gusdev-gusdev — Topics concerning GUS development

Re: [GUSDEV] 5/27 GUS 3.5 Development Status

[Jian Lu <jl...@vb...>]

The report I sent out returned to me. It seems like mail.sourceforge.net 
blocks the mail with .zip extension. So I change the file extension to 
cheat the mail server. When you receive the file, change the file 
extension to zip.

The attached is the comparison report of GUS 3.0 and 3.5 schema. It is 
based on our project GUS schema at VBI. It could be different from yours 
depending on your GUS version. Use it as a reference.

Michael Saffitz wrote:

>GUS 3.5 Development Status
>
>This is an updated 3.5 status report.  Also, please look for the
>announcement of the GUS Workshop, scheduled for July 6-8 in Philadelphia.
>As always, please let me know if you have any questions or concerns.
>
>Important!  While components of GUS 3.5 are finalized and the overall system
>is nearing release, it is NOT YET READY for use and attempting to do so in a
>production environment, or even in a test environment in which GUS 3.0
>exists MAY RESULT IN DATA LOSS.  You have been warned!  Do NOT use the GUS
>3.5 cvs branches for any other purpose than GUS 3.5 development, and only
>after having read and fully understanding the relevant documentation.
>
>* Schema
>
>Completed and frozen for release.
>
>* Plugins
>
>Work is underway to update the supported plugins for GUS 3.5.  Roughly a
>quarter are complete and tested.  Roughly another quarter are nearly
>complete but not yet fully tested.  It's my hope that all plugins will be
>completed close to 6/3.
>
>* Application Framework
>
>The Application framework is now functioning properly with PostgreSQL.
>There have been other small changes to remove obsolete code and fix small
>bugs.
>
>The Java object model will need some review to address persistent compile
>issues and a continued reliance on RAD3 (instead of RAD).
>
>* Administrative Functions & Installing
>
>There was a large bug that created incorrect views.  This has been changed.
>Also, the PostgreSQL installer has been rewritten and now properly creates
>views and rules for updating views.
>
>The bootstrap data still awaits addressing.
>
>* Documentation
>
>Documentation work is underway.  Ed Robinson's plugin guide is being
>incorporated into the GUS Developers guide, and I've been working on
>combining the existing installation guides into a single guide that's been
>updated for 3.5.
>
>* Upgrading
>
>As mentioned, this will occur last.  Jian Lu from VBI has produced a HTML
>file outlining the differences between 3.0 and 3.5.  It's quite large (3.5
>MB), but hopefully he'll post it or compress it and send it to the list.
>
>
>
>
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[GUSDEV] 5/27 GUS 3.5 Development Status

[Michael S. <msa...@pc...>]

GUS 3.5 Development Status

This is an updated 3.5 status report.  Also, please look for the
announcement of the GUS Workshop, scheduled for July 6-8 in Philadelphia.
As always, please let me know if you have any questions or concerns.

Important!=A0 While components of GUS 3.5 are finalized and the overall syste=
m
is nearing release, it is NOT YET READY=A0for use and attempting to do so in =
a
production environment, or even in a test environment in which GUS 3.0
exists MAY RESULT IN DATA LOSS.=A0 You have been warned!=A0 Do NOT=A0use the GUS
3.5 cvs branches for any other purpose than GUS 3.5 development, and only
after having read and fully understanding the relevant documentation.

* Schema

Completed and frozen for release.

* Plugins

Work is underway to update the supported plugins for GUS 3.5.  Roughly a
quarter are complete and tested.  Roughly another quarter are nearly
complete but not yet fully tested.  It's my hope that all plugins will be
completed close to 6/3.

* Application Framework

The Application framework is now functioning properly with PostgreSQL.
There have been other small changes to remove obsolete code and fix small
bugs.

The Java object model will need some review to address persistent compile
issues and a continued reliance on RAD3 (instead of RAD).

* Administrative Functions & Installing

There was a large bug that created incorrect views.  This has been changed.
Also, the PostgreSQL installer has been rewritten and now properly creates
views and rules for updating views.

The bootstrap data still awaits addressing.

* Documentation

Documentation work is underway.  Ed Robinson's plugin guide is being
incorporated into the GUS Developers guide, and I've been working on
combining the existing installation guides into a single guide that's been
updated for 3.5.

* Upgrading

As mentioned, this will occur last.  Jian Lu from VBI has produced a HTML
file outlining the differences between 3.0 and 3.5.  It's quite large (3.5
MB), but hopefully he'll post it or compress it and send it to the list.

[GUSDEV] Announcement: GUS Workshop

[Michael S. <msa...@pc...>]

We're very excited to announce preliminary details and call for
presentations for the GUS Workshop.   The workshop will be held July 6-8, at
the Computational Biology Informatics Laboratory (CBIL) at the University of
Pennsylvania in Philadelphia.

The goal of the workshop is to bring together GUS users and developers in a
setting where users can learn and address issues, and developers can receive
feedback from users and plan for future releases of GUS.  There will be an
emphasis on getting real work done-- installing GUS, running plugins,
upgrading to 3.5 (which will be released by then).

If you're interested in speaking at the Workshop, please send a brief
overview of your talk to gus...@pc... by June 3rd.

Also, we're trying to get an early head count for planning.  If you're
thinking about attending, please email gus...@pc....

