gmod-resources — Discuss resource, including issues surrounding cross-speices similarities

[Gmod-resources] Re: [GMOD-devel] Common MOD URL for genome data?

[Aaron J. M. <am...@pc...>]

in your example URL's, "my.org/genome(s)/..."

Is this just to denote the special "data dump" section of the website? 
And if so, isn't there a more specific word to be used (e.g. "data" or 
"access" or "download" or such)?

Also, I think the whole must/may criteria is moot.  Everything is "may", 
there's nothing I "must" do ;)

some additional paths to possibly provide:

/help    # Don's suggested default "index" page
/version # Todd's suggestion of current release version
/listing # a tab-delim list of available data, in various versions,
          # species and formats

My vote for common options:
   version
   species (by scientific name, by taxon id, ?)
   format (default FASTA or GFF, as apropos)

And I realize my URL path syntax for specifying options is just candy 
coating over the CGI GET syntax, but I think that cleaner URLs are 
generally more humanly robust for memorization and publication.  We'll 
follow the community "spec" (whatever it is), but will likely implement 
the URL path syntax also (if necessary).

I also agree that we should provide both singular and plural forms of 
URL paths for convenience.

-Aaron

Don Gilbert wrote:

> Todd, others,
> 
> Sounds like there is general support.  For specifics, my own quick thoughts are it
> would be easier, maybe better, to start with one top level folder, and put the 
> options off of that, with some "MUST" options, and many "MAY" options.  I would probably
> prefer this sort of organization:
> 
>   my.org/genome{s}/    
>     -- return information/help page with links, MUST offer
>    { plurals are tricky - do people remember them? }
>   my.org/genome/dna  == return full genome dna in fasta format  
>          genome/genome == alias to /dna
>   my.org/genome/protein{s} == return " proteins in fasta
>          genome/proteome  == alias to proteins
>   my.org/genome/transcript{s} ==  transcripts in fasta
> 	 genome/transcriptome  == alias to transcripts 
>   my.org/genome/feature{s} ==  features in GFF
>          genome/gff  == alias to features
> 
>    -- other options as people want to support them
>        genome/versions/ ...
>        genome/species/ ..
>    -- and/or use CGI options for these "?species=x&version=y"
> 
> But we should decide what good common terms above and option names are.
> 
> -- Don
> 
> 
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[Gmod-resources] Re: [GMOD-devel] Common MOD URL for genome data?

[Don G. <gil...@bi...>]

Todd, others,

Sounds like there is general support.  For specifics, my own quick thoughts are it
would be easier, maybe better, to start with one top level folder, and put the 
options off of that, with some "MUST" options, and many "MAY" options.  I would probably
prefer this sort of organization:

  my.org/genome{s}/    
    -- return information/help page with links, MUST offer
   { plurals are tricky - do people remember them? }
  my.org/genome/dna  == return full genome dna in fasta format  
         genome/genome == alias to /dna
  my.org/genome/protein{s} == return " proteins in fasta
         genome/proteome  == alias to proteins
  my.org/genome/transcript{s} ==  transcripts in fasta
	 genome/transcriptome  == alias to transcripts 
  my.org/genome/feature{s} ==  features in GFF
         genome/gff  == alias to features

   -- other options as people want to support them
       genome/versions/ ...
       genome/species/ ..
   -- and/or use CGI options for these "?species=x&version=y"

But we should decide what good common terms above and option names are.

-- Don

[Gmod-resources] Re: [GMOD-devel] Common MOD URL for genome data?

[Todd H. <ha...@cs...>]

Hi Don - 

I definitely think the MODs should implement this as discussed at the last
meeting.  Currently, WormBase uses an Apache handler to map URLs to files --
or if need be, database dump scripts.

Currently, we have
    /genome
    /proteome
    /transcriptome
    /laboratories   // a list of labs and IDs, admittedly worm specific

When appropriate, URLs also accept a "species=" parameter.

I'd also like to suggest two additional URLs:

    /version   // The current version or release of the MOD
    /defaults  //  A key=value listing of appropriate defaults for the MOD

These last two options are used by my Bio::GMOD module which aims to provide
a unified perl API to the MODs.  (I haven't officially announced the module
yet while I polish some details and add some documentation).

