[Bioperl-guts-l] bioperl-live/doc/howto/sgml Beginners.xml, 1.36, 1.37

Brian Osborne bosborne at pub.open-bio.org
Mon Jul 25 03:25:28 EDT 2005


Update of /home/repository/bioperl/bioperl-live/doc/howto/sgml
In directory pub.open-bio.org:/tmp/cvs-serv18654

Modified Files:
	Beginners.xml 
Log Message:
Edits


Index: Beginners.xml
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/doc/howto/sgml/Beginners.xml,v
retrieving revision 1.36
retrieving revision 1.37
diff -C2 -d -r1.36 -r1.37
*** Beginners.xml	23 Jun 2005 15:19:32 -0000	1.36
--- Beginners.xml	25 Jul 2005 07:25:26 -0000	1.37
***************
*** 20,24 ****
        <surname>Osborne</surname>
        <authorblurb>
! 		  <para>Bioperl contributor</para>
        </authorblurb>
        <affiliation>
--- 20,24 ----
        <surname>Osborne</surname>
        <authorblurb>
! 		  <para><ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> contributor</para>
        </authorblurb>
        <affiliation>
***************
*** 69,80 ****
        <para>
  		  This is a HOWTO written in DocBook (XML) that talks about using
! 		  Bioperl, for biologists who would like to learn more
! 		  about writing their own bioinformatics scripts using Bioperl. 
        </para>
  		<para>
! 		  What is Bioperl? It is an open source bioinformatics toolkit
  		  used by researchers all over the world. If you're looking for
  		  a script built to fit your exact need it's likely 
! 		  you won't find it in Bioperl. What you will find is a
  		  diverse set of Perl modules that will enable you to write
  		  your own script, and a commmunity of people who are willing 
--- 69,80 ----
        <para>
  		  This is a HOWTO written in DocBook (XML) that talks about using
! 		  <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink>, for biologists who would like to learn more
! 		  about writing their own bioinformatics scripts using <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink>. 
        </para>
  		<para>
! 		  What is <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink>? It is an open source bioinformatics toolkit
  		  used by researchers all over the world. If you're looking for
  		  a script built to fit your exact need it's likely 
! 		  you won't find it in <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink>. What you will find is a
  		  diverse set of Perl modules that will enable you to write
  		  your own script, and a commmunity of people who are willing 
***************
*** 93,101 ****
  		about learning more about the programming side of bioinformatics.
  		In this HOWTO you'll see discussions of some of the common uses
! 		of Bioperl, 
  		like sequence analysis with BLAST and retrieving sequences from 
  		public databases. You'll also see how to
! 		write Bioperl scripts that chain these tasks together, that's
! 		how you'll be able to do really powerful things with Bioperl.
      </para>
      <para>
--- 93,101 ----
  		about learning more about the programming side of bioinformatics.
  		In this HOWTO you'll see discussions of some of the common uses
! 		of <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink>, 
  		like sequence analysis with BLAST and retrieving sequences from 
  		public databases. You'll also see how to
! 		write <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> scripts that chain these tasks together, that's
! 		how you'll be able to do really powerful things with <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink>.
      </para>
      <para>
***************
*** 105,109 ****
  		to not introduce too much unfamiliar material. 
  		However, there will be an introducton to modularity, or objects. This is 
! 		one of the aspects of the Bioperl package that you'll have
  		to come to grips with as you attempt more complex tasks with
  		your scripts.
--- 105,109 ----
  		to not introduce too much unfamiliar material. 
  		However, there will be an introducton to modularity, or objects. This is 
! 		one of the aspects of the <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> package that you'll have
  		to come to grips with as you attempt more complex tasks with
  		your scripts.
***************
*** 123,127 ****
  			 excellent introductory tool, it is not object-oriented and
  		  can't be extended. What we're
! 		  attempting here is to introduce Bioperl and show you
  		  ways to expand your new-found skills.
