Hi Mary,<br><br>Sarah Richardson from Johns Hopkins, Scott Cain from GMOD, and Peter Ruzanov from the University of Toronto all provided feedback on the GBrowse tutorial. I've included their comments (and mine) below, sometimes verbatim. (Reviewers: Please feel free to correct any errors or omissions.)<br>
<br>Overall we liked it a lot. It is very good. This will be a great resource to GBrowse users.<br><br>Our concerns are listed below. All but one of them are small. The one large concern is that the tutorial covers an old version of GBrowse. See below for more.<br>
<br>Please let us know if you have any questions or comments.<br><br>Thanks,<br><br>Dave C.<br><br><br><b>Big Picture<br></b><br>We liked it and were impressed by how thorough it is. Specific comments:<br>* I like it, a lot.<br>
* I think it is very thorough!<br>* I was quite impressed with the quality of presented material - the slides were easy to read and narration is also very nicely done. I especially liked the examples section and the additional material available for download. This is quite a departure from a plain html documentation, I have always had a feeling that [technologically] scientific material presented on the Internet is behind the advertisement/entertainment industry, and not always look as cool as it should. In that regard, I liked this tutorial very much.<br>
<br><br><b>GBrowse Version:<br></b><br>All of us had concerns about the version of GBrowse that is covered in the tutorial. The tutorial uses release 1.68. The current production release is 1.69 and It includes many look and feel and functionality changes compared to 1.68. MGI does not have plans to migrate to 1.69, but many other places have and most remaining places will. It has many features that make the upgrade attractive.<br>
<br>Some options to address this:<br><br>1. Redo the whole tutorial using a 1.69 browser such as WormBase's. Include the many new new features. We can imagine this idea might not be enthusiastically welcomed.<br><br>
2. Add a 1.69 browser to the GBrowse Tours section (e.g., WormBase) that emphasizes what's new in 1.69. (Or this could be added to the main section as well, but that may be more work.) Modify the MGI part of the tutorial to clearly specify it uses version 1.68, and say that new 1.69 features are covered later in the tutorial.<br>
<br>Adding 1.69 coverage will give the tutorial a much longer shelf life.<br><br><br>The next release, GBrowse 2.0 is likely to also introduce several more interface changes (and lots of behind the scene changes). Also, an alternative to GBrowse currently called both GBrowse 3.0 and JBrowse will likely be out in the next year or so. JBrowse is not expected to replace GBrowse, but rather to be an alternative.<br>
<br>Version matters with GBrowse. Any tutorial on it should clearly say what version it covers (and that most functionality remains the same across versions).<br><br><br><b>URLs and Help:<br></b><br>The URLs for the GBrowse documentation home page have been rationalized. Please update all URLs in the HTML and presentation to point to <br>
<a href="http://gmod.org/wiki/GBrowse">http://gmod.org/wiki/GBrowse</a><br><br>A couple of places mention Lincoln's CSHL e-mail address for help. Lincoln's involvement with CSHL is decreasing. We recommend promoting the GBrowse mailing list for help instead:<br>
<a href="mailto:gmod-gbrowse@lists.sourceforge.net">gmod-gbrowse@lists.sourceforge.net</a> and<br> <a href="https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse">https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse</a><br>
<br><br><b>Jim Watson Genome:<br></b><br>Two sections cover/mention the Jim Watson genome viewer with some enthusiasm about Jim. Given Watson's well-documented belief system, two of the reviewers, myself included, were not comfortable with this enthusiasm. <br>
<br>Some options to consider<br>* Sticking with Jim<br> * Perhaps with less enthusiasm<br> * Discussing something that isn't his allele status for a crippling genetic disease.<br>* Switching to Craig Venter<br> * <a href="http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/cvsequence/">http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/cvsequence/</a><br>
