treebase-devel — TreeBASE developer mailing list

[Treebase-devel] cool GSOC projects with Mesquite?

[Arlin S. <ar...@um...>]

Hi.  Not sure if this is the right Mesquite list, because I'm trying  
to reach developers, rather than users, with some ideas for summer  
projects.  Some interest has been expressed in 2 Mesquite-related GSOC  
(Google summer-of-code) proposals, for inclusion in the NESCent- 
organized "phylosoc" package of proposals.  Google provides summer  
support for work on open-source projects.

What these potential projects would need from you folks is a a)  
programmer committed to serving as a mentor, and b) a compelling write- 
up.

If you might be interested, read on...

One proposal is for a graphical UI to design workflow descriptions

  http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011#Graphical_UI_for_designing_phylo_workflow_descriptions

Annotating workflows is a stumbling block in creating re-useable  
phylogenetic records.  The idea here is that users would use drag-an- 
drop tools to compose a phylogenetics workflow (with pipes or flow- 
chart icons or whatever), and this would be converted into a set of  
annotations useful for an archival record.  An example of this sort of  
thing, executed with Google Web Toolkit, would be http://exon.niaid.nih.gov/mobyleWorkflow 
.   Ultimately (when hooked up to the right back-end) this could be  
used to create executable workflow descriptions.  Some folks have  
suggested that Mesquite would provide an ideal framework for  
developing this.  Vivek Gopalan (who developed the example above) is  
one mentor, but we would need an experienced Mesquite programmer to  
join with us.

The second idea, which is not on the proposals page yet, is an  
intelligent submission tool for TreeBASE.  Mesquite is ideal for this  
because TreeBASE already recommends that users format their NEXUS  
files using Mesquite, for compatibility.

Ideally this tool would solve 2 main problems, using some intelligence  
to aid the user.  Bill Piel reports that a major stumbling block in  
submission is that users start the process with separate 1) tree and  
2) alignment (or other char matrix) with non-matching OTU names.  This  
corresponds to my own experience trying to re-use other people's  
data.  Finding an optimal name-match (the submission tool could  
propose a match to the user for manual verification) turns out to be a  
simple and well-studied problem in CS called "the marriage problem".    
The second major stumbling block is that, in order to annotate  
provenance, users need to match up (tediously) GenBank accession  
numbers and species identifiers.   In the case of sequence alignments,  
an intelligent tool could leverage NCBI services to guess the  
accession and species (i.e., BLAST it).  Given accessions, an  
intelligent tool could supply NCBI species ids (an even easier  
problem).  Initially, this tool could create a NEXUS file with a  
TreeBASE block containing the annotations (in the future, presumably  
the preferred format will be NeXML).

What makes the second proposal sexy is the use of intelligence to aid  
the user.   Again, Mesquite might provide an ideal development platform.

For either proposal, let me know ASAP if you are interested.  The GSOC  
project proposals need to be finished up this week.  Thanks for your  
time,

Arlin
-------
Arlin Stoltzfus (ar...@um...)
Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
IBBR, 9600 Gudelsky Drive, Rockville, MD
tel: 240 314 6208; web: www.molevol.org

Re: [Treebase-devel] NeXML submissions to TreeBASE as GSOC project?

[Rutger V. <rut...@gm...>]

I'm interested in (co-)mentoring that.

On Thu, Mar 3, 2011 at 1:25 PM, Arlin Stoltzfus <ar...@um...> wrote:
> I'd like to suggest-- to anyone who might be interested in serving as a
> mentor-- implementing NeMXL submissions to TreeBASE as a possible GSOC
> project.   The idea would be to reduce the amount of user interaction with
> TreeBASE, supporting direct submission of critical information represented
> in the NeXML file, including the usual matrix and trees, as well as
> * GenBank accessions
> * links from OTUs to taxon concepts
> * methodological links from a matrix to a tree
> * authors and contact information
> This would open the door for the development of third-party annotation tools
> or phylogeny inference tools that generate submission-ready NeXML files that
> meet a minimal standard (like MIAPA if it exists).  A bioinformatics grad
> student in Jim Leebens-Mack's lab is gearing up to develop such a submission
> tool this spring.
> A further project might be to develop and implement a web services protocol
> so that annotation clients can submit to TreeBASE.
> Arlin
>
> Begin forwarded message:
>
> From: Rutger Vos <rut...@gm...>
> Date: March 3, 2011 5:38:55 AM EST
> To: Arlin Stoltzfus <ar...@um...>
> Cc: William Piel <wil...@ya...>, Enrico Pontelli
> <epo...@cs...>, Jim Leebens-Mack <jle...@pl...>,
> "mar...@gm... panahiazar" <mar...@gm...>
> Subject: Re: MIAPA demo & GSOC projects: TreeBASE, NeXML coordination
> It would be great if NeXML submissions to TreeBASE could be a GSoC
> project, but that does mean that whoever (else) wants to mentor that
> should sign themselves up to the PhyloSoC wiki in rather short order:
> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011
>
> On Wed, Mar 2, 2011 at 3:43 PM, Arlin Stoltzfus <ar...@um...> wrote:
>
> Enrico, Bill--
>
> Some of us (Jim, Maryam, Rutger and I) have been having a discussion about a
>
> MIAPA demo project this spring that may lead to GSOC projects and to
>
> long-term funding.
>
> A likely target is a submission tool that would facilitate the annotation of
>
> methods and the creation of an archive-ready record.  I did a
>
> proof-of-concept of this a few years ago
>
> (https://www.nescent.org/wg_evoinfo/Supporting_MIAPA#Proof-of-concept_.28annotation_software.29).
>
>  We would use external vocabularies (many useful sources have been
>
> identified) and represent annotations using meta statements in NeXML.
>
> Maryam (PhD student in bioinformatics, CS background) has some months to
>
> devote to this project while working with Jim.  So, this (or something like
>
> it) is really going to happen over the next few months.
>
> We agreed it would be good to get Enrico and Bill involved to talk about
>
> possible GSOC projects, and how to leverage this into other, larger plans.
>
> For instance, a GSOC project to modify TreeBASE to allow NeXML submissions
>
> would be timely.  More generally, it would be nice to demo a web services
>
> architecture for submission, so that various clients could submit records.
>
>  For several years, Enrico has wanted to apply computational intelligence to
>
> workflow description and execution.
>
> Here is one vision for an overall strategy:
>
>  http://www.evoio.org/wiki/DemonstrationProject#An_overall_strategy
>
> If you are interested, please join us for a teleconference on Friday at
>
> 10:00 am.  Enrico already has expressed interest.  Bill, let me know if you
>
> are interested.  Regards,
>
> Arlin
>
> -------
>
> Arlin Stoltzfus (ar...@um...)
>
> Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
>
> IBBR, 9600 Gudelsky Drive, Rockville, MD
>
> tel: 240 314 6208; web: www.molevol.org
>
>
>
>
>
> --
> Dr. Rutger A. Vos
> School of Biological Sciences
> Philip Lyle Building, Level 4
> University of Reading
> Reading
> RG6 6BX
> United Kingdom
> Tel: +44 (0) 118 378 7535
> http://www.nexml.org
> http://rutgervos.blogspot.com
>
> -------
> Arlin Stoltzfus (ar...@um...)
> Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
> IBBR, 9600 Gudelsky Drive, Rockville, MD
> tel: 240 314 6208; web: www.molevol.org
>
> ------------------------------------------------------------------------------
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>
>



