[Bioperl-l] FW: release of cipres portal for tree inference

[Hilmar Lapp]

Just HTTP, no CORBA or other stuff needed client-side.

Ultimately it would of course be nice if they offered a more SOA  
compliant interface too, to obviate the screen-scraping need.  
However, if I understand the UI correctly the screen scraping is - if  
at all - only needed for walking through the steps, and for  
extracting the location of the result. The result itself is in NEXUS  
format, as a separate file.

	-hilmar

On May 20, 2007, at 1:06 AM, Jason Stajich wrote:

> technically remoteblast is in bioperl-live, but for historical/ease  
> of user-install purposes (i.e. so many people want to use blast out  
> of the box, we kept it in bioperl-live to not force them to install  
> bioperl-run).
>
> I think it would be great to have the interface - can we do it all  
> via HTTP or will it require some installation of client software  
> and/or CORBA?
>
> -jason
> On May 19, 2007, at 7:19 PM, Hilmar Lapp wrote:
>
>> I guess so. That's where RemoteBlast is too, if I'm not mistaken?
>>
>> What sucks about the UI from a programming perspective is that it
>> goes through multiple screens. There may be a lot of screen-scraping.
>>
>> 	-hilmar
>>
>> On May 19, 2007, at 10:10 PM, Chris Fields wrote:
>>
>>> I think it would be worthwhile.  Would we place it in bioperl-run?
>>>
>>> chris
>>>
>>> On May 19, 2007, at 8:36 PM, Hilmar Lapp wrote:
>>>
>>>> FYI. Is it worth thinking about implementing a remote access
>>>> interface to the CIPRES tree inference tools, similar to what we  
>>>> have
>>>> for RemoteBlast?
>>>>
>>>> 	-hilmar
>>>>
>>>> Begin forwarded message:
>>>>
>>>> From: "Vision, Todd (Biology)" <tjv at bio.unc.edu>
>>>> Date: May 16, 2007 6:48:49 AM EDT
>>>> Subject: FW: release of cipres portal for tree inference
>>>>
>>>> The CIPRES Central Resource team is pleased to announce the first
>>>> public
>>>> release of the CIPRES portal for Tree Inference.
>>>>
>>>> The portal is based on capabilities exposed by the Cipres software
>>>> libraries, which were constructed as a Joint Effort between Mark
>>>> Holder
>>>> at Florida State University and the SDSC SW engineering team led by
>>>> Terri Liebowitz.
>>>>
>>>> It currently presents Parsimony (PAUP) and Likelihood (GARLI and
>>>> RAxML)
>>>> tools with or without boosting >from RecIDCM3 created by Usman
>>>> Roshan and
>>>> co-workers. Nexus and Phylip files are currently supported.
>>>>
>>>> The site is available to all, and is underwritten by the CIPRES
>>>> cluster
>>>> at SDSC.
>>>>
>>>> The portal is fully supported by the SDSC team, with contributions
>>>> and
>>>> new features introduced by the team in collaboration with Mark  
>>>> Holder
>>>> and Rutger Vos. At present weekly releases are made with  
>>>> improvements
>>>> and new features.
>>>>
>>>> You can visit the portal at the Cipres Web Site.
>>>>
>>>> http://www.phylo.org/sub_sections/portal.htm
>>>>
>>>> Please forward this information to anyone you feel may find the
>>>> portal useful.
>>>>
>>>> On behalf of the whole CIPRES team,
>>>>
>>>> Mark
>>>>
>>>> Mark A. Miller, PhD
>>>> Principal Investigator, Biology
>>>> San Diego Supercomputer Center
>>>> University of California, San Diego
>>>> La Jolla, CA, 92093-0505
>>>> Tel: 858-822-0866
>>>> Fax: 858-822-3610
>>>>
>>>> -- 
>>>> ===========================================================
>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>> ===========================================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>
>> -- 
>> ===========================================================
>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>> ===========================================================
>>
>>
>>
>>
>>
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>
> --
> Jason Stajich
> jason at bioperl.org
> http://jason.open-bio.org/
>
>

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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