From cb063440ce7652ea082e4ab9f002700b1cb0837f Mon Sep 17 00:00:00 2001
From: jae <>
Date: Fri, 7 Jun 2013 23:04:04 +0000
Subject: [PATCH] fix nupic links

---
 LDP/howto/linuxdoc/AI-Alife-HOWTO.sgml | 108 ++++++++++++++-----------
 1 file changed, 61 insertions(+), 47 deletions(-)

diff --git a/LDP/howto/linuxdoc/AI-Alife-HOWTO.sgml b/LDP/howto/linuxdoc/AI-Alife-HOWTO.sgml
index bdefb0a6..8f0a9e09 100644
--- a/LDP/howto/linuxdoc/AI-Alife-HOWTO.sgml
+++ b/LDP/howto/linuxdoc/AI-Alife-HOWTO.sgml
@@ -45,6 +45,10 @@ GNU/Linux specifically in mind.
 
 <itemize>
 
+    <item>v3.2 -
+
+    <p>New entries: <ref id="Simbrain">, <ref id="lens">.
+
     <item>v3.1 -
 
     <p>New entries: <ref id="SimpleAI">.
@@ -1392,7 +1396,7 @@ United States.
     <label id="Baysian Modeling">
     <tag/Software for Flexible Bayesian Modeling/
       <itemize>
-        <item>Web site: <htmlurl url="http://www.cs.utoronto.ca/&tilde;radford/fbm.software.html" name="www.cs.utoronto.ca/&tilde;radford/fbm.software.html">
+        <item>Web site: <htmlurl url="http://www.cs.utoronto.ca/&tilde;radford/fbm.software.html">
       </itemize>
 
       This software implements flexible Bayesian models for regression
@@ -1406,7 +1410,7 @@ United States.
     <label id="BELIEF">
       <tag/BELIEF/
       <itemize>
-        <item>Web site: <htmlurl url="http://www.cs.cmu.edu/afs/cs/project/ai-repository/ai/areas/reasonng/probabl/belief/" name="www.cs.cmu.edu/afs/cs/project/ai-repository/ai/areas/reasonng/probabl/belief/">
+        <item>Web site: <htmlurl url="http://www.cs.cmu.edu/afs/cs/project/ai-repository/ai/areas/reasonng/probabl/belief/">
       </itemize>
 
 
@@ -1427,8 +1431,7 @@ United States.
     <tag/bpnn.py/
         <itemize>
             <item>Web site: <htmlurl
-                url="http://arctrix.com/nas/python/bpnn.py"
-                name="http://arctrix.com/nas/python/bpnn.py">
+                url="http://arctrix.com/nas/python/bpnn.py">
         </itemize>
 
         A simple back-propogation ANN in Python.
@@ -1437,8 +1440,7 @@ United States.
     <label id="brain">
     <tag/brain/
         <itemize>
-            <item>Web site: <htmlurl
-                url="http://harthur.github.com/brain/">
+            <item>Web site: <htmlurl url="http://harthur.github.com/brain/">
         </itemize>
 
         Brain is a lightweight JavaScript library for  neural networks. It
@@ -1448,8 +1450,7 @@ United States.
     <label id="brain-simulator">
     <tag/brain-simulator/
         <itemize>
-            <item>Web site: <htmlurl
-                url="http://www.briansimulator.org/">
+            <item>Web site: <htmlurl url="http://www.briansimulator.org/">
         </itemize>
 
         Brian is a clock-driven simulator for spiking neural networks. It is
@@ -1499,8 +1500,7 @@ United States.
     <label id="CONICAL">
     <tag/CONICAL/
         <itemize>
-          <item>Web site: <htmlurl
-                  url="http://strout.net/conical/" name="strout.net/conical/">
+          <item>Web site: <htmlurl url="http://strout.net/conical/">
         </itemize>
 
         CONICAL is a C++ class library for building simulations common
@@ -1517,8 +1517,7 @@ United States.
     <label id="Encog">
     <tag/Encog/
         <itemize>
-            <item>Web site: <htmlurl
-                url="http://www.heatonresearch.com/">
+            <item>Web site: <htmlurl url="http://www.heatonresearch.com/">
         </itemize>
 
         Encog is an advanced neural network and machine learning framework.
@@ -1534,8 +1533,7 @@ United States.
     <label id="FANN">
     <tag/FANN/
         <itemize>
-            <item>Web site: <htmlurl
-                url="http://leenissen.dk/fann/">
+            <item>Web site: <htmlurl url="http://leenissen.dk/fann/">
         </itemize>
 
