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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Hi Dave<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Again, thank you for your thorough reply.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>I will walk through the GBrowse tutorial in the very near
future. I have been hesitant in doing this because it would require me to download
things to my laptop and start playing around with them. But my current laptop
is belongs to my company (Popular Genetics) and not my client (i.e. The Centre
for Applied Genomics) so I’ve been worried I might start breaking things
(a broken laptop means business comes to a halt). I’ve got an older laptop
that I am reconfiguring and eventually will install a Unix OS (probably CentOS
as recommended on the GMOD pages) – I will then be in a much better
position for downloading, installing, and monkeying around with GBrowse and such.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Your description of the annotation pipeline sheds some light on
an area of GBrowse that presented a fair bit of confusion to me. I now
understand that the data behind some of the tracks is obtained from an “eternal
source” – such as NCBI or UCSC – and then converted to an “internal
source” that can be read by GBrowse. The bottom line is that I finally
understand where this data originates and how it fits in the GBrowse world.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>I will try to create a diagram of what I understand about
GBrowse and how it interacts with other GMOD components and a database. If this
diagram turns out to be of any value to the GMOD community (especially newbies
like me), you will be welcome to post it on the wiki (provided I get around to
creating it!).<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>I genuinely appreciate your help with all of this – it is
terrific to have you as a resource!<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Cheers,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Margie<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'>
<p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:
"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;
font-family:"Tahoma","sans-serif"'> Dave Clements, GMOD Help Desk
[mailto:gmodhelp@googlemail.com] <br>
<b>Sent:</b> December-08-08 4:11 PM<br>
<b>To:</b> Margie Manker<br>
<b>Cc:</b> GMOD Help Desk<br>
<b>Subject:</b> Re: [Gmod-help] new database and GBrowse<o:p></o:p></span></p>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Hi Margie<br clear=all>
<o:p></o:p></p>
<p>You will still need an adaptor such as Bio::DB::GFF (GFF2) or
Bio::DB::SeqFeature::Store (GFF3) to provide data to GBrowse. However,
you won't need other components such as Chado, Apollo, or CMAP. You can
write your own adaptor if you choose, but this is non-trivial and you are
instead encouraged to write a program to generate GFF3 & FASTA files from
your database and then use something like bp_seqfeature_load.pl (a bioperl
program) to load the data into a MySQL DB that GBrowse will then read.<o:p></o:p></p>
<p>I don't think there is any specific documentation on how to write a GBrowse
adaptor. (Scott, Lincoln, please chime in if you disagree.) If you
still want to go down this path, I would start by looking at the Chado adaptor
(Bio::DB::Das::Chado), which is inside the GBrowse distribution.<o:p></o:p></p>
<p>If you haven't already done so, I encourage you to walk through the GBrowse
tutorial, actually do an installation and playing with the configuration.
At the end of the tutorial it tells you how to hook GBrowse up to a
database instead of running it from flat files. Installing the
prequisites for for GBrowse will take some effort (usually BioPerl and libgd) but
once you have it up and running, the tutorial is pretty straightforward.<o:p></o:p></p>
<p>I'm not familiar with the history or details of the Database of Genomic
Variants (DGV), but I'll take a stab at your questions. The data behind
tracks such as RefSeq and UCSC segmental duplications were generated by NCBI
(certainly) and UCSC (probably) and made available in some common
bioinformatics file format (if you are lucky, GFF3). NCBI and UCSC ran
pipelines to generate these data, but as a consumer of the data, you don't need
to know all the details of how those pipelines worked, just what the output
formats are. The data was generated against a specific build of the
reference human genome.<o:p></o:p></p>
<p>To create the DGV GBrowse instance the site admins needed to get data files
describing the reference genome, the RefSeq genes, the UCSC segmental
duplications, and so on.<o:p></o:p></p>
<p>For any file that is not already in GFF2/3, they need to translate the data
into GFF2/3. If they were lucky, those programs already existed.