-- 
Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
Reading
RG6 6BX
United Kingdom
Tel: +44 (0) 118 378 7535
http://www.nexml.org
http://rutgervos.blogspot.com

[Treebase-devel] NeXML submissions to TreeBASE as GSOC project?

[Arlin S. <ar...@um...>]

I'd like to suggest-- to anyone who might be interested in serving as  
a mentor-- implementing NeMXL submissions to TreeBASE as a possible  
GSOC project.   The idea would be to reduce the amount of user  
interaction with TreeBASE, supporting direct submission of critical  
information represented in the NeXML file, including the usual matrix  
and trees, as well as
* GenBank accessions
* links from OTUs to taxon concepts
* methodological links from a matrix to a tree
* authors and contact information

This would open the door for the development of third-party annotation  
tools or phylogeny inference tools that generate submission-ready  
NeXML files that meet a minimal standard (like MIAPA if it exists).  A  
bioinformatics grad student in Jim Leebens-Mack's lab is gearing up to  
develop such a submission tool this spring.

A further project might be to develop and implement a web services  
protocol so that annotation clients can submit to TreeBASE.

Arlin

Begin forwarded message:

> From: Rutger Vos <rut...@gm...>
> Date: March 3, 2011 5:38:55 AM EST
> To: Arlin Stoltzfus <ar...@um...>
> Cc: William Piel <wil...@ya...>, Enrico Pontelli <epo...@cs... 
> >, Jim Leebens-Mack <jle...@pl...>, "mar...@gm... 
>  panahiazar" <mar...@gm...>
> Subject: Re: MIAPA demo & GSOC projects: TreeBASE, NeXML coordination
>
> It would be great if NeXML submissions to TreeBASE could be a GSoC
> project, but that does mean that whoever (else) wants to mentor that
> should sign themselves up to the PhyloSoC wiki in rather short order:
> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011
>
> On Wed, Mar 2, 2011 at 3:43 PM, Arlin Stoltzfus <ar...@um...> wrote:
>> Enrico, Bill--
>>
>> Some of us (Jim, Maryam, Rutger and I) have been having a  
>> discussion about a
>> MIAPA demo project this spring that may lead to GSOC projects and to
>> long-term funding.
>>
>> A likely target is a submission tool that would facilitate the  
>> annotation of
>> methods and the creation of an archive-ready record.  I did a
>> proof-of-concept of this a few years ago
>> (https://www.nescent.org/wg_evoinfo/Supporting_MIAPA#Proof-of-concept_.28annotation_software.29) 
>> .
>>  We would use external vocabularies (many useful sources have been
>> identified) and represent annotations using meta statements in NeXML.
>>
>> Maryam (PhD student in bioinformatics, CS background) has some  
>> months to
>> devote to this project while working with Jim.  So, this (or  
>> something like
>> it) is really going to happen over the next few months.
>>
>> We agreed it would be good to get Enrico and Bill involved to talk  
>> about
>> possible GSOC projects, and how to leverage this into other, larger  
>> plans.
>> For instance, a GSOC project to modify TreeBASE to allow NeXML  
>> submissions
>> would be timely.  More generally, it would be nice to demo a web  
>> services
>> architecture for submission, so that various clients could submit  
>> records.
>>  For several years, Enrico has wanted to apply computational  
>> intelligence to
>> workflow description and execution.
>>
>> Here is one vision for an overall strategy:
>>
>>  http://www.evoio.org/wiki/DemonstrationProject#An_overall_strategy
>>
>> If you are interested, please join us for a teleconference on  
>> Friday at
>> 10:00 am.  Enrico already has expressed interest.  Bill, let me  
>> know if you
>> are interested.  Regards,
>>
>> Arlin
>> -------
>> Arlin Stoltzfus (ar...@um...)
>> Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
>> IBBR, 9600 Gudelsky Drive, Rockville, MD
>> tel: 240 314 6208; web: www.molevol.org
>>
>>
>
>
>
> -- 
> Dr. Rutger A. Vos
> School of Biological Sciences
> Philip Lyle Building, Level 4
> University of Reading
> Reading
> RG6 6BX
> United Kingdom
> Tel: +44 (0) 118 378 7535
> http://www.nexml.org
> http://rutgervos.blogspot.com

-------
Arlin Stoltzfus (ar...@um...)
Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
IBBR, 9600 Gudelsky Drive, Rockville, MD
tel: 240 314 6208; web: www.molevol.org

Re: [Treebase-devel] How do you align >100,000 sequences?

[Arlin S. <ar...@um...>]

I started a wiki page for use-cases (relevant to MIAPA, TreeBASE, etc)  
that focus on replication, re-use, aggregation, re-purposing, meta- 
analysis, and integration:

   http://www.evoio.org/wiki/UseCases

You should be able to sign up for access if you do not have it already.

Right now the list is empty.  However, there have been several good  
discussions of use-cases over the past 2 months.  I encourage those  
who are interested to transfer some of that material to the wiki,  
where it can become a shared resource.

