusoz, Tom~C Freeman, Akira Funahashi, Samik
- Ghosh, Akiya Jouraku, Sohyoung Kim, Fedor Kolpakov, Augustin Luna, Sven
- Sahle, Esther Schmidt, Steven Watterson, Guanming Wu, Igor Goryanin,
- Douglas~B Kell, Chris Sander, Herbert Sauro, Jacky~L Snoep, Kurt Kohn, and
- Hiroaki Kitano.
-\newblock The systems biology graphical notation.
-\newblock {\em Nat Biotechnol}, 27(8):735--741, 2009.
-\newblock 10.1038/nbt.1558.
-
-\bibitem{Moodie:2011}
-Stuart Moodie, Nicolas Le~Nov\`{e}re, Emek Demir, Huaiyu Mi, and Alice
- Vill\'{e}ger.
-\newblock Systems biology graphical notation: Process description language
- level 1.
-\newblock {\em Nature Precedings}, 2011.
-
-\bibitem{Courtot:2011}
-M.~Courtot, N.~Juty, C.~Kn{\"u}pfer, D.~Waltemath, A.~Zhukova, A.~Dr{\"a}ger,
- M.~Dumontier, A.~Finney, M.~Golebiewski, J.~Hastings, et~al.
-\newblock Controlled vocabularies and semantics in systems biology.
-\newblock {\em Molecular systems biology}, 7(1), 2011.
-
-\bibitem{Hucka:2003}
-M.~Hucka, A.~Finney, H.~M. Sauro, H.~Bolouri, J.~C. Doyle, H.~Kitano, A.~P.
- Arkin, B.~J. Bornstein, D.~Bray, A.~Cornish-Bowden, A.~A. Cuellar, S.~Dronov,
- E.~D. Gilles, M.~Ginkel, V.~Gor, I.~I. Goryanin, W.~J. Hedley, T.~C. Hodgman,
- J.-H. Hofmeyr, P.~J. Hunter, N.~S. Juty, J.~L. Kasberger, A.~Kremling,
- U.~Kummer, N.~Le~Nov\`{e}re, L.~M. Loew, D.~Lucio, P.~Mendes, E.~Minch, E.~D.
- Mjolsness, Y.~Nakayama, M.~R. Nelson, P.~F. Nielsen, T.~Sakurada, J.~C.
- Schaff, B.~E. Shapiro, T.~S. Shimizu, H.~D. Spence, J.~Stelling,
- K.~Takahashi, M.~Tomita, J.~Wagner, and J.~Wang.
-\newblock The {S}ystems {B}iology {M}arkup {L}anguage ({SBML}): A medium for
- representation and exchange of biochemical network models.
-\newblock {\em Bioinformatics}, 19(4):524--531, 2003.
-
-\end{thebibliography}
+\begin{thebibliography}{1}
+
+\bibitem{LeNovere:2009p1}
+N~Le~Nov\`{e}re, Michael Hucka, Huaiyu Mi, Stuart Moodie, Falk Schreiber,
+ Anatoly Sorokin, Emek Demir, Katja Wegner, Mirit~I Aladjem, M~Sarala
+ Wimalaratne, Frank~T Bergman, Ralph Gauges, Peter Ghazal, Hideya Kawaji,
+ Lu~Li, Yukiko Matsuoka, Alice Villeger, Sarah~E Boyd, Laurence Calzone,
+ M\'{e}lanie Courtot, Ugur Dogrusoz, Tom~C Freeman, Akira Funahashi, Samik
+ Ghosh, Akiya Jouraku, Sohyoung Kim, Fedor Kolpakov, Augustin Luna, Sven
+ Sahle, Esther Schmidt, Steven Watterson, Guanming Wu, Igor Goryanin,
+ Douglas~B Kell, Chris Sander, Herbert Sauro, Jacky~L Snoep, Kurt Kohn, and
+ Hiroaki Kitano.
+\newblock The systems biology graphical notation.
+\newblock {\em Nat Biotechnol}, 27(8):735--741, 2009.
+\newblock 10.1038/nbt.1558.
+
+\bibitem{Moodie:2011}
+Stuart Moodie, Nicolas Le~Nov\`{e}re, Emek Demir, Huaiyu Mi, and Alice
+ Vill\'{e}ger.
+\newblock Systems biology graphical notation: Process description language
+ level 1.
+\newblock {\em Nature Precedings}, 2011.
+
+\bibitem{Junker:2012}
+Astrid Junker, Anatoly Sorokin, Tobias Czauderna, Falk Schreiber, and Alexander
+ Mazein.
+\newblock Wiring diagrams in biology: towards the standardized representation
+ of biological information.
+\newblock {\em Trends in Biotechnology}, 30(11):555--557, 2012.
+
+\bibitem{Courtot:2011}
+M.~Courtot, N.~Juty, C.~Kn{\"u}pfer, D.~Waltemath, A.~Zhukova, A.~Dr{\"a}ger,
+ M.~Dumontier, A.~Finney, M.~Golebiewski, J.~Hastings, et~al.
+\newblock Controlled vocabularies and semantics in systems biology.
+\newblock {\em Molecular systems biology}, 7(1), 2011.
+
+\bibitem{Hucka:2003}
+M.~Hucka, A.~Finney, H.~M. Sauro, H.~Bolouri, J.~C. Doyle, H.~Kitano, A.~P.
+ Arkin, B.~J. Bornstein, D.~Bray, A.~Cornish-Bowden, A.~A. Cuellar, S.~Dronov,
+ E.~D. Gilles, M.~Ginkel, V.~Gor, I.~I. Goryanin, W.~J. Hedley, T.~C. Hodgman,
+ J.-H. Hofmeyr, P.~J. Hunter, N.~S. Juty, J.~L. Kasberger, A.~Kremling,
+ U.~Kummer, N.~Le~Nov\`{e}re, L.~M. Loew, D.~Lucio, P.~Mendes, E.~Minch, E.~D.
+ Mjolsness, Y.~Nakayama, M.~R. Nelson, P.~F. Nielsen, T.~Sakurada, J.~C.
+ Schaff, B.~E. Shapiro, T.~S. Shimizu, H.~D. Spence, J.~Stelling,
+ K.~Takahashi, M.~Tomita, J.~Wagner, and J.~Wang.
+\newblock The {S}ystems {B}iology {M}arkup {L}anguage ({SBML}): A medium for
+ representation and exchange of biochemical network models.
+\newblock {\em Bioinformatics}, 19(4):524--531, 2003.
+
+\end{thebibliography}
Modified: ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.bib
===================================================================
--- ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.bib 2012-11-28 18:21:05 UTC (rev 849)
+++ ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.bib 2012-11-28 21:29:17 UTC (rev 850)
@@ -120,6 +120,16 @@
pages = {1-13}
}
+@Article{Junker:2012,
+ author = {Astrid Junker and Anatoly Sorokin and Tobias Czauderna and Falk Schreiber and Alexander Mazein},
+ title = {Wiring diagrams in biology: towards the standardized representation of biological information},
+ journal = {Trends in Biotechnology},
+ year = {2012},
+ volume = {30},
+ number = {11},
+ pages = {555-557},
+}
+
@InProceedings{Maimon:2001,
author = {Ron Maimon and Sam Browning},
title = {Diagrammatic notation and computational structure of gene networks},
@@ -175,14 +185,14 @@
number = "1",
pages = "9-36",
year = "1976",
- url = "citeseer.ist.psu.edu/519283.html"
+ url = "citeseer.ist.psu.edu/519283.html"
}
%% This BibTeX bibliography file in UTF-8 format was created using Papers.