Todd


> On 3/3/05 12:38 PM, Don Gilbert wrote:

> 
> Dear MOD folks,
> 
> Do you think we should arrange to have a common URL to locate genome
> data?   The value to this is making it easier for anyone looking for
> dna, protein, feature data for a given genome (or all of them).
> 
> Common urls would be something like this:
> my.org/genome?species=x [&version=y]   == dna fasta
> my.org/proteome?species=x ...    == protein fasta
> my.org/transcriptome? ...        == transcript fasta
> 
> and I guess add gff or include it as option above ?
> my.org/genomefeatures?...
> 
> I would vote for keeping the above options fairly simple, not
> necessarily comprehensive for all possible data choices.
> Also I'd suggest a common URL for information (e.g. a web page
> that lists the particulars for a MOD).
> my.org/genomes/help  or equivalent
> 
> One can think of variants on the above:
> my.org/genomes/dna, genome/proteins, genome/gff, genomes/help, ...
> The main thing is some agreement and folks who will
> implement this.  
> 
> = Don Gilbert
> 
> From: Kara Dolinski <ka...@ge...>
> | Thanks for the info, and thanks for the reminder about Lincoln's idea;
> | I had totally forgotten about it!  I think it's a great idea--it'd be
> | fabulous to have a standard URL to get these common files that we all
> | provide.  No matter how hard we all try, it is still pretty darn hard
> | to make it easy for people to navigate our ftp sites.  A
> | standard/common URL to get at least the basic files would do wonders.
> | I think beginning with DNA and protein fasta files for all ORFs + a gff
> | file would be a great start.
> | 
> | Should we send a message to a gmod list and see if we can decide on the
> | URL, then work on implementation?  Should be pretty straightforward to
> | do, I think....
> | 
> | -Kara
> 
> On Mar 2, 2005, at 5:29 PM, Don Gilbert wrote:
> 
>> 
>> Kara,
>> 
>> Find drosophila genome data including gff at
>> http://flybase.net/annot/#Data
>> the gff section (for each of two species).
>> 
>> Lincoln Stein thought we (mods) should all be serving bulk genome data
>> sets thru
>> a common url (that is wormbase.org/genome/xxx, flybase.net/genome/xxx,
>> yeastgenome.org/genome/...).
>> I don't recall what the specific url was, but if we all used the same
>> one, it would
>> make it easier to find these things.
>> 
>> Ah, notes help - October GMOD meeting - you were there also?
>>  sample standard urls something like this:
>>  my.org/genome?species=x [&version=y]   == dna fasta
>>  my.org/proteome?species=x ...    == protein fasta
>>  my.org/transcriptome? ...        == transcript fasta
>> 
>> and I guess add gff or include it as option above ?
>>  my.org/genomefeatures?...
>> 
>> I'm not sure what options we would be expected to all support.
> 
> 
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[Gmod-resources] Re: [GMOD-devel] Common MOD URL for genome data?

[Todd H. <ha...@cs...>]

Hi Don - 

I definitely think the MODs should implement this as discussed at the last
meeting.  Currently, WormBase uses an Apache handler to map URLs to files --
or if need be, database dump scripts.

Currently, we have
    /genome
    /proteome
    /transcriptome
    /laboratories   // a list of labs and IDs, admittedly worm specific

When appropriate, URLs also accept a "species=" parameter.

I'd also like to suggest two additional URLs:

    /version   // The current version or release of the MOD
    /defaults  //  A key=value listing of appropriate defaults for the MOD

These last two options are used by my Bio::GMOD module which aims to provide
a unified perl API to the MODs.  (I haven't officially announced the module
yet while I polish some details and add some documentation).

Todd


> On 3/3/05 12:38 PM, Don Gilbert wrote:

> 
> Dear MOD folks,
> 
> Do you think we should arrange to have a common URL to locate genome
> data?   The value to this is making it easier for anyone looking for
> dna, protein, feature data for a given genome (or all of them).
> 
> Common urls would be something like this:
> my.org/genome?species=x [&version=y]   == dna fasta
> my.org/proteome?species=x ...    == protein fasta
> my.org/transcriptome? ...        == transcript fasta
> 
> and I guess add gff or include it as option above ?
> my.org/genomefeatures?...
> 
> I would vote for keeping the above options fairly simple, not
> necessarily comprehensive for all possible data choices.
> Also I'd suggest a common URL for information (e.g. a web page
> that lists the particulars for a MOD).
> my.org/genomes/help  or equivalent
> 
> One can think of variants on the above:
> my.org/genomes/dna, genome/proteins, genome/gff, genomes/help, ...
> The main thing is some agreement and folks who will
> implement this.  
> 
> = Don Gilbert
> 
> From: Kara Dolinski <ka...@ge...>
> | Thanks for the info, and thanks for the reminder about Lincoln's idea;
> | I had totally forgotten about it!  I think it's a great idea--it'd be
> | fabulous to have a standard URL to get these common files that we all
> | provide.  No matter how hard we all try, it is still pretty darn hard
> | to make it easy for people to navigate our ftp sites.  A
> | standard/common URL to get at least the basic files would do wonders.
> | I think beginning with DNA and protein fasta files for all ORFs + a gff
> | file would be a great start.
> | 
> | Should we send a message to a gmod list and see if we can decide on the
> | URL, then work on implementation?  Should be pretty straightforward to
> | do, I think....
> | 
> | -Kara
> 
> On Mar 2, 2005, at 5:29 PM, Don Gilbert wrote:
> 
>> 
>> Kara,
>> 
>> Find drosophila genome data including gff at
>> http://flybase.net/annot/#Data
>> the gff section (for each of two species).
>> 
>> Lincoln Stein thought we (mods) should all be serving bulk genome data
>> sets thru
>> a common url (that is wormbase.org/genome/xxx, flybase.net/genome/xxx,
>> yeastgenome.org/genome/...).
>> I don't recall what the specific url was, but if we all used the same
>> one, it would
>> make it easier to find these things.
>> 
>> Ah, notes help - October GMOD meeting - you were there also?
>>  sample standard urls something like this:
>>  my.org/genome?species=x [&version=y]   == dna fasta
>>  my.org/proteome?species=x ...    == protein fasta
>>  my.org/transcriptome? ...        == transcript fasta
>> 
>> and I guess add gff or include it as option above ?
>>  my.org/genomefeatures?...
>> 
>> I'm not sure what options we would be expected to all support.
> 
> 
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[Gmod-resources] Re: [GMOD-devel] Common MOD URL for genome data?

[Aaron J. M. <am...@pc...>]

FYI, if/when a consensus is reached, the ApiDB databases (PlasmoDB, 
ToxoDB, CryptoDB, etc.) will follow suit.

I'd be happy with the virtual path based solution, and even happier if 
it was extended to include the possibility for different formats:

my.org/genome      # dna fasta, current version
my.org/genome/v4.4 # dna fasta, version 4.4

my.org/proteome/v4.3     # protein fasta, version 4.3
my.org/proteome/v4.3/gff # GFF of protein-encoding (CDS) features
my.org/proteome/gff/v4.3 # same, order shouldn't matter
my.org/v4.3/gff/proteome # same, ditto

I'd argue that "v4.3" and such strings be very "weakly typed", i.e. 
they're just tags that represent different instances of the dataset. 
This way I can also get:

my.org/proteome/gff/glimmerM/v4.3
my.org/proteome/gff/twinscan/v4.4

While this last bit looks hard, it actually isn't with the right Apache 
configuration ... but maybe this is overkill?  And it leaves open the 
problem of how would one find out what possible datasets/tags/formats 
are available (besides a separate download index HTML page) ... should 
my.org/proteome/list provide a flat list of available URLs?

