gmod-devel — GMOD developer's mailing list

[GMOD-devel] Re: [Open-bio-l] Schema for genes & features & mappings to assemblies

[Ewan B. <bi...@eb...>]

On Tue, 23 Apr 2002, Elia Stupka wrote:

> > Ensembl's sweet spot is assemblies+automatic pipeline (ala Ensembl). Most
> > people get put off by how much "stuff" there is inside Ensembl but infact
> 
> I just had to jump in here. We over here would be keen and are working on
> getting more into bioperl, biosql and bioperl-pipeline. Ideally I think we
> should aim at allowing people the same sweet automatic feeling that
> ensembl has for genome annotation become one of the many sweet features of
> a bioperl-pipeline. With the notable difference that it would be just one
> of the many sweet spots in that it could be used also for much smaller
> jobs (a simple blast pipeline for lab sequences for example) with the same
> ease, and knows how to interact with multiple dbs,etc.

I think what is happening here is very natural (Ensembl expertise
trickling down in some sense without us entangling people in Ensembl's
schedule - which is often pretty forced). 


I *do* think people will be surprised and how clean the next generation
Ensembl schema is, which we are working on in a very steady manner and
adaptors. It really unifies lots of ideas that have been floating around
for a while in a clean-and-explicit schema, with a clean-and-explicit code
layer on top. However, BioSQL is also very clean.

> 
> > The big benefits are (a) schema and data which can be downloaded for
> > human, mouse, zebra, fugu, (and soon... anopheles) which is guarenteed to
> > work (b) very functional web site which is portable (c) ability to run
> > automatic systems which scale into a "please completely annotate this
> > genome in 2 weeks" scale
> 
> I admit I cannot see any of us or bioperl moving soon to some fancy
> website building and it'd be useless. Probably more on the lines of
> genquire, or a bioperl-gui... but apart from that there would be no issue
> once things are setup to port bioperl-pipeline over to ensembl with a
> couple of parsers or the other way around.
> 

Flexiblity and reuse here are watchwords. David - I think you are best off
backing BioSQL - it is the schema which represents the most complete and
shared view of dna+features.


We do need to discuss assemblies. I vote for "flat" one level assemblies
(set of contigs form a chromosome), ala Ensembl, as I believe that the
assummed heirarichal nature of assemblies is (a) mainly a consequence of
how it is put together and the intermedaites in the heirarchies between
contigs of DNA and chromosomes are nearly never stable (b) means you
always have to use software to do conversions and can never do it easily
with SQL (PL/SQL probably can...).


Other options are :

  (a) multi-level (thomas')

  (b) zero level (Lincoln likes this). The schema stores contigs as
"features" on DNA Sequences which are chromosome length.




> Elia
> 
> 
> 
> ********************************
> * http://www.fugu-sg.org/~elia *
> * tel:    +65 874 1467         *
> * mobile: +65 90307613         *
> * fax:    +65 777 0402         *
> ********************************
> 
> 
> _______________________________________________
> Open-Bio-l mailing list
> Ope...@op...
> http://open-bio.org/mailman/listinfo/open-bio-l
> 

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<bi...@eb...>. 
-----------------------------------------------------------------

[GMOD-devel] Re: [Open-bio-l] Schema for genes & features & mappings to assemblies

[Elia S. <el...@fu...>]

> Ensembl's sweet spot is assemblies+automatic pipeline (ala Ensembl). Most
> people get put off by how much "stuff" there is inside Ensembl but infact

I just had to jump in here. We over here would be keen and are working on
getting more into bioperl, biosql and bioperl-pipeline. Ideally I think we
should aim at allowing people the same sweet automatic feeling that
ensembl has for genome annotation become one of the many sweet features of
a bioperl-pipeline. With the notable difference that it would be just one
of the many sweet spots in that it could be used also for much smaller
jobs (a simple blast pipeline for lab sequences for example) with the same
ease, and knows how to interact with multiple dbs,etc.

> The big benefits are (a) schema and data which can be downloaded for
> human, mouse, zebra, fugu, (and soon... anopheles) which is guarenteed to
> work (b) very functional web site which is portable (c) ability to run
> automatic systems which scale into a "please completely annotate this
> genome in 2 weeks" scale

I admit I cannot see any of us or bioperl moving soon to some fancy
website building and it'd be useless. Probably more on the lines of
genquire, or a bioperl-gui... but apart from that there would be no issue
once things are setup to port bioperl-pipeline over to ensembl with a
couple of parsers or the other way around.