More details, including an agenda, registration details, etc., etc. will be
available in the next couple of weeks.  In the meantime, if you have any
questions, please email gus...@pc....

Thanks,

The GUS Team

[GUSDEV] BLAST Feature Similarity data

[Amruta J. <am...@st...>]

Hi,

I need plug-ins to load and dump BLAST Feature Similarity data to/from GUS.
Does the current distribution of GUS have these ? (I couldn't find any)
Please can someone make these avaiable.

thanks,

Regards,
Amruta
---
Research Assistant,
Relman Lab,
Stanford University,
CA - 94305.

Re: [GUSDEV] GUS BOSC meeting?

[<ju...@cs...>]

Michael Saffitz <msa...@pc...> writes:
>
> There wasn't sufficient interest to justify a GUS meeting at BOSC.  We're
> working an alternative that would allow GUS developers and users to come
> together in early July for a few days of intense workshops, presentations,
> and coding jamborees.  We hope to have more details in the coming days and
> weeks.

Please keep me informed. I would very much like to present as well as
attend.

Josef


Josef Jurek, Ph.D.

Daphne Preuss Laboratory
Molecular Genetics and Cell Biology
The University of Chicago
ju...@cs...

voice: (773) 834-3985
fax:   (773) 702-6648

Re: [GUSDEV] Documentation Site

[Michael S. <msa...@pc...>]

Hi Ed,

This is great-- thanks.

I'd like to get as much of this as possible into GUS 3.5 as the "official"
documentation.  GUS 3.5 documentation will be in the ubiquitous docbook
format, which is XML based and allows for effort-less transformations into
XML, PDF, HTML, and other formats.  The documentation will be maintained in
CVS as a GUS Component.

Ed-- Would you be willing to convert your Developer's Guide (as a start)
into a docbook chapter (on Plugin Development) for the GUS Developer's
Guide?  If you don't have the time or interest, I'd be happy to do the
conversion, but in that case I'd want to make sure that any future changes
to your document are incorporated into the GUS versions as well.

Also, please keep in mind for the bootstrapping documents-- this process
will be changing in 3.5, which is due in the next few weeks.  Thus, it may
make more sense for us to speak to come to a consensus on what data needs to
be loaded, and the best way to load it as part of the initial install
process before you spend too much documenting processes that may change.

Thanks again for all this work-- I think it really contributes to the
accessibility and understanding of GUS and (provided you're ok with it) is a
great contribution to the project.

--Mike

On 5/23/05 1:14 PM, "Ed Robinson" <ero...@ug...> wrote:

> Jessie Kissinger asked me to make my better, internal, lab
> documentation for gus avaiable for a number of new people on
> this list.  We now have a location on our lab website where
> this material can be accessed:
> 
> http://mango.ctegd.uga.edu/jkissingLab/gus_docs/
> 
> 
> Please note, everything on this site is a work in progress!
> This is especially true of the plugins!!!
> 
> One item more experienced GUS users might be interested in is
> a rough draft of a developers guide to GUS which is being
> discussed here and at CBIL.  If any of the more experienced
> GUS developers on this list would like to add their comments
> to this document, please send them to me so I can add them to
> the working draft.  We would very much appreciate your input!
> 
> Also, one item which Jessie wants me to document
> for the new folks is the GUS bootstrapping process and
> plugin dependencies contingent upon this bootstrapping.
> I do not yet have such a document.  However,
> I will write one now that she has asked for
> it.  In the meantime, I will be placing a modified
> version of the LoadPFam.pm plugin and the documentation
> for this plugin on this site.  This plugin should
> make the importance of these contingencies apparent to new
> users.
> 
> Please check on this site regularly.  There will be multiple
> updates each day over the next couple of weeks.
> 
> 
> -Ed
> -----------------
> Ed Robinson
> Center for Tropical and Emerging Global Diseases
> University of Georgia, Athens, GA 30602
> ero...@ug.../(706)542.1447/254.8883
> 
> 
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Re: [GUSDEV] GUS BOSC meeting?

[Michael S. <msa...@pc...>]

Hi Josef,

There wasn't sufficient interest to justify a GUS meeting at BOSC.  We're
working an alternative that would allow GUS developers and users to come
together in early July for a few days of intense workshops, presentations,
and coding jamborees.  We hope to have more details in the coming days and
weeks.

Thanks,

Mike

On 5/23/05 11:46 AM, "ju...@cs..." <ju...@cs...> wrote:

> Is the GUS meeting still on during the BOSC 2005 in Detroit?
> I would very much like to attend such a meeting.
> 
> Thank,
> 
> 
> Josef Jurek, Ph.D.
> 
> Daphne Preuss Laboratory
> Molecular Genetics and Cell Biology
> The University of Chicago
> ju...@cs...
> 
> voice: (773) 834-3985
> fax:   (773) 702-6648
> 
> 
> 
> 
> 
> 
> 
> -------------------------------------------------------
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> Want to be the first software developer in space?
> Enter now for the Oracle Space Sweepstakes!
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> _______________________________________________
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> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

[GUSDEV] Documentation Site

[Ed R. <ero...@ug...>]

Jessie Kissinger asked me to make my better, internal, lab
documentation for gus avaiable for a number of new people on 
this list.  We now have a location on our lab website where 
this material can be accessed:

http://mango.ctegd.uga.edu/jkissingLab/gus_docs/


Please note, everything on this site is a work in progress! 
This is especially true of the plugins!!!