Once the data is in GFF they can load it into a GBrowse database and then
show it in GBrowse.<o:p></o:p></p>
<p>There may be other data at DGV that was locally created, perhaps the all
CNV's track. In this case, a lot more work had to be done to get the data
from whatever format it was in, into GFF so it could be loaded into the DB, and
then seen by GBrowse.<o:p></o:p></p>
<p>All GBrowse instances get their data from somewhere (see <a
href="http://gmod.org/wiki/GBrowse_Adaptors">http://gmod.org/wiki/GBrowse_Adaptors</a>).
Is that somewhere external? "External" and "Internal"
may not be meaningful here. GBrowse is a Perl program that reads its data
from a data source. A more useful question might be "Does the data
source exist solely to provide data to GBrowse?" The answer to that
question is most often Yes. Most users probably did not have Bio:DB::GFF
or Bio::DB::SeqFeature::Store databases prior to installing GBrowse.<o:p></o:p></p>
<p>Please let me know if any of this is not clear or if you have other
questions. Please don't hesitate to call/Skype/Aim/Ichat me.<o:p></o:p></p>
<p>Thanks,<o:p></o:p></p>
<p>Dave C<o:p></o:p></p>
<div>
<p class=MsoNormal>On Mon, Dec 8, 2008 at 11:04 AM, Margie Manker <<a
href="mailto:manker@populargenetics.ca">manker@populargenetics.ca</a>>
wrote:<o:p></o:p></p>
<div>
<div>
<p><span style='font-size:11.0pt;color:#1F497D'>Hi Dave</span><o:p></o:p></p>
<p><span style='font-size:11.0pt;color:#1F497D'> </span><o:p></o:p></p>
<p><span style='font-size:11.0pt;color:#1F497D'>I have had a chance to review
your comments in detail and have a couple of follow-up questions for you:</span><o:p></o:p></p>
<p><span style='font-size:11.0pt;color:#1F497D'> </span><o:p></o:p></p>
<p style='text-indent:-18.0pt'><span style='font-size:11.0pt;color:#1F497D'>1)</span><span
style='font-size:7.0pt;color:#1F497D'> </span><span
style='font-size:11.0pt;color:black'>"</span>It is possible to use GBrowse
as a standalone tool, without any other GMOD tools. A lot of people
actually do this. It sounds like this might work fine for
you." <span style='font-size:11.0pt;color:#943634'>-- If I use
GBrowse as a stand-alone tool, do I still need an adaptor (such as
Bio::DB::GFF)? If not, I would conclude that GBrowse can be customized to read
directly from my custom database. Is this correct? If I can use GBrowse without
any other GMOD components, where is the best place to look at documentation
specifically on how to do this?</span><o:p></o:p></p>
<p><span style='color:#1F497D'> </span><o:p></o:p></p>
<p style='text-indent:-18.0pt'><span style='font-size:11.0pt;color:#1F497D'>2)</span><span
style='font-size:7.0pt;color:#1F497D'> </span><span
style='font-size:11.0pt;color:#943634'>Annotation Pipeline: I am still unclear
as to what is part of the annotation pipeline. For example, the tracks in the
Database of Genomic Variants (i.e. Genome Browser: <a
href="http://projects.tcag.ca/cgi-bin/variation/gbrowse/hg18/" target="_blank"><span
style='color:#943634'>http://projects.tcag.ca/cgi-bin/variation/gbrowse/hg18/</span></a>
) display data such as RefSeq genes, UCSC segmental duplications, Clones, OMIM
disease genes, etc. Where do these data come from? Are files downloaded,
stored, and then read by the pipeline? Are these data part of GBrowse somehow?
