[Gmod-help] Grant sponsored GBrowse tutorial from OpenHelix

Wed Nov 26 18:10:35 EST 2008

Hi Mary,

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.)

Overall we liked it a lot.  It is very good.  This will be a great resource
to GBrowse users.

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.

Please let us know if you have any questions or comments.

Thanks,

Dave C.

*Big Picture
*
We liked it and were impressed by how thorough it is.  Specific comments:
* I like it, a lot.
* I think it is very thorough!
* 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.

*GBrowse Version:
*
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.

Some options to address this:

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.

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.

Adding 1.69 coverage will give the tutorial a much longer shelf life.

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.

Version matters with GBrowse.  Any tutorial on it should clearly say what
version it covers (and that most functionality remains the same across
versions).

*URLs and Help:
*
The URLs for the GBrowse documentation home page have been rationalized.
Please update all URLs in the HTML and presentation to point to
  http://gmod.org/wiki/GBrowse

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:
  gmod-gbrowse at lists.sourceforge.net and
  https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

*Jim Watson Genome:
*
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.

Some options to consider
* Sticking with Jim
  * Perhaps with less enthusiasm
  * Discussing something that isn't his allele status for a crippling
genetic disease.
* Switching to Craig Venter
  * http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/cvsequence/

*Introduction and Credits
*
This section mentions that this tutorial only covers usage, not installation
and configuration.  This would be a good place to say something like:

  If you are interested in GBrowse installation and configuration
  documentation and an HTML tutorial are also available:
    http://gmod.org/wiki/GBrowse
    http://gmod.org/gbrowse-cgi/tutorial/tutorial.html

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.

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).

*Layout and Basic Search*

This and the next section change quite a bit in release 1.69

*Basic Annotation Controls.
*
There is no wiggle / density / intensity data shown in any examples.  This
should be added, either here or in the GBrowse Tours section.

*Advanced Annotation Controls
*
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.

2. The narrator says "Edit your text file."  Shouldn't this be "Edit a copy
of your text file?"

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.

*GBrowse Tours*

Narrator says
  Flybase has 12 different strains
Should say
 12 different species.

*Summary*

No comments.

*Exercises / Handouts
*
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.

On Wed, Nov 5, 2008 at 6:31 AM, Mary Mangan <mmangan at openhelix.com> wrote:

> Hi Dave and GMOD team--
>
> That's terrific, thanks!  We are finding a lot of interest in this tutorial
> and I think it will be very popular.
>
> Let me know if you have any questions on any aspect of this.
>
> Best regards,
>
> Mary
>
> -----Original Message-----
> From: Dave Clements, GMOD Help Desk [mailto:gmodhelp at googlemail.com]
> Sent: Tuesday, November 04, 2008 7:26 PM
> To: Mary Mangan
> Cc: GMOD Help Desk
> Subject: Re: [Gmod-help] Grant sponsored GBrowse tutorial from OpenHelix
>
> Dear Mary,
>
> Thank you for contacting us about the GBrowse tutorial created by
> OpenHelix.  It has great promise for making GBrowse easier to use.
>
> I would be happy to share the tutorial with a few select peoplein the
> GMOD project and then compile our feedback before sending it back to
> you.
>
> Once the tutorial becomes publicly available, I would also be happy to
> link to it and promote it from the GMOD web site.
>
> I will get back to you before November 28.
>
> Please let me know if you have any questions.
>
> Thanks,
>
> Dave Clements
> GMOD Help Desk
>
>
> On Mon, Nov 3, 2008 at 1:25 PM, Mary Mangan <mmangan at openhelix.com> wrote:
> > Hello GMOD team-
> >
> >
> >
> > You may be aware that we have developed online tutorial suite on GBrowse.
> > These materials are introductory in nature, providing awareness and
> > understanding of the data contents and search types available.  Basic
> > features of the navigation, search and display options are our focus.
>  The
> > suite includes a training movie, slides, handouts, and exercises.
> >
> >
> >
> > We offer this tutorial among our 60 tutorial suites available through
> paid
> > subscription.  However, we have recently received funding from NHGRI to
> > offer a number of model organism database tutorial suites free to the
> public
> > in 2009.  GBrowse is one of the tutorial suites that will be offered
> under
> > this program.
> >
> >
> >
> > We would like to offer you the opportunity to review the materials before
> we
> > make them freely available.  If needed, we can make an updates tutorial
> > suite before we launch.  If you could review these materials and return a
> > collection of comments to us by November 28, we can update the materials
> > with an expected launch in January 2009.
> >
> >
> >
> > We intend to have outreach around these materials using a number of
> > strategies.  We hope that this will drive new users to your site, and
> enable
> > them to be more effective database users.
> >
> >
> >
> > There is no cost to you for this.  The funding comes from a supplement to
> > our NIH grant 9R44HG004531-02A2.  We will be pleased to share usage data
> > with you if desired.
> >
> >
> >
> > To access the materials:
> >
> > URL: http://openhelix.com/downloads/gbrowse/gbrowse_home.shtml
> >
> > Login: gbrowsereview
> >
> > Password: gmod123
> >
> >
> >
> > Please let us know if you have any issues during the review phase.
> >
> >
> >
> > We hope that you will find this to be a useful opportunity and a benefit
> to
> > biomedical researchers all over the world.
> >
> >
> >
> > We look forward to your response.
> >
> >
> >
> > Best regards,
> >
> >
> >
> > Mary
> >
> >
> >
> >
> >
> >
> >
> > Mary E. Mangan, PhD
> >
> > President
> >
> > OpenHelix LLC
> >
> > 65 Main St.
> >
> > Somerville, MA 02145
> >
> > Phone:  888-861-5051 x9
> >
> > mmangan at openhelix.com
> >
> > www.openhelix.com
> >
> > www.openhelix.com/blog
> >
> >
>
>
>
> --
> Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback
>
>
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