Arlin

On Feb 14, 2011, at 10:22 PM, Rutger Vos wrote:

> Hi guys,
>
> Brian has an interesting use case:
>
> ---------- Forwarded message ----------
> From: Brian T. Foley <bt...@la...>
> Date: Thu, Feb 10, 2011 at 11:44 PM
> Subject: Re: How do you align >100,000 sequences?
> To: Rutger Vos <rut...@gm...>
> Cc: bt...@la...
>
>
> OK.  I guess I can see some uses of such a thing, even if it is not  
> true
> phylogenetics, or the best method.
>
> Tree building is done in other fields besides biology, so there may be
> tools in use by computer scientists or librarians or something, that  
> could
> work better or fast than the tools I am used to in biology.
>
> I was quite interested after poking around in TreeBase a bit  
> yesterday.  I
> still don't find it easy to find my way to the data sets I'd like,  
> but the
> more I try the easier it is getting.
>
> Keep me, and the HIV Databases, in mind if you have questions about  
> large
> sets.  Viruses leave no fossils and they all look alike for the most  
> part,
> so all we have is phylogeny, and we do a lot of it.
>
> It looks like TreeBase is more about storing data produced by others,
> rather than building new trees or helping researchers put together a  
> new
> data set.  HIV Database is rather the opposite, but I've long  
> thought it
> would be very nice if we provided trees and NEXUS files.  Maybe it  
> would
> make sense to store them in TreeBase with a link to the TreeBase entry
> from our database.
>
> Brian
>
> > Dear Brian,
> >
> > I actually sent my query on behalf of someone else, so I can't  
> vouch for
> > how
> > or why he did things the way he did them. I know that he has
> > Smith-Waterman
> > distances between all pairs of proteins in the set, but that he  
> doesn't
> > actually have one multiple sequence alignment for the whole set. My
> > understanding is that the proteins are very, very divergent in  
> some cases,
> > so I doubt trying to align them would make any sense at all (and,  
> perhaps,
> > neither would using the SW distances as a metric on which to base  
> a tree,
> > but that's his business).
> >
> > Best wishes,
> >
> > Rutger
> >
>
>
>
> -- 
> Dr. Rutger A. Vos
> School of Biological Sciences
> Philip Lyle Building, Level 4
> University of Reading
> Reading
> RG6 6BX
> United Kingdom
> Tel: +44 (0) 118 378 7535
> http://www.nexml.org
> http://rutgervos.blogspot.com
>
> -- 
> You received this message because you are subscribed to the Google
> Groups "MIAPA" group.
> For more options, visit this group at
> http://groups.google.com/group/miapa-discuss?hl=en

-------
Arlin Stoltzfus (ar...@um...)
Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
IBBR, 9600 Gudelsky Drive, Rockville, MD
tel: 240 314 6208; web: www.molevol.org

[Treebase-devel] Fwd: How do you align >100,000 sequences?

[Rutger V. <rut...@gm...>]

Hi guys,

Brian has an interesting use case:

---------- Forwarded message ----------
From: Brian T. Foley <bt...@la...>
Date: Thu, Feb 10, 2011 at 11:44 PM
Subject: Re: How do you align >100,000 sequences?
To: Rutger Vos <rut...@gm...>
Cc: bt...@la...


OK.  I guess I can see some uses of such a thing, even if it is not true
phylogenetics, or the best method.

Tree building is done in other fields besides biology, so there may be
tools in use by computer scientists or librarians or something, that could
work better or fast than the tools I am used to in biology.

I was quite interested after poking around in TreeBase a bit yesterday.  I
still don't find it easy to find my way to the data sets I'd like, but the
more I try the easier it is getting.

Keep me, and the HIV Databases, in mind if you have questions about large
sets.  Viruses leave no fossils and they all look alike for the most part,
so all we have is phylogeny, and we do a lot of it.

It looks like TreeBase is more about storing data produced by others,
rather than building new trees or helping researchers put together a new
data set.  HIV Database is rather the opposite, but I've long thought it
would be very nice if we provided trees and NEXUS files.  Maybe it would
make sense to store them in TreeBase with a link to the TreeBase entry
from our database.

Brian

> Dear Brian,
>
> I actually sent my query on behalf of someone else, so I can't vouch for
> how
> or why he did things the way he did them. I know that he has
> Smith-Waterman
> distances between all pairs of proteins in the set, but that he doesn't
> actually have one multiple sequence alignment for the whole set. My
> understanding is that the proteins are very, very divergent in some cases,
> so I doubt trying to align them would make any sense at all (and, perhaps,
> neither would using the SW distances as a metric on which to base a tree,
> but that's his business).
>
> Best wishes,
>
> Rutger
>



-- 
Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
Reading
RG6 6BX
United Kingdom
Tel: +44 (0) 118 378 7535
http://www.nexml.org
http://rutgervos.blogspot.com

Re: [Treebase-devel] DOI links in the interface

[William P. <wil...@ya...>]

On Feb 3, 2011, at 1:07 AM, Rutger Vos wrote:

> 
> Actually if this were using JSTL on the code that renders the UI then
> it is easy to check for both conditions simultaneously - testing
> (<c:if/>) for the ${variable} yields false for null and empty string.
> So that should be an easy fix if someone knows the jsp that is
> responsible.
> 
> 
> treebase-web/src/main/webapp/WEB-INF/pages/search/studyList.jsp (line 48 indeed tests for null instead of true)

I created a bug for this and assigned it to Harry.

bp

Re: [Treebase-devel] DOI links in the interface

[Rutger V. <rut...@gm...>]

>
>
> Actually if this were using JSTL on the code that renders the UI then
> it is easy to check for both conditions simultaneously - testing
> (<c:if/>) for the ${variable} yields false for null and empty string.
> So that should be an easy fix if someone knows the jsp that is
> responsible.
>
>
treebase-web/src/main/webapp/WEB-INF/pages/search/studyList.jsp (line 48
indeed tests for null instead of true)

-- 
Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
Reading
RG6 6BX
United Kingdom
Tel: +44 (0) 118 378 7535
http://www.nexml.org
http://rutgervos.blogspot.com

Re: [Treebase-devel] DOI links in the interface

[Hilmar L. <hl...@ne...>]

On Feb 2, 2011, at 11:02 PM, William Piel wrote:

> Either the entry form should be designed to enter NULL for blank  
> values, or the hyperlink should not be presented to users when the  
> DOI is blank.  Anyone prefer one solution over the other?