         Fast Artificial Neural Network Library is a free open source neural
@@ -1553,8 +1551,7 @@ United States.
     <label id="ffnet">
     <tag/ffnet/
         <itemize>
-            <item>Web site: <htmlurl
-                url="http://ffnet.sourceforge.net/">
+            <item>Web site: <htmlurl url="http://ffnet.sourceforge.net/">
         </itemize>
 
         ffnet is a fast and easy-to-use feed-forward neural network training
@@ -1585,9 +1582,7 @@ United States.
     <label id="Matrix Class">
     <tag/Matrix Class/
         <itemize>
-	    <item>FTP site: <htmlurl
-                url="ftp://ftp.cs.ucla.edu/pub/"
-                name="ftp.cs.ucla.edu/pub/">
+	    <item>FTP site: <htmlurl url="ftp://ftp.cs.ucla.edu/pub/">
         </itemize>
 
         A simple, fast, efficient C++ Matrix class designed for
@@ -1644,8 +1639,8 @@ United States.
     <label id="NuPIC">
     <tag/NuPIC/
         <itemize>
-            <item>Web site: http://www.numenta.org/
-            <item>Web site: https://github.com/numenta/nupic
+            <item>Web site: <htmlurl url="http://www.numenta.org/">
+            <item>Web site: <htmlurl url="https://github.com/numenta/nupic">
         </itemize>
 
         The Numenta Platform for Intelligent Computing (NuPIC) is built around
@@ -1658,9 +1653,7 @@ United States.
     <label id="Pulcinella">
     <tag/Pulcinella/
 	<itemize>
-        <item>Web site: <htmlurl
-            url="http://iridia.ulb.ac.be/pulcinella/"
-            name="iridia.ulb.ac.be/pulcinella/">
+        <item>Web site: <htmlurl url="http://iridia.ulb.ac.be/pulcinella/">
     </itemize>
 
       Pulcinella is written in CommonLisp, and appears as a library of
@@ -1679,8 +1672,7 @@ United States.
     <tag/scnANNlib/
         <itemize>
             <item>Web site: <htmlurl
-                url="http://www.sentinelchicken.org/projects/scnANNlib/"
-                name="www.sentinelchicken.org/projects/scnANNlib/">
+                url="http://www.sentinelchicken.org/projects/scnANNlib/">
         </itemize>
 
         SCN Artificial Neural Network Library provides a programmer with a
@@ -1750,8 +1742,7 @@ United States.
     <tag/Various (C++) Neural Networks/
      <itemize>
         <item>Web site: <htmlurl
-            url="http://www.dontveter.com/nnsoft/nnsoft.html"
-            name="www.dontveter.com/nnsoft/nnsoft.html">
+            url="http://www.dontveter.com/nnsoft/nnsoft.html">
     </itemize>
 
       Example neural net codes from the book, <htmlurl
@@ -1790,7 +1781,7 @@ United States.
       <label id="Aspirin-MIGRANES">
       <tag/Aspirin - MIGRAINES/ (am6.tar.Z on ftp site)
       <itemize>
-	    <item>FTP site: <htmlurl url="ftp://sunsite.unc.edu/pub/academic/computer-science/neural-networks/programs/Aspirin/" name="sunsite.unc.edu/pub/academic/computer-science/neural-networks/programs/Aspirin/">
+	    <item>FTP site: <htmlurl url="ftp://sunsite.unc.edu/pub/academic/computer-science/neural-networks/programs/Aspirin/">
       </itemize>
 
 
@@ -1892,8 +1883,7 @@ United States.
     <tag/Jbpe/
         <itemize>
             <item>Web site: <htmlurl
-                url="http://cs.felk.cvut.cz/&tilde;koutnij/studium/jbpe.html"
-                name="cs.felk.cvut.cz/&tilde;koutnij/studium/jbpe.html">
+                url="http://cs.felk.cvut.cz/&tilde;koutnij/studium/jbpe.html">
         </itemize>
 
         Jbpe is a back-propagation neural network editor/simulator.
@@ -1911,11 +1901,29 @@ United States.
         </itemize>
 
