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[Gmod-apollo-cmts] SF.net SVN: gmod:[23958] apollo/trunk/doc/html/userguide.html
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From: <no...@us...> - 2010-10-13 00:25:41
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Revision: 23958
http://gmod.svn.sourceforge.net/gmod/?rev=23958&view=rev
Author: nomi
Date: 2010-10-13 00:25:31 +0000 (Wed, 13 Oct 2010)
Log Message:
-----------
Removed links to todos.
Fixed text and link to Dolan.
Modified Paths:
--------------
apollo/trunk/doc/html/userguide.html
Modified: apollo/trunk/doc/html/userguide.html
===================================================================
--- apollo/trunk/doc/html/userguide.html 2010-10-12 21:38:30 UTC (rev 23957)
+++ apollo/trunk/doc/html/userguide.html 2010-10-13 00:25:31 UTC (rev 23958)
@@ -260,7 +260,7 @@
<p>
Apollo is a Java application that you can download and run on your
computer (Windows, Linux, or Mac OS X--earlier Mac versions are not
-supported). You can get Apollo <a href="/">here</a>.
+supported). You can get Apollo <a href="/current/">here</a>.
When you
install Apollo, a JVM is bundled with it, unless you are on Mac OS X.
</p><h3>Getting the appropriate Java on a Mac</h3>
@@ -430,10 +430,9 @@
non-FlyBase data. Also, it cannot yet handle macros, and it doesn't yet deal with
some types of "non-Apollo" data such as feature_cvterms.
Theoretically, you can use Apollo as a converter between Chado XML and GAME, but we are still
-debugging that conversion. Please see <a target="todo" href="http://apollo.berkeleybop.org/todo">doc/todo</a>
-for a list of known issues with the Chado XML adapter.
+debugging that conversion.
</p><p>
-The <a href="/game.rng.txt">GAME XML</a> adapter
+The <a href="/current/game.rng.txt">GAME XML</a> adapter
was written to handle Drosophila data in the older GAME XML format. You should be
able to use it to read other types of annotation data in GAME XML format, but you
will need to change the tiers file.
@@ -458,11 +457,11 @@
gene name (if you selected type gene) or scaffold ID (if you selected
golden_path_region). An example of a fruitfly gene is "cact". An
example scaffold ID is AE003603. </p><p>
-The Chado adapter has known bugs that are described in
-<a target="todo" href="http://apollo.berkeleybop.org/chado/chado-jdbc-todo">doc/chado/chado-jdbc-todo</a>. For example,
+The Chado adapter has known bugs.
+For example,
if you request a region that doesn't exist, Apollo will
seize up. Also the dashed contig result lines that are present from
-the GAME Adapter are not coming up yet. See chado-jdbc-todo for the full listing.
+the GAME Adapter are not coming up yet.
</p><p>
Also, if you ask the server for data by chromosome region (e.g.,
2L:10000-20000), you may get an entire scaffold that includes the requested
@@ -2033,7 +2032,7 @@
"Edit->Removed gapped columns" will remove the gapped columns (all
dashes). So this will remove the gaps of the intron, but the genomic
sequence of the intron remains.
-On our <a target="todo" href="http://apollo.berkeleybop.org/todo">todo list</a> is adding a menu item to remove the whole intron,
+On our todo list is adding a menu item to remove the whole intron,
gaps and genomic.
</p><p>
Columns can be selected/deselected by clicking above the sequences. A red square
@@ -2086,11 +2085,7 @@
</p><p>
Also be aware that Jalview uses a lot of memory, and that if you launch multiple
Jalview windows, Apollo may run out of memory.
-</p><p>
-Known Jalview bugs are listed in the <a target="todo" href="http://apollo.berkeleybop.org/todo">doc/todo</a> file.
-If you encounter a problem that is not listed in that file, please report it via
-the <a href="http://sourceforge.net/tracker/?func=add&group_id=27707&atid=462763">
-SourceForge Apollo bug tracker</a> or via the <a href="#mailing">Apollo mailing list</a>.
+</p>
</p><h3><a name="Graphs"></a>Viewing graph data</h3>
<p>
@@ -2213,7 +2208,7 @@
a genome, you may be interested in using Apollo as a curation tool. This section explains
how to use Apollo's annotation curation and editing capabilities.
<p>
-If you want to edit annotations, Chado XML or <a href="/game.rng.txt">GAME XML</a> format works the best. Ensembl GFF format
+If you want to edit annotations, Chado XML or <a href="/current/game.rng.txt">GAME XML</a> format works the best. Ensembl GFF format
(which is also used by the Ensembl server) is not a rich enough data format to
use for curating annotations. If you turn on editing in gff.style, you will find
that it doesn't work right.
@@ -2247,7 +2242,7 @@
save GAME 1.0; true means save GAME 1.1).
</p><p>
Apollo supports several output formats, including <a href="http://www.sanger.ac.uk/Software/formats/GFF/">Ensembl GFF</a>
-format and <a href="/game.rng.txt">GAME XML</a>. The GFF format is simpler (though less rich)
+format and <a href="/current/game.rng.txt">GAME XML</a>. The GFF format is simpler (though less rich)
and more compact. It is a good format for representing simple computational
results, but is not the best choice for saving annotations.
</p><p>
@@ -4107,8 +4102,7 @@
apollo (though they are not by chado). These do not show up as features
in the main window, rather they show up as sequence errors in the exon
detail editor, with a base pair turned orange. The main window just
-displays an orange vertical line for these. <br>
- </p>
+displays an orange vertical line for these.</p>
<p>Select your database from the pull-down menu next to Chado
Database.
Then select a region to display. The list for Type of Region includes
@@ -4131,9 +4125,10 @@
</p><h3>Contributed Apollo Documentation</h3>
<a name="Contributed"></a>
-<h4>DNA Learning Center at Gramene</h4>
-There is a series of Quicktime recordings about using Apollo at <a href="http://www.dnalc.org/gramene/clips/">Gramene</a>.
-<p>
+<h4>DNA Learning Center</h4>
+<p>The Dolan DNA Learning Center at Cold Spring Harbor Laboratory uses Apollo to teach students how to annotate genomes.
+Visit the <a target="_new" href="http://www.dynamicgene.org/annotation/annotation.html">Dynamic Gene</a> annotation page
+to check it out!</p>
</p><h2>Acknowledgements</h2>
<a name="acknowledgements"></a>
@@ -4141,7 +4136,7 @@
<p></p><hr><p>
<!-- hhmts start -->
-Last modified: Tue Oct 12 14:00:27 PDT 2010
+Tue Oct 12 17:06:37 PDT 2010
<!-- hhmts end -->
</p></output></li></body></html>
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