%% http://mekentosj.com/papers/
@article{LeNovere:2009p1,
-author = {Le Nov\`{e}re, N and Michael Hucka and Huaiyu Mi and Stuart Moodie and Falk Schreiber and Anatoly Sorokin and Emek Demir and Katja Wegner and Aladjem, Mirit I and Wimalaratne, M Sarala and Bergman, Frank T and Ralph Gauges and Peter Ghazal and Hideya Kawaji and Lu Li and Yukiko Matsuoka and Alice Villeger and Boyd, Sarah E and Laurence Calzone and M\'{e}lanie Courtot and Ugur Dogrusoz and Freeman, Tom C and Akira Funahashi and Samik Ghosh and Akiya Jouraku and Sohyoung Kim and Fedor Kolpakov and Augustin Luna and Sven Sahle and Esther Schmidt and Steven Watterson and Guanming Wu and Igor Goryanin and Kell, Douglas B and Chris Sander and Herbert Sauro and Snoep, Jacky L and Kurt Kohn and Hiroaki Kitano},
+author = {Le Nov\`{e}re, N and Michael Hucka and Huaiyu Mi and Stuart Moodie and Falk Schreiber and Anatoly Sorokin and Emek Demir and Katja Wegner and Aladjem, Mirit I and Wimalaratne, M Sarala and Bergman, Frank T and Ralph Gauges and Peter Ghazal and Hideya Kawaji and Lu Li and Yukiko Matsuoka and Alice Villeger and Boyd, Sarah E and Laurence Calzone and M\'{e}lanie Courtot and Ugur Dogrusoz and Freeman, Tom C and Akira Funahashi and Samik Ghosh and Akiya Jouraku and Sohyoung Kim and Fedor Kolpakov and Augustin Luna and Sven Sahle and Esther Schmidt and Steven Watterson and Guanming Wu and Igor Goryanin and Kell, Douglas B and Chris Sander and Herbert Sauro and Snoep, Jacky L and Kurt Kohn and Hiroaki Kitano},
journal = {Nat Biotechnol},
title = {The Systems Biology Graphical Notation},
note = {10.1038/nbt.1558},
@@ -212,4 +222,3 @@
year = 2010,
howpublished = {Available via the World Wide Web at \url{http://www.omg.org/spec/UML/2.1.2/Superstructure/PDF/}},
}
-
Modified: ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.blg
===================================================================
--- ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.blg 2012-11-28 18:21:05 UTC (rev 849)
+++ ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.blg 2012-11-28 21:29:17 UTC (rev 850)
@@ -1,49 +1,7 @@
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-A level-1 auxiliary file: sources/introduction.aux
-A level-1 auxiliary file: sources/symbols.aux
-A level-1 auxiliary file: sources/build.aux
-A level-1 auxiliary file: sources/refcard.aux
-The style file: unsrt.bst
-Database file #1: sbgn_PD-level1-user.bib
-You've used 4 entries,
- 1791 wiz_defined-function locations,
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-and the built_in function-call counts, 1971 in all, are:
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-> -- 302
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-- -- 98
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-type$ -- 0
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-width$ -- 5
-write$ -- 47
+This is BibTeX, Version 0.99dThe top-level auxiliary file: sbgn_PD-level1-user.aux
+A level-1 auxiliary file: sources/introduction.aux
+A level-1 auxiliary file: sources/symbols.aux
+A level-1 auxiliary file: sources/build.aux
+A level-1 auxiliary file: sources/refcard.aux
+The style file: unsrt.bst
+Database file #1: sbgn_PD-level1-user.bib
Modified: ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log
===================================================================
--- ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log 2012-11-28 18:21:05 UTC (rev 849)
+++ ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log 2012-11-28 21:29:17 UTC (rev 850)
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|
From: <stu...@us...> - 2012-11-28 18:21:16
|
Revision: 849
http://sbgn.svn.sourceforge.net/sbgn/?rev=849&view=rev
Author: stumoodie
Date: 2012-11-28 18:21:05 +0000 (Wed, 28 Nov 2012)
Log Message:
-----------
Reorganised so restructured spec worked.
Modified Paths:
--------------
ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
Added Paths:
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ProcessDiagram/trunk/Specification/validation-rules/
Removed Paths:
-------------
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ProcessDiagram/trunk/images/
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Modified: ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
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(Binary files differ)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <le...@us...> - 2012-11-28 09:38:59
|
Revision: 848
http://sbgn.svn.sourceforge.net/sbgn/?rev=848&view=rev
Author: lenov
Date: 2012-11-28 09:38:48 +0000 (Wed, 28 Nov 2012)
Log Message:
-----------
Removed Paths:
-------------
ProcessDiagram/trunk/README.txt
Deleted: ProcessDiagram/trunk/README.txt
===================================================================
--- ProcessDiagram/trunk/README.txt 2012-11-05 23:28:47 UTC (rev 847)
+++ ProcessDiagram/trunk/README.txt 2012-11-28 09:38:48 UTC (rev 848)
@@ -1,13 +0,0 @@
-
- Specification for the
-
- ----------------------------------------
- Systems Biology Graphical Notation (SBGN)
- Process Diagrams Level 1.1
- ----------------------------------------
-
- For more information about SBGN, visit:
- http://sbgn.org
-
- Please join the sbgn-discuss mailing list by visiting
- http://www.sbgn.org/Forums
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <le...@us...> - 2012-11-05 23:28:56
|
Revision: 847
http://sbgn.svn.sourceforge.net/sbgn/?rev=847&view=rev
Author: lenov
Date: 2012-11-05 23:28:47 +0000 (Mon, 05 Nov 2012)
Log Message:
-----------
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From: <le...@us...> - 2012-11-05 23:18:30
|
Revision: 846
http://sbgn.svn.sourceforge.net/sbgn/?rev=846&view=rev
Author: lenov
Date: 2012-11-05 23:18:21 +0000 (Mon, 05 Nov 2012)
Log Message:
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From: <le...@us...> - 2012-11-05 23:10:48
|
Revision: 845
http://sbgn.svn.sourceforge.net/sbgn/?rev=845&view=rev
Author: lenov
Date: 2012-11-05 23:10:38 +0000 (Mon, 05 Nov 2012)
Log Message:
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From: <le...@us...> - 2012-10-07 21:53:15
|
Revision: 844
http://sbgn.svn.sourceforge.net/sbgn/?rev=844&view=rev
Author: lenov
Date: 2012-10-07 21:53:09 +0000 (Sun, 07 Oct 2012)
Log Message:
-----------
Removed Paths:
-------------
ProcessDiagram/trunk/Makefile
Deleted: ProcessDiagram/trunk/Makefile
===================================================================
--- ProcessDiagram/trunk/Makefile 2012-10-07 21:52:50 UTC (rev 843)
+++ ProcessDiagram/trunk/Makefile 2012-10-07 21:53:09 UTC (rev 844)
@@ -1,38 +0,0 @@
-# =============================================================================
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- -rm -f *.tmp
- -rm -f *.prv
- -rm -f sbgn_PD-level1.fdb_latexmk
-
-dist_clean: clean
- -rm -f *.pdf
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <le...@us...> - 2012-10-07 21:52:56
|
Revision: 843
http://sbgn.svn.sourceforge.net/sbgn/?rev=843&view=rev
Author: lenov
Date: 2012-10-07 21:52:50 +0000 (Sun, 07 Oct 2012)
Log Message:
-----------
Added Paths:
-----------
ProcessDiagram/trunk/Specification/Makefile
Copied: ProcessDiagram/trunk/Specification/Makefile (from rev 839, ProcessDiagram/trunk/Makefile)
===================================================================
--- ProcessDiagram/trunk/Specification/Makefile (rev 0)
+++ ProcessDiagram/trunk/Specification/Makefile 2012-10-07 21:52:50 UTC (rev 843)
@@ -0,0 +1,38 @@
+# =============================================================================
+# $Id$
+# Top-level Makefile for the SBGN Process Diagram specification.