 
+    <label id="lens">
+    <tag/lens/
+        <itemize>
+            <item>Web site: <htmlurl
+                url="http://tedlab.mit.edu/~dr/Lens/">
+        </itemize>
+
+        Lens is an efficient, yet flexible, neural network simulator that runs
+        on a variety of platforms, is able to handle large, complex
+        simulations, but is also reasonably easy for novices to operate. Lens
+        has three main design objectives:
+
+        <itemize>
+          <item>Speed: Both in performance and development time.
+          <item>Flexibility: Hundreds of scriptable functions and components.
+          <item>Customizability: Modular code to allow for easy extensions.
+        </itemize>
+
+
     <label id="Nengo">
     <tag/Nengo/
         <itemize>
-            <item>Web site: <htmlurl
-                url="http://www.nengo.ca/">
+            <item>Web site: <htmlurl url="http://www.nengo.ca/">
         </itemize>
 
         Nengo (Nengo Neural Simulator) is a graphical and scripting based
@@ -1943,8 +1951,7 @@ United States.
     <tag/Neural Network Generator/
         <itemize>
             <item>FTP site: <htmlurl
-                url="ftp://ftp.idsia.ch/pub/rafal/"
-                name="ftp.idsia.ch/pub/rafal">
+                url="ftp://ftp.idsia.ch/pub/rafal/">
         </itemize>
 
       The Neural Network Generator is a genetic algorithm for the
@@ -1964,9 +1971,7 @@ United States.
       <label id="NEURON">
       <tag/NEURON/
         <itemize>
-            <item>Web site: <htmlurl
-                url="http://www.neuron.yale.edu/"
-                name="www.neuron.yale.edu/">
+            <item>Web site: <htmlurl url="http://www.neuron.yale.edu/">
         </itemize>
 
       NEURON is an extensible nerve modeling and simulation
@@ -2028,7 +2033,7 @@ United States.
       <label id="RNS">
       <tag/RNS/
     	<itemize>
-            <item>Web site: <htmlurl url="http://www.cs.cmu.edu/afs/cs/project/ai-repository/ai/areas/neural/systems/rns/" name="www.cs.cmu.edu/afs/cs/project/ai-repository/ai/areas/neural/systems/rns/">
+            <item>Web site: <htmlurl url="http://www.cs.cmu.edu/afs/cs/project/ai-repository/ai/areas/neural/systems/rns/">
         </itemize>
 
       RNS (Recurrent Network Simulator) is a simulator for recurrent
@@ -2056,7 +2061,7 @@ United States.
     <tag/Semantic Networks in Python/
       <itemize>
         <item>Web site: <htmlurl
-        url="http://strout.net/info/coding/python/ai/index.html" name="strout.net/info/coding/python/ai/index.html">
+            url="http://strout.net/info/coding/python/ai/index.html">
       </itemize>
 
       The semnet.py module defines several simple classes for
@@ -2083,6 +2088,19 @@ United States.
       about a set of objects, and query them for logical conclusions.
 
 
+    <label id="Simbrain">
+    <tag/Simbrain/
+        <itemize>
+            <item>Web site: <htmlurl url="http://www.simbrain.net/">
+        </itemize>
+
+        SIMBRAIN is a free tool for building, running, and analyzing
+        neural-networks (computer simulations of brain circuitry). Simbrain
+        aims to be as visual and easy-to-use as possible. Unique features of
+        Simbrain include its integrated "world components" and its ability to
+        represent a network's state space. Simbrain is written in Java.
+
+
     <label id="SNNS">
     <tag/SNNS/
       <itemize>
@@ -2104,11 +2122,9 @@ United States.
       <tag/TOOLDIAG/
         <itemize>
             <item>Web site: <htmlurl
-                url="http://www.inf.ufes.br/&tilde;thomas/home/soft.html"
-                name="www.inf.ufes.br/&tilde;thomas/home/soft.html">
+                url="http://www.inf.ufes.br/&tilde;thomas/home/soft.html">
             <item>Alt site: <htmlurl
-                url="http://www.cs.cmu.edu/afs/cs/project/ai-repository/ai/areas/neural/systems/tooldiag/0.html"
-                name="http://www.cs.cmu.edu/afs/cs/project/ai-repository/ai/areas/neural/systems/tooldiag/0.html">
+                url="http://www.cs.cmu.edu/afs/cs/project/ai-repository/ai/areas/neural/systems/tooldiag/0.html">
         </itemize>
 
       TOOLDIAG is a collection of methods for statistical pattern
@@ -2123,9 +2139,7 @@ United States.
     <label id="XNBC">
     <tag/XNBC/
         <itemize>
-            <item>Web site: <htmlurl
-                url="http://www.b3e.jussieu.fr/xnbc/"
-                name="www.b3e.jussieu.fr/xnbc/">
+            <item>Web site: <htmlurl url="http://www.b3e.jussieu.fr/xnbc/">
         </itemize>
 
 	XNBC v8 is a simulation tool for the neuroscientists interested in