Actually if this were using JSTL on the code that renders the UI then  
it is easy to check for both conditions simultaneously - testing  
(<c:if/>) for the ${variable} yields false for null and empty string.  
So that should be an easy fix if someone knows the jsp that is  
responsible.

	-hilmar

-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================

Re: [Treebase-devel] DOI links in the interface

[William P. <wil...@ya...>]

On Feb 2, 2011, at 7:42 PM, Rutger Vos wrote:

> There is probably an empty string (but not null) for the DOI field for those records.

Correct. This is a bug. The "http://dx.doi.org" hyperlink is provided for all non-NULL values, however when users enter citation information in which the DOI entry is left blank, the field is filled with "blank" rather than NULL. Hence a hyperlink to nowhere is displayed. 

Either the entry form should be designed to enter NULL for blank values, or the hyperlink should not be presented to users when the DOI is blank.  Anyone prefer one solution over the other?

bp

Re: [Treebase-devel] DOI links in the interface

[Hilmar L. <hl...@ne...>]

So that could be corrected at the SQL level, no? Bill or Harry -  
interested in taking a crack?

	-hilmar

On Feb 2, 2011, at 7:42 PM, Rutger Vos wrote:

> There is probably an empty string (but not null) for the DOI field  
> for those records.
>
> On Thu, Feb 3, 2011 at 3:50 AM, Hilmar Lapp <hl...@ne...> wrote:
> I'm wondering what's going on with the DOI links in the search results
> interface. As an example, search for author 'Lutzoni' - several of the
> rows have DOI links that go to http://dx.doi.org without the actual
> DOI appended. Is this because the DOI is missing (and then why is the
> link not showing to begin with for other rows?), or because of some
> failure to properly append the DOI?
>
>        -hilmar
> --
> ===========================================================
> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
>
>
>
>
> ------------------------------------------------------------------------------
> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
> Finally, a world-class log management solution at an even better  
> price-free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
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> _______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>
>
>
> -- 
> Dr. Rutger A. Vos
> School of Biological Sciences
> Philip Lyle Building, Level 4
> University of Reading
> Reading
> RG6 6BX
> United Kingdom
> Tel: +44 (0) 118 378 7535
> http://www.nexml.org
> http://rutgervos.blogspot.com

-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================

Re: [Treebase-devel] DOI links in the interface

[Rutger V. <rut...@gm...>]

There is probably an empty string (but not null) for the DOI field for those
records.

On Thu, Feb 3, 2011 at 3:50 AM, Hilmar Lapp <hl...@ne...> wrote:

> I'm wondering what's going on with the DOI links in the search results
> interface. As an example, search for author 'Lutzoni' - several of the
> rows have DOI links that go to http://dx.doi.org without the actual
> DOI appended. Is this because the DOI is missing (and then why is the
> link not showing to begin with for other rows?), or because of some
> failure to properly append the DOI?
>
>        -hilmar
> --
> ===========================================================
> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
>
>
>
>
>
> ------------------------------------------------------------------------------
> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
> Finally, a world-class log management solution at an even better
> price-free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d
> _______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>



-- 
Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
Reading
RG6 6BX
United Kingdom
Tel: +44 (0) 118 378 7535
http://www.nexml.org
http://rutgervos.blogspot.com

[Treebase-devel] DOI links in the interface

[Hilmar L. <hl...@ne...>]

I'm wondering what's going on with the DOI links in the search results  
interface. As an example, search for author 'Lutzoni' - several of the  
rows have DOI links that go to http://dx.doi.org without the actual  
DOI appended. Is this because the DOI is missing (and then why is the  
link not showing to begin with for other rows?), or because of some  
failure to properly append the DOI?

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================

[Treebase-devel] purl.org down

[Hilmar L. <hl...@ne...>]

Not funny. It says "Service Unavailable", and "too many concurrent  
requests." So all our canonical URIs are unreachable right now.

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================

Re: [Treebase-devel] [Nexml-discuss] iEvoBio registration is open. Data integration challenge!

[Hilmar L. <hl...@ne...>]

Great suggestion indeed. Also a good example for data integration with  
the purpose of discovering something you hadn't known before, which  
personally I think is what's going to be to compel the audience.  
Though obviously I don't know how the submissions are going to turn out.

Great to see though that this is sparking ideas and discussion even  
before the website's official existence :)

	-hilmar

On Jan 20, 2011, at 4:12 PM, Arlin Stoltzfus wrote:

> start with user-input gene (protein) tree, get taxids for species
> sources of genes, use species list to extract species tree from ToL,
> run a reconcile-tree algorithm, display the reconcile-tree with
> duplications, add GO annotations and colorize them to reveal
> functional shifts in paralogous subfamilies.
>
> if the starting tree is from treebase, the first two steps are done
> already (in many cases).
>
> but  that's a heavy load.
>
> arlin
>
> On Jan 20, 2011, at 3:56 PM, Rutger Vos wrote:
>
>> Mmmm... yeah, I guess it would make more sense for the message to  
>> come
>> out of @ievobio rather than being picked up by someone in the
>> twittersphere stumbling across the registration page. That said, it
>> would be interesting to think about how some projects near and dear  
>> to
>> our hearts might be parts in a data integration challenge. For
>> example: traverse the ToL (with a new visualizer, e.g. jsPhyloSVG)
>> that can attach clickable PhyloWS query URLs to nodes in the ToL  
>> which
>> lead you to any trees in TreeBASE for that (higher or terminal)  
>> taxon.
>>
>> On Thu, Jan 20, 2011 at 1:40 PM, Hilmar Lapp <hl...@ne...>
>> wrote:
>>> Registration isn't quite open yet - we depend on Evolution for
>>> that, which
>>> needs a few days more. We won't be silent about it either when that
>>> happens
>>> :-)
>>>
>>>       -hilmar
>>>
>>> On Jan 20, 2011, at 3:56 AM, Rutger Vos wrote:
>>>
>>>> http://ievobio.org/challenge.html
>>>>
>>>> --
>>>> Dr. Rutger A. Vos
>>>> School of Biological Sciences
>>>> Philip Lyle Building, Level 4
>>>> University of Reading
>>>> Reading
>>>> RG6 6BX
>>>> United Kingdom
>>>> Tel: +44 (0) 118 378 7535
>>>> http://www.nexml.org
>>>> http://rutgervos.blogspot.com
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Protect Your Site and Customers from Malware Attacks
>>>> Learn about various malware tactics and how to avoid them.
>>>> Understand
>>>> malware threats, the impact they can have on your business, and
>>>> how you
>>>> can protect your company and customers by using code signing.
>>>> http://p.sf.net/sfu/oracle-sfdevnl
>>>> _______________________________________________
>>>> Treebase-devel mailing list
>>>> Tre...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>>>
>>> --
>>> ===========================================================
>>> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
>>> ===========================================================
>>>
>>>
>>>
>>>
>>
>>
>>
>> -- 
>> Dr. Rutger A. Vos
>> School of Biological Sciences
>> Philip Lyle Building, Level 4
>> University of Reading
>> Reading
>> RG6 6BX
>> United Kingdom
>> Tel: +44 (0) 118 378 7535
>> http://www.nexml.org
>> http://rutgervos.blogspot.com
>>
>> ------------------------------------------------------------------------------
>> Protect Your Site and Customers from Malware Attacks
>> Learn about various malware tactics and how to avoid them. Understand
>> malware threats, the impact they can have on your business, and how
>> you
>> can protect your company and customers by using code signing.
>> http://p.sf.net/sfu/oracle-sfdevnl
>> _______________________________________________
>> Nexml-discuss mailing list
>> Nex...@li...
>> https://lists.sourceforge.net/lists/listinfo/nexml-discuss
>
> -------
> Arlin Stoltzfus (ar...@um...)
> Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
> IBBR, 9600 Gudelsky Drive, Rockville, MD
> tel: 240 314 6208; web: www.molevol.org
>
>
> ------------------------------------------------------------------------------
> Protect Your Site and Customers from Malware Attacks
> Learn about various malware tactics and how to avoid them. Understand
> malware threats, the impact they can have on your business, and how  
> you
> can protect your company and customers by using code signing.
> http://p.sf.net/sfu/oracle-sfdevnl
> _______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel

-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================

Re: [Treebase-devel] [Nexml-discuss] iEvoBio registration is open. Data integration challenge!

[Rutger V. <rut...@gm...>]

On Thu, Jan 20, 2011 at 9:12 PM, Arlin Stoltzfus <ar...@um...> wrote:
> start with user-input gene (protein) tree, get taxids for species
> sources of genes, use species list to extract species tree from ToL,
> run a reconcile-tree algorithm, display the reconcile-tree with
> duplications, add GO annotations and colorize them to reveal
> functional shifts in paralogous subfamilies.
>
> if the starting tree is from treebase, the first two steps are done
> already (in many cases).
>
> but  that's a heavy load.

Very useful, though.

-- 
Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
Reading
RG6 6BX
United Kingdom
Tel: +44 (0) 118 378 7535
http://www.nexml.org
http://rutgervos.blogspot.com

Re: [Treebase-devel] [Nexml-discuss] iEvoBio registration is open. Data integration challenge!

[Arlin S. <ar...@um...>]

start with user-input gene (protein) tree, get taxids for species  
sources of genes, use species list to extract species tree from ToL,  
run a reconcile-tree algorithm, display the reconcile-tree with  
duplications, add GO annotations and colorize them to reveal  
functional shifts in paralogous subfamilies.

if the starting tree is from treebase, the first two steps are done  
already (in many cases).

but  that's a heavy load.

arlin

On Jan 20, 2011, at 3:56 PM, Rutger Vos wrote:

> Mmmm... yeah, I guess it would make more sense for the message to come
> out of @ievobio rather than being picked up by someone in the
> twittersphere stumbling across the registration page. That said, it
> would be interesting to think about how some projects near and dear to
> our hearts might be parts in a data integration challenge. For
> example: traverse the ToL (with a new visualizer, e.g. jsPhyloSVG)
> that can attach clickable PhyloWS query URLs to nodes in the ToL which
> lead you to any trees in TreeBASE for that (higher or terminal) taxon.
>
> On Thu, Jan 20, 2011 at 1:40 PM, Hilmar Lapp <hl...@ne...>  
> wrote:
>> Registration isn't quite open yet - we depend on Evolution for  
>> that, which
>> needs a few days more. We won't be silent about it either when that  
>> happens
>> :-)
>>
>>        -hilmar
>>
>> On Jan 20, 2011, at 3:56 AM, Rutger Vos wrote:
>>
>>> http://ievobio.org/challenge.html
>>>
>>> --
>>> Dr. Rutger A. Vos
>>> School of Biological Sciences
>>> Philip Lyle Building, Level 4
>>> University of Reading
>>> Reading
>>> RG6 6BX
>>> United Kingdom
>>> Tel: +44 (0) 118 378 7535
>>> http://www.nexml.org
>>> http://rutgervos.blogspot.com
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Protect Your Site and Customers from Malware Attacks
>>> Learn about various malware tactics and how to avoid them.  
>>> Understand
>>> malware threats, the impact they can have on your business, and  
>>> how you
>>> can protect your company and customers by using code signing.
>>> http://p.sf.net/sfu/oracle-sfdevnl
>>> _______________________________________________
>>> Treebase-devel mailing list
>>> Tre...@li...
>>> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>>
>> --
>> ===========================================================
>> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
>> ===========================================================
>>
>>
>>
>>
>
>
>
> -- 
> Dr. Rutger A. Vos
> School of Biological Sciences
> Philip Lyle Building, Level 4
> University of Reading
> Reading
> RG6 6BX
> United Kingdom
> Tel: +44 (0) 118 378 7535
> http://www.nexml.org
> http://rutgervos.blogspot.com
>
> ------------------------------------------------------------------------------
> Protect Your Site and Customers from Malware Attacks
> Learn about various malware tactics and how to avoid them. Understand
> malware threats, the impact they can have on your business, and how  
> you
> can protect your company and customers by using code signing.
> http://p.sf.net/sfu/oracle-sfdevnl
> _______________________________________________
> Nexml-discuss mailing list
> Nex...@li...
> https://lists.sourceforge.net/lists/listinfo/nexml-discuss

-------
Arlin Stoltzfus (ar...@um...)
Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
IBBR, 9600 Gudelsky Drive, Rockville, MD
tel: 240 314 6208; web: www.molevol.org

Re: [Treebase-devel] iEvoBio registration is open. Data integration challenge!