+#
+# $HeadURL$
+# =============================================================================
+
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+
+MAIN = sbgn_PD-level1
+
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+BIBTEX = bibtex
+
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+ $(MAKE) -C examples
+ $(MAKE) -C images
+ $(LATEX) $(MAIN).tex
+ $(LATEX) $(MAIN).tex
+ $(BIBTEX) $(MAIN)
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+
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+ $(MAKE) -C images clean
+ $(MAKE) -C examples clean
+ -rm -f *.bbl
+ -rm -f *.blg
+ -rm -f *.out
+ -rm -f *.dvi
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+ -rm -f *.aux
+ -rm -f *.log
+ -rm -f *.tmp
+ -rm -f *.prv
+ -rm -f sbgn_PD-level1.fdb_latexmk
+
+dist_clean: clean
+ -rm -f *.pdf
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <le...@us...> - 2012-10-07 21:51:37
|
Revision: 842
http://sbgn.svn.sourceforge.net/sbgn/?rev=842&view=rev
Author: lenov
Date: 2012-10-07 21:51:29 +0000 (Sun, 07 Oct 2012)
Log Message:
-----------
Added Paths:
-----------
ProcessDiagram/trunk/Specification/
ProcessDiagram/trunk/Specification/sbgn_PD-level1.bib
ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf
ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex
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Removed Paths:
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ProcessDiagram/trunk/sbgn_PD-level1.bib
ProcessDiagram/trunk/sbgn_PD-level1.pdf
ProcessDiagram/trunk/sbgn_PD-level1.tex
Copied: ProcessDiagram/trunk/Specification/sbgn_PD-level1.bib (from rev 839, ProcessDiagram/trunk/sbgn_PD-level1.bib)
===================================================================
--- ProcessDiagram/trunk/Specification/sbgn_PD-level1.bib (rev 0)
+++ ProcessDiagram/trunk/Specification/sbgn_PD-level1.bib 2012-10-07 21:51:29 UTC (rev 842)
@@ -0,0 +1,196 @@
+@Article{Cook:2001,
+ author = {Daniel L. Cook and J. F. Farley and S. J. Tapscott},
+ title = {A basis for a visual language for describing, archiving and analyzing functional
+models of complex biological systems},
+ journal = {Genome Biology},
+ year = {2001},
+ volume = {2},
+ number = {4},
+ pages = {research0012.1-research0012.10.}
+}
+
+@Article{Demir:2002,
+ author = {Demir, E. and Babur, O. and Dogrusoz., U and Gursoy, A. and Nisanci, G. and Cetin-Atalay, R. and Ozturk, M.},
+ title = {PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways},
+ journal = {Bioinformatics},
+ year = {2002},
+ volume = {18},
+ number = {7},
+ pages = {996-1003}
+}
+
+@Article{Demir:2004,
+ author = {Demir, E. and Babur, O. and Dogrusoz, U. and Gursoy, A. and Ayaz, A. and Gulesir, G. and Nisanci, G. and Cetin-Atalay, R.},
+ title = {An ontology for collaborative construction and analysis of cellular pathways},
+ journal = {Bioinformatics},
+ year = {2004},
+ volume = {20},
+ number = {3},
+ pages = {349-356}
+}
+
+@Book{DiBattista:1998,
+ author = {{D}i {B}attista, G. and Eades, P. and Tamassia, R. and Tollis, I.G.},
+ title = {Graph Drawing: Algorithms for the Visualization of Graphs},
+ year = {1998},
+ publisher = {Prentice Hall},
+ address = {New Jersey},
+}
+
+@Book{Kaufmann:2001,
+ author = {Kaufmann, M. and Wagner, D.},
+ title = {Drawing Graphs: Methods and Models},
+ year = {2001},
+ volume = {2025},
+ series = {Lecture Notes in Computer Science Tutorial},
+ publisher = {Springer},
+}
+
+@article{Hucka:2003,
+ AUTHOR = {Hucka, M. and Finney, A. and Sauro, H.~M. and Bolouri, H.
+ and Doyle, J.~C. and Kitano, H. and Arkin, A.~P.
+ and Bornstein, B.~J. and Bray, D. and Cornish-Bowden, A.
+ and Cuellar, A.~A. and Dronov, S. and Gilles, E.~D.
+ and Ginkel, M. and Gor, V. and Goryanin, I.~I.
+ and Hedley, W.~J. and Hodgman, T.~C. and Hofmeyr, J.-H.
+ and Hunter, P.~J. and Juty, N.~S. and Kasberger, J.~L.
+ and Kremling, A. and Kummer, U. and Le Nov\`{e}re, N.
+ and Loew, L.~M. and Lucio, D. and Mendes, P. and Minch, E.
+ and Mjolsness, E.~D. and Nakayama, Y. and Nelson, M.~R.
+ and Nielsen, P.~F. and Sakurada, T. and Schaff, J.~C.
+ and Shapiro, B.~E. and Shimizu, T.~S. and Spence, H.~D.
+ and Stelling, J. and Takahashi, K. and Tomita, M.