-Aaron

Don Gilbert wrote:
> Dear MOD folks,
> 
> Do you think we should arrange to have a common URL to locate genome
> data?   The value to this is making it easier for anyone looking for
> dna, protein, feature data for a given genome (or all of them).
> 
> Common urls would be something like this:
>   my.org/genome?species=x [&version=y]   == dna fasta
>   my.org/proteome?species=x ...    == protein fasta
>   my.org/transcriptome? ...        == transcript fasta
> 
> and I guess add gff or include it as option above ?
>   my.org/genomefeatures?...
> 
> I would vote for keeping the above options fairly simple, not
> necessarily comprehensive for all possible data choices.
> Also I'd suggest a common URL for information (e.g. a web page
> that lists the particulars for a MOD).
>   my.org/genomes/help  or equivalent
>   
> One can think of variants on the above:
>   my.org/genomes/dna, genome/proteins, genome/gff, genomes/help, ...
> The main thing is some agreement and folks who will
> implement this.   
> 
> = Don Gilbert
> 
> From: Kara Dolinski <ka...@ge...>
> | Thanks for the info, and thanks for the reminder about Lincoln's idea; 
> | I had totally forgotten about it!  I think it's a great idea--it'd be 
> | fabulous to have a standard URL to get these common files that we all 
> | provide.  No matter how hard we all try, it is still pretty darn hard 
> | to make it easy for people to navigate our ftp sites.  A 
> | standard/common URL to get at least the basic files would do wonders.  
> | I think beginning with DNA and protein fasta files for all ORFs + a gff 
> | file would be a great start.
> | 
> | Should we send a message to a gmod list and see if we can decide on the 
> | URL, then work on implementation?  Should be pretty straightforward to 
> | do, I think....
> | 
> | -Kara
> 
> On Mar 2, 2005, at 5:29 PM, Don Gilbert wrote:
> 
> 
>>Kara,
>>
>>Find drosophila genome data including gff at 
>>http://flybase.net/annot/#Data
>>the gff section (for each of two species).
>>
>>Lincoln Stein thought we (mods) should all be serving bulk genome data 
>>sets thru
>>a common url (that is wormbase.org/genome/xxx, flybase.net/genome/xxx,
>>yeastgenome.org/genome/...).
>>I don't recall what the specific url was, but if we all used the same 
>>one, it would
>>make it easier to find these things.
>>
>>Ah, notes help - October GMOD meeting - you were there also?
>> sample standard urls something like this:
>> my.org/genome?species=x [&version=y]   == dna fasta
>> my.org/proteome?species=x ...    == protein fasta
>> my.org/transcriptome? ...        == transcript fasta
>>
>>and I guess add gff or include it as option above ?
>> my.org/genomefeatures?...
>>
>>I'm not sure what options we would be expected to all support.
> 
> 
> 
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[Gmod-resources] Common MOD URL for genome data?

[Don G. <gil...@bi...>]

Dear MOD folks,

Do you think we should arrange to have a common URL to locate genome
data?   The value to this is making it easier for anyone looking for
dna, protein, feature data for a given genome (or all of them).

Common urls would be something like this:
  my.org/genome?species=x [&version=y]   == dna fasta
  my.org/proteome?species=x ...    == protein fasta
  my.org/transcriptome? ...        == transcript fasta

and I guess add gff or include it as option above ?
  my.org/genomefeatures?...

I would vote for keeping the above options fairly simple, not
necessarily comprehensive for all possible data choices.
Also I'd suggest a common URL for information (e.g. a web page
that lists the particulars for a MOD).
  my.org/genomes/help  or equivalent
  
One can think of variants on the above:
  my.org/genomes/dna, genome/proteins, genome/gff, genomes/help, ...
The main thing is some agreement and folks who will
implement this.   

= Don Gilbert

From: Kara Dolinski <ka...@ge...>
| Thanks for the info, and thanks for the reminder about Lincoln's idea; 
| I had totally forgotten about it!  I think it's a great idea--it'd be 
| fabulous to have a standard URL to get these common files that we all 
| provide.  No matter how hard we all try, it is still pretty darn hard 
| to make it easy for people to navigate our ftp sites.  A 
| standard/common URL to get at least the basic files would do wonders.  
| I think beginning with DNA and protein fasta files for all ORFs + a gff 
| file would be a great start.
| 
| Should we send a message to a gmod list and see if we can decide on the 
| URL, then work on implementation?  Should be pretty straightforward to 
| do, I think....
| 
| -Kara

On Mar 2, 2005, at 5:29 PM, Don Gilbert wrote:

>
> Kara,
>
> Find drosophila genome data including gff at 
> http://flybase.net/annot/#Data
> the gff section (for each of two species).
>
> Lincoln Stein thought we (mods) should all be serving bulk genome data 
> sets thru
> a common url (that is wormbase.org/genome/xxx, flybase.net/genome/xxx,
> yeastgenome.org/genome/...).
> I don't recall what the specific url was, but if we all used the same 
> one, it would
> make it easier to find these things.
>
> Ah, notes help - October GMOD meeting - you were there also?
>  sample standard urls something like this:
>  my.org/genome?species=x [&version=y]   == dna fasta
>  my.org/proteome?species=x ...    == protein fasta
>  my.org/transcriptome? ...        == transcript fasta
>
> and I guess add gff or include it as option above ?
>  my.org/genomefeatures?...
>
> I'm not sure what options we would be expected to all support.