[Rutger V. <rut...@gm...>]

Mmmm... yeah, I guess it would make more sense for the message to come
out of @ievobio rather than being picked up by someone in the
twittersphere stumbling across the registration page. That said, it
would be interesting to think about how some projects near and dear to
our hearts might be parts in a data integration challenge. For
example: traverse the ToL (with a new visualizer, e.g. jsPhyloSVG)
that can attach clickable PhyloWS query URLs to nodes in the ToL which
lead you to any trees in TreeBASE for that (higher or terminal) taxon.

On Thu, Jan 20, 2011 at 1:40 PM, Hilmar Lapp <hl...@ne...> wrote:
> Registration isn't quite open yet - we depend on Evolution for that, which
> needs a few days more. We won't be silent about it either when that happens
> :-)
>
>        -hilmar
>
> On Jan 20, 2011, at 3:56 AM, Rutger Vos wrote:
>
>> http://ievobio.org/challenge.html
>>
>> --
>> Dr. Rutger A. Vos
>> School of Biological Sciences
>> Philip Lyle Building, Level 4
>> University of Reading
>> Reading
>> RG6 6BX
>> United Kingdom
>> Tel: +44 (0) 118 378 7535
>> http://www.nexml.org
>> http://rutgervos.blogspot.com
>>
>>
>> ------------------------------------------------------------------------------
>> Protect Your Site and Customers from Malware Attacks
>> Learn about various malware tactics and how to avoid them. Understand
>> malware threats, the impact they can have on your business, and how you
>> can protect your company and customers by using code signing.
>> http://p.sf.net/sfu/oracle-sfdevnl
>> _______________________________________________
>> Treebase-devel mailing list
>> Tre...@li...
>> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>
> --
> ===========================================================
> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
>
>
>
>



-- 
Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
Reading
RG6 6BX
United Kingdom
Tel: +44 (0) 118 378 7535
http://www.nexml.org
http://rutgervos.blogspot.com

Re: [Treebase-devel] iEvoBio registration is open. Data integration challenge!

[Hilmar L. <hl...@ne...>]

Registration isn't quite open yet - we depend on Evolution for that,  
which needs a few days more. We won't be silent about it either when  
that happens :-)

	-hilmar

On Jan 20, 2011, at 3:56 AM, Rutger Vos wrote:

> http://ievobio.org/challenge.html
>
> -- 
> Dr. Rutger A. Vos
> School of Biological Sciences
> Philip Lyle Building, Level 4
> University of Reading
> Reading
> RG6 6BX
> United Kingdom
> Tel: +44 (0) 118 378 7535
> http://www.nexml.org
> http://rutgervos.blogspot.com
>
> ------------------------------------------------------------------------------
> Protect Your Site and Customers from Malware Attacks
> Learn about various malware tactics and how to avoid them. Understand
> malware threats, the impact they can have on your business, and how  
> you
> can protect your company and customers by using code signing.
> http://p.sf.net/sfu/oracle-sfdevnl
> _______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel

-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================

[Treebase-devel] iEvoBio registration is open. Data integration challenge!

[Rutger V. <rut...@gm...>]

http://ievobio.org/challenge.html

-- 
Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
Reading
RG6 6BX
United Kingdom
Tel: +44 (0) 118 378 7535
http://www.nexml.org
http://rutgervos.blogspot.com

Re: [Treebase-devel] Issues with Treebase Configuration

[Shyket, H. <har...@ya...>]

Hi Vladimir,

Thank you for the advice, it did the trick!

As for the environment, it's a Ubuntu(10.0) VM running Tomcat 5.5.31 and Java 1.5.0.  That's the environment, I do my build on my Windows PC using Eclipse (Galileo) with a J2SE 1.5 build path.

Thanks,

Harry Shyket
Digitial Media Specialist
Yale University Peabody Museum
ph. 203-436-9428
har...@ya...

From: Vladimir Gapeyev [mailto:vla...@du...]
Sent: Thursday, January 06, 2011 10:50 AM
To: Shyket, Harry
Cc: William Halliday Piel; TreeBASE devel
Subject: Fwd: Issues with Treebase Configuration



On Jan 5, 2011, at 11:52 AM, Shyket, Harry wrote:


From: "Shyket, Harry" <har...@ya...<mailto:har...@ya...>>
Date: January 5, 2011 11:52:30 AM EST
To: "vla...@du...<mailto:vla...@du...>" <vla...@du...<mailto:vla...@du...>>
Cc: William Halliday Piel <pi...@tr...<mailto:pi...@tr...>>
Subject: Issues with Treebase Configuration

Hi Vladimir,

I am having issues with my Treebase setup.  I followed the instructions on the wiki.   I built using Eclipse on my PC and then deployed the WAR file to a virtual environment (Ubuntu).  I worked through a couple of errors, but the latest one seems to be the webservice that's causing the site not to work.  I have attached both the treebase.log file as well as the catalina.out file.

Any help with this issue would be appreciated.

Thanks,

Harry Shyket
Digitial Media Specialist
Yale University Peabody Museum
ph. 203-436-9428
har...@ya...<mailto:har...@ya...>

[Treebase-devel] Fwd: Issues with Treebase Configuration

[Vladimir G. <vla...@du...>]

On Jan 5, 2011, at 11:52 AM, Shyket, Harry wrote:

> From: "Shyket, Harry" <har...@ya...>
> Date: January 5, 2011 11:52:30 AM EST
> To: "vla...@du..." <vla...@du...>
> Cc: William Halliday Piel <pi...@tr...>
> Subject: Issues with Treebase Configuration
>
> Hi Vladimir,
>
> I am having issues with my Treebase setup.  I followed the  
> instructions on the wiki.   I built using Eclipse on my PC and then  
> deployed the WAR file to a virtual environment (Ubuntu).  I worked  
> through a couple of errors, but the latest one seems to be the  
> webservice that’s causing the site not to work.  I have attached  
> both the treebase.log file as well as the catalina.out file.
>
> Any help with this issue would be appreciated.
>
> Thanks,
>
> Harry Shyket
> Digitial Media Specialist
> Yale University Peabody Museum
> ph. 203-436-9428
> har...@ya...
>


Hi Harry,

The logs appear similar to the problem I ran into after Java updates  
over the summer (I run a Mac, with Java from Apple) -- see treebase- 
dev messages from Sep 9 2010.  With people here who work with J2EE way  
more than I do, we tracked the problem to the xercesImpl-2.4.0.jar  
being on the way (as I recall it supplies outdated implementations  
that overwrite newer ones, now in the standard library).