One item more experienced GUS users might be interested in is
a rough draft of a developers guide to GUS which is being
discussed here and at CBIL.  If any of the more experienced
GUS developers on this list would like to add their comments
to this document, please send them to me so I can add them to
the working draft.  We would very much appreciate your input!

Also, one item which Jessie wants me to document
for the new folks is the GUS bootstrapping process and 
plugin dependencies contingent upon this bootstrapping.  
I do not yet have such a document.  However, 
I will write one now that she has asked for 
it.  In the meantime, I will be placing a modified 
version of the LoadPFam.pm plugin and the documentation 
for this plugin on this site.  This plugin should
make the importance of these contingencies apparent to new
users.

Please check on this site regularly.  There will be multiple
updates each day over the next couple of weeks.


-Ed
-----------------
Ed Robinson
Center for Tropical and Emerging Global Diseases
University of Georgia, Athens, GA 30602
ero...@ug.../(706)542.1447/254.8883

Re: [GUSDEV] blastSimilarity

[<ju...@cs...>]

I wrote:
>
> From where does one obtain the utility 'blastSimilarity'?
>

I ask because Steve Fisher's recent mail indicates that
this utility is useful in conjunction with LoadBlastSimFast:

     From: Steve Fischer <sfi...@pc...>
     Date: Fri, 11 Feb 2005 08:56:26 -0500
     Message-ID: <420...@pc...>
     To: Poliana Mateus <pol...@gm...>
     Subject: Re: [Gusdev-gusdev] parseBlastFilesForSimilarity.pl
     Cc: gus...@li...

     poliana-

     oops, the usage statement for LoadBlastSimFast is out of date.   it
     should instruct you to use the blastSimilarity command.

     LoadBlastSimFast makes a big assumption, that the subject and query
     sequences are in GUS, and their def. lines have GUS primary keys.

     Are your sequences already loaded into GUS?

     steve

and a Google search on 'blastSimilarity' yields almost nothing.

In addition, or possibly instead of, could someone share with me
a sample input file for LoadBlastSimFast?

Thank you for your help.






Josef Jurek, Ph.D.

Daphne Preuss Laboratory
Molecular Genetics and Cell Biology
The University of Chicago
ju...@cs...

voice: (773) 834-3985
fax:   (773) 702-6648

[GUSDEV] GUS BOSC meeting?

[<ju...@cs...>]

Is the GUS meeting still on during the BOSC 2005 in Detroit?
I would very much like to attend such a meeting.

Thank,


Josef Jurek, Ph.D.

Daphne Preuss Laboratory
Molecular Genetics and Cell Biology
The University of Chicago
ju...@cs...

voice: (773) 834-3985
fax:   (773) 702-6648

Re: [GUSDEV] Preliminary 3.5 Schema

[Jian Lu <jl...@vb...>]

Hi Mike,

Here are what I found from different documents which show difference.

  	Gus 3.5 Road Map 	schemaBrowser35 (online) 	gus_35 (distributed 
schema file)
table name 	  	DoTS::AASequenceImp 	DoTS.AASequence 
  	  	DoTS::AAFeatureImp 	DoTS.AAFeature
  	  	DoTS::NASequenceImp 	DoTS.NASequence 
  	  	DoTS::NAFeatureImp 	DoTS.NAFeature
  	  	  	 
column 	SRes.ExternalDatabase remove lowercase_name column 
lowercase_name column exists 	lowercase_name column is gone


Also, for DoTS::AASequenceImp and DoTS::NASequenceImp, the online 
schemaBrowser35 doesn't display for details of columns.

Thanks,

Jian

Michael Saffitz wrote:

>
> All,
>
> The latest proposed GUS 3.5 schema is attached.  This draft has 
> numerous changes since the previous release, including the addition of 
> a few dozen missing views, the changes outlined below, and other cleanup.
>
> This draft has a small error in which the first subclass for a 
> particular superclass appears twice.  I'm trying to track down and 
> resolve that, but it appears to only affect this simple text reports, 
> not the actual DDL. Schemas and tables are in alphabetical order, but 
> capitalization is wreaking a little bit of havok on that.  I hope to 
> fix that in a future draft as well.
>
> There are some additional PROT changes that this draft does not 
> include.  I will send another draft Wednesday with those changes.
>
> Please submit comments/changes/etc. as soon as possible.  The 3.5 
> schema is scheduled to be frozen at the end of this week and all 
> resources will turn at that time to preparing the application level 
> code for release.
>
> Thanks,
>
> Mike
>
> DoTS:
>
> * Drop DoTS.PlasmoAPFeature view
>
> * Drop DoTS.MassSpecSummary
>
> * DoTS.GeneFeatureSeqOverlap.SIMILARITY_ID will have a foreign key 
> constraint to DoTS.SIMILARITY
>
> * DoTS.NASequenceImp.SOURCE_NA_SEQUENCE_ID will have a foreign key 
> constraint to DoTS.NASequenceImp
>
> * DoTS.SecondaryStructure.AA_SEQUENCE_ID will have a foreign key 
> constraint to DoTS.AASequenceImp.  
> DoTS.SecondaryStructure.PRED_ALG_INVOCATION_ID will have a foreign key 
> constraint to Core.AlgorithmInvocation.
>
> * DoTS.SecondaryStructureCall.Secondary_Structure_ID will have a 
> foreign key constraint to DoTS.SecondaryStructure
>
> * DoTS.AASequenceEnzymeClass.AA_Sequence_ID will have a foreign key 
> constraint to DoTS.AASequenceImp, and 
> DoTS.AASequenceEnzymeClass.EC_ASSIGNMENT_CONTACT_ID will have a 
> foreign key constraint to SRES.CONTACT
>
> * DoTS.ConsistentAlignment.SIMILARITY_ID will have a foreign key 
> constraint to DoTS.Similarity
>
> * DoTS.RejectedMotif.External_Database_Id will have a foreign key 
> constraint to SRes.ExternalDatabase. 
> DoTS.RejectedMotif.External_Database_release_id will have a foreign 
> key constraint to SRes.ExternalDatabaseRelease
>
> * DoTS.Similarity.Subject_Table_ID and DoTS.Similarity.Query_Table_id 
> will have foreign key constraints to core.tableinfo
>
> * DoTS.PlasmoMap has been renamed to DoTS.MicroSatelliteMap
>
> Prot:
>
> * Prot.OntologyEntry has been removed
>
> * Prot.StudyAssay has been added.
>
> * Prot.StudyDesignAssay has been added
>
> * Prot.StudyBioMaterial has been added
>
> * Prot.AcquisitionChannel has been added
>
> SRes:
>
> * SRes.ExternalDatabaseKeyword has been moved to DoTS
>
> RAD:
>
> * RAD.ScanAlyzeElementResult.top,left,bot,right have had _coordinate 
> appended to them
>
> * The RAD.DataTransformationResult has been added as a view on 
> RAD.AnalysisResultImp
>
> * RAD.ReporterArray has been renamed to RAD.ArrayDesign.  This impacts 
> the following changes:
>  - RAD.ArrayAnnotation -> RAD.ArrayDesignAnnotation
>  - RAD.ArrayGroup -> RAD.ArrayDesignGroup
>  - RAD.ArrayGroupLink -> RAD.ArrayDesignGroupLink
>  - and associated column changes
>
> * RAD.CompositeElementGus has been dropped
>
> * RAD.MageDocumentation and RAD.Mage_ML have been dropped.
>
> * RAD.Channel has been removed
>
> Study:
>
> * Study.Ontology* tables have been dropped.  This includes ontology, 
> ontologyannotation, ontologyrelationship, ontologyterm, ontologytype.  
> This DOES NOT include study.ontologyentry.
>
> * Study.BioSample, Study.BioSource, and Study.LabeledExtract have been 
> added as views on Study.BioMaterial
>
> * Moved Study.BioMaterialMeasurement to Prot and a copy to RAD.
>
> * Study.Parameter* tables have been moved to prot.  This includes 
> parameter, parameterinstance, parameterizable, 
> parameterizableinstance, and paramterizablelink
>
> --On April 21, 2005 3:20:15 PM -0400 Michael Saffitz 
> <msa...@pc...> wrote:
>
>>
>> Since releasing the preliminary 3.5 schema, the following changes have
>> been proposed.  The list below only covers App, SRes, and Core-- other
>> schema changes will come early next week.
>>
>> The scheduled freeze date for the 3.5 schema is 4/29.  If there are no
>> objections to the items below, Core and App will be frozen for 3.5 on
>> 4/25 (more SRes changes may be coming early next week).
>>
>> Consult the road map for full changes.  The list below are just new
>> changes since sending this previous email.  They'll be added to the road
>> map after feedback from the list is received.
>>
>> App:
>>
>> * The App schema has been deprecated.  The remaining few tables that 
>> were
>> in app will be moved to non-GUS project specific schema (i.e. a Study
>> Annotator schema).
>>
>> Core:
>>
>> * The workflow tables have been deprecated as they were never actually
>> used.  This includes core.workflowstatus, core.workflowedge,
>> core.workflowinit, core.workflowedgesql, core.workflow,
>> core.workflowblackboard, and core.workflowstatus
>>
>> * core.generaldocumentation is tentatively deprecated, pending the lack
>> of objections from this list.
>>
>> * core.userdatabase is tenetively deprecated, pending the lack of
>> objections from this list.
>>
>> SRes (tentative, pending more review)
>>
>> * SRes.SequenceOntology.SO_ID will be a VARCHAR(12), not a NUMBER(10)
>>
>> * SRes.MGEDOntologyRelationship will be named SRes.OntologyRelationship
>>
>> * SRes.MGEDOntologyTerm will be named SRes.OntologyTerm
>>
>> * SRes.BibliographicReference.authors will be nullable, to support the
>> alternative BibRefAuthor linking table.
>> SRes.BibliographicReference.External_Database_Release_ID will gain 
>> the FK
>> the ExternalDatabaseRelease table
>>
>> * SRes.BibRefAnnotation is tentatively deprecated, pending the lack of
>> objections from this list.
>>
>> Thanks,
>>
>> Mike
>>
>>
>> --On April 7, 2005 1:53:44 PM -0400 Michael Saffitz
>> <msa...@pc...> wrote:
>>
>>>
>>> All,
>>>
>>> Development work on the GUS 3.5 Schema is nearing completion, and we'd
>>> like to take this opportunity to solicit community feedback and provide
>>> the 3.5 schema for review.
>>>
>>> With the 3.5 Schema nearly finalized, we're now turning our 
>>> attention to
>>> ensuring compatibility in the object layer and with plugins for 3.5. 
>>> Once
>>> done, GUS 3.5 will be ready for release.  It's my hope that that 
>>> will be
>>> as soon as possible, but I'm hesitant to give a firm date.
>>>
>>> The attached file contains the 3.5 schema, in a simple text summary
>>> format.  When reviewing the file, please keep the following in mind:
>>>
>>> * I've done a very preliminary analysis of the file--- there may be
>>> glaring mistakes/omissions.
>>>
>>> * All tables and views in GUS 3.5 are versioned, and the version
>>> tables/views are not displayed.
>>>
>>> * All tables and views in GUS 3.5 contain the standard housekeeping
>>> columns, which are also not displayed.
>>>
>>> * Subclass tables (marked by "extends superclass" where superclass 
>>> is the
>>> name of the parent table) only have the columns added by the subclass
>>> displayed.  For example, if the superclass has columns a, b, c, and d,
>>> then the subclass will display the column e but have all five 
>>> columns in
>>> the database.
>>>
>>> * This is an object-centric display-- the method of subclassing 
>>> (i.e. use
>>> of imp tables) is not changing.  As a result, Imp tables are not
>>> displayed, nor are super/sub classes flagged as views.
>>>
>>> * The Type of a column with a foreign key is the name of the foreign 
>>> key
>>> table.  For example, a table with a column NA_FEATURE_ID with a foreign
>>> key to DoTS.NAFEATURE will have a type of DoTSS.NAFEATURE.  This is the
>>> only way foreign keys are displayed in this view.
>>>
>>> * All tables first column serves as the Primary key.  There is no
>>> denotation for the primary key (although it will also appear as an 
>>> index
>>> against the first column).  Some tables are missing primary keys in 
>>> this
>>> document-- it will be fixed soon.
>>>
>>> * All indexes for a table are displayed.
>>>
>>> Please let me know if you have any questions/concerns.
>>>
>>> Thanks,
>>>
>>> Mike
>>
>>
>>
>>
>>
>>
>>
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>
>
>
>