[Gmod-resources] RFA for generic tools for MODs

[Lincoln S. <ls...@cs...>]

Hi all,

Please have a look at this new RFA from NIHGMS:

	http://grants.nih.gov/grants/guide/pa-files/PA-04-135.html

It appears to be very much in line with the GMOD project.  If any 
groups wish to apply for this, let Scott and myself know so that we 
can provide a strongly worded letter of support.

Lincoln

-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724

Re: [Gmod-resources] cross-species gene similarity compute criteria? [BMS specs]

[Don G. <gil...@bi...>]

Here are the blast specs for the cross-species gene similarity compute run
at Bristol Myer Squibb, available at GMOD.

http://prdownloads.sourceforge.net/gmod/Refseq_Genome_TBLASTX.tar.gz
README:
Cross species comparisons of RefSeq and Yeast transcripts aligned to genomes using
TBLASTX.

        Nathan Siemers
        Donald Jackson

The enclosed files contain the results of large scale tblastx analyses
of refseq and yeast ORF transcript information onto the genomes of
yeast, drosophila, and C. elegans genomes.  Analyses were run via
NCBI blastall 2.2.1 on 32 Processor SGI Origin 2000 and 3000 series
machines, with the following parameters:

-b 1 -v 1 -e 0.00001 -p tblastx

Thus *only* the top hit from any transcript onto a genome is saved (if
its probability of significance is less than 1e-5).  

-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- gil...@in...--http://marmot.bio.indiana.edu/

[Gmod-resources] cross-species gene similarity compute criteria?

[Don G. <gil...@bi...>]

What  blast or other protocols do we want for  cross-species gene
similarity computes, so that any model organism database would be happy
using the results?   Any of you who do or have done such computations, please
comment on your criteria and methods for calculating gene similarities.

For euGenes.org's gene similarity computes, we've used just a simple
protein-gene species x species blast (see
http://euGenes.org:7072/all/hgsummary.html)

This is a computed gene homology or similarity using reference protein sequences
identified by the source databases.  A BLAST of all these sequences is computed,
each sequence against all others, using specific parameters given below
(specifically an E value at or below 1e-30). 

The sequences used in these calculations are found in the "Reference proteins"
data files in each organism's folder.  This summary is determined from the
"Homologous genes table" data files also in each folder. 

The counts in the [above url] table are of the number of available genes for an organism,
and those which have one or more significant homologs in the other organisms.
Percentages are the count of genes with any homolog (one or several) in another
organism, divided by the total available genes in that organism (x 100). 

For gene reports, we use the criteria of picking the most
significant (E value) match from each species, plus any other matches within
10% of that E value.

Similarity computations, using NCBI BLASTP 2.2.6 : 

orglist=(Fruitfly Human Mouse Mosquito Weed Worm Yeast Zebrafish Rat Rice E_coli
Chimp)

foreach org1 in (orglist)
  foreach org2 in (orglist)
   blastall -v 10 -b 10 -m 9 -a 4  -p blastp -e 1e-30 -d org1/refprot.fasta -i
org2/refprot.fasta 
  end
end

-- Don
-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- gil...@in...--http://marmot.bio.indiana.edu/

[Gmod-resources] Re: [GMOD-devel] Apple to give 5 mini-clusters

[Brian O'C. <boc...@uc...>]

Allen Day wrote:

>On Tue, 11 May 2004, Scott Cain wrote:
>
>  
>
>>On Tue, 2004-05-11 at 12:59, Lincoln Stein wrote:
>>    
>>
>>>A cluster of 4 nodes is not really going to be adequate for decent 
>>>cross species comparison.  It would make a great test bed for a 
>>>prototype MOD web site, though.  You would designate one of the nodes 
>>>to run the database, another to run the web site, a third to run 
>>>BLAST, and a fourth for developing the next release.
>>>
>>>I think we can make a good argument for making the cluster into a 
>>>hardware reference platform for a generic MOD, and skip the cross 
>>>species comparison altogether unless someone like Jason thinks that 
>>>we could an all-against-all BLAST across six species on a 4-node 
>>>cluster in reasonable time.
>>>
>>>I'm willing to do the writeup if I get to have the system in my 
>>>office.
>>>      
>>>
>>:-)  I was thinking in my basement.  I suppose it may not be heavy duty
>>enough to do all v all BLASTs (although, if it were BLASTP, it might
>>have a shot).  The app could say that it could be used as test cluster
>>for determining needs for bigger (imply, Apple) cluster.
>>    
>>
>
>i was thinking in our server room, we have gigabit uplink :).  i agree
>that we can make a strong argument here for a GMOD site test bed.  i do
>think though that lincoln would be an appropriate person to spearhead the
>application composition with his superb writing skillz.
>
>-allen
>
I was just saying we need to get a Mac to test the GMOD install :-)