+ and Wagner, J. and Wang, J.},
+ TITLE = {The {S}ystems {B}iology {M}arkup {L}anguage ({SBML}): A Medium
+ for Representation and Exchange of Biochemical Network Models},
+ JOURNAL = {Bioinformatics},
+ VOLUME = {19},
+ NUMBER = {4},
+ PAGES = {524-531},
+ YEAR = 2003
+}
+
+@Article{Kitano:2003,
+ author = {Hiroaki Kitano},
+ title = {A graphical notation for biochemical networks},
+ journal = {BioSilico},
+ year = {2003},
+ volume = {1},
+ pages = {169-176}
+}
+
+@Article{Kitano:2005,
+ author = {Hiroaki Kitano and Akira Funahashi and Yukiko Matsuoka and Kanae Oda},
+ title = {Using process diagrams for the graphical representation of biological networks},
+ journal = {Nature Biotechnology},
+ year = {2005},
+ volume = {23},
+ number = {8},
+ pages = {961-966}
+}
+
+@Article{Kohn:1999,
+ author = {Kurt W. Kohn},
+ title = {Molecular Interaction Map of the Mammalian Cell Cycle Control and {DNA} Repair Systems},
+ journal = {Molecular Biology of the Cell},
+ year = {1999},
+ volume = {10},
+ number = {8},
+ pages = {2703-2734}
+}
+
+@Article{Kohn:2006,
+ author = {Kurt W. Kohn and Mirit I. Aladjem and J. N. Weinstein and Y. Pommier},
+ title = {Molecular interaction maps of bioregulatory networks: A general rubric for systems biology},
+ journal = {Molecular Biology of the Cell},
+ year = {2006},
+ volume = {17},
+ number = {1},
+ pages = {1-13}
+}
+
+@InProceedings{Maimon:2001,
+ author = {Ron Maimon and Sam Browning},
+ title = {Diagrammatic notation and computational structure of gene networks},
+ booktitle = {Proceedings of the 2nd International Conference on Systems Biology},
+ year = {2001},
+ editor = {Hiroaki Kitano},
+ pages = {311-317},
+ address = {Madison, WI},
+ publisher = {Omnipress}
+}
+
+@Article{Michal:1998,
+ author = {Gerhard Michal},
+ title = {On Representation of Metabolic Pathways},
+ journal = {BioSystems},
+ year = {1998},
+ volume = {47},
+ pages = {1-7},
+}
+
+@Article{Moodie:2006,
+ author = {Stuart L. Moodie and Anatoly A. Sorokin and Igor Goryanin and Peter Ghazal},
+ title = {A Graphical Notation to Describe the Logical Interactions of Biological Pathways},
+ journal = {Journal of Integrative Bioinformatics},
+ year = {2006},
+ volume = {3},
+ pages = {36}
+}
+
+@Article{Pirson:2000,
+ author = {I. Pirson and N. Fortemaison and C. Jacobs and S. Dremier and J. E. Dumont and C. Maenhaut},
+ title = {The visual display of regulatory information and networks},
+ journal = {Trends in Cell Biology},
+ year = {2000},
+ volume = {10},
+ number = {10},
+ pages = {404-408}
+}
+
+@article{Chen:1976,
+ author = "Peter Pin-Shan S. Chen",
+ title = "The Entity-Relationship Model: Toward a Unified View of Data",
+ journal = "ACM Transactions on Database Systems",
+ volume = "1",
+ number = "1",
+ pages = "9-36",
+ year = "1976",
+ url = "citeseer.ist.psu.edu/519283.html"
+}
+
+%% This BibTeX bibliography file in UTF-8 format was created using Papers.
+%% http://mekentosj.com/papers/
+
+@article{Novere:2009p1,
+author = {Nicolas Novere and Michael Hucka and Huaiyu Mi and Stuart Moodie and Falk Schreiber and Anatoly Sorokin and Emek Demir and Katja Wegner and Mirit Aladjem and Sarala Wimalaratne and Frank Bergman and Ralph Gauges and Peter Ghazal and Hideya Kawaji and Lu Li and Yukiko Matsuoka and Alice Villeger and Sarah Boyd and Laurence Calzone and Melanie Courtot and Ugur Dogrusoz and Tom Freeman and Akira Funahashi and Samik Ghosh and Akiya Jouraku and Sohyoung Kim and Fedor Kolpakov and Augustin Luna and Sven Sahle and Esther Schmidt and Steven Watterson and Guanming Wu and Igor Goryanin and Douglas Kell and Chris Sander and Herbert Sauro and Jacky Snoep and Kurt Kohn and Hiroaki Kitano},
+journal = {Nat Biotech},
+title = {The Systems Biology Graphical Notation},
+note = {10.1038/nbt.1558},
+number = {8},
+pages = {735--741},
+volume = {27},
+year = {2009},
+date-added = {2009-08-26 14:04:26 +0100},
+date-modified = {2009-08-26 14:04:26 +0100},
+doi = {10.1038/nbt.1558},
+URL = {http://dx.doi.org/10.1038/nbt.1558},
+uri = {papers://77A5F866-15B8-4DD4-868D-FB8B6E3E7794/Paper/p1},
+rating = {0}
+}
+
+@misc{sbmll3core,
+title = {{The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core}},
+author = {Michael Hucka and Frank T. Bergmann and Stefan Hoops and Sarah M. Keating and Sven Sahle and James C. Schaff and Lucian P. Smith and Darren J. Wilkinson},
+year = 2007,
+month = {November},
+howpublished = {Available via the World Wide Web at \url{http://sbml.org/Documents/Specifications}},
+}
+
+@misc{umlspec,
+title = {{OMG Unified Modeling Language (OMG UML), Superstructure, V2.1.2}},
+author = {Object management Group},
+year = 2010,
+howpublished = {Available via the World Wide Web at \url{http://www.omg.org/spec/UML/2.1.2/Superstructure/PDF/}},
+}
+
Copied: ProcessDiagram/trunk/Specification/sbgn_PD-level1.pdf (from rev 839, ProcessDiagram/trunk/sbgn_PD-level1.pdf)
===================================================================
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Copied: ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex (from rev 839, ProcessDiagram/trunk/sbgn_PD-level1.tex)
===================================================================
--- ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex (rev 0)
+++ ProcessDiagram/trunk/Specification/sbgn_PD-level1.tex 2012-10-07 21:51:29 UTC (rev 842)
@@ -0,0 +1,62 @@
+% =============================================================================
+% $Id$
+% Top-level latex file for the SBGN Process Description specification document.
+%
+% $HeadURL$
+% =============================================================================
+
+\documentclass[11pt,oneside]{book}
+
+
+%% ----------------------------------------------------------------------------
+%% Layout customizations and macro definitions.
+%% ----------------------------------------------------------------------------
+
+\input{sources/latex-style}
+\input{sources/latex-macros}
+
+
+%% ----------------------------------------------------------------------------
+\begin{document}
+%% ----------------------------------------------------------------------------
+
+\frontmatter
+
+\input{sources/front-page}
+\input{sources/toc}
+
+\mainmatter
+\linenumbers
+
+\include{sources/introduction}
+\include{sources/concepts}
+\include{sources/glyphs}
+\include{sources/layout}
+
+
+\include{sources/acknowledgments}
+
+\appendix
+
+\include{sources/examples}
+\include{sources/refcard}
+\include{sources/validation}
+\include{sources/working}
+\include{sources/revision_history}
+
+\backmatter
+
+\clearpage
+\bibliographystyle{unsrt}
+\bibliography{sbgn_PD-level1}
+
+
+%% ----------------------------------------------------------------------------
+\end{document}
+%% ----------------------------------------------------------------------------
+
+
+% The following is for [X]Emacs users. Please leave in place.