        </para>
--- 123,127 ----
  			 excellent introductory tool, it is not object-oriented and
  		  can't be extended. What we're
! 		  attempting here is to introduce <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> and show you
  		  ways to expand your new-found skills.
        </para>
***************
*** 130,136 ****
  
    <section id="installation">
!     <title>Installing Bioperl</title>
      <para>
! 		The first thing to determine is the Bioperl platform - Unix or
  		Windows? Here are some things to consider, if you're choosing 
  		between the two.
--- 130,136 ----
  
    <section id="installation">
!     <title>Installing <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink></title>
      <para>
! 		The first thing to determine is the <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> platform - Unix or
  		Windows? Here are some things to consider, if you're choosing 
  		between the two.
***************
*** 159,163 ****
  		  <member>
  			 There may be an administrator taking care of the machine - maybe
! 			 she'll even install Bioperl for you! Ask and see.
  		  </member>
  		</simplelist>
--- 159,163 ----
  		  <member>
  			 There may be an administrator taking care of the machine - maybe
! 			 she'll even install <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> for you! Ask and see.
  		  </member>
  		</simplelist>
***************
*** 197,201 ****
  		  </member>
  		  <member>
! 			 Plenty of Bioperl users run it on Windows.
  		  </member>
  		</simplelist>
--- 197,201 ----
  		  </member>
  		  <member>
! 			 Plenty of <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> users run it on Windows.
  		  </member>
  		</simplelist>
***************
*** 239,244 ****
  				On Windows, messages like "Error: Failed to download URL
  				http://bioperl.org/DIST/GD.ppd", or "Not found". The 
! 				explanation is that Bioperl does not supply every
! 				accessory module that's necessary to run all of Bioperl.
  				You'll need to search other repositories to install
  				all of these accessory modules. See the
--- 239,244 ----
  				On Windows, messages like "Error: Failed to download URL
  				http://bioperl.org/DIST/GD.ppd", or "Not found". The 
! 				explanation is that <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> does not supply every
! 				accessory module that's necessary to run all of <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink>.
  				You'll need to search other repositories to install
  				all of these accessory modules. See the
***************
*** 254,258 ****
  				could not find a particular module and the explanation
  				usually is that this module is not installed. You can
! 				either install Bundle::Bioperl or install that specific
  				module by hand. See 
  <ulink
--- 254,258 ----
  				could not find a particular module and the explanation
  				usually is that this module is not installed. You can
! 				either install Bundle::<ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> or install that specific
  				module by hand. See 
  <ulink
***************
*** 265,270 ****
  				Seeing messages like "Tests Failed". If you see an 
  				error during installation consider whether
! 				this problem is going to affect your use of Bioperl. There
! 				are almost 800 modules in Bioperl, and ten times that many
  				tests are run during the installation. If there's a
  				complaint about GD it's only relevant if you want to 
--- 265,270 ----
  				Seeing messages like "Tests Failed". If you see an 
  				error during installation consider whether
! 				this problem is going to affect your use of <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink>. There
! 				are almost 800 modules in <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink>, and ten times that many
  				tests are run during the installation. If there's a
  				complaint about GD it's only relevant if you want to 
***************
*** 273,277 ****
  				you're reading XML files. Yes, you could try and make
  				each and every test pass, but that may be a lot of work, with much
! 				of it fixing modules that aren't in Bioperl itself.
  			 </para>
  		  </listitem>
--- 273,277 ----
  				you're reading XML files. Yes, you could try and make
  				each and every test pass, but that may be a lot of work, with much
! 				of it fixing modules that aren't in <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> itself.
  			 </para>
  		  </listitem>
***************
*** 283,288 ****
      <title>Getting Assistance</title>
      <para>
! 		People will run into problems installing Bioperl or writing 
! 		scripts using Bioperl, nothing unusual about that. If you need 
  		assistance the way to get it is to mail bioperl-l at bioperl.org.
  		There are a good number of helpful people who regularly read
--- 283,288 ----
      <title>Getting Assistance</title>
      <para>
! 		People will run into problems installing <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> or writing 
! 		scripts using <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink>, nothing unusual about that. If you need 
  		assistance the way to get it is to mail bioperl-l at bioperl.org.
  		There are a good number of helpful people who regularly read
***************
*** 296,300 ****
  		<orderedlist>
  		  <listitem>
! 			<para> The version of Bioperl you're working with. </para>
  		  </listitem>
  		  <listitem>
--- 296,300 ----
  		<orderedlist>
  		  <listitem>
! 			<para> The version of <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> you're working with. </para>
  		  </listitem>
  		  <listitem>
***************
*** 327,331 ****
  		  And every once in a while, not often, an email will go
  		  unanswered because the
! 		  the tone is unpleasant. Bioperl
  		  is a 100% volunteer effort, we all have other jobs, 
  		  complaining about bugs or lack of
--- 327,331 ----
  		  And every once in a while, not often, an email will go
  		  unanswered because the
! 		  the tone is unpleasant. <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink>
  		  is a 100% volunteer effort, we all have other jobs, 
  		  complaining about bugs or lack of
***************
*** 452,456 ****
  		Our first script will create a sequence. Well, not just a sequence,
  		you will be creating a "sequence object", since
! 		Bioperl is written in an object-oriented way. Why be
  		object-oriented? Why introduce these odd or intrusive notions into
  		software that should be "biological" or "intuitive"? The reason is 
--- 452,456 ----
  		Our first script will create a sequence. Well, not just a sequence,
  		you will be creating a "sequence object", since
! 		<ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> is written in an object-oriented way. Why be
  		object-oriented? Why introduce these odd or intrusive notions into
  		software that should be "biological" or "intuitive"? The reason is 
***************
*** 469,474 ****
  	 </para>
  	 <para>
! 		All objects in Bioperl are created by specific
! 		Bioperl modules, so if you want to create an object you're also going
  		to have to tell Perl which module to use. Let's add another line:
      </para>	
--- 469,474 ----
  	 </para>
  	 <para>
! 		All objects in <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> are created by specific
! 		<ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> modules, so if you want to create an object you're also going
  		to have to tell Perl which module to use. Let's add another line:
      </para>	
***************
*** 491,497 ****
  		The 
  <ulink url="http://doc.bioperl.org/releases/bioperl-1.4/Bio/Seq.html"><citetitle>Bio::Seq</citetitle></ulink> module is one of the central modules in
! 		Bioperl. The analogous 
  <ulink url="http://doc.bioperl.org/releases/bioperl-1.4/Bio/Seq.html"><citetitle>Bio::Seq</citetitle></ulink> object, or "Sequence object", or
! 		"Seq object", is ubiquitous in Bioperl, it contains 
  		a single sequence and associated names, identifiers, and
  		properties. Let's create a very simple sequence object at
--- 491,497 ----
  		The 
  <ulink url="http://doc.bioperl.org/releases/bioperl-1.4/Bio/Seq.html"><citetitle>Bio::Seq</citetitle></ulink> module is one of the central modules in
! 		<ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink>. The analogous 
  <ulink url="http://doc.bioperl.org/releases/bioperl-1.4/Bio/Seq.html"><citetitle>Bio::Seq</citetitle></ulink> object, or "Sequence object", or
! 		"Seq object", is ubiquitous in <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink>, it contains 
  		a single sequence and associated names, identifiers, and
  		properties. Let's create a very simple sequence object at
***************
*** 512,521 ****
  		That's it! The variable <varname>$seq_obj</varname> is the
  		Sequence object, a simple one, containing just a sequence.
! 		Note that the code tells Bioperl that the sequence is DNA
  		(the choices here are 'dna', 'rna', and 'protein'), this is
! 		the wise thing to do. If you don't tell Bioperl it will attempt 
  		to guess the alphabet. Normally it guesses correctly but if your sequence
  		has lots of odd or ambiguous characters, such as N or X,
! 		Bioperl's guess may be incorrect and this may lead to some
  		problems.
  	 </para>
--- 512,521 ----
  		That's it! The variable <varname>$seq_obj</varname> is the
  		Sequence object, a simple one, containing just a sequence.
! 		Note that the code tells <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> that the sequence is DNA
  		(the choices here are 'dna', 'rna', and 'protein'), this is
! 		the wise thing to do. If you don't tell <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> it will attempt 
  		to guess the alphabet. Normally it guesses correctly but if your sequence
  		has lots of odd or ambiguous characters, such as N or X,
! 		<ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink>'s guess may be incorrect and this may lead to some
  		problems.
  	 </para>
***************
*** 523,527 ****
  		<ulink url="http://doc.bioperl.org/releases/bioperl-1.4/Bio/Seq.html"><citetitle>Bio::Seq</citetitle></ulink> objects can be created manually, as above, but
  		they're also create automatically in many operations
! 		in Bioperl, for example when alignment files or database
  		entries or BLAST reports are parsed.
  	 </para>      
--- 523,527 ----
  		<ulink url="http://doc.bioperl.org/releases/bioperl-1.4/Bio/Seq.html"><citetitle>Bio::Seq</citetitle></ulink> objects can be created manually, as above, but
  		they're also create automatically in many operations
! 		in <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink>, for example when alignment files or database
  		entries or BLAST reports are parsed.
  	 </para>      
***************
*** 529,533 ****
  		Any time you explicitly create an object, you
  		will use this <function>new()</function> method. The syntax of this
! 		line is one you'll see again and again in Bioperl: the name
  		of the object or variable, the module name, the 
  		<emphasis>-></emphasis> symbol, the
--- 529,533 ----
  		Any time you explicitly create an object, you
  		will use this <function>new()</function> method. The syntax of this
! 		line is one you'll see again and again in <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink>: the name
  		of the object or variable, the module name, the 
  		<emphasis>-></emphasis> symbol, the
***************
*** 618,622 ****
  		By using 
  <ulink url="http://doc.bioperl.org/releases/bioperl-1.4/Bio/SeqIO.html"><citetitle>Bio::SeqIO</citetitle></ulink> in this manner you will be able to get input
! 		and make output for all of the sequence file formats supported by Bioperl
  		(the <ulink url="http://bioperl.org/HOWTOs/SeqIO/index.html"><citetitle>SeqIO HOWTO</citetitle></ulink> has a complete list of supported formats).
  		The way you create <classname>Bio::SeqIO</classname> objects is 
--- 618,622 ----
  		By using 
  <ulink url="http://doc.bioperl.org/releases/bioperl-1.4/Bio/SeqIO.html"><citetitle>Bio::SeqIO</citetitle></ulink> in this manner you will be able to get input
! 		and make output for all of the sequence file formats supported by <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink>
  		(the <ulink url="http://bioperl.org/HOWTOs/SeqIO/index.html"><citetitle>SeqIO HOWTO</citetitle></ulink> has a complete list of supported formats).
  		The way you create <classname>Bio::SeqIO</classname> objects is 
***************
*** 721,725 ****
  		files. This is understandable in some respects. You
  		may have read about Perl's <function>open</function>
! 		function, and Bioperl's way of retrieving sequences may look odd
  		and overly complicated, at first. But don't use
  		<function>open</function>! Using <function>open</function> 
--- 721,725 ----
  		files. This is understandable in some respects. You
  		may have read about Perl's <function>open</function>
! 		function, and <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink>'s way of retrieving sequences may look odd
  		and overly complicated, at first. But don't use
  		<function>open</function>! Using <function>open</function> 
***************
*** 728,732 ****
  		the SeqIO object, it's built to open and parse all
  		the common sequence formats, it can read and write to files,
! 		and it's built to operate with all the other Bioperl 
  		modules that you will want to use. 
  	 </para>
--- 728,732 ----
  		the SeqIO object, it's built to open and parse all
  		the common sequence formats, it can read and write to files,
! 		and it's built to operate with all the other <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> 
  		modules that you will want to use. 
  	 </para>
***************
*** 776,780 ****
  		will be identical to
  		to the Sequence object we created manually in our first example.
! 		This is another idiom that's used frequently in Bioperl, the
  		next_&lt;something&gt; method. You'll come across the same idea
  		in the <function>next_aln</function> method of 
--- 776,780 ----
  		will be identical to
  		to the Sequence object we created manually in our first example.
! 		This is another idiom that's used frequently in <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink>, the
  		next_&lt;something&gt; method. You'll come across the same idea
  		in the <function>next_aln</function> method of 
***************
*** 813,816 ****
--- 813,829 ----
  		correctly for every single format.
  	 </para>
+     <tip>
+       <para>
+ 		  It may be useful to specify the alphabet, using the
+ 		  "-alphabet" argument. What this does is to tell <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> not to
+ 		  try to determine the alphabet ("dna", "rna", "protein"). This helps
+ 		  when <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> guesses incorrectly (e.g. <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> is going to
+ 		  guess that the protein sequence "GATC" is DNA) or if there are odd 
+ 		  characters in the sequence that
+ 		  SeqIO may object to (e.g. "-"). Set "-alphabet" to a value
+ 		  when reading sequences and SeqIO will not examine those sequence.
+       </para>
+     </tip>
+ 
    </section>
  
***************
*** 818,822 ****
  	 <title>Retrieving a sequence from a database</title>
  	 <para>
! 		One of the strengths of Bioperl is that it allows you to retrieve
  		sequences from all sorts of sources, files, remote databases,
  		local databases, regardless of their format. Let's use this 
--- 831,835 ----
  	 <title>Retrieving a sequence from a database</title>
  	 <para>
! 		One of the strengths of <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> is that it allows you to retrieve
  		sequences from all sorts of sources, files, remote databases,
  		local databases, regardless of their format. Let's use this 
***************
*** 831,835 ****
  <para></para>
  	 <para>
! 		We could also query SwissProt, GenPept, EMBL, SeqHound, or RefSeq in an 
  		analogous fashion (e.g "use Bio::DB::SwissProt"). Now we'll
  		create the object:
--- 844,850 ----
  <para></para>
  	 <para>
! 		We could also query <ulink
! 		href="http://www.expasy.ch"><citetitle>SwissProt</citetitle></ulink>,
! 		GenPept, EMBL, <ulink href="http://www.blueprint.org/seqhound"><citetitle>SeqHound</citetitle>, or RefSeq in an 
  		analogous fashion (e.g "use Bio::DB::SwissProt"). Now we'll
  		create the object:
***************
*** 887,892 ****
  		<para>
  		  This capability to query by string and field is only available
! 		  for GenBank as of Bioperl version 1.5, queries to other
! 		  databases, like Swissprot or EMBL, are limited to identifiers
  		  and accessions.
  		</para>
--- 902,907 ----
  		<para>
  		  This capability to query by string and field is only available
! 		  for GenBank as of <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> version 1.5, queries to other
! 		  databases, like <ulink href="http://www.expasy.ch"><citetitle>Swissprot</citetitle></ulink> or EMBL, are limited to identifiers
  		  and accessions.
  		</para>
***************
*** 1334,1338 ****
  		you noticed that there's an awful lot of
  		information missing. All of this missing information is stored in
! 		what Bioperl calls Features and Annotations, see the
  		<ulink
  		  url="http://bioperl.org/HOWTOs/Feature-Annotation/index.html"><citetitle>Feature and Annotation HOWTO</citetitle></ulink> if you'd like to learn more about this.
--- 1349,1353 ----
  		you noticed that there's an awful lot of
  		information missing. All of this missing information is stored in
! 		what <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> calls Features and Annotations, see the
  		<ulink
  		  url="http://bioperl.org/HOWTOs/Feature-Annotation/index.html"><citetitle>Feature and Annotation HOWTO</citetitle></ulink> if you'd like to learn more about this.
***************
*** 1431,1443 ****
  		formats. The reason is that there are no rules governing how 
  		one interconverts formats, meaning how Genbank creates fasta
! 		files from Genbank files may be different from how SwissProt
  		performs the same interconversion. Again, until the
  		organizations creating these databases agree on standard sets
! 		of names and formats all the Bioperl authors can do is do 
  		make reasonable choices.
  	 </para>
  	 <note>
  		<para>
! 		  Yes, Bioperl could follow the
  		  conventions of a single organization like Genbank such that
  		  <function>display_id</function> returns the same value when
--- 1446,1459 ----
  		formats. The reason is that there are no rules governing how 
  		one interconverts formats, meaning how Genbank creates fasta
! 		files from Genbank files may be different from how 
! <ulink href="http://www.expasy.ch"><citetitle>SwissProt</citetitle></ulink>
  		performs the same interconversion. Again, until the
  		organizations creating these databases agree on standard sets
! 		of names and formats all the <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> authors can do is do 
  		make reasonable choices.
  	 </para>
  	 <note>
  		<para>
! 		  Yes, <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> could follow the
  		  conventions of a single organization like Genbank such that
  		  <function>display_id</function> returns the same value when
***************
*** 1450,1454 ****
  	 <para></para>
  	 <para>
! 		Let's use a Swissprot file as our last example. The input entry
  		looks like this:
  	 </para>
--- 1466,1470 ----
  	 <para></para>
  	 <para>
! 		Let's use a <ulink href="http://www.expasy.ch"><citetitel>Swissprot</citetitle></ulink> file as our last example. The input entry
  		looks like this:
  	 </para>
***************
*** 1539,1543 ****
  	 <para>
  		<table>
! 		  <title>Values from Swissprot</title>
  		  <tgroup cols="2">
  			 <thead>
--- 1555,1559 ----
  	 <para>
  		<table>
! 		  <title>Values from <ulink href="http://www.expasy.ch"><citetitle>Swissprot<citetitle></ulink></title>
  		  <tgroup cols="2">
  			 <thead>
***************
*** 1592,1596 ****
  	 <para>
  		You have access to a large number of sequence analysis programs 
! 		within Bioperl. Typically this means you have a means to run
  		the program and frequently a means of parsing the resulting 
  		output, or report, as well. Certainly the most popular 
--- 1608,1612 ----
  	 <para>
  		You have access to a large number of sequence analysis programs 
! 		within <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink>. Typically this means you have a means to run
  		the program and frequently a means of parsing the resulting 
  		output, or report, as well. Certainly the most popular 
***************
*** 1663,1667 ****
  <ulink
  		  url="http://doc.bioperl.org/releases/bioperl-1.4/Bio/Tools/Run/StandAloneBlast.html"><citetitle>Bio::Tools::Run::StandAloneBlast</citetitle></ulink> 
! 		that have nothing to do with Bioperl. Make sure that BLAST is 
  		set up properly and running before you attempt to script it
  		using 
--- 1679,1683 ----
  <ulink
  		  url="http://doc.bioperl.org/releases/bioperl-1.4/Bio/Tools/Run/StandAloneBlast.html"><citetitle>Bio::Tools::Run::StandAloneBlast</citetitle></ulink> 
! 		that have nothing to do with <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink>. Make sure that BLAST is 
  		set up properly and running before you attempt to script it
  		using 
***************
*** 1674,1678 ****
  	 </para>
  	 <para>
! 		Bioperl enables you to run a wide variety of bioinformatics
  		programs but in order to do so, in most cases, you will need
  		to install the accessory bioperl-run package. In addition 
--- 1690,1694 ----
  	 </para>
  	 <para>
! 		<ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> enables you to run a wide variety of bioinformatics
  		programs but in order to do so, in most cases, you will need
  		to install the accessory bioperl-run package. In addition 
***************
*** 1689,1693 ****
  	 <title>Indexing for Fast Retrieval</title>
  	 <para>
! 		One of the under-appreciated features of Bioperl is its ability
  		to index sequence files. The idea is that you would create some sequence
  		file locally and create an index file for it that enables you to 
--- 1705,1709 ----
  	 <title>Indexing for Fast Retrieval</title>
  	 <para>
! 		One of the under-appreciated features of <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> is its ability
  		to index sequence files. The idea is that you would create some sequence
  		file locally and create an index file for it that enables you to 
***************
*** 1841,1848 ****
  
    <section id="more">
! 	 <title>More on Bioperl</title>
  	 <para>
  		Perhaps this article has gotten you interested in learning a
! 		bit more about Bioperl. Here are some other things you might 
  		want to look at:
  	 </para>
--- 1857,1864 ----
  
    <section id="more">
! 	 <title>More on <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink></title>
  	 <para>
  		Perhaps this article has gotten you interested in learning a
! 		bit more about <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink>. Here are some other things you might 
  		want to look at:
  	 </para>
***************
*** 1870,1877 ****
  		  </para></listitem>
  		  <listitem><para>
! 				Bioperl scripts. You'll find them in the scripts/ directory
! 				and in the examples/ directory of the Bioperl package.
  				The former contains more carefully written and documented
! 				scripts that can be installed along with Bioperl. You should
  				feel free to contribute scripts to either of these 
  				directories. There's also a complete list of scripts,
--- 1886,1893 ----
  		  </para></listitem>
  		  <listitem><para>
! 				<ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> scripts. You'll find them in the scripts/ directory
! 				and in the examples/ directory of the <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> package.
  				The former contains more carefully written and documented
! 				scripts that can be installed along with <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink>. You should
  				feel free to contribute scripts to either of these 
  				directories. There's also a complete list of scripts,
***************
*** 1910,1914 ****
  	 </para>
  	 <para>
! 		Read about any module, including any of the Bioperl modules:
  		<programlisting>
  >perldoc Bio::SeqIO
--- 1926,1930 ----
  	 </para>
  	 <para>
! 		Read about any module, including any of the <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> modules:
  		<programlisting>
  >perldoc Bio::SeqIO
***************
*** 1995,1999 ****
  		That's the sort of explanation you'll get in programming
  		books, but what is a Perl object really? Usually a hash.
! 		In Bioperl the data that the object contains is stored in a 
  		single, complex hash and the object, like 
  		<varname>$seq_obj</varname>,
--- 2011,2015 ----
  		That's the sort of explanation you'll get in programming
  		books, but what is a Perl object really? Usually a hash.
! 		In <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> the data that the object contains is stored in a 
  		single, complex hash and the object, like 
  		<varname>$seq_obj</varname>,
***************
*** 2001,2009 ****
  		that the object can use are also stored in this hash as
  		particular kinds of references. You could say that an
! 		object in Bioperl is a special kind of hash reference.
  	 </para>
  
  	 <para>
! 		Bioperl uses the object-oriented paradigm, and here are
  		some texts if you want to learn more:
  	 </para>
--- 2017,2025 ----
  		that the object can use are also stored in this hash as
  		particular kinds of references. You could say that an
! 		object in <ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> is a special kind of hash reference.
  	 </para>
  
  	 <para>
! 		<ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> uses the object-oriented paradigm, and here are
  		some texts if you want to learn more:
  	 </para>
***************
*** 2017,2021 ****
  		  <listitem>
  			 <para>               
! 				The <ulink url="http://bioperl.org/Core/Latest/biodesign.html"><citetitle>Bioperl design documentation</citetitle></ulink>, for anyone who'd like
  				to write their own modules. 
  			 </para>
--- 2033,2037 ----
  		  <listitem>
  			 <para>               
! 				The <ulink url="http://bioperl.org/Core/Latest/biodesign.html"><citetitle><ulink href="http://bioperl.org"><citetitle>Bioperl</citetitle></ulink> design documentation</citetitle></ulink>, for anyone who'd like
  				to write their own modules. 
  			 </para>



More information about the Bioperl-guts-l mailing list