<br><br><b>Introduction and Credits<br></b><br>This section mentions that this tutorial only covers usage, not installation and configuration. This would be a good place to say something like: <br><br> If you are interested in GBrowse installation and configuration<br>
documentation and an HTML tutorial are also available:<br> <a href="http://gmod.org/wiki/GBrowse">http://gmod.org/wiki/GBrowse</a><br> <a href="http://gmod.org/gbrowse-cgi/tutorial/tutorial.html">http://gmod.org/gbrowse-cgi/tutorial/tutorial.html</a><br>
<br>This section also talks about "Model Organism Databases". "Model" is a loaded term implying organisms with a long history of research and large research communities (think yeast, fly, mouse, worm). As the tutorial points out, GBrowse is used in both large and small communities.<br>
<br>So, even though there is an "M" in GMOD we'd like the tutorial not to emphasize that. Perhaps the tutorial could mention that GBrowse is relatively easy to install and is in use by over 100 groups around the world, some of them with only EST data (an no reference sequence).<br>
<br><br><b>Layout and Basic Search</b><br><br>This and the next section change quite a bit in release 1.69<br><br><br><b>Basic Annotation Controls.<br></b><br>There is no wiggle / density / intensity data shown in any examples. This should be added, either here or in the GBrowse Tours section.<br>
<br><br><b>Advanced Annotation Controls<br></b><br>1. The slides/handout only mention the reports and analysis menu once, and only in the context of wormbase, and the exercises don't touch it at all, which it seems to me is a pretty big omission when it appears at the top of every page in two of their example gbrowse installations and every other gbrowse installation I have ever seen. You can't miss it. I know plugins are varied in installation, implementation, and support, but it seems it would be simple enough to cover perhaps downloading a sequence file or adding restriction site annotation to the view, as those plugins are pretty universally used. I especially say this because I know there can be some confusion over the "Go" and "Configure" buttons, and what happens when you hit configure instead of go inside a plugin configuration menu, etc.<br>
<br>2. The narrator says "Edit your text file." Shouldn't this be "Edit a copy of your text file?"<br><br>3. If someone told me to upload my annotation data to some server and didn't discuss the disposition of the data, whether or not it was stored or visible to other users, I'd be skeptical. I think the tutorial should be more clear that uploading in this sense is not a contribution to the installation or a publication. The GBrowse disclaimer is briefly visible in the tutorial but having it explicitly stated that the data is still private would be good.<br>
<br><br><b>GBrowse Tours</b><br><br>Narrator says<br> Flybase has 12 different strains<br>Should say<br> 12 different species.<br><br><br><b>Summary</b><br><br>No comments.<br><br><br><b>Exercises / Handouts<br></b><br>The handouts are black and white versions of the color slides. I thought this caused an unnecessary loss of information - segments about highlighting features, for example, are rendered a little less intelligible and the agenda slides don't show any advancement. GBrowse uses color so effectively it seems a shame to have such flat slides - and if the user wants them printed in black and white he can always convert them.<br>
<br><br><div class="gmail_quote">On Wed, Nov 5, 2008 at 6:31 AM, Mary Mangan <span dir="ltr"><<a href="mailto:mmangan@openhelix.com">mmangan@openhelix.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Dave and GMOD team--<br>
<br>
That's terrific, thanks! We are finding a lot of interest in this tutorial<br>
and I think it will be very popular.<br>
<br>
Let me know if you have any questions on any aspect of this.<br>
<br>
Best regards,<br>