+% Local Variables:
+% TeX-master: t
+% End:
Deleted: ProcessDiagram/trunk/sbgn_PD-level1.bib
===================================================================
--- ProcessDiagram/trunk/sbgn_PD-level1.bib 2012-10-07 21:47:30 UTC (rev 841)
+++ ProcessDiagram/trunk/sbgn_PD-level1.bib 2012-10-07 21:51:29 UTC (rev 842)
@@ -1,196 +0,0 @@
-@Article{Cook:2001,
- author = {Daniel L. Cook and J. F. Farley and S. J. Tapscott},
- title = {A basis for a visual language for describing, archiving and analyzing functional
-models of complex biological systems},
- journal = {Genome Biology},
- year = {2001},
- volume = {2},
- number = {4},
- pages = {research0012.1-research0012.10.}
-}
-
-@Article{Demir:2002,
- author = {Demir, E. and Babur, O. and Dogrusoz., U and Gursoy, A. and Nisanci, G. and Cetin-Atalay, R. and Ozturk, M.},
- title = {PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways},
- journal = {Bioinformatics},
- year = {2002},
- volume = {18},
- number = {7},
- pages = {996-1003}
-}
-
-@Article{Demir:2004,
- author = {Demir, E. and Babur, O. and Dogrusoz, U. and Gursoy, A. and Ayaz, A. and Gulesir, G. and Nisanci, G. and Cetin-Atalay, R.},
- title = {An ontology for collaborative construction and analysis of cellular pathways},
- journal = {Bioinformatics},
- year = {2004},
- volume = {20},
- number = {3},
- pages = {349-356}
-}
-
-@Book{DiBattista:1998,
- author = {{D}i {B}attista, G. and Eades, P. and Tamassia, R. and Tollis, I.G.},
- title = {Graph Drawing: Algorithms for the Visualization of Graphs},
- year = {1998},
- publisher = {Prentice Hall},
- address = {New Jersey},
-}
-
-@Book{Kaufmann:2001,
- author = {Kaufmann, M. and Wagner, D.},
- title = {Drawing Graphs: Methods and Models},
- year = {2001},
- volume = {2025},
- series = {Lecture Notes in Computer Science Tutorial},
- publisher = {Springer},
-}
-
-@article{Hucka:2003,
- AUTHOR = {Hucka, M. and Finney, A. and Sauro, H.~M. and Bolouri, H.
- and Doyle, J.~C. and Kitano, H. and Arkin, A.~P.
- and Bornstein, B.~J. and Bray, D. and Cornish-Bowden, A.
- and Cuellar, A.~A. and Dronov, S. and Gilles, E.~D.
- and Ginkel, M. and Gor, V. and Goryanin, I.~I.
- and Hedley, W.~J. and Hodgman, T.~C. and Hofmeyr, J.-H.
- and Hunter, P.~J. and Juty, N.~S. and Kasberger, J.~L.
- and Kremling, A. and Kummer, U. and Le Nov\`{e}re, N.
- and Loew, L.~M. and Lucio, D. and Mendes, P. and Minch, E.
- and Mjolsness, E.~D. and Nakayama, Y. and Nelson, M.~R.
- and Nielsen, P.~F. and Sakurada, T. and Schaff, J.~C.
- and Shapiro, B.~E. and Shimizu, T.~S. and Spence, H.~D.
- and Stelling, J. and Takahashi, K. and Tomita, M.
- and Wagner, J. and Wang, J.},
- TITLE = {The {S}ystems {B}iology {M}arkup {L}anguage ({SBML}): A Medium
- for Representation and Exchange of Biochemical Network Models},
- JOURNAL = {Bioinformatics},
- VOLUME = {19},
- NUMBER = {4},
- PAGES = {524-531},
- YEAR = 2003
-}
-
-@Article{Kitano:2003,
- author = {Hiroaki Kitano},
- title = {A graphical notation for biochemical networks},
- journal = {BioSilico},
- year = {2003},
- volume = {1},
- pages = {169-176}
-}
-
-@Article{Kitano:2005,
- author = {Hiroaki Kitano and Akira Funahashi and Yukiko Matsuoka and Kanae Oda},
- title = {Using process diagrams for the graphical representation of biological networks},
- journal = {Nature Biotechnology},
- year = {2005},
- volume = {23},
- number = {8},
- pages = {961-966}
-}
-
-@Article{Kohn:1999,
- author = {Kurt W. Kohn},
- title = {Molecular Interaction Map of the Mammalian Cell Cycle Control and {DNA} Repair Systems},
- journal = {Molecular Biology of the Cell},
- year = {1999},
- volume = {10},
- number = {8},
- pages = {2703-2734}
-}
-
-@Article{Kohn:2006,
- author = {Kurt W. Kohn and Mirit I. Aladjem and J. N. Weinstein and Y. Pommier},
- title = {Molecular interaction maps of bioregulatory networks: A general rubric for systems biology},
- journal = {Molecular Biology of the Cell},
- year = {2006},
- volume = {17},
- number = {1},
- pages = {1-13}
-}
-
-@InProceedings{Maimon:2001,
- author = {Ron Maimon and Sam Browning},
- title = {Diagrammatic notation and computational structure of gene networks},
- booktitle = {Proceedings of the 2nd International Conference on Systems Biology},
- year = {2001},
- editor = {Hiroaki Kitano},
- pages = {311-317},
- address = {Madison, WI},
- publisher = {Omnipress}
-}
-
-@Article{Michal:1998,
- author = {Gerhard Michal},
- title = {On Representation of Metabolic Pathways},
- journal = {BioSystems},
- year = {1998},
- volume = {47},
- pages = {1-7},
-}
-
-@Article{Moodie:2006,
- author = {Stuart L. Moodie and Anatoly A. Sorokin and Igor Goryanin and Peter Ghazal},
- title = {A Graphical Notation to Describe the Logical Interactions of Biological Pathways},
- journal = {Journal of Integrative Bioinformatics},
- year = {2006},
- volume = {3},
- pages = {36}
-}
-
-@Article{Pirson:2000,
- author = {I. Pirson and N. Fortemaison and C. Jacobs and S. Dremier and J. E. Dumont and C. Maenhaut},
- title = {The visual display of regulatory information and networks},
- journal = {Trends in Cell Biology},
- year = {2000},
- volume = {10},
- number = {10},
- pages = {404-408}
-}
-
-@article{Chen:1976,
- author = "Peter Pin-Shan S. Chen",
- title = "The Entity-Relationship Model: Toward a Unified View of Data",
- journal = "ACM Transactions on Database Systems",
- volume = "1",
- number = "1",
- pages = "9-36",
- year = "1976",
- url = "citeseer.ist.psu.edu/519283.html"
-}
-
-%% This BibTeX bibliography file in UTF-8 format was created using Papers.
