From fbc198360c448f0303cfb4d007ec3ed5a91f5ef0 Mon Sep 17 00:00:00 2001
From: Brian Osborne <briano@bioteam.net>
Date: Sat, 26 Dec 2015 14:01:34 -0500
Subject: [PATCH] Convert to Markdown

---
 INSTALL   | 21 ++++++++-------------
 README.md | 10 +++-------
 2 files changed, 11 insertions(+), 20 deletions(-)

diff --git a/INSTALL b/INSTALL
index bbbf1ef..742cbe1 100644
--- a/INSTALL
+++ b/INSTALL
@@ -1,26 +1,21 @@
 bioperl-network Installation
 
-1. Requirements
-2. Installing bioperl-network (Unix or Cygwin)
-
-1. Requirements 
+REQUIREMENTS 
 
 Perl 5.6.1 is required, but 5.8 or greater is recommended.
 
 The bioperl-network package depends on the core BioPerl package. See  
-the BioPerl INSTALL file for instructions for downloading and installing 
-BioPerl. You should install at least the corresponding version of Bioperl: 
-since this is bioperl-network 1.6, bioperl 1.6 or greater is recommended.
+the BioPerl INSTALL file (http://bioperl.org/INSTALL.html) for instructions 
+for downloading and installing BioPerl. You should install at least the 
+corresponding version of Bioperl: since this is bioperl-network 1.6, bioperl 
+1.6 or greater is recommended.
 
-bioperl-network also depends on Perl's Graph package. See CPAN at 
-www.perl.org for instructions on downloading and installing Graph,
-use Graph version .86 or greater.
+bioperl-network also requires Perl's Graph package, https://metacpan.org/pod/Graph
 
 Reading PSI XML files using bioperl-network requires the XML::Twig 
-module. See CPAN at www.perl.org for instructions on downloading 
-and installing XML::Twig.
+module. See https://metacpan.org/pod/XML::Twig.
 
-2. Installing bioperl-network (Unix, Mac OS X and Cygwin)
+INSTALLING BIOPERL-NETWORK (UNIX, MAC OS X AND CYGWIN)
   
 Using CPAN:
 
diff --git a/README.md b/README.md
index 360c17f..7411ec9 100644
--- a/README.md
+++ b/README.md
@@ -22,8 +22,7 @@ A node is one or more BioPerl sequence objects, a Bio::Seq or
 Bio::Seq::RichSeq object. Since a node can contain more than one
 Sequence object it can represent protein complexes as well as proteins.
 Essentially the node can be any Bioperl object that implements the
-Bio::AnnotatableI and Bio::IdentifiableI interfaces. This is relevant since the 
-identities of nodes are determined by their identifiers.
+Bio::AnnotatableI and Bio::IdentifiableI interfaces. This is relevant since the identities of nodes are determined by their identifiers.
 
 The bioperl-network modules use Perl's Graph::Undirected 
 module and inherit its formal model as well. An edge corresponds to a 
@@ -39,13 +38,10 @@ identifier, add and delete components (nodes, interactions, and
 edges), count all components of a certain type, get all components of
 a certain type, and get subgraphs. Then you have all the functionality
 of Perl's Graph in addition such as traversal using different
-algorithms, getting interior and exterior nodes, and getting all  
-connected subgraphs. Graph is quite rich in functionality, this list
-is only a small subset of available methods, see the documentation 
-for Graph for more detail (http://search.cpan.org/~jhi/Graph/lib/Graph.pod).
+algorithms, getting interior and exterior nodes, and getting all connected subgraphs. Graph is quite rich in functionality, this list is only a small subset of available methods, see the documentation for Graph for more detail (https://metacpan.org/pod/Graph).
 
 For more detailed documentation also see the
-Bio::Network::ProteinNet module.
+https://metacpan.org/pod/Bio::Network::ProteinNet module.
 
 
 ## Status
-- 
2.11.4.GIT