[Simbiome-feedback] RE: Simbiome Resource Inventory - Beta Review

[Jon Dugan]

Michael,

Thank you for your comments!

As for suggesting new entries, I would be glad to enter them for now.
I went ahead and added Proshape by Patrice Koehl.

http://simbiome.org/resource/show/75

Any user can create entries once they set up a user account, however,
those entries are not viewable on the site until they are approved.
Site admins (who I assume might eventually be you, Russ, Vijay,
Micahel, others?) can then make entries viewable to the world when
logged in.  Currently I'm the only site admin.

There are two X-plor packages listed now:
http://simbiome.org/resource/show/35 (X-plor) and
http://simbiome.org/resource/show/38 (XPLOR-NIH)
I went in and cross linked them to each other.

I'll add Netlib and MSD now.


The reason for having feedback come to a list (simbiome-feedback)
instead of me supports exactly your suggestion.  I'll go ahead and add
you now so you can see beta feedback.  


Regards,
Jon

650 799 5369






On Tue, May 02, 2006 at 08:11:38AM -0700, Michael Levitt wrote:
> Dear Jon,
> 
>    The interface is clean and the information is well-presented. 
> I could see nothing to be removed .  As for adding, this is a 
> slow process that we need to think about more.  It also will
> likely make the resource deeper is certain narrow areas.
> Do you have  a format for suggesting additional areas?
> 
>    Actually, I would add a link to ProShape, Patrice Koehl's 
> exceptionally fast and robust software for protein geometry.
> (see: http://nook.cs.ucdavis.edu:8080/~koehl/research.html).
> I am sure this is much better than Surfnet.
> 
>    Also, Axel Brunger is now at Stanford so it X-PLOR still at Yale.
> There is a better package based on explore but in the public
> domain (I think) managed by Marius Clore at NIH.
> 
>    Another useful link is EBI MSD (Molecular Structure Database)
> which has better biological units in PQS.  A link to netlib, the database
> of legacy software with some amazing numerical routines is also 
> good.
> 
>     Michael
> 
> PS:  Perhaps set up a mailing list of your beta testers so that each 
> of our emails go to all the others.  That way, our memories will be 
> collectively jogged to add new resources.  To this end, I am copying my
> email
> to Sherm, Vijay and Russ.
> 
> -----Original Message-----
> From: owner-simbiosfac at lists.Stanford.EDU
> [mailto:owner-simbiosfac at lists.Stanford.EDU] On Behalf Of Jon Dugan
> Sent: Tuesday, May 02, 2006 12:21 AM
> To: Simbios Participants; Simbios Faculty
> Subject: Simbiome Resource Inventory - Beta Review
> 
> 
> Dear Simbios Participants and Faculty,
> 
> 
> As you may know we've been built an online resource inventory for the
> Simbios Center - we've called it the "Simbiome".  Back in February, we
> polled members of the Center for suggestions on what resources should
> initially be on the list.
> 
> Before we release Simbiome for public use, we would like your feedback.
> Specifically, we want you to look at the resources listed and let us know if
> there are ones we should add, or ones listed that should be removed. 
> 
> 
> The site is here:	http://simbiome.org
> 
> To access the site, use 
> 			UserName: beta
> 			Password: 123123
> 
> 
> There are instructions on the front page for what (& how) to review.
> Specifically, please go to the "List all resources" page
> 	      http://simbiome.org/resource/list and read through and see if
> there are other, trusted resources that you think we should recommend.
> 
> 
> You can reply to this email (simbiome-feedback at simtk.org) with suggestions,
> feedback, and helpful criticism.  Your time and feedback are greatly
> appreciated.  Please reply by May 8 (this week).
> 
> If you get really excited and want to add resources yourself - sign up for
> an user account and start adding!  Feedback on this process would be great
> too.
> 
> 
> Thank you.
> 
> 
> Regards,
> Jon
> 
> 
> 650 799 5369
> 
> 
> 
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