--Brian

[Gmod-resources] Re: [GMOD-devel] Apple to give 5 mini-clusters

[Allen D. <all...@uc...>]

On Tue, 11 May 2004, Scott Cain wrote:

> On Tue, 2004-05-11 at 12:59, Lincoln Stein wrote:
> > A cluster of 4 nodes is not really going to be adequate for decent 
> > cross species comparison.  It would make a great test bed for a 
> > prototype MOD web site, though.  You would designate one of the nodes 
> > to run the database, another to run the web site, a third to run 
> > BLAST, and a fourth for developing the next release.
> > 
> > I think we can make a good argument for making the cluster into a 
> > hardware reference platform for a generic MOD, and skip the cross 
> > species comparison altogether unless someone like Jason thinks that 
> > we could an all-against-all BLAST across six species on a 4-node 
> > cluster in reasonable time.
> > 
> > I'm willing to do the writeup if I get to have the system in my 
> > office.
> 
> :-)  I was thinking in my basement.  I suppose it may not be heavy duty
> enough to do all v all BLASTs (although, if it were BLASTP, it might
> have a shot).  The app could say that it could be used as test cluster
> for determining needs for bigger (imply, Apple) cluster.

i was thinking in our server room, we have gigabit uplink :).  i agree
that we can make a strong argument here for a GMOD site test bed.  i do
think though that lincoln would be an appropriate person to spearhead the
application composition with his superb writing skillz.

-allen

> 
> Scott
> 
> > 
> > Lincoln
> > 
> > On Monday 10 May 2004 09:35 pm, Scott Cain wrote:
> > > Hi,
> > >
> > > I'm forwarding an email from Chris Dagdigian from the bioperl
> > > mailing list.  I think we could put together an application for
> > > GMOD to use both as a development box for GMOD applications as well
> > > as a compute cluster for cross species comparisons.  Would anybody
> > > be willing to take the lead?  The application deadline is June 13.
> > >
> > > Thanks,
> > > Scott
> > >
> > > From Chris:
> > >
> > > Hi folks,
> > >
> > > Apologies for the semi off topic posting but I think it may be
> > > appropriate because I know lots of people doing really clever
> > > informatics stuff tend to be on the open-bio.org mailing lists.
> > >
> > > I want to make sure many of the small group, individuals and DIY
> > > types hear about this as they can probably benefit the most from a
> > > influx of hardware.
> > >
> > > In short, Apple just announced a program to give away 5 fully
> > > provisioned mini-clusters (4 Xserve G5 nodes) in a judged process
> > > specifically aimed at bioinformatics types. Awards are announced on
> > > 29 June 2004.
> > >
> > > The URL is here:
> > > http://www.apple.com/science/clusteraward/
> > >
> > > Regards,
> > > Chris
> 

[Gmod-resources] Re: [GMOD-devel] Apple to give 5 mini-clusters

[Scott C. <ca...@cs...>]

On Tue, 2004-05-11 at 12:59, Lincoln Stein wrote:
> A cluster of 4 nodes is not really going to be adequate for decent 
> cross species comparison.  It would make a great test bed for a 
> prototype MOD web site, though.  You would designate one of the nodes 
> to run the database, another to run the web site, a third to run 
> BLAST, and a fourth for developing the next release.
> 
> I think we can make a good argument for making the cluster into a 
> hardware reference platform for a generic MOD, and skip the cross 
> species comparison altogether unless someone like Jason thinks that 
> we could an all-against-all BLAST across six species on a 4-node 
> cluster in reasonable time.
> 
> I'm willing to do the writeup if I get to have the system in my 
> office.