i.e. does GBrowse fetch data from an external source (external to my
database/in-house information system) and display it to users? </span><o:p></o:p></p>
<p><span style='font-size:11.0pt;color:#943634'> </span><o:p></o:p></p>
<p><span style='font-size:11.0pt;color:#1F497D'>I think I will be getting ever
closer to a better understanding of GMOD and GBrowse if you are able to provide
further insight to the above topics.</span><o:p></o:p></p>
<p><span style='font-size:11.0pt;color:#1F497D'> </span><o:p></o:p></p>
<p><span style='font-size:11.0pt;color:#1F497D'>Again, thank you very much for
your help with this. It is much appreciated and I look forward to the
opportunity to, in turn, help others in our GMOD community.</span><o:p></o:p></p>
<p><span style='font-size:11.0pt;color:#1F497D'> </span><o:p></o:p></p>
<p><span style='font-size:11.0pt;color:#1F497D'>Cheers!</span><o:p></o:p></p>
<div>
<p><span style='font-size:11.0pt;color:#1F497D'> </span><o:p></o:p></p>
<p><span style='font-size:11.0pt;color:#1F497D'>Margie </span><o:p></o:p></p>
<p><span style='font-size:11.0pt;color:#943634'> </span><o:p></o:p></p>
<p><span style='font-size:11.0pt;color:#943634'> </span><o:p></o:p></p>
<p><span style='font-size:11.0pt;color:#1F497D'> </span><o:p></o:p></p>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'>
<p><b><span lang=EN-US style='font-size:10.0pt'>From:</span></b><span
lang=EN-US style='font-size:10.0pt'> Dave Clements, GMOD Help Desk [mailto:<a
href="mailto:gmodhelp@googlemail.com" target="_blank">gmodhelp@googlemail.com</a>]
<br>
<b>Sent:</b> December-04-08 7:30 PM<br>
<b>To:</b> Margie Manker<br>
<b>Cc:</b> GMOD Help Desk<br>
<b>Subject:</b> Re: [Gmod-help] new database and GBrowse</span><o:p></o:p></p>
</div>
<p> <o:p></o:p></p>
</div>
<p>Hi Margie,<o:p></o:p></p>
<div>
<div>
<p>I remember speaking with you in Toronto. I hope that you are still enjoying
working in biology!<o:p></o:p></p>
<div>
<blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;
margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt'>
<div>
<div>
<p style='text-indent:-18.0pt'>-<span style='font-size:7.0pt'>
</span>I am creating two new database schemas that will contain mostly genomic
variation data as well as some phenotype data. These data will also include
information on a study, methods, platforms, subjects, samples, etc.<o:p></o:p></p>
<p style='text-indent:-18.0pt'>-<span style='font-size:7.0pt'>
</span>I would like to create a schema that suits the needs of our
organization. I have reviewed Chado in some detail and it does not suit the
needs of our organization. Ideally, our own schema should be used and I would
like to continue with this approach.<o:p></o:p></p>
</div>
</div>
</blockquote>
<div>
<p>Can you describe what you found lacking in Chado? This will help us
improve it in the near future: Chado is extendable and NESCent (<a
href="http://nescent.org" target="_blank">nescent.org</a>) has developed a
natural diversity module for Chado. This is still in Beta (and is likely to
change before it is released). It is based on the GDPDM, which is used at
Gramene and MaizeGenetics for this purpose. One of my deliverables for
2009 is to get the natural diversity module out of Beta and into production
Chado.<o:p></o:p></p>
</div>
<div>
<p>Several things should help this along. One is a NESCent working group
that needs this to be done, and secondly we are trying to schedule a GMOD
natural diversity hackathon for 2009 that will move this work forward. <o:p></o:p></p>
</div>
<div>
<p>If you are interested the natural diversity module and GDPDM are described
at:<o:p></o:p></p>
</div>
<div>
<p> <a
href="http://heliconiusdb.svn.sourceforge.net/viewvc/heliconiusdb/trunk/schema/doc/"
target="_blank">http://heliconiusdb.svn.sourceforge.net/viewvc/heliconiusdb/trunk/schema/doc/</a><o:p></o:p></p>
</div>
<div>
<p> <a href="http://www.maizegenetics.net/gdpdm/" target="_blank">http://www.maizegenetics.net/gdpdm/</a><o:p></o:p></p>
</div>
<div>
<p>I think all this work may come too late for your needs. However, I
encourage you to look at the current beta release as a possible solution.