-%% http://mekentosj.com/papers/
-
-@article{Novere:2009p1,
-author = {Nicolas Novere and Michael Hucka and Huaiyu Mi and Stuart Moodie and Falk Schreiber and Anatoly Sorokin and Emek Demir and Katja Wegner and Mirit Aladjem and Sarala Wimalaratne and Frank Bergman and Ralph Gauges and Peter Ghazal and Hideya Kawaji and Lu Li and Yukiko Matsuoka and Alice Villeger and Sarah Boyd and Laurence Calzone and Melanie Courtot and Ugur Dogrusoz and Tom Freeman and Akira Funahashi and Samik Ghosh and Akiya Jouraku and Sohyoung Kim and Fedor Kolpakov and Augustin Luna and Sven Sahle and Esther Schmidt and Steven Watterson and Guanming Wu and Igor Goryanin and Douglas Kell and Chris Sander and Herbert Sauro and Jacky Snoep and Kurt Kohn and Hiroaki Kitano},
-journal = {Nat Biotech},
-title = {The Systems Biology Graphical Notation},
-note = {10.1038/nbt.1558},
-number = {8},
-pages = {735--741},
-volume = {27},
-year = {2009},
-date-added = {2009-08-26 14:04:26 +0100},
-date-modified = {2009-08-26 14:04:26 +0100},
-doi = {10.1038/nbt.1558},
-URL = {http://dx.doi.org/10.1038/nbt.1558},
-uri = {papers://77A5F866-15B8-4DD4-868D-FB8B6E3E7794/Paper/p1},
-rating = {0}
-}
-
-@misc{sbmll3core,
-title = {{The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core}},
-author = {Michael Hucka and Frank T. Bergmann and Stefan Hoops and Sarah M. Keating and Sven Sahle and James C. Schaff and Lucian P. Smith and Darren J. Wilkinson},
-year = 2007,
-month = {November},
-howpublished = {Available via the World Wide Web at \url{http://sbml.org/Documents/Specifications}},
-}
-
-@misc{umlspec,
-title = {{OMG Unified Modeling Language (OMG UML), Superstructure, V2.1.2}},
-author = {Object management Group},
-year = 2010,
-howpublished = {Available via the World Wide Web at \url{http://www.omg.org/spec/UML/2.1.2/Superstructure/PDF/}},
-}
-
Deleted: ProcessDiagram/trunk/sbgn_PD-level1.pdf
===================================================================
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Deleted: ProcessDiagram/trunk/sbgn_PD-level1.tex
===================================================================
--- ProcessDiagram/trunk/sbgn_PD-level1.tex 2012-10-07 21:47:30 UTC (rev 841)
+++ ProcessDiagram/trunk/sbgn_PD-level1.tex 2012-10-07 21:51:29 UTC (rev 842)
@@ -1,62 +0,0 @@
-% =============================================================================
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-% =============================================================================
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-\documentclass[11pt,oneside]{book}
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-
-%% ----------------------------------------------------------------------------
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-%% ----------------------------------------------------------------------------
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-%% ----------------------------------------------------------------------------
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-
-\include{sources/acknowledgments}
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-\appendix
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-\include{sources/examples}
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-\include{sources/validation}
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-
-\clearpage
-\bibliographystyle{unsrt}
-\bibliography{sbgn_PD-level1}
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-
-%% ----------------------------------------------------------------------------
-\end{document}
-%% ----------------------------------------------------------------------------
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-
-% The following is for [X]Emacs users. Please leave in place.
-% Local Variables:
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This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <le...@us...> - 2012-10-07 21:47:39
|
Revision: 841
http://sbgn.svn.sourceforge.net/sbgn/?rev=841&view=rev
Author: lenov
Date: 2012-10-07 21:47:30 +0000 (Sun, 07 Oct 2012)
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From: <le...@us...> - 2012-10-07 21:40:38
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Revision: 840
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Date: 2012-10-07 21:40:29 +0000 (Sun, 07 Oct 2012)
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Modified: ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log
===================================================================
--- ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log 2012-08-14 22:52:38 UTC (rev 839)
+++ ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log 2012-10-07 21:40:29 UTC (rev 840)
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[truncated message content] |
|
From: <ali...@us...> - 2012-08-14 22:52:47
|
Revision: 839
http://sbgn.svn.sourceforge.net/sbgn/?rev=839&view=rev
Author: alice_villeger
Date: 2012-08-14 22:52:38 +0000 (Tue, 14 Aug 2012)
Log Message:
-----------
fixed a few typos and added internal links
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--- ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.aux 2012-07-18 07:12:59 UTC (rev 838)
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===================================================================
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<use images/or.pdf>) (./sources/not.tex
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File: images/not.pdf Graphic file (type pdf)
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osphate.
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+<use images/submap-unfolded.pdf>)) [25 <./images/submap-folded.pdf> <./images/s
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(./sources/build.tex
Chapter 3.
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File: images/hemoglobin-macromolecule.pdf Graphic file (type pdf)
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+<use images/hemoglobin-macromolecule.pdf> [27 <./images/MAPK-OneVar.pdf> <./ima
ges/MAPK-TwoVar.pdf>]
-<images/hemoglobin-multimer.pdf, id=494, 419.5675pt x 284.06125pt>
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File: images/hemoglobin-multimer.pdf Graphic file (type pdf)
<use images/hemoglobin-multimer.pdf>
-<images/hemoglobin-complex.pdf, id=495, 729.72626pt x 418.56375pt>
+<images/hemoglobin-complex.pdf, id=500, 729.72626pt x 418.56375pt>
File: images/hemoglobin-complex.pdf Graphic file (type pdf)
-<use images/hemoglobin-complex.pdf>)) [27 <./images/hemoglobin-macromolecule.pd
+<use images/hemoglobin-complex.pdf>)) [28 <./images/hemoglobin-macromolecule.pd
f> <./images/hemoglobin-multimer.pdf> <./images/hemoglobin-complex.pdf>]
\openout2 = `sources/refcard.aux'.
-(./sources/refcard.tex <images/refcard.pdf, id=532, 798.985pt x 551.05875pt>
+(./sources/refcard.tex <images/refcard.pdf, id=537, 798.985pt x 551.05875pt>
File: images/refcard.pdf Graphic file (type pdf)
-<use images/refcard.pdf>) [28
+<use images/refcard.pdf>) [29
<./images/refcard.pdf>]
-(./sbgn_PD-level1-user.bbl) [29
+(./sbgn_PD-level1-user.bbl) [30
@@ -1487,10 +1493,10 @@
(./sources/introduction.aux) (./sources/symbols.aux) (./sources/build.aux)
(./sources/refcard.aux)) )
Here is how much of TeX's memory you used:
- 5628 strings out of 493848
- 77686 string characters out of 1152824
- 154142 words of memory out of 3000000
- 8561 multiletter control sequences out of 15000+50000
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32i,8n,32p,1395b,298s stack positions out of 5000i,500n,10000p,200000b,50000s
@@ -1504,9 +1510,9 @@
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8a.pfb>
-Output written on sbgn_PD-level1-user.pdf (30 pages, 1405964 bytes).
+Output written on sbgn_PD-level1-user.pdf (31 pages, 1427319 bytes).