Elia



********************************
* http://www.fugu-sg.org/~elia *
* tel:    +65 874 1467         *
* mobile: +65 90307613         *
* fax:    +65 777 0402         *
********************************

[GMOD-devel] Re: [Open-bio-l] Schema for genes & features & mappings to assemblies

[Ewan B. <bi...@eb...>]

On Mon, 22 Apr 2002, Thomas Down wrote:

> On Mon, Apr 22, 2002 at 02:36:18PM -0700, Hilmar Lapp wrote:
> > 
> > 	- biosql is for sequences and features, not mappings to 
> >  assemblies (is that intended to be added, too, or is it beyond its scope? )
> 
> Hi...
> 
> There was a bit of discussion of assemblies at Cape Town,
> but I don't think it was terribly conclusive.
> 
> I did actually write a little BioSQL schema extension
> for supporting assemblies, and prototyped some support for
> it in the BioJava-BioSQL code.  So it's certainly possible.
> The particular approach I took wasn't universally well
> received, though, since I designed it to support nested
> assemblies (i.e. a fragment of an assembly can itself be
> an assembly).  That's nice in that you can actually model
> the whole assembly process (right down to the individual
> sequencing reads, if you feel like it). But does mean
> that all the `assembly-munging' code will probably need
> to be put in your object layer, rather than handling
> the assembly directly in the SQL queries.
> 
> If you think BioSQL + assemblies might fit your requirements,
> it could be worth re-starting this debate.

Yup - I agree on thomas view and I think it would be fine to put in
assemblies into BioSQL.


Ensembl's sweet spot is assemblies+automatic pipeline (ala Ensembl). Most
people get put off by how much "stuff" there is inside Ensembl but infact
the schema is pretty simple and the complexity is mainly because it has
been an active project for 3 years with numerous silly deadlines drop on
it from above. Finally people get the heebee-jeebies because Ensembl is
such a big group with lots of internal drivers that people get worrried
that they don't get any say and just get swept along.



The big benefits are (a) schema and data which can be downloaded for
human, mouse, zebra, fugu, (and soon... anopheles) which is guarenteed to
work (b) very functional web site which is portable (c) ability to run
automatic systems which scale into a "please completely annotate this
genome in 2 weeks" scale



BioSQL's advantages is that it is more project neutral and the feature
ontology stuff is better worked out whereas Ensembl is deliberately
"flat".




> 
>     Thomas.
> _______________________________________________
> Open-Bio-l mailing list
> Ope...@op...
> http://open-bio.org/mailman/listinfo/open-bio-l
> 

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<bi...@eb...>. 
-----------------------------------------------------------------

[GMOD-devel] Re: [Open-bio-l] Schema for genes & features & mappings to assemblies

[Chris M. <cj...@bd...>]

On Mon, 22 Apr 2002, Hilmar Lapp wrote:

> First off, apologies to all who get this twice or multiple times.
>
> We're setting out to build a database to integrate genes, features,
> mappings between genes, mappings between genes and features, and
> mappings of features and genes to genome assemblies, all from different
> sources, for browsing, visualization, and fast queries (NOT for
> editing).
>
> I'd like to steal as much as possible from what's out there already,
> which is why I'm writing (surprise surprise).
>
> I'm having some difficulties finding the right pointers to schemas
> underpinning the genome databases, but I'm sure I just haven't been
> looking enough. Any piece of information you can give me would be
> greatly appreciated.
>
> What I understand so far (correct me where I'm wrong):
>
> 	- biosql is for sequences and features, not mappings to assemblies
> (is that intended to be added, too, or is it beyond its scope? )
> 	- GGB is running off the schema in Bio::DB:GFF, which is not
> biosql compatible (Lincoln? If so, do you have any plans to change
> that?)
> 	- Apollo doesn't run off any particular schema (is that true?),
> but rather pulls data through adaptors/APIs
> 	- Wormbase is an AceDB
> 	- the Ensembl schema excels at modeling contigs and assemblies
> (but is probably 5x more than what I want; is there a piece one could
> prune that encompasses what I'm after?)
>
> What about Flybase? Chris M. would that be you? Someone told me since
> he's leading biosql too you could just use that and get the essence of
> flybase along with it.

FlyBase uses GadFly for its annotation database; you can find more here:
www.fruitfly.org/developers.

biosql has a some of gadfly's essence sprinkled onto it but there's still
various differences.

biosql has adaptors for the bioperl objects whereas gadfly has adaptors to
it's own (not quite bioperl compliant) perl object model

> While waiting for responses (hoping that there are going to be some :) I
> thought I reverse engineer ERDs from the DDL I find in biosql and
> Bio::DB::GFF, because I hate trying to understand a schema based on
> CREATE TABLE statements. Let me know if that's already been done and I
> just overlooked the respective URLs. Also, we'll eventually implement
> this database in Oracle, and my understanding is that none of the things
> I mentioned is in or has been ported to Oracle (the latter may be,
> better yet, hopefully is, wrong).

there really needs to be some kind of website for biosql set up. I hope
folks aren't waiting on me to do this, i'm rubbish at that sort of thing.

in the biosql repository, in docs/biosql-schema.html, there is an
automatically generated html doc of the schema, with all foreign keys
bidirectionally hyperlinked. not quite an ER diagram, but it's better than
a manually generated diagram that gets out of sync with the schema.

the postgres schema gets automatically generated from the mysql one, which
is regarded as the source one. it should be easy to generate oracle too.

Right now the script for doing the conversion is pretty hacky - I'm just
about to commit a replacement.

there are also some postgres specific extensions. Some of these such as
views should work on oracle but the pg functions will need porting if you
decide to use them.

I promise to write some more docs on biosql this week - if someone could
get the basic framework for a website for it set up on open-bio that'd be
great

> 	-hilmar
>

[GMOD-devel] Re: [Open-bio-l] Schema for genes & features & mappings to assemblies

[Thomas D. <td...@sa...>]

On Mon, Apr 22, 2002 at 02:36:18PM -0700, Hilmar Lapp wrote:
> 
> 	- biosql is for sequences and features, not mappings to 
>  assemblies (is that intended to be added, too, or is it beyond its scope? )

Hi...

There was a bit of discussion of assemblies at Cape Town,
but I don't think it was terribly conclusive.

I did actually write a little BioSQL schema extension
for supporting assemblies, and prototyped some support for
it in the BioJava-BioSQL code.  So it's certainly possible.
The particular approach I took wasn't universally well
received, though, since I designed it to support nested
assemblies (i.e. a fragment of an assembly can itself be
an assembly).  That's nice in that you can actually model
the whole assembly process (right down to the individual
sequencing reads, if you feel like it). But does mean
that all the `assembly-munging' code will probably need
to be put in your object layer, rather than handling
the assembly directly in the SQL queries.

If you think BioSQL + assemblies might fit your requirements,
it could be worth re-starting this debate.

    Thomas.

[GMOD-devel] Schema for genes & features & mappings to assemblies

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

First off, apologies to all who get this twice or multiple times.

We're setting out to build a database to integrate genes, features, =
mappings between genes, mappings between genes and features, and =
mappings of features and genes to genome assemblies, all from different =
sources, for browsing, visualization, and fast queries (NOT for =
editing).

I'd like to steal as much as possible from what's out there already, =
which is why I'm writing (surprise surprise).

I'm having some difficulties finding the right pointers to schemas =
underpinning the genome databases, but I'm sure I just haven't been =
looking enough. Any piece of information you can give me would be =
greatly appreciated.

What I understand so far (correct me where I'm wrong):

	- biosql is for sequences and features, not mappings to assemblies (is =
that intended to be added, too, or is it beyond its scope? )
	- GGB is running off the schema in Bio::DB:GFF, which is not biosql =
compatible (Lincoln? If so, do you have any plans to change that?)
	- Apollo doesn't run off any particular schema (is that true?), but =
rather pulls data through adaptors/APIs
	- Wormbase is an AceDB
	- the Ensembl schema excels at modeling contigs and assemblies (but is =
probably 5x more than what I want; is there a piece one could prune that =
encompasses what I'm after?)

What about Flybase? Chris M. would that be you? Someone told me since =
he's leading biosql too you could just use that and get the essence of =
flybase along with it.

While waiting for responses (hoping that there are going to be some :) I =
thought I reverse engineer ERDs from the DDL I find in biosql and =
Bio::DB::GFF, because I hate trying to understand a schema based on =
CREATE TABLE statements. Let me know if that's already been done and I =
just overlooked the respective URLs. Also, we'll eventually implement =
this database in Oracle, and my understanding is that none of the things =
I mentioned is in or has been ported to Oracle (the latter may be, =
better yet, hopefully is, wrong).

	-hilmar
--=20
-------------------------------------------------------------
Hilmar Lapp                            email: la...@gn...
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------

[GMOD-devel] Re: Bio Graphics Panel

[ShengQiang S. <ss...@bd...>]

On Tue, 16 Apr 2002, ShengQiang Shu wrote:

>
> hi, all. I was trying to catch up with all changes in Bio Graphics under
> gmod. It seems that callback in panel does not work any more. I
> dynamically set bgcolor/fgcolor using configure method, e.g
>
> $track->configure(blahblah,
> 		  -bgcolor =>
> 			sub {
> 			   my $sf = shift;
> 			   return ($sf->something ? color1 : color2)}
> 		);
>
> it used to work. Any track with this kind of configure call has no glyph
> drawn out, but label is visible.
>

ok, found what is the problem. it enforces that a feature be a
Bio::FeatureI when getting option value from callback. Our gadfly model
conforms to Bio::FeatureI, but does not inherit from it. Chris, can we
make our seq feature obj inherit from Bio::FeatureI



Shu

[GMOD-devel] Bio Graphics Panel

[ShengQiang S. <ss...@bd...>]

hi, all. I was trying to catch up with all changes in Bio Graphics under
gmod. It seems that callback in panel does not work any more. I
dynamically set bgcolor/fgcolor using configure method, e.g

$track->configure(blahblah,
		  -bgcolor =>
			sub {
			   my $sf = shift;
			   return ($sf->something ? color1 : color2)}
		);

it used to work. Any track with this kind of configure call has no glyph
drawn out, but label is visible.

appreciate any insight on this.



Shu

Re: [GMOD-devel] Label not showing

[Marco V. <mav...@ma...>]

Hi Lincoln,
 I've download the Bioperl v1.01 from CVS and the labels are showing 
now. That was the problem as you said, thank you very much.
Maybe you could  mention this on INSTALL file on " 8. BIOPERL VERSIONS".

Marco.


Lincoln Stein wrote:

>Hi Marco,
>
>I loaded up your sample data on my test system, and I don't have any problem 
>with the labels showing up.  Here is an example region:
>
>http://brie2.cshl.org:8081/db/seq/gbrowse?name=Chromosome6%3A25190695..25200694;source=melanoma;width=800;label=BLASTN
>
>The configuration file you sent me also worked fine as is.  After I confirmed 
>that it was working, I did make a few small changes to improve the way the 
>BLAST hits are drawn (changed dashed line to solid line and removed the 
>uninformative description below).  Here is the new stanza:
>
>
>[BLASTN]
>feature       = alignment:blastn
>glyph         = segments
>bgcolor       = lightgrey
>fgcolor       = black
>height        = 6
>connector     = solid
>key           = BLASTN Hits
>
>Is it possible that you are using an old version of BioPerl?   I recommend 
>version 1.01 or higher -- you have to download the 1.0 distribution, and then 
>apply a patch that is in the GBrowse distribution.
>
>If this isn't the problem, we'll have to explore more esoteric problems like 
>the version of mysql, Perl and Apache that you are using.
>
>Lincoln
>
>On Monday 15 April 2002 15:41, you wrote:
>
>>I've attached the selects
>>Marco.
>>
>>Lincoln Stein wrote:
>>
>>>Hello Marco,
>>>
>>>I would like to test whether the data looks OK when it is loaded into the
>>>database.  Could you run these commands for me from the mysql database in
>>>which your melanoma data is loaded:
>>>
>>>	mysql> select * from fdata limit 10;
>>>	mysql> select * from fgroup limit 10;
>>>	mysql> select * from ftype limit 10;
>>>	mysql> select * from fattribute limit 10;
>>>
>>>Thanks a lot,
>>>
>>>Lincoln
>>>
>>>On Friday 12 April 2002 19:08, you wrote:
>>>
>>>>If you are courious about the output you can access the server at:
>>>>
>>>>This link for D.Melanogaster test:
>>>>
>>>>http://143.107.223.178/cgi-bin/gbrowse?name=2L%3A9497921..9499920&source=
>>>>fl y&width=800&label=TRANS-GENE-BLASTX%20Hits-REP-CLO-SCAFF
>>>>
>>>>And this is my sequences set:
>>>>
>>>>http://143.107.223.178/cgi-bin/gbrowse?name=Chromosome1%3A6216431..621743
>>>>0& source=melanoma&width=800&label=BLASTN
>>>>
>>>>Marco.
>>>>PS: Be patience 'cause the server is a test server (Intel very slow)
>>>>
>
>----------------------------------------
>Content-Type: text/plain; charset="iso-8859-1"; name="melanoma.querys"
>Content-Transfer-Encoding: 7bit
>Content-Description: 
>----------------------------------------
>

-- 
#Marco Aurélio Valtas Cunha
#Laboratório de Bioinformática
#Hemocentro de Ribeirão Preto
#Faculdade de Medicina de Ribeirão Preto
#Universidade de São Paulo
#Tel 55 16 3963-9300 R: 9603
#homepage http://bit.fmrp.usp.br
#e-mail: mav...@ma...

Re: [GMOD-devel] Label not showing

[Marco V. <mav...@ma...>]

Oh my... ( Pretty alignment, no?! :) )
 Well, I will look on BioPerl version and more.  When I get  some info I 
e-mail to you.
Thanks for you time.
Marco.

Lincoln Stein wrote:

>Hi Marco,
>
>I loaded up your sample data on my test system, and I don't have any problem 
>with the labels showing up.  Here is an example region:
>
>http://brie2.cshl.org:8081/db/seq/gbrowse?name=Chromosome6%3A25190695..25200694;source=melanoma;width=800;label=BLASTN
>
>The configuration file you sent me also worked fine as is.  After I confirmed 
>that it was working, I did make a few small changes to improve the way the 
>BLAST hits are drawn (changed dashed line to solid line and removed the 
>uninformative description below).  Here is the new stanza:
>
>
>[BLASTN]
>feature       = alignment:blastn
>glyph         = segments
>bgcolor       = lightgrey
>fgcolor       = black
>height        = 6
>connector     = solid
>key           = BLASTN Hits
>
>Is it possible that you are using an old version of BioPerl?   I recommend 
>version 1.01 or higher -- you have to download the 1.0 distribution, and then 
>apply a patch that is in the GBrowse distribution.
>
>If this isn't the problem, we'll have to explore more esoteric problems like 
>the version of mysql, Perl and Apache that you are using.
>
>Lincoln
>
>On Monday 15 April 2002 15:41, you wrote:
>
>>I've attached the selects
>>Marco.
>>
>>Lincoln Stein wrote:
>>
>>>Hello Marco,
>>>
>>>I would like to test whether the data looks OK when it is loaded into the
>>>database.  Could you run these commands for me from the mysql database in
>>>which your melanoma data is loaded:
>>>
>>>	mysql> select * from fdata limit 10;
>>>	mysql> select * from fgroup limit 10;
>>>	mysql> select * from ftype limit 10;
>>>	mysql> select * from fattribute limit 10;
>>>
>>>Thanks a lot,
>>>
>>>Lincoln
>>>
>>>On Friday 12 April 2002 19:08, you wrote:
>>>
>>>>If you are courious about the output you can access the server at:
>>>>
>>>>This link for D.Melanogaster test:
>>>>
>>>>http://143.107.223.178/cgi-bin/gbrowse?name=2L%3A9497921..9499920&source=
>>>>fl y&width=800&label=TRANS-GENE-BLASTX%20Hits-REP-CLO-SCAFF
>>>>
>>>>And this is my sequences set:
>>>>
>>>>http://143.107.223.178/cgi-bin/gbrowse?name=Chromosome1%3A6216431..621743
>>>>0& source=melanoma&width=800&label=BLASTN
>>>>
>>>>Marco.
>>>>PS: Be patience 'cause the server is a test server (Intel very slow)
>>>>
>
>----------------------------------------
>Content-Type: text/plain; charset="iso-8859-1"; name="melanoma.querys"
>Content-Transfer-Encoding: 7bit
>Content-Description: 
>----------------------------------------
>

-- 
#Marco Aurélio Valtas Cunha
#Laboratório de Bioinformática
#Hemocentro de Ribeirão Preto
#Faculdade de Medicina de Ribeirão Preto
#Universidade de São Paulo
#Tel 55 16 3963-9300 R: 9603
#homepage http://bit.fmrp.usp.br
#e-mail: mav...@ma...

Re: [GMOD-devel] Label not showing

[Marco V. <mav...@ma...>]

Here is
 From ChangeLog:
1.38    Mon Apr  8 21:16:12 EDT 2002

I think I can add that i'm starting with GMOD and maybe you should look 
on basic problems of configuration too.  What I'm trying is use the 
drosophila configuration on my sequences. The GFF file has no more 
information beside what I sended.
To test I have the fly.gff on my server too and all look ok.
Some thought about this?
Marco.

Lincoln Stein wrote:

>The GFF looks fine so the problem isn't immediately obvious.  Could you send 
>the versions and/or modification dates of the software you are using?  
>There's been a lot of change in recent days.
>
>Lincoln
>
>On Friday 12 April 2002 16:56, Marco Valtas wrote:
>
>>I'm trying to get my label showing but it's seems impossible, here's a
>>sample of gff
>>
>>Chromosome6     arm     Component       1       25259406        .
>>+       .       Sequence "Chromosome6"
>>Chromosome6     blastn  similarity      12265899        12266072
>>5.0e-38 +       .       Target
>>"Sequence:RC6-AN0069-290900-021-A02" 16 192
>>
>>The map is working and [BLAST N] label is 1 , but no matter how much
>>zoom I can't view some notation. I've tryied Note: too but didn't worked.
>>
>>What's is the commons pitfalls for this problem?
>>
>>Best Regards
>>Marco.
>>
>

-- 
#Marco Aurélio Valtas Cunha
#Laboratório de Bioinformática
#Hemocentro de Ribeirão Preto
#Faculdade de Medicina de Ribeirão Preto
#Universidade de São Paulo
#Tel 55 16 3963-9300 R: 9603
#homepage http://bit.fmrp.usp.br

[GMOD-devel] Label not showing

[Marco V. <mav...@ma...>]

I'm trying to get my label showing but it's seems impossible, here's a 
sample of gff

Chromosome6     arm     Component       1       25259406        .       
+       .       Sequence "Chromosome6"
Chromosome6     blastn  similarity      12265899        12266072        
5.0e-38 +       .       Target
"Sequence:RC6-AN0069-290900-021-A02" 16 192

The map is working and [BLAST N] label is 1 , but no matter how much 
zoom I can't view some notation. I've tryied Note: too but didn't worked.

What's is the commons pitfalls for this problem?

Best Regards
Marco.

-- 
#Marco Aurélio Valtas Cunha
#Laboratório de Bioinformática
#Hemocentro de Ribeirão Preto
#Faculdade de Medicina de Ribeirão Preto
#Universidade de São Paulo
#Tel 55 16 3963-9300 R: 9603
#homepage http://bit.fmrp.usp.br
#e-mail:

[GMOD-devel] gbrowse plugin architecture

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

Hi Jason,

The latest GBrowse version now has a plugin architecture for dumpers
and other types of analysis programs.  I've written a couple of sample
dumpers (FASTA and GFF dumping) and have a README-PLUGINS file that
describes how the plugins work.

In addition ot the dumpers there's a kind of plugin that will do a
search on the database and propose a series of matching regions (like
a BLAST search).  These are then displayed in a list that shows the
matches on the chromosome.  Another type of plugin adds new
annotations to the display; (restriction sites, CG islands).  These
plugins are described in the README, but I haven't quite finished the
implementation.

If you are still working on this, you can check out the latest version
from the GMOD CVS.

Lincoln

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
ls...@cs...			                  Cold Spring Harbor, NY
Positions available at my lab: see http://stein.cshl.org/#hire
========================================================================

[GMOD-devel] RE: SOAP expert

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

Hi Tim,

That's great!  I hadn't expected a response to the want ad so soon.
You are talking about the GMOD project, right?

Here's the plan...  We're developing a common infrastructure for
describing biological data using XSL and WSDL, and would like to
develop SOAP services on top of them.  We've got some parts of the
schemas more-or-less ready for this (to the group: I'm thinking of the
GO and DAS schemas).  If you're interested in getting started right
away, you can do some background reading at the following URLs:

	  www.geneontology.org
	  www.biodas.org
	  www.biomoby.org

Read a bit and then we'll discuss a specific role for you in the
project.

Best,

Lincoln

Tim Burns writes:
 > Hi,
 > I've done some work with SOAP and am interested in doing 
 > some work for your project.  I've been programming for 
 > about 5 years and did mathematics before that.  I work for 
 > Pharmacia in the genomics group so this would help me a lot 
 > with work that we intend to do.
 > Best regards,
 > Tim
 > 

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
ls...@cs...			                  Cold Spring Harbor, NY
Positions available at my lab: see http://stein.cshl.org/#hire
========================================================================

[GMOD-devel] bop

[Suzanna L. <su...@bd...>]

now installed in cvs repository.

still work to do (as usual), particular a good test/example

-S

Re: [GMOD-devel] New home page, generic genome browser, labdoc online

[Chris M. <cj...@fr...>]

On Thu, 3 Jan 2002, Lincoln Stein wrote:

> Hi Everyone,
> 
> I've revamped the GMOD home page completely.  It's reasonably useful
> now and gives people a better sense of what's going on.  (Of course, I
> would love it if someone who has some artistic talent could take a
> look at it and suggest improvements.)
> 
> Meanwhile, I've added the following projects to the release list:
> 
>    Generic Genome Browser -- now a separate project, complete with
> 			  documentation and test data
> 
>    LabDoc -- the system we use at WormBase/CSHL for managing our SOPs
> 
> I would suggest linking to the GMOD home page from your respective
> MODs.
> 
> Any other packages that we can make available at this point?
> 
> Best,
> 
> Lincoln
> 
> PS: Chris, if you could add a section about Dag-Edit to the home page,
> that would be great!

Done. Apollo and BOP coming soon...
 
> 
> -- 
> ========================================================================
> Lincoln D. Stein                           Cold Spring Harbor Laboratory
> ls...@cs...			                  Cold Spring Harbor, NY
> Positions available at my lab: see http://stein.cshl.org/#hire
> ========================================================================
> 
> _______________________________________________
> Gmod-devel mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-devel
> 

Re: [GMOD-devel] New home page, generic genome browser, labdoc online

[Allen D. <all...@1-...>]

Hey, this is site is looking a lot better.  I think labdoc needs to move
to its own package though, instead of being released under the gmod
package.  Will someone create it or give me permission to do so please?

-Allen

On Thu, 3 Jan 2002, Lincoln Stein wrote:

> Hi Everyone,
>
> I've revamped the GMOD home page completely.  It's reasonably useful
> now and gives people a better sense of what's going on.  (Of course, I
> would love it if someone who has some artistic talent could take a
> look at it and suggest improvements.)
>
> Meanwhile, I've added the following projects to the release list:
>
>    Generic Genome Browser -- now a separate project, complete with
> 			  documentation and test data
>
>    LabDoc -- the system we use at WormBase/CSHL for managing our SOPs
>
> I would suggest linking to the GMOD home page from your respective
> MODs.
>
> Any other packages that we can make available at this point?
>
> Best,
>
> Lincoln
>
> PS: Chris, if you could add a section about Dag-Edit to the home page,
> that would be great!
>
>
>

[GMOD-devel] New home page, generic genome browser, labdoc online

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

Hi Everyone,

I've revamped the GMOD home page completely.  It's reasonably useful
now and gives people a better sense of what's going on.  (Of course, I
would love it if someone who has some artistic talent could take a
look at it and suggest improvements.)

Meanwhile, I've added the following projects to the release list:

   Generic Genome Browser -- now a separate project, complete with
			  documentation and test data

   LabDoc -- the system we use at WormBase/CSHL for managing our SOPs

I would suggest linking to the GMOD home page from your respective
MODs.

Any other packages that we can make available at this point?

Best,

Lincoln

PS: Chris, if you could add a section about Dag-Edit to the home page,
that would be great!


-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
ls...@cs...			                  Cold Spring Harbor, NY
Positions available at my lab: see http://stein.cshl.org/#hire
========================================================================