When I actually get to work on this (probably starting in February) I may
ask you for any insights you have and for a copy of your schema. If you are
really lucky (!) I might even ask if you are interested in attending the
hackathon. :-)<o:p></o:p></p>
</div>
<blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;
margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt'>
<div>
<div>
<p style='text-indent:-18.0pt'>-<span style='font-size:7.0pt'>
</span>We will most likely employ GBrowse as the genome browser for display of
data in the above databases.<o:p></o:p></p>
<p style='text-indent:-18.0pt'>-<span style='font-size:7.0pt'>
</span>My highest level questions that I have yet to find appropriate answers
to are these:<o:p></o:p></p>
<p style='margin-left:72.0pt;text-indent:-18.0pt'><span style='font-family:
"Courier New"'>o</span><span style='font-size:7.0pt'> </span>Can I
use my own schema to build the database which underlies Gbrowse? If so, will a
separate 'Bio::DB::GFF' database need to be created to act as a bridge between
my database and Gbrowse?<o:p></o:p></p>
<p style='margin-left:72.0pt;text-indent:-18.0pt'><span style='font-family:
"Courier New"'>o</span><span style='font-size:7.0pt'> </span>What
components would I most likely need from GMOD to get my database and GBrowse to
work together?<o:p></o:p></p>
<p style='text-indent:-18.0pt'>-<span style='font-size:7.0pt'>
</span>From what I can determine based on the documentation, I should be able
to use my own database schema to underlie GBrowse. It looks like my database
would require a GBrowse adaptor (Bio::DB::GFF??) and GBrowse. It also looks
like I might need an annotation pipeline, too.<o:p></o:p></p>
<p style='text-indent:-18.0pt'>-<span style='font-size:7.0pt'>
</span>Other questions that arise are:<o:p></o:p></p>
<p style='margin-left:72.0pt;text-indent:-18.0pt'><span style='font-family:
"Courier New"'>o</span><span style='font-size:7.0pt'> </span>What
is "Bio::DB::GFF"? Is it a database? Schema? Adaptor?<o:p></o:p></p>
<p style='margin-left:72.0pt;text-indent:-18.0pt'><span style='font-family:
"Courier New"'>o</span><span style='font-size:7.0pt'> </span>Where does
annotation data come from? What is the annotation pipeline?<o:p></o:p></p>
</div>
</div>
</blockquote>
<div>
<p>GBrowse uses adaptors to read different data sources. The data source
can be flat files (GFF3 + FASTA if you want the sequence), or databases, or any
other data source you can imagine. I believe that all adaptors are
written in Perl. Each adaptor has an expected input format. The
database adaptors expect a specific schema to talk to. <o:p></o:p></p>
</div>
<div>
<p>So Bio::DB::GFF is a Perl module that is a GBrowse adaptor. It expects
to read from a database with a specific schema. (Bio::DB::GFF also
assumes GFF2, a now deprecated format.)<o:p></o:p></p>
</div>
<div>
<p>However, writing an adaptor is not a small undertaking. Probably a
much easier way to tackle this is to write a program to export GFF3 and FASTA
formatted files from your database and then load it into a into a
Bio::DB::SeqFeature::Store MySQL database. This will likely be faster
than running directly off of your source database. GFF3 is a flat file
format for specifying genomic features (genes, exons, SNPs, ...) and relationships
between them. FASTA is a flat file format for specifying sequence.<o:p></o:p></p>
</div>
<div>
<p>Since you have a custom database, there is not going to be any program that
will create GFF3 or FASTA for you. FASTA should be trivial to create (if you
have the sequence). GFF3 will require more work. Some code you
could look at for inspiration is the GMODTools suite (<a
href="http://gmod.org/wiki/GMODTools" target="_blank">http://gmod.org/wiki/GMODTools</a>).
It does conversion from several formats to GFF3.<o:p></o:p></p>
</div>
<div>
<p>Where does annotation data come from? From an annotation pileline!<o:p></o:p></p>
</div>
<div>
<p>Wait. That answer isn't helpful, darnit. A pipeline is usually a
series (thus a pipeline) of programs that performs some analysis on sequence.