PDF statistics:
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0 named destinations out of 1000 (max. 500000)
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+ 306 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/build.aux
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/build.aux 2012-07-17 23:22:09 UTC (rev 837)
+++ ProcessDiagram/trunk/UserManual/sources/build.aux 2012-07-18 07:12:59 UTC (rev 838)
@@ -1,25 +1,25 @@
\relax
\citation{Hucka:2003}
-\@writefile{toc}{\contentsline {chapter}{\numberline {3}Building a SBGN Process Description map\xspace }{25}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {3}Building a SBGN Process Description map\xspace }{26}}
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\@writefile{lot}{\addvspace {10\p@ }}
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-\@writefile{lof}{\contentsline {figure}{\numberline {3.1}{\ignorespaces Phosphorylation of ERK by MEK, where ERK is represented by three different macromolecules.}}{25}}
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-\@writefile{lof}{\contentsline {figure}{\numberline {3.2}{\ignorespaces Phosphorylation of ERK by MEK, where ERK is represented by three different states, non-phosphorylated, mono-phosphorylated and bi-phosphorylated.}}{26}}
-\newlabel{fig:MAPK-OneVar}{{3.2}{26}}
-\@writefile{lof}{\contentsline {figure}{\numberline {3.3}{\ignorespaces Phosphorylation of ERK by MEK, where each phosphorylated form of ERK is represented.}}{26}}
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-\@writefile{lof}{\contentsline {figure}{\numberline {3.4}{\ignorespaces Hemoglobin oxygenation using \emph {macromolecules}.}}{27}}
-\newlabel{fig:hemoglobin-macromolecule}{{3.4}{27}}
-\@writefile{lof}{\contentsline {figure}{\numberline {3.5}{\ignorespaces legend}}{27}}
-\newlabel{fig:hemoglobin-multimer}{{3.5}{27}}
-\@writefile{lof}{\contentsline {figure}{\numberline {3.6}{\ignorespaces legend}}{27}}
-\newlabel{fig:hemoglobin-complex}{{3.6}{27}}
+\newlabel{chp:build}{{3}{26}}
+\@writefile{toc}{\contentsline {section}{\numberline {3.1}How to choose the symbols to use?}{26}}
+\newlabel{sec:choose}{{3.1}{26}}
+\@writefile{lof}{\contentsline {figure}{\numberline {3.1}{\ignorespaces Phosphorylation of ERK by MEK, where ERK is represented by three different macromolecules.}}{26}}
+\newlabel{fig:MAPK-NoVar}{{3.1}{26}}
+\@writefile{lof}{\contentsline {figure}{\numberline {3.2}{\ignorespaces Phosphorylation of ERK by MEK, where ERK is represented by three different states, non-phosphorylated, mono-phosphorylated and bi-phosphorylated.}}{27}}
+\newlabel{fig:MAPK-OneVar}{{3.2}{27}}
+\@writefile{lof}{\contentsline {figure}{\numberline {3.3}{\ignorespaces Phosphorylation of ERK by MEK, where each phosphorylated form of ERK is represented.}}{27}}
+\newlabel{fig:MAPK-TwoVar}{{3.3}{27}}
+\@writefile{lof}{\contentsline {figure}{\numberline {3.4}{\ignorespaces Hemoglobin oxygenation using \emph {macromolecules}.}}{28}}
+\newlabel{fig:hemoglobin-macromolecule}{{3.4}{28}}
+\@writefile{lof}{\contentsline {figure}{\numberline {3.5}{\ignorespaces legend}}{28}}
+\newlabel{fig:hemoglobin-multimer}{{3.5}{28}}
+\@writefile{lof}{\contentsline {figure}{\numberline {3.6}{\ignorespaces legend}}{28}}
+\newlabel{fig:hemoglobin-complex}{{3.6}{28}}
\@setckpt{sources/build}{
-\setcounter{page}{28}
+\setcounter{page}{29}
\setcounter{equation}{0}
\setcounter{enumi}{0}
\setcounter{enumii}{0}
Modified: ProcessDiagram/trunk/UserManual/sources/multimer.tex
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/multimer.tex 2012-07-17 23:22:09 UTC (rev 837)
+++ ProcessDiagram/trunk/UserManual/sources/multimer.tex 2012-07-18 07:12:59 UTC (rev 838)
@@ -9,3 +9,12 @@
\caption{The \PD glyph for \glyph{multimer}. }
\label{fig:multimer}
\end{figure}
+
+Examples of \glyph{multimers} are presented in \fig{multimer-examples}.
+
+\begin{figure}[H]
+ \centering
+ \includegraphics[scale = 0.5]{images/multimer-examples}
+ \caption{Examples of \glyph{multimers}. From left to right: pentameric nicotinic receptor in the open state, tetramer of oxygenated globin.}
+ \label{fig:multimer-examples}
+\end{figure}
\ No newline at end of file
Modified: ProcessDiagram/trunk/UserManual/sources/multimer.tex~
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/multimer.tex~ 2012-07-17 23:22:09 UTC (rev 837)
+++ ProcessDiagram/trunk/UserManual/sources/multimer.tex~ 2012-07-18 07:12:59 UTC (rev 838)
@@ -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/refcard.aux
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/refcard.aux 2012-07-17 23:22:09 UTC (rev 837)
+++ ProcessDiagram/trunk/UserManual/sources/refcard.aux 2012-07-18 07:12:59 UTC (rev 838)
@@ -1,6 +1,6 @@
\relax
\@setckpt{sources/refcard}{
-\setcounter{page}{29}
+\setcounter{page}{30}
\setcounter{equation}{0}
\setcounter{enumi}{0}
\setcounter{enumii}{0}
Modified: ProcessDiagram/trunk/UserManual/sources/symbols.aux
===================================================================
--- ProcessDiagram/trunk/UserManual/sources/symbols.aux 2012-07-17 23:22:09 UTC (rev 837)
+++ ProcessDiagram/trunk/UserManual/sources/symbols.aux 2012-07-18 07:12:59 UTC (rev 838)
@@ -45,161 +45,163 @@
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\newlabel{fig:multimer}{{2.12}{8}}
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-\newlabel{sec:decorations}{{2.2}{8}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.13}{\ignorespaces Examples of \emph {multimers}. From left to right: pentameric nicotinic receptor in the open state, tetramer of oxygenated globin.}}{9}}
+\newlabel{fig:multimer-examples}{{2.13}{9}}
+\@writefile{toc}{\contentsline {section}{\numberline {2.2}Decorations of the entity pool nodes}{9}}
+\newlabel{sec:decorations}{{2.2}{9}}
\@writefile{toc}{\contentsline {subsection}{\numberline {2.2.1}Glyph: \emph {Unit of information}}{9}}
\newlabel{sec:unitInfo}{{2.2.1}{9}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.13}{\ignorespaces The Process Description\xspace glyph for \emph {unit of information}.}}{9}}
-\newlabel{fig:unitInfo}{{2.13}{9}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.14}{\ignorespaces The Process Description\xspace glyph for \emph {unit of information}.}}{9}}
+\newlabel{fig:unitInfo}{{2.14}{9}}
\@writefile{toc}{\contentsline {subsection}{\numberline {2.2.2}Glyph: \emph {State variable}}{9}}
\newlabel{sec:stateVariable}{{2.2.2}{9}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.14}{\ignorespaces The Process Description\xspace glyph for \emph {state variable}.}}{9}}
-\newlabel{fig:state-var}{{2.14}{9}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.15}{\ignorespaces The Process Description\xspace glyph for \emph {state variable}.}}{10}}
+\newlabel{fig:state-var}{{2.15}{10}}
\@writefile{toc}{\contentsline {subsection}{\numberline {2.2.3}Glyph: \emph {Clone marker}}{10}}
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-\@writefile{lof}{\contentsline {figure}{\numberline {2.16}{\ignorespaces The Process Description\xspace glyph for \emph {labeled clone marker} applied to a \emph {multimer} of \emph {macromolecules}.}}{10}}
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-\@writefile{toc}{\contentsline {subsection}{\numberline {2.2.4}Controlled vocabularies used in SBGN Process Description\xspace Level\nobreakspace {}1\xspace }{10}}
-\newlabel{sec:CVs}{{2.2.4}{10}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.16}{\ignorespaces The Process Description\xspace glyph for \emph {simple clone marker} applied to a \emph {simple chemical}}}{10}}
+\newlabel{fig:simpleCloneMarker}{{2.16}{10}}
\citation{Courtot:2011}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.17}{\ignorespaces The Process Description\xspace glyph for \emph {labeled clone marker} applied to a \emph {multimer} of \emph {macromolecules}.}}{11}}
+\newlabel{fig:labeledCloneMarker}{{2.17}{11}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.2.4}Controlled vocabularies used in SBGN Process Description\xspace Level\nobreakspace {}1\xspace }{11}}
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-\@writefile{toc}{\contentsline {subsubsection}{Macromolecule covalent modifications}{11}}
-\newlabel{sec:covalent-mod-cv}{{2.2.4}{11}}
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+\@writefile{toc}{\contentsline {subsubsection}{Macromolecule covalent modifications}{12}}
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[truncated message content] |
|
From: <le...@us...> - 2012-07-17 23:22:18
|
Revision: 837
http://sbgn.svn.sourceforge.net/sbgn/?rev=837&view=rev
Author: lenov
Date: 2012-07-17 23:22:09 +0000 (Tue, 17 Jul 2012)
Log Message:
-----------
Modified Paths:
--------------
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log
ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.pdf
ProcessDiagram/trunk/UserManual/sources/build.aux
ProcessDiagram/trunk/UserManual/sources/complex.tex
ProcessDiagram/trunk/UserManual/sources/complex.tex~
ProcessDiagram/trunk/UserManual/sources/genetic.tex
ProcessDiagram/trunk/UserManual/sources/genetic.tex~
ProcessDiagram/trunk/UserManual/sources/refcard.aux
ProcessDiagram/trunk/UserManual/sources/symbols.aux
Added Paths:
-----------
ProcessDiagram/trunk/UserManual/images/complex-examples.eps
ProcessDiagram/trunk/UserManual/images/complex-examples.png
ProcessDiagram/trunk/UserManual/images/complex-examples.svg
ProcessDiagram/trunk/UserManual/images/multimer-examples.svg
Added: ProcessDiagram/trunk/UserManual/images/complex-examples.eps
===================================================================
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+%%EndProlog
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Modified: ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.log
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[truncated message content] |
|
From: <le...@us...> - 2012-07-17 21:32:25
|
Revision: 836
http://sbgn.svn.sourceforge.net/sbgn/?rev=836&view=rev
Author: lenov
Date: 2012-07-17 21:32:16 +0000 (Tue, 17 Jul 2012)
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[truncated message content] |
|
From: <le...@us...> - 2012-07-16 22:38:14
|
Revision: 835
http://sbgn.svn.sourceforge.net/sbgn/?rev=835&view=rev
Author: lenov
Date: 2012-07-16 22:38:05 +0000 (Mon, 16 Jul 2012)
Log Message:
-----------
Modified Paths:
--------------
ProcessDiagram/trunk/UserManual/images/MAPK-only.eps
ProcessDiagram/trunk/UserManual/images/MAPK-only.pdf
ProcessDiagram/trunk/UserManual/images/MAPK-only.png
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ProcessDiagram/trunk/UserManual/images/refcard.pdf
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ProcessDiagram/trunk/UserManual/sbgn_PD-level1-user.blg
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/CVs.tex~
ProcessDiagram/trunk/UserManual/sources/association.tex
ProcessDiagram/trunk/UserManual/sources/association.tex~
ProcessDiagram/trunk/UserManual/sources/build.aux
ProcessDiagram/trunk/UserManual/sources/build.tex
ProcessDiagram/trunk/UserManual/sources/build.tex.backup
ProcessDiagram/trunk/UserManual/sources/build.tex~
ProcessDiagram/trunk/UserManual/sources/catalysis.tex
ProcessDiagram/trunk/UserManual/sources/catalysis.tex~
ProcessDiagram/trunk/UserManual/sources/interpret.aux
ProcessDiagram/trunk/UserManual/sources/introduction.tex
ProcessDiagram/trunk/UserManual/sources/introduction.tex~
ProcessDiagram/trunk/UserManual/sources/necessary_stim.tex
ProcessDiagram/trunk/UserManual/sources/necessary_stim.tex~
ProcessDiagram/trunk/UserManual/sources/phenotype.tex
ProcessDiagram/trunk/UserManual/sources/phenotype.tex~
ProcessDiagram/trunk/UserManual/sources/process.tex
ProcessDiagram/trunk/UserManual/sources/process.tex~
ProcessDiagram/trunk/UserManual/sources/refcard.aux
ProcessDiagram/trunk/UserManual/sources/stimulation.tex
ProcessDiagram/trunk/UserManual/sources/stimulation.tex~
ProcessDiagram/trunk/UserManual/sources/symbols.aux
Modified: ProcessDiagram/trunk/UserManual/images/MAPK-only.eps
===================================================================
--- ProcessDiagram/trunk/UserManual/images/MAPK-only.eps 2012-07-16 18:40:29 UTC (rev 834)
+++ ProcessDiagram/trunk/UserManual/images/MAPK-only.eps 2012-07-16 22:38:05 UTC (rev 835)
@@ -1,6 +1,6 @@
%!PS-Adobe-3.0 EPSF-3.0
%%Creator: cairo 1.10.2 (http://cairographics.org)
-%%CreationDate: Fri Jul 13 19:02:40 2012
+%%CreationDate: Mon Jul 16 22:57:53 2012
%%Pages: 1
%%BoundingBox: 0 -1 344 332
%%DocumentData: Clean7Bit
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@@ -1008,6 +1013,10 @@
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11 dict begin
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Encoding 2 /uni003A put
Encoding 3 /uni0035 put
Encoding 4 /uni0032 put
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[truncated message content] |
|
From: <le...@us...> - 2012-07-16 18:40:39
|
Revision: 834
http://sbgn.svn.sourceforge.net/sbgn/?rev=834&view=rev
Author: lenov
Date: 2012-07-16 18:40:29 +0000 (Mon, 16 Jul 2012)
Log Message:
-----------
Modified Paths:
--------------
ProcessDiagram/trunk/UserManual/images/MAPK-TwoVar.eps
ProcessDiagram/trunk/UserManual/images/MAPK-TwoVar.pdf
ProcessDiagram/trunk/UserManual/images/MAPK-TwoVar.svg
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Added Paths:
-----------
ProcessDiagram/trunk/UserManual/images/MAPK-twoVar.png
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ProcessDiagram/trunk/UserManual/images/stimulation-reversible.png
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Modified: ProcessDiagram/trunk/UserManual/images/MAPK-TwoVar.eps
===================================================================
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showpage
%%Trailer
Modified: ProcessDiagram/trunk/UserManual/images/MAPK-TwoVar.pdf
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