Somehow this problem does not rise at our linux server that runs  
treebase, perhaps for using OpenJDK instead of Sun/Apple.  What is  
your environment?

I currently work around the problem in a very clumsy way: Instead of  
dropping treebase-web.war into $CATALINA_HOME/webapps/ and letting  
tomcat unpack it, I unpack it myself, excluding xercesImpl, and move  
the result to $CATALINA_HOME/webapps/, i.e.

unzip -q treebase/treebase-web/target/treebase-web.war -x WEB-INF/lib/ 
xercesImpl-2.4.0.jar  -d $CATALINA_HOME/webapps/treebase
-web

Hopefully, this will work for you.

The proper solution would be revising treebase build process and  
pruning out lots of outdated and unused jars that linger there.

--VG

Re: [Treebase-devel] NEXML export really, really slow

[William P. <wil...@ya...>]

On Dec 15, 2010, at 3:08 AM, Roderic Page wrote:

> However, generating the NEXML file can take what seems like an age,  
> particularly for large data sets.

Yup. Caching would help a lot. But we also need to address what I think is the main cause of this problem: the matrixelement table, that is now probably larger than 200 GB -- so PostgreSQL is not performing well with it. The result is that morphological matrices are very slow to download -- and some are big enough that we get a proxy time-out before the data have been assembled. This is particularly true for matrices with a nucleotide-indel mix, since they are both big and require access to this table. Ideally, any predefined datatypes (ie DNA and protein) should not store records in the matrixelement table -- that would shrink it by several orders of magnitude, with big performance gains. 

bp

Re: [Treebase-devel] NEXML export really, really slow

[Rutger V. <rut...@gm...>]

On Wed, Dec 15, 2010 at 7:59 AM, Roderic Page <r....@bi...> wrote:
>
>
> On 15 Dec 2010, at 10:45, Rutger Vos wrote:
>
>> Can I quote that in the endorsement section on the NeXML website? i.e.:
>>
>> "pretty unpleasant to deal with" -- Rod Page, Glasgow
>
> XML is one way to serialise data, and it can be verbose and ugly. OK, pretty
> much anytime it's used things get verbose and ugly. I totally get the
> rationale for using it, and NeXML has some nice features, I'm just not a big
> fan of XML. It makes sense in document mark-up where structure and order
> matter (e.g., the NLM mark-up for journal articles) but for moving objects
> around it is a pain. JSON makes life a lot easier (and by this I don't mean
> some JSON version of an XML document).

I was just teasing, not expecting a serious response. I'm well aware
of the pros and cons of XML; there are certainly some weird, weird
design choices in there (for starters, why do we need closing tags
anyway?) but for many use cases, on balance, it's the best we have
right now. In the context you're interested in, with couchdb and
things happening inside a browser, JSON is obviously much nicer to
work with.

>> On the matter at hand, a reverse proxy that caches anything static
>> would be great to have, agreed. Is squid still the thing to use?
>
> Call me old fashioned, but why not just dump the NexML files to disk,
> updating if and when source data changes? You've a couple of thousand
> documents, most will be rarely used, but it's the first time the document is
> created that is the killer. I've no experience with reverse proxies, but
> presumably the document has to exist before it can be cached, and the issue
> here is the time it takes to create the document, not serve it.

Yeah, that's probably easier. Generate them all once a month (+make
any new ones from new submissions as they are encountered) and return
those on request. Also, zip them up, generate an MD5 checksum and
that's your dump.

>> On Wednesday, December 15, 2010, Roderic Page <r....@bi...>
>> wrote:
>>>
>>> I've been downloading NEXML files from TreeBASE with a view to making
>>> a local copy in CouchDB. TreeBASE NEXML is pretty unpleasant to deal
>>> with, but it does give me a complete summary of a study.
>>>
>>> However, generating the NEXML file can take what seems like an age,
>>> particularly for large data sets. I've written a script to harvest
>>> NEXML for each study, but this regularly times out. Is there anyway
>>> this could be speed up, perhaps by having TreeBASE cache NEXML files
>>> so users are grabbing a text document, not forcing live queries to the
>>> database?
>>>
>>> Regards
>>>
>>> Rod
>>> ---------------------------------------------------------
>>> Roderic Page
>>> Professor of Taxonomy
>>> Institute of Biodiversity, Animal Health and Comparative Medicine
>>> College of Medical, Veterinary and Life Sciences
>>> Graham Kerr Building
>>> University of Glasgow
>>> Glasgow G12 8QQ, UK
>>>
>>> Email: r....@bi...
>>> Tel: +44 141 330 4778
>>> Fax: +44 141 330 2792
>>> AIM: rod...@ai...
>>> Facebook: http://www.facebook.com/profile.php?id=1112517192
>>> Twitter: http://twitter.com/rdmpage
>>> Blog: http://iphylo.blogspot.com
>>> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Lotusphere 2011
>>> Register now for Lotusphere 2011 and learn how
>>> to connect the dots, take your collaborative environment
>>> to the next level, and enter the era of Social Business.
>>> http://p.sf.net/sfu/lotusphere-d2d
>>> _______________________________________________
>>> Treebase-devel mailing list
>>> Tre...@li...
>>> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>>>
>>
>> --
>> Dr. Rutger A. Vos
>> School of Biological Sciences
>> Philip Lyle Building, Level 4
>> University of Reading
>> Reading
>> RG6 6BX
>> United Kingdom
>> Tel: +44 (0) 118 378 7535
>> http://www.nexml.org
>> http://rutgervos.blogspot.com
>>
>
> ---------------------------------------------------------
> Roderic Page
> Professor of Taxonomy
> Institute of Biodiversity, Animal Health and Comparative Medicine
> College of Medical, Veterinary and Life Sciences
> Graham Kerr Building
> University of Glasgow
> Glasgow G12 8QQ, UK
>
> Email: r....@bi...
> Tel: +44 141 330 4778
> Fax: +44 141 330 2792
> AIM: rod...@ai...
> Facebook: http://www.facebook.com/profile.php?id=1112517192
> Twitter: http://twitter.com/rdmpage
> Blog: http://iphylo.blogspot.com
> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
>
>
>
>
>
>
>
>