For example, you might have an already annotated reference genome, and a
slew of short sequences reads from ESTs* from the latest high-throughput
sequencer and you want to annotate the reference genome with the new data.
your pipeline might be:<o:p></o:p></p>
</div>
<div>
<p>1. Assemble the short reads into a series of contigs (put the short reads
together into longer chunks, hopefully each as long as the complete EST).
<o:p></o:p></p>
</div>
<div>
<p>2. Align the contigs to the reference genome (figure out where they came
from)<o:p></o:p></p>
</div>
<div>
<p>3. Create a GFF3 file and a FASTA file (not sure on the FASTA) describing
where each EST aligns to and load it into GBrowse.<o:p></o:p></p>
</div>
<div>
<p>All of these steps may involve heavy magic. Fortunately, most of that
magic is already done by the people who have written the programs to do the
steps.<o:p></o:p></p>
</div>
<div>
<p>ESTs = a relatively easy way to find out what part of the genome is being
transcribed (what the active genes are)<o:p></o:p></p>
</div>
<blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;
margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt'>
<div>
<div>
<p>As I said, I am relatively new to GMOD and I find the online documentation
is plentiful, but not easily navigated by the newbie. After two weeks of
reading the documentation I find I am now going in circles looking for answers to
my questions – and information on how to design an information system
employing components of GMOD. <o:p></o:p></p>
<p>Ideally a diagram that displays a database and how it interacts with the
components of GMOD would be great to see. I haven't yet found anything like this
in the documentation. At the very least, if someone could steer me in the right
direction as far as what components I should focus on and what specific
documentation I can read, it would be appreciated.<o:p></o:p></p>
</div>
</div>
</blockquote>
<div>
<p>It is possible to use GBrowse as a standalone tool, without any other GMOD
tools. A lot of people actually do this. It sounds like this might
work fine for you. <o:p></o:p></p>
</div>
<div>
<p>Thanks for the documentation suggestions. We just did a community
survey and one of the top priorities for the help desk was improving the documentation.
Look for progress in 2009.<o:p></o:p></p>
</div>
<div>
<p>Finally, although you didn't ask for it, I can think of two GBrowse
instances that might show datatypes that are sort of similar to what you are
doing:<o:p></o:p></p>
</div>
<div>
<p> <a href="http://hapmap.org" target="_blank">http://hapmap.org</a><o:p></o:p></p>
</div>
<div>
<p> <a
href="http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/jwsequence/"
target="_blank">http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/jwsequence/</a>
or<o:p></o:p></p>
</div>
<div>
<p> <a
href="http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/cvsequence/"
target="_blank">http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/cvsequence/</a><o:p></o:p></p>
</div>
<div>
<p>Please let em know if you have any questions or comments.<o:p></o:p></p>
</div>
<div>
<p>Dave C<o:p></o:p></p>
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<div>
<p>541 914 6324<o:p></o:p></p>
</div>
<div>
<p>AIM or Skype user: tnabtaf <o:p></o:p></p>
</div>
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margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt'>
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<p> <o:p></o:p></p>
<p>Any assistance you can provide on these questions would be tremendously appreciated.
And if I can, in turn, provide some input on how to create some
"newbie" documentation, I will do so – to help others in my
situation.<o:p></o:p></p>
<p> <o:p></o:p></p>
<p>Also…I have 15 years' experience working with relational
databases…but not genomic databases…so you can assume a level of
technical understanding, but with the caveat that genomic databases are new
territory for me.<o:p></o:p></p>
<p> <o:p></o:p></p>
<p>Thanks so much for your time.<o:p></o:p></p>
<p> <o:p></o:p></p>
<p>Kind regards,<o:p></o:p></p>
<p> <o:p></o:p></p>
<p><span style='color:#888888'>Margie Manker</span><o:p></o:p></p>
</div>
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</blockquote>
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