[GUSDEV] blastSimilarity

[<ju...@cs...>]

From where does one obtain the utility 'blastSimilarity'?

Thank you for your help;  Josef



Josef Jurek, Ph.D.

Daphne Preuss Laboratory
Molecular Genetics and Cell Biology
The University of Chicago
ju...@cs...

voice: (773) 834-3985
fax:   (773) 702-6648

Re: [GUSDEV] GUS 3.5 Development Status

[Jian Lu <jl...@vb...>]

Junmin,

Could you point to me where to get GUS3.5 installation package? I would 
like to install GUS 3.5 schema for evaluation.
Thanks,
Jian

Junmin Liu wrote:

> Hi, there,
> Just want to share my experiences of install GUS 35 when I followed 
> the attached guide.
>
> The build system will automatically generate the $GUS_CONFIG_FILE by 
> setting up the $PROJECT_HOME/install/gus.config, but it will NOT 
> replaced it when it exists.
>
> BTW, GUS_CONFIG_FILE=/home/YOUR_USERNAME/gus35/gus.properties
>
> When I first build GUS 35, I wrongly set up the
> dbiDsn=dbi:Oracle:host=cbildb;sid=plugindev;port=1521
> in my gus.config.
>
> did a build which automatically generates the $GUS_CONFIG_FILE, got 
> the error complaining about the "plugindev" not exist.
>
> then reset it in gus.confgi to
> dbiDsn=dbi:Oracle:host=cbildb;sid=plugdev;port=1521
>
> But the build didn't rewrite the old $GUS_CONFIG_FILE which still had 
> the wrong dbiDsn, so the build fails since the build depends on the 
> $GUS_CONFIG_FILE, and even worse, it just fails without printing out 
> any error logs.
>
> So you have to check the $GUS_CONFIG_FILE to see if everything is set 
> right there.
> --junmin
>
>
> -------------------------------------------------------
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Re: [GUSDEV] GUS 3.5 Development Status

[Junmin L. <ju...@pc...>]

Hi, there,
Just want to share my experiences of install GUS 35 when I followed the 
attached guide.

The build system will automatically generate the $GUS_CONFIG_FILE by 
setting up the $PROJECT_HOME/install/gus.config, but it will NOT replaced 
it when it exists.

BTW, GUS_CONFIG_FILE=/home/YOUR_USERNAME/gus35/gus.properties

When I first build GUS 35, I wrongly set up the
dbiDsn=dbi:Oracle:host=cbildb;sid=plugindev;port=1521
in my gus.config.

did a build which automatically generates the $GUS_CONFIG_FILE, got the 
error complaining about the "plugindev" not exist.

then reset it in gus.confgi to
dbiDsn=dbi:Oracle:host=cbildb;sid=plugdev;port=1521

But the build didn't rewrite the old $GUS_CONFIG_FILE which still had the 
wrong dbiDsn, so the build fails since the build depends on the 
$GUS_CONFIG_FILE, and even worse, it just fails without printing out any 
error logs.