:-)  I was thinking in my basement.  I suppose it may not be heavy duty
enough to do all v all BLASTs (although, if it were BLASTP, it might
have a shot).  The app could say that it could be used as test cluster
for determining needs for bigger (imply, Apple) cluster.

Scott

> 
> Lincoln
> 
> On Monday 10 May 2004 09:35 pm, Scott Cain wrote:
> > Hi,
> >
> > I'm forwarding an email from Chris Dagdigian from the bioperl
> > mailing list.  I think we could put together an application for
> > GMOD to use both as a development box for GMOD applications as well
> > as a compute cluster for cross species comparisons.  Would anybody
> > be willing to take the lead?  The application deadline is June 13.
> >
> > Thanks,
> > Scott
> >
> > From Chris:
> >
> > Hi folks,
> >
> > Apologies for the semi off topic posting but I think it may be
> > appropriate because I know lots of people doing really clever
> > informatics stuff tend to be on the open-bio.org mailing lists.
> >
> > I want to make sure many of the small group, individuals and DIY
> > types hear about this as they can probably benefit the most from a
> > influx of hardware.
> >
> > In short, Apple just announced a program to give away 5 fully
> > provisioned mini-clusters (4 Xserve G5 nodes) in a judged process
> > specifically aimed at bioinformatics types. Awards are announced on
> > 29 June 2004.
> >
> > The URL is here:
> > http://www.apple.com/science/clusteraward/
> >
> > Regards,
> > Chris
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         ca...@cs...
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory

[Gmod-resources] Re: [GMOD-devel] Apple to give 5 mini-clusters

[Lincoln S. <ls...@cs...>]

A cluster of 4 nodes is not really going to be adequate for decent 
cross species comparison.  It would make a great test bed for a 
prototype MOD web site, though.  You would designate one of the nodes 
to run the database, another to run the web site, a third to run 
BLAST, and a fourth for developing the next release.

I think we can make a good argument for making the cluster into a 
hardware reference platform for a generic MOD, and skip the cross 
species comparison altogether unless someone like Jason thinks that 
we could an all-against-all BLAST across six species on a 4-node 
cluster in reasonable time.

I'm willing to do the writeup if I get to have the system in my 
office.

Lincoln

On Monday 10 May 2004 09:35 pm, Scott Cain wrote:
> Hi,
>
> I'm forwarding an email from Chris Dagdigian from the bioperl
> mailing list.  I think we could put together an application for
> GMOD to use both as a development box for GMOD applications as well
> as a compute cluster for cross species comparisons.  Would anybody
> be willing to take the lead?  The application deadline is June 13.
>
> Thanks,
> Scott
>
> From Chris:
>
> Hi folks,
>
> Apologies for the semi off topic posting but I think it may be
> appropriate because I know lots of people doing really clever
> informatics stuff tend to be on the open-bio.org mailing lists.
>
> I want to make sure many of the small group, individuals and DIY
> types hear about this as they can probably benefit the most from a
> influx of hardware.
>
> In short, Apple just announced a program to give away 5 fully
> provisioned mini-clusters (4 Xserve G5 nodes) in a judged process
> specifically aimed at bioinformatics types. Awards are announced on
> 29 June 2004.
>
> The URL is here:
> http://www.apple.com/science/clusteraward/
>
> Regards,
> Chris

-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724

[Gmod-resources] Apple to give 5 mini-clusters

[Scott C. <ca...@cs...>]

Hi,

I'm forwarding an email from Chris Dagdigian from the bioperl mailing
list.  I think we could put together an application for GMOD to use both
as a development box for GMOD applications as well as a compute cluster
for cross species comparisons.  Would anybody be willing to take the
lead?  The application deadline is June 13.

Thanks,
Scott

>From Chris:

Hi folks,

Apologies for the semi off topic posting but I think it may be 
appropriate because I know lots of people doing really clever 
informatics stuff tend to be on the open-bio.org mailing lists.

I want to make sure many of the small group, individuals and DIY types
hear about this as they can probably benefit the most from a influx of
hardware.

In short, Apple just announced a program to give away 5 fully 
provisioned mini-clusters (4 Xserve G5 nodes) in a judged process 
specifically aimed at bioinformatics types. Awards are announced on 29
June 2004.

The URL is here:
http://www.apple.com/science/clusteraward/

Regards,
Chris
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         ca...@cs...
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory