<commit_before><div>
<h1>RAST, Version 2</h1>

<a target=_blank_ href="http://rast.nmpdr.org/rast.cgi">RAST</a> is a set of tools that support
the construction of  automated annotation
systems that accepts as input a set of contigs from a genome and produces as output
the initial annotations needed to support researchers in their efforts to study the genome.  
Since the initial publication of <a target=_blank_ href="http://www.ncbi.nlm.nih.gov/pubmed/18261238">
The RAST Server: rapid annotations using subsystems technology</a> in 2008,
over 150,000 requests for genome annotations have been processed, at a current rate of 1,200 jobs per week.  
<p>

As demand for ever more accurate annotations and the number of
newly-sequenced genomes increases, there is a growing demand for "the
next generation" of the RAST technology (RAST2).  This new version of the 
architecture makes it possible to construct custom pipelines,
 integrate new bioinformatic tools, and make the developed pipelines
easily accessible by a large user community.


</div>
<div>


<h3> Getting Started </h3>

<p> 
In order to run the RAST2 tools, you must either download the Kbase app dmg 
<a target=_blank_ href="http://kbase.us/developer-zone/tutorials/getting-started/installing-the-kbase-dmg">here</a>,
or use the
<a target=_blank_ href="http://www.kbase.us/services/docs/invocation/Iris">IRIS</a> environment. 
An introduction to IRIS can be found  <a target=_blank_ href="http://kbase.us/for-users/get-started">here</a>.  
</p>

<p>
There are advantages to using either tool.  The KBase app runs a bash shell on your
machine with all of the necessary scripts installed and is therefore easier to use for processing batches of genomes.  
On the other hand, the IRIS environment requires no installation, is always up to date, and is 
ideal for small numbers of genomes.
</p>

<p>
If you are following this tutorial with the KBase app, no login is required.  If you use <a target=_blank_ href="http://kbase.us/services/docs/invocation/Iris/iris.html">IRIS</a>, you
must first login by typing "login" and then "some user name".  It is not necessary that you register, but you 
should remember your user name so that you can retrieve your data later.  
</p>


</div>
<div>


<p>
If you want to step through the tutorial, you can download the  E. coli K-12 contig in fasta format from KBase.  To download this genome open a command window in the KBase app or in the IRIS command window and type:
</p>

<pre>
    <code title ="iris-tutorial"> echo "kb|g.0" | genomes_to_contigs  | contigs_to_sequences &gt; E_coli.contig </code>  
</pre>
"kb|g.0" is the KBase identifier for E. coli K-12.  "genomes_to_contigs" provides the contig ids (there is only one for this genome),
and "contigs_to_sequences" returns the sequence in fasta format.  There is a large body of scripts and database acquisition tools that 
that are visible in the "command list" side bar in IRIS which can also be implemented in the KBase.app.  Tutorials for these scripts exist on the KBase website,
 and all scripts contain a help (-h) option. When the time comes, you can manually upload your own genome (contigs in fasta format) to the IRIS environment by clicking on the up arrow button on the bottom left-hand side of the page below the file browser window.
</p>


</div>
<div>


<h3> Choices in using the RAST2 tools </h3>

<p>
The RAST2 environment is designed so that users can compose annotation
pipelines, and then run those pipelines to annotate genomes.
There is a rich and growing body of annotation tools that we have either built or
imported from other groups, and these offer a framework for incrementally constructing<commit_msg>editing code tags<commit_after><div>
<h1>RAST, Version 2</h1>

<a target=_blank_ href="http://rast.nmpdr.org/rast.cgi">RAST</a> is a set of tools that support
the construction of  automated annotation
systems that accepts as input a set of contigs from a genome and produces as output
the initial annotations needed to support researchers in their efforts to study the genome.  
Since the initial publication of <a target=_blank_ href="http://www.ncbi.nlm.nih.gov/pubmed/18261238">
The RAST Server: rapid annotations using subsystems technology</a> in 2008,
over 150,000 requests for genome annotations have been processed, at a current rate of 1,200 jobs per week.  
<p>

As demand for ever more accurate annotations and the number of
newly-sequenced genomes increases, there is a growing demand for "the
next generation" of the RAST technology (RAST2).  This new version of the 
architecture makes it possible to construct custom pipelines,
 integrate new bioinformatic tools, and make the developed pipelines
easily accessible by a large user community.


</div>
<div>


<h3> Getting Started </h3>

<p> 
In order to run the RAST2 tools, you must either download the Kbase app dmg 
<a target=_blank_ href="http://kbase.us/developer-zone/tutorials/getting-started/installing-the-kbase-dmg">here</a>,
or use the
<a target=_blank_ href="http://www.kbase.us/services/docs/invocation/Iris">IRIS</a> environment. 
An introduction to IRIS can be found  <a target=_blank_ href="http://kbase.us/for-users/get-started">here</a>.  
</p>

<p>
There are advantages to using either tool.  The KBase app runs a bash shell on your
machine with all of the necessary scripts installed and is therefore easier to use for processing batches of genomes.  
On the other hand, the IRIS environment requires no installation, is always up to date, and is 
ideal for small numbers of genomes.
</p>

<p>
If you are following this tutorial with the KBase app, no login is required.  If you use <a target=_blank_ href="http://kbase.us/services/docs/invocation/Iris/iris.html">IRIS</a>, you
must first login by typing "login" and then "some user name".  It is not necessary that you register, but you 
should remember your user name so that you can retrieve your data later.  
</p>


</div>
<div>


<p>
If you want to step through the tutorial, you can download the  E. coli K-12 contig in fasta format from KBase.  To download this genome open a command window in the KBase app or in the IRIS command window and type:
</p>

<pre>
    <code title ="iris-tutorial"> echo </code> "kb|g.0" | genomes_to_contigs  | contigs_to_sequences &gt; E_coli.contig   
</pre>
"kb|g.0" is the KBase identifier for E. coli K-12.  "genomes_to_contigs" provides the contig ids (there is only one for this genome),
and "contigs_to_sequences" returns the sequence in fasta format.  There is a large body of scripts and database acquisition tools that 
that are visible in the "command list" side bar in IRIS which can also be implemented in the KBase.app.  Tutorials for these scripts exist on the KBase website,
 and all scripts contain a help (-h) option. When the time comes, you can manually upload your own genome (contigs in fasta format) to the IRIS environment by clicking on the up arrow button on the bottom left-hand side of the page below the file browser window.
</p>


</div>
<div>


<h3> Choices in using the RAST2 tools </h3>

<p>
The RAST2 environment is designed so that users can compose annotation
pipelines, and then run those pipelines to annotate genomes.
There is a rich and growing body of annotation tools that we have either built or
imported from other groups, and these offer a framework for incrementally constructing
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