[Avida-SVN] r3400 - in development: Avida.xcodeproj documentation
brysonda at myxo.css.msu.edu
brysonda at myxo.css.msu.edu
Fri Sep 11 10:25:15 PDT 2009
Author: brysonda
Date: 2009-09-11 13:25:15 -0400 (Fri, 11 Sep 2009)
New Revision: 3400
Added:
development/documentation/avida_overview.html
Modified:
development/Avida.xcodeproj/project.pbxproj
development/documentation/cpu_tour.html
development/documentation/index.html
development/documentation/main.css
Log:
Update the documentation:
- reorganize the index categories
- add a short overview page
- add a note about circular memory spaces
- a few changes to the css styles
Modified: development/Avida.xcodeproj/project.pbxproj
===================================================================
--- development/Avida.xcodeproj/project.pbxproj 2009-09-11 16:42:59 UTC (rev 3399)
+++ development/Avida.xcodeproj/project.pbxproj 2009-09-11 17:25:15 UTC (rev 3400)
@@ -452,6 +452,7 @@
70211A5B0ECBD531004A293A /* cRCObject.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cRCObject.h; sourceTree = "<group>"; };
70211A5C0ECBD531004A293A /* cRCObject.cc */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = cRCObject.cc; sourceTree = "<group>"; };
70211A6C0ECBDB72004A293A /* tRCPtr.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = tRCPtr.h; sourceTree = "<group>"; };
+ 70217EAE105AB75500F2789F /* avida_overview.html */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text.html.documentation; path = avida_overview.html; sourceTree = "<group>"; };
7023EC330C0A426900362B9C /* libavida-core.a */ = {isa = PBXFileReference; explicitFileType = archive.ar; includeInIndex = 0; path = "libavida-core.a"; sourceTree = BUILT_PRODUCTS_DIR; };
7027621909D73E5900741717 /* cOrgSourceMessage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cOrgSourceMessage.h; sourceTree = "<group>"; };
7027621A09D73E7700741717 /* cOrgSinkMessage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cOrgSinkMessage.h; sourceTree = "<group>"; };
@@ -1191,6 +1192,7 @@
children = (
707415C70AA7E4100064A546 /* main.css */,
70A33CC00D878407008EF976 /* as_overview.html */,
+ 70217EAE105AB75500F2789F /* avida_overview.html */,
704D57210AA53F8600207FC1 /* code_standards.html */,
707CE7500AA334120022D19C /* analyze.html */,
707CE7490AA333060022D19C /* actions.html */,
Added: development/documentation/avida_overview.html
===================================================================
--- development/documentation/avida_overview.html (rev 0)
+++ development/documentation/avida_overview.html 2009-09-11 17:25:15 UTC (rev 3400)
@@ -0,0 +1,44 @@
+<html>
+<head>
+ <title>Avida : Overview</title>
+ <link rel="stylesheet" type="text/css" href="main.css" />
+</head>
+<body>
+
+<div class="revision">
+Revised 2009-09-11 DMB
+</div>
+
+<p><a href="index.html">Return to the Index</a></p>
+<hr />
+
+<div align="center">
+<h1>Overview</h1>
+</div>
+
+<p>
+Avida is a software platform for experiments with self-replicating and evolving computer programs. It provides detailed
+control over experimental settings and protocols, a large array of measurement tools, and sophisticated methods to analyze
+and post-process experimental data.
+</p>
+<p>
+In Avida, each digital organism is a self-contained computing automaton that has the ability to construct new automata.
+The organism is responsible for building the genome (computer program) that will control its offspring automaton, and
+handing that genome to the Avida world. Avida will then construct virtual hardware for the genome to be run on, and
+determine how this new organism should be placed into the population. In a typical Avida experiment, a successful
+organism attempts to make an identical copy of its own genome, and Avida randomly places that copy into the population,
+typically by replacing another member of the population.
+</p>
+<p>
+In principle, the only assumption made about these self-replicating automata in the core Avida software is that their
+initial state can be described by a string of symbols (their genome) and that it is possible through processing these
+symbols to autonomously produce offspring organisms. However, in practice our work has focused on automata with a simple
+von Neumann architecture that operate on an assembly-like language inspired by the Tierra system. Future research projects
+will likely have us implement additional oranism instantiations to allow us to explore additional biological questions.
+</p>
+
+<hr />
+<p><a href="index.html">Return to the Index</a></p>
+
+</body>
+</html>
Modified: development/documentation/cpu_tour.html
===================================================================
--- development/documentation/cpu_tour.html 2009-09-11 16:42:59 UTC (rev 3399)
+++ development/documentation/cpu_tour.html 2009-09-11 17:25:15 UTC (rev 3400)
@@ -6,7 +6,7 @@
<body>
<div class="revision">
-Revised 2006-09-05 DMB
+Revised 2009-09-11 DMB
</div>
<p><a href="index.html">Return to the Index</a></p>
@@ -32,7 +32,9 @@
<ul>
<li>A <strong style="color: #006666">memory</strong> that consists of a sequence
of instructions, each associated with a set of flags to denote if the
- instruction has been executed, copied, mutated, etc.</li>
+ instruction has been executed, copied, mutated, etc. Memory is treated
+ as circular, such that execution will loop back to the first instruction
+ after the last instruction has been executed</li>
<li>An <strong style="color: #880088">instruction pointer</strong> (IP) that
indicates the next site in the memory to be executed.</li>
<li>Three <strong style="color: #FF8888">registers</strong> that can be used
Modified: development/documentation/index.html
===================================================================
--- development/documentation/index.html 2009-09-11 16:42:59 UTC (rev 3399)
+++ development/documentation/index.html 2009-09-11 17:25:15 UTC (rev 3400)
@@ -21,47 +21,55 @@
<h2>General Information</h2>
-<p>
-<a href="cpu_tour.html">A Guided Tour of an Ancestor and its Hardware</a>
-<br /><a href="structure.html">The Directory and File Structure</a>
-<br /><a href="svn.html">Using Subversion to Obtain Avida</a>
-<br />[@TODO]<a href="as_overview.html">The Avida Scripting Language</a>
-<br /><a href="flamegraph.html">Creating a Flame Graph</a>
-</p>
+<ul>
+<li><a href="avida_overview.html">Overview</a></li>
+<li><a href="cpu_tour.html">A Guided Tour of an Ancestor and its Hardware</a></li>
+<li><a href="structure.html">The Directory and File Structure</a></li>
+<li><a href="svn.html">Using Subversion to Obtain Avida</a></li>
+<li><a href="as_overview.html">The Avida Scripting Language</a></li>
+</ul>
-<h2>Configuration Files</h2>
+<h2>Configuration and Command Reference</h2>
-<p>
-<a href="config.html">Setting up the Avida Configuration File</a>
-<br /><a href="energy_model.html">Energy model configuration</a>
-<br /><a href="inst_set.html">Setting up the Instruction Set</a>
-<br /><a href="events.html">Guidelines to setting up the Events File</a>
-<br /><a href="environment.html">Guidelines to setting up Environments</a>
-<br /><a href="analyze.html">Guidelines to Analyze Mode</a>
-<br /><a href="analyze_samples.html">Sample Analyze Programs</a>
-<br /><a href="actions.html">List of Actions</a>
-<br /><a href="configurations.html">Example configurations from published work</a>
-</p>
+<ul>
+<li><a href="config.html">Setting up the Avida Configuration File</a></li>
+<li><a href="energy_model.html">Energy model configuration</a></li>
+<li><a href="inst_set.html">Setting up the Instruction Set</a></li>
+<li><a href="events.html">Guidelines to setting up the Events File</a></li>
+<li><a href="environment.html">Guidelines to setting up Environments</a></li>
+<li><a href="analyze.html">Guidelines to Analyze Mode</a></li>
+<li><a href="analyze_samples.html">Sample Analyze Programs</a></li>
+<li><a href="actions.html">List of Actions</a></li>
+</ul>
-<h2>Guides to Modifying the Avida Source Code</h2>
+<h2>Experiment and Analysis Guides</h2>
-<p>
-<a href="code_c++_intro.html">A Conceptual Introduction to C++ in Avida</a>
-<br /><a href="code_death_birth.html">Guide to the Death/Birth Cycle</a>
-<br /><a href="code_life_cycle.html">Guide to an Avidan Life Cycle</a>
-<br /><a href="code_genome.html">The Building Blocks of the Virtual CPU</a>
-<br /><a href="code_environment.html">The Environment Source Code</a>
-</p>
-<p>
-<a href="code_standards.html">Coding Standards</a>
-<br /><a href="code_instruction.html">Instruction Implemention Checklist</a>
-<br /><a href="code_task.html">Environment Task Implementation Checklist</a>
-</p>
+<ul>
+<li><a href="configurations.html">Example configurations from published work</a></li>
+<li><a href="flamegraph.html">Creating a Flame Graph</a></li>
+</ul>
+
+<h2>Development Reference</h2>
+<p>Guides and guidelines for modifying the Avida source code.</p>
+
+<ul>
+<li><a href="code_c++_intro.html">A Conceptual Introduction to C++ in Avida</a></li>
+<li><a href="code_death_birth.html">Guide to the Death/Birth Cycle</a></li>
+<li><a href="code_life_cycle.html">Guide to an Avidan Life Cycle</a></li>
+<li><a href="code_genome.html">The Building Blocks of the Virtual CPU</a></li>
+<li><a href="code_environment.html">The Environment Source Code</a></li>
+</ul>
+<ul>
+<li><a href="code_standards.html">Coding Standards</a></li>
+<li><a href="code_instruction.html">Instruction Implemention Checklist</a></li>
+<li><a href="code_task.html">Environment Task Implementation Checklist</a></li>
+</ul>
+
<div>
-Revised 2006-08-30 DMB
+Revised 2009-09-11 DMB
</div>
</body>
Modified: development/documentation/main.css
===================================================================
--- development/documentation/main.css 2009-09-11 16:42:59 UTC (rev 3399)
+++ development/documentation/main.css 2009-09-11 17:25:15 UTC (rev 3400)
@@ -1,3 +1,14 @@
+body, table {
+ font: 10pt 'Lucida Grande', Verdana, sans-serif;
+}
+
+a {
+ text-decoration: none;
+}
+a:hover {
+ text-decoration: underline;
+}
+
pre, .sub {
margin-left: 10px;
}
@@ -2,2 +13,5 @@
+pre, code, kbd {
+ font: 9pt 'Monaco', monospace, Verdana, sans-serif;
+}
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