-- 
Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
Reading
RG6 6BX
United Kingdom
Tel: +44 (0) 118 378 7535
http://www.nexml.org
http://rutgervos.blogspot.com

Re: [Treebase-devel] NEXML export really, really slow

[Roderic P. <r....@bi...>]

On 15 Dec 2010, at 10:45, Rutger Vos wrote:

> Can I quote that in the endorsement section on the NeXML website?  
> i.e.:
>
> "pretty unpleasant to deal with" -- Rod Page, Glasgow

XML is one way to serialise data, and it can be verbose and ugly. OK,  
pretty much anytime it's used things get verbose and ugly. I totally  
get the rationale for using it, and NeXML has some nice features, I'm  
just not a big fan of XML. It makes sense in document mark-up where  
structure and order matter (e.g., the NLM mark-up for journal  
articles) but for moving objects around it is a pain. JSON makes life  
a lot easier (and by this I don't mean some JSON version of an XML  
document).

>
> On the matter at hand, a reverse proxy that caches anything static
> would be great to have, agreed. Is squid still the thing to use?

Call me old fashioned, but why not just dump the NexML files to disk,  
updating if and when source data changes? You've a couple of thousand  
documents, most will be rarely used, but it's the first time the  
document is created that is the killer. I've no experience with  
reverse proxies, but presumably the document has to exist before it  
can be cached, and the issue here is the time it takes to create the  
document, not serve it.

Rod

>
> On Wednesday, December 15, 2010, Roderic Page <r....@bi...>  
> wrote:
>> I've been downloading NEXML files from TreeBASE with a view to making
>> a local copy in CouchDB. TreeBASE NEXML is pretty unpleasant to deal
>> with, but it does give me a complete summary of a study.
>>
>> However, generating the NEXML file can take what seems like an age,
>> particularly for large data sets. I've written a script to harvest
>> NEXML for each study, but this regularly times out. Is there anyway
>> this could be speed up, perhaps by having TreeBASE cache NEXML files
>> so users are grabbing a text document, not forcing live queries to  
>> the
>> database?
>>
>> Regards
>>
>> Rod
>> ---------------------------------------------------------
>> Roderic Page
>> Professor of Taxonomy
>> Institute of Biodiversity, Animal Health and Comparative Medicine
>> College of Medical, Veterinary and Life Sciences
>> Graham Kerr Building
>> University of Glasgow
>> Glasgow G12 8QQ, UK
>>
>> Email: r....@bi...
>> Tel: +44 141 330 4778
>> Fax: +44 141 330 2792
>> AIM: rod...@ai...
>> Facebook: http://www.facebook.com/profile.php?id=1112517192
>> Twitter: http://twitter.com/rdmpage
>> Blog: http://iphylo.blogspot.com
>> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
>>
>>
>>
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Lotusphere 2011
>> Register now for Lotusphere 2011 and learn how
>> to connect the dots, take your collaborative environment
>> to the next level, and enter the era of Social Business.
>> http://p.sf.net/sfu/lotusphere-d2d
>> _______________________________________________
>> Treebase-devel mailing list
>> Tre...@li...
>> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>>
>
> -- 
> Dr. Rutger A. Vos
> School of Biological Sciences
> Philip Lyle Building, Level 4
> University of Reading
> Reading
> RG6 6BX
> United Kingdom
> Tel: +44 (0) 118 378 7535
> http://www.nexml.org
> http://rutgervos.blogspot.com
>

---------------------------------------------------------
Roderic Page
Professor of Taxonomy
Institute of Biodiversity, Animal Health and Comparative Medicine
College of Medical, Veterinary and Life Sciences
Graham Kerr Building
University of Glasgow
Glasgow G12 8QQ, UK

Email: r....@bi...
Tel: +44 141 330 4778
Fax: +44 141 330 2792
AIM: rod...@ai...
Facebook: http://www.facebook.com/profile.php?id=1112517192
Twitter: http://twitter.com/rdmpage
Blog: http://iphylo.blogspot.com
Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html

Re: [Treebase-devel] NEXML export really, really slow

[Rutger V. <rut...@gm...>]

Can I quote that in the endorsement section on the NeXML website? i.e.:

"pretty unpleasant to deal with" -- Rod Page, Glasgow

On the matter at hand, a reverse proxy that caches anything static
would be great to have, agreed. Is squid still the thing to use?

On Wednesday, December 15, 2010, Roderic Page <r....@bi...> wrote:
> I've been downloading NEXML files from TreeBASE with a view to making
> a local copy in CouchDB. TreeBASE NEXML is pretty unpleasant to deal
> with, but it does give me a complete summary of a study.
>
> However, generating the NEXML file can take what seems like an age,
> particularly for large data sets. I've written a script to harvest
> NEXML for each study, but this regularly times out. Is there anyway
> this could be speed up, perhaps by having TreeBASE cache NEXML files
> so users are grabbing a text document, not forcing live queries to the
> database?
>
> Regards
>
> Rod
> ---------------------------------------------------------
> Roderic Page
> Professor of Taxonomy
> Institute of Biodiversity, Animal Health and Comparative Medicine
> College of Medical, Veterinary and Life Sciences
> Graham Kerr Building
> University of Glasgow
> Glasgow G12 8QQ, UK
>
> Email: r....@bi...
> Tel: +44 141 330 4778
> Fax: +44 141 330 2792
> AIM: rod...@ai...
> Facebook: http://www.facebook.com/profile.php?id=1112517192
> Twitter: http://twitter.com/rdmpage
> Blog: http://iphylo.blogspot.com
> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
>
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
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-- 
Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
Reading
RG6 6BX
United Kingdom
Tel: +44 (0) 118 378 7535
http://www.nexml.org
http://rutgervos.blogspot.com