Thanks Dave!<br><br>
<div><span class="gmail_quote">On 10/30/07, <b class="gmail_sendername">GMOD Help Desk</b> <<a href="mailto:help@gmod.org">help@gmod.org</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hello Mark,<br><br>Responses to some of your questions are below. I have CC'd this<br>message to the GBrowse and CMap e-mail lists because there are people
<br>on those lists who can probably answer the other questions.<br><br>Dave Clements<br>GMOD Help Desk<br><br>On Oct 30, 2007 7:08 AM, Mark Mandel <<a href="mailto:mandel01@gmail.com">mandel01@gmail.com</a>> wrote:<br>
> Hello Helpdesk,<br>><br>> I am working on building a "model organism" resource for Vibrio fischeri and<br>> the GMOD resources seem very appealing. I am writing because I found your<br>> "GMOD for the Biologist" page in your Wiki and that fits me very well, so I
<br>> wanted some feedback before I get started.<br>><br>> My goals are to have an easily searchable interface for the V. fischeri<br>> ES114 genome (which we have recently resequenced and reannotated), which it
<br>> seems that gbrowse will accomplish very well! Looking toward the future,<br>> there are additional features that will be particularly valuable:<br>><br>> 1. links to papers that are related to the genes involved (we have a curated
<br>> list of Pubmed ID's at this point but will want to add to it).<br>> 2. user-added gene annotations or information as gene names and annotations<br>> change.<br>> 3. comparative genomics with other bacterial strains of this species, since
<br>> others are in the pipeline to be sequenced. I saw the cmap page but wasn't<br>> sure if this was well-adaptable to bacterial genomes.<br><br>GBrowse is indeed the tool you want for displaying the sequence and
<br>the annotation. How are you currently making and recording your<br>annotations? Apollo is another GMOD component that might be able to<br>help with that.<br><br>I am not sure if GBrowse can link to papers. This may require GBrowse
<br>to run on Chado. Can someone on the GBrowse list address this<br>question?<br><br>GMOD components are widely used with bacteria. I do not know if CMap<br>is in use with bacterial maps or not. Ben (or anyone else on the CMap
<br>list), do you know of any sites using CMap with bacteria?<br><br>> I am going to start installing the basic gbrowse w/gff annotations and see<br>> how it goes, but if you had any other comments (or knew of other examples of
<br>> smaller bacterial comparative genomics/annotation projects) that would be<br>> appreciated.<br><br>See <a href="http://gmod.org/wiki/index.php/GMOD_Users">http://gmod.org/wiki/index.php/GMOD_Users</a> for a partial list of
<br>sites that use GMOD components. That page also lists GBrowse users at<br>the end. Unfortunately this list is several years old and without<br>links.<br><br>> In general most of my database work has been in Microsoft Access (I use
<br>> Windows), and I have a rudimentary Python and Perl knowledge that I am<br>> working on enhancing. But I am principally a *biologist* and most<br>> importantly want to build a system that will be easy to maintain and keep
<br>> up-to-date, not one that is always waiting for me to learn some more<br>> programming!!<br><br>With GBrowse, you almost certainly won't have to do significant (or<br>maybe even any) Perl coding. You will need to know how to install
<br>things. Windows is a supported platform, but it is probably the least<br>used platform in the GMOD world. Questions that are Windows specific<br>will have a smaller pool of people that are able to respond.<br><br>> Thanks in advance for any comments.
<br>><br>> Regards,<br>> Mark Mandel<br>><br>> <a href="mailto:mandel01@gmail.com">mandel01@gmail.com</a><br>> <a href="http://www.vfdna.org/">http://www.vfdna.org/</a><br>> _______________________________________________
<br>> Wg-emod mailing list<br>> <a href="mailto:Wg-emod@nescent.org">Wg-emod@nescent.org</a><br>> <a href="https://lists.nescent.org/mailman/listinfo/wg-emod">https://lists.nescent.org/mailman/listinfo/wg-emod</a>
<br>><br>><br></blockquote></div><br>