<font color="#888888"><br>
Mary<br>
</font><div><div></div><div class="Wj3C7c"><br>
-----Original Message-----<br>
From: Dave Clements, GMOD Help Desk [mailto:<a href="mailto:gmodhelp@googlemail.com">gmodhelp@googlemail.com</a>]<br>
Sent: Tuesday, November 04, 2008 7:26 PM<br>
To: Mary Mangan<br>
Cc: GMOD Help Desk<br>
Subject: Re: [Gmod-help] Grant sponsored GBrowse tutorial from OpenHelix<br>
<br>
Dear Mary,<br>
<br>
Thank you for contacting us about the GBrowse tutorial created by<br>
OpenHelix. It has great promise for making GBrowse easier to use.<br>
<br>
I would be happy to share the tutorial with a few select peoplein the<br>
GMOD project and then compile our feedback before sending it back to<br>
you.<br>
<br>
Once the tutorial becomes publicly available, I would also be happy to<br>
link to it and promote it from the GMOD web site.<br>
<br>
I will get back to you before November 28.<br>
<br>
Please let me know if you have any questions.<br>
<br>
Thanks,<br>
<br>
Dave Clements<br>
GMOD Help Desk<br>
<br>
<br>
On Mon, Nov 3, 2008 at 1:25 PM, Mary Mangan <<a href="mailto:mmangan@openhelix.com">mmangan@openhelix.com</a>> wrote:<br>
> Hello GMOD team-<br>
><br>
><br>
><br>
> You may be aware that we have developed online tutorial suite on GBrowse.<br>
> These materials are introductory in nature, providing awareness and<br>
> understanding of the data contents and search types available. Basic<br>
> features of the navigation, search and display options are our focus. The<br>
> suite includes a training movie, slides, handouts, and exercises.<br>
><br>
><br>
><br>
> We offer this tutorial among our 60 tutorial suites available through paid<br>
> subscription. However, we have recently received funding from NHGRI to<br>
> offer a number of model organism database tutorial suites free to the<br>
public<br>
> in 2009. GBrowse is one of the tutorial suites that will be offered under<br>
> this program.<br>
><br>
><br>
><br>
> We would like to offer you the opportunity to review the materials before<br>
we<br>
> make them freely available. If needed, we can make an updates tutorial<br>
> suite before we launch. If you could review these materials and return a<br>
> collection of comments to us by November 28, we can update the materials<br>
> with an expected launch in January 2009.<br>
><br>
><br>
><br>
> We intend to have outreach around these materials using a number of<br>
> strategies. We hope that this will drive new users to your site, and<br>
enable<br>
> them to be more effective database users.<br>
><br>
><br>
><br>
> There is no cost to you for this. The funding comes from a supplement to<br>
> our NIH grant 9R44HG004531-02A2. We will be pleased to share usage data<br>
> with you if desired.<br>
><br>
><br>
><br>
> To access the materials:<br>
><br>
> URL: <a href="http://openhelix.com/downloads/gbrowse/gbrowse_home.shtml" target="_blank">http://openhelix.com/downloads/gbrowse/gbrowse_home.shtml</a><br>
><br>
> Login: gbrowsereview<br>
><br>
> Password: gmod123<br>
><br>
><br>
><br>
> Please let us know if you have any issues during the review phase.<br>
><br>
><br>
><br>
> We hope that you will find this to be a useful opportunity and a benefit<br>
to<br>
> biomedical researchers all over the world.<br>
><br>
><br>
><br>
> We look forward to your response.<br>
><br>
><br>
><br>
> Best regards,<br>
><br>
><br>
><br>
> Mary<br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
> Mary E. Mangan, PhD<br>
><br>
> President<br>
><br>
> OpenHelix LLC<br>
><br>
> 65 Main St.<br>
><br>
> Somerville, MA 02145<br>
><br>
> Phone: 888-861-5051 x9<br>
><br>
> <a href="mailto:mmangan@openhelix.com">mmangan@openhelix.com</a><br>
><br>
> <a href="http://www.openhelix.com" target="_blank">www.openhelix.com</a><br>
><br>
> <a href="http://www.openhelix.com/blog" target="_blank">www.openhelix.com/blog</a><br>
><br>
><br>
<br>
<br>
<br>
--<br>
Was this helpful? Let us know at <a href="http://gmod.org/wiki/Help_Desk_Feedback" target="_blank">http://gmod.org/wiki/Help_Desk_Feedback</a><br>
<br>
</div></div></blockquote></div><br>