So you have to check the $GUS_CONFIG_FILE to see if everything is set 
right there.
--junmin

[GUSDEV] GUS 3.5 Development Status

[Michael S. <msa...@pc...>]

GUS 3.5 Development Status

Since recently freezing the schema, there's been a lot of work =20
getting all of the pieces in place for the GUS 3.5 release.  This =20
email is an effort to summarize the progress and coordinate efforts =20
for those that are interested in assisting.  I've outlined the major =20
components of GUS and/or focus areas for 3.5 below, and tried to =20
provide as much detail as possible about what's planned for GUS 3.5 =20
and the current status.

Important!  While components of GUS 3.5 are finalized and the overall =20=

system is nearing release, it is NOT YET READY for use and attempting =20=

to do so in a production environment, or even in a test environment =20
in which GUS 3.0 exists MAY RESULT IN DATA LOSS.  You have been =20
warned!  Do NOT use the GUS 3.5 cvs branches for any other purpose =20
than GUS 3.5 development, and only after having read and fully =20
understanding the relevant documentation.

* Schema

As mentioned above, the schema for GUS 3.5 has been frozen, and no =20
new changes are being permitted.  There are already several issues =20
identified and changes that have been suggested, however.  As a =20
result, we expect to have a GUS 3.5.1 release very shortly after the =20
GUS 3.5 release that will incorporate these items.  All items for =20
3.5.1 should be entered in the tracker as an issue against 3.5.

* Plugins

With the Schema frozen, the primary focus of development has been =20
updating the plugins to ensure compatibility with schema changes and =20
to make necessary changes to the APIs (see below).  If you're =20
interested in assisting with this progress, please see the attached =20
guide.

* Application Framework

GUS 3.5 has no additional functionality planned for the application =20
framework.  The only changes being made are the introduction of =20
PostgreSQL compatibility, and fixes to address issues in the existing =20=

functionality or necessitated by changes in the schema.  One such =20
instance is the move to a GUS-wide versioning system, used by the =20
plugins to ensure compatibility.  In GUS 3.0, plugins could =20
optionally specify the required versions of specific schemas (i.e. =20
DoTS version 2.0, RAD version 3).  GUS 3.5 requires plugins to =20
specify the required version of GUS (i.e. 3.5) against which to run.

* Administrative Functions & Installing

GUS 3.5 contains a whole new administrative system, used mostly at =20
this point for installing the schema and tracking changes.  This =20
system is mostly complete: the components that generate and install =20
the PostgreSQL schema require some additional work to properly deal =20
with subclassing.

In addition to the administrative installer, there is some work still =20=

to be done in identifying and managing the installation of bootstrap =20
data into new GUS instances.

* Documentation

GUS 3.5 will contain consolidated and greatly improved =20
documentation.  The official documentation for GUS will be in the =20
ubiquitous docbook XML format, exported for end-user use as both HTML =20=

and PDF, and available for conversion into alternative formats.  The =20
intent is to provide several "books": a Getting Started Guide,  a =20
Users Guide, and a Developers Guide.

Please email me if you're interested in writing one or more chapters =20
for these books.  If you've previously provided documentation, =20
chances are I'll be contacting you in the near future to recruit you =20
to write documentation.

* Upgrading

The last focus area for GUS 3.5 I want to mention are upgrade scripts =20=

and instructions for moving from GUS 3.0 to 3.5.  Due to the =20
unstructured nature of the previous releases of GUS, these scripts =20
will provide general instructions for upgrading (and upgrade =20
validation mechanisms through the new administrative system)-- user =20
intervention, thought, and guidance will be required.  Some upgrade =20
scripts have already been created, however, the bulk of this work is =20
being delayed until all other GUS 3.5 components have been finalized.


=EF=BF=BC=

[GUSDEV] Update to LoadPfam.pm LoadEnzymDatabase.pm, LoadNRDB.pm

[Ed R. <ero...@ug...>]

For the ApiDB project, we need to make a number of
modifications to some of the plugins that require divisions in
the ExternalDatabase and ExternalDatabaseRelease tables.  All
of the changes we are making to these plugins are backwards
compatable and require boolean flags to implement our needs. 
With the change to the 3.5 schema coming up, we run the risk
of making the ApiDB project a permanent fork off of the main
GUS development path.  In order to avoid this, can whomever is
presently responsible for these plugins please let me know so
I can send you our changes so they can get into the main GUS
CVS?  These changes will not affect the existing functionality
of these plugins, but they are show-stoppers for us.

Thanks in advance,
-Ed

-----------------
Ed Robinson
Center for Tropical and Emerging Global Diseases
University of Georgia, Athens, GA 30602
ero...@ug.../(706)542.1447/254.8883

Re: [GUSDEV] GUS 3.5 Schema -- Final

[Junmin L. <ju...@pc...>]

Actually I can answer my own question.
https://www.cbil.upenn.edu/tracker/buglist.cgi?regetlastlist=1

--junmin


On Mon, 9 May 2005, Junmin Liu wrote:

> Does anyone out there know where is the GUS tracker mentioned in Mike's 
> email? I think Mike is on vacation now.
> I need to make some changes to the GUS3.5 schema and want to know where I put 
> them?
> --junmin
>
>
> On Tue, 3 May 2005, Michael Saffitz wrote:
>
>> 
>> 
>> All,
>> 
>> The final schema for GUS 3.5 is attached.  Any changes at this point should 
>> be entered in the GUS Tracker for inclusion in a future release of GUS.
>> 
>> Work is now underway in readying plugins and the application framework for 
>> GUS 3.5, as well as documentation development.  Please let me know if you 
>> have any questions or would like to help out in any way.
>> 
>> Thanks,
>> 
>> Mike
>> 
>> 
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: NEC IT Guy Games.
> Get your fingers limbered up and give it your best shot. 4 great events, 4
> opportunities to win big! Highest score wins.NEC IT Guy Games. Play to
> win an NEC 61 plasma display. Visit http://www.necitguy.com/?r=20
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

Re: [GUSDEV] GUS 3.5 Schema -- Final

[Junmin L. <ju...@pc...>]

Does anyone out there know where is the GUS tracker mentioned in Mike's 
email? I think Mike is on vacation now.
I need to make some changes to the GUS3.5 schema and want to know where I 
put them?
--junmin


On Tue, 3 May 2005, Michael Saffitz wrote:

>
>
> All,
>
> The final schema for GUS 3.5 is attached.  Any changes at this point should 
> be entered in the GUS Tracker for inclusion in a future release of GUS.
>
> Work is now underway in readying plugins and the application framework for 
> GUS 3.5, as well as documentation development.  Please let me know if you 
> have any questions or would like to help out in any way.
>
> Thanks,
>
> Mike
>
>

Re: [GUSDEV] Another GBParser error :-/

[Thomas O. <ot...@fi...>]

Hi,

I think that you inserted twice the taxonomie... so it gives back two 
result. You will have to delete one... take the modification_date in the 
where select.

Cheers,
Thomas
fab...@de... wrote:

>Hello all,
>
>our GBParser initial error was solved (Thanks Jeetendra, Thomas and Pablo)...
>now we have another one. Running the plugin "ga GUS::Common::Plugin::GBParser
>--file=sequences.gb --gbRel=145.0 --db_rel_id=62" we're getting the following
>messages:
>
>...
>RUN     1037631..1047290
>RUN     1047319..1050482
>RUN     1052519..1054589
>RUN     1059492..1060087
>VLD     CBIL::Bio::GenBank::Features    1
>VLD     CBIL::Bio::GenBank::Origin      1
>Fri May  6 14:38:56 2005        STATUS  N=1 ACC=NC_000521       
>TOTAL_OBJECTS=17
>
>ERROR TaxonName: retrieveFromDB: select * from SRes.TaxonName where  name_class
>= ? and  name = ?       2 rows returned!
>
>ERROR TaxonName: retrieveFromDB: select * from SRes.TaxonName where  name_class
>= ? and  name = ?       2 rows returned!
>Fri May  6 14:39:40 2005        INVALID QUALIFIER       GUS::Model::DoTS::Source
>       ::      mol_type        ::      genomic DNA
>
>DBD::Pg::st execute failed: ERROR:  duplicate key violates unique constraint
>"pk_externaldatabase" at
>/usr/local/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147, <GEN0>
>line 26148.
>Fri May  6 14:39:41 2005        Genbank entries inserted= 0;  updated= 0; total
>#(inserted::updated::deleted)=19::::
>
>Fri May  6 14:39:41 2005        FAILURES        Unable to process 2 entries. See
>gbparserFailures/
>Fri May  6 14:39:41 2005        RESULT  Genbank entries inserted= 0;  updated=
>0;  failed= 2
>
>
>
>
>
>Our gbparserFailures/errors file has:
>
>SQL ERROR!! involving
>
>    INSERT INTO SRes.ExternalDatabase (  group_write, other_read, group_read,
>lowercase_name, name, user_read, row_user_id, external_database_id,
>modification_date, other_write, row_alg_invocation_id, row_project_id,
>row_group_id, user_write )
>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?, ?, ? )
> Values: 1, 1, 1, geneid, GeneID, 1, 1, 8, 0, 62, 1, 1, 1 at
>/usr/local/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 187
>       
>GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x8bd1cf0)','\x{a}
>SQL ERROR!! involving\x{a} \x{a}    INSERT INTOSRes.ExternalDataba...') called
>at /usr/local/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
>       
>GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x8bd1cf0)','GUS::ObjRelP::DbiDbHandle::st=HASH(0x94eed78)','ARRAY(0x94eedb4)','\x{a}
>   INSERT INTO SRes.ExternalDatabase (  group_write, other_...') called at
>/usr/local/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 689
>
>
>We're sure that our --db_rel_id=62 as shown here:
>
>gus=# select edbr.external_database_release_id 
>      from sres.externaldatabase edb, sres.externaldatabaserelease edbr
>      where edb.external_database_id = edbr.external_database_id
>      and edb.name = 'GenBank';
>
> external_database_release_id
>------------------------------
>                           62
>(1 row)
>
>
>Does anyone can help us to identify the trouble?
>
>Thanks a lot.
>
>
>----------------------------------------------------------------
>This message was sent using IMP, the Internet Messaging Program.
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by: NEC IT Guy Games.
>Get your fingers limbered up and give it your best shot. 4 great events, 4
>opportunities to win big! Highest score wins.NEC IT Guy Games. Play to
>win an NEC 61 plasma display. Visit http://www.necitguy.com/?r 
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>  
>

[GUSDEV] Another GBParser error :-/

[<fab...@de...>]

Hello all,

our GBParser initial error was solved (Thanks Jeetendra, Thomas and Pablo=
)...
now we have another one. Running the plugin "ga GUS::Common::Plugin::GBPa=
rser
--file=3Dsequences.gb --gbRel=3D145.0 --db_rel_id=3D62" we're getting the=
 following
messages:

...
RUN     1037631..1047290
RUN     1047319..1050482
RUN     1052519..1054589
RUN     1059492..1060087
VLD     CBIL::Bio::GenBank::Features    1
VLD     CBIL::Bio::GenBank::Origin      1
Fri May  6 14:38:56 2005        STATUS  N=3D1 ACC=3DNC_000521      =20
TOTAL_OBJECTS=3D17

ERROR TaxonName: retrieveFromDB: select * from SRes.TaxonName where  name=
_class
=3D ? and  name =3D ?       2 rows returned!

ERROR TaxonName: retrieveFromDB: select * from SRes.TaxonName where  name=
_class
=3D ? and  name =3D ?       2 rows returned!
Fri May  6 14:39:40 2005        INVALID QUALIFIER       GUS::Model::DoTS:=
:Source
       ::      mol_type        ::      genomic DNA

DBD::Pg::st execute failed: ERROR:  duplicate key violates unique constra=
int
"pk_externaldatabase" at
/usr/local/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147, <GE=
N0>
line 26148.
Fri May  6 14:39:41 2005        Genbank entries inserted=3D 0;  updated=3D=
 0; total
#(inserted::updated::deleted)=3D19::::

Fri May  6 14:39:41 2005        FAILURES        Unable to process 2 entri=
es. See
gbparserFailures/
Fri May  6 14:39:41 2005        RESULT  Genbank entries inserted=3D 0;  u=
pdated=3D
0;  failed=3D 2





Our gbparserFailures/errors file has:

SQL ERROR!! involving

    INSERT INTO SRes.ExternalDatabase (  group_write, other_read, group_r=
ead,
lowercase_name, name, user_read, row_user_id, external_database_id,
modification_date, other_write, row_alg_invocation_id, row_project_id,
row_group_id, user_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?, ?, ? )
 Values: 1, 1, 1, geneid, GeneID, 1, 1, 8, 0, 62, 1, 1, 1 at
/usr/local/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 187
      =20
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=3DHASH(0x8bd1=
cf0)','\x{a}
SQL ERROR!! involving\x{a} \x{a}    INSERT INTOSRes.ExternalDataba...') c=
alled
at /usr/local/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
      =20
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=3DHASH(0x8b=
d1cf0)','GUS::ObjRelP::DbiDbHandle::st=3DHASH(0x94eed78)','ARRAY(0x94eedb=
4)','\x{a}
   INSERT INTO SRes.ExternalDatabase (  group_write, other_...') called a=
t
/usr/local/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 689


We're sure that our --db_rel_id=3D62 as shown here:

gus=3D# select edbr.external_database_release_id=20
      from sres.externaldatabase edb, sres.externaldatabaserelease edbr
      where edb.external_database_id =3D edbr.external_database_id
      and edb.name =3D 'GenBank';

 external_database_release_id
------------------------------
                           62
(1 row)


Does anyone can help us to identify the trouble?

Thanks a lot.


----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.

[GUSDEV] Re: GUS @ BOSC?

[Trish W. <wh...@pc...>]

To confirm, yes Steve did give a talk at the BOSC last year.

Sounds like having a GUS meeting and a presentation is a great idea!

Trish


> Subject: Re: [GUSDEV] GUS @ BOSC?
>
> Oh sure, in Scotland!  Lucky devils.
>
> -Aaron
> Haiming Wang wrote:
>
>> I think Steve might have given a talk about GUS at BOSC2004.
>> http://open-bio.org/bosc2004/accepted_abstracts.html#abstracts
>>
>> -Haiming
>>
>> Aaron J. Mackey wrote:
>>
>>> As a BOSC organizer this year, I can almost guarantee that if there
>>> was someone who wanted to give a talk on GUS (status, future plans,
>>> etc), that the talk would be accepted (has there ever been a GUS talk
>>> at BOSC?)  Perhaps a lightning talk even?
>>>
>>> -Aaron
>>>
>>> Michael Saffitz wrote:
>>>
>>>>
>>>> Since there wasn't any interest in a GUS meetup at the
>>>> Bioinformatics  Hackathon, we'd thought we'd see if there was greater
>>>> interest for a  GUS meeting/hackathon/get together in conjunction
>>>> with BOSC/ISMB:
>>>>
>>>> http://open-bio.org/bosc2005/
>>>>
>>>> Anyone out there interested in GUS User group meetings?
>>>>
>>>> --Mike
>>>>
>>>>
>>>> On Apr 22, 2005, at 6:36 PM, Michael Saffitz wrote:
>>>>
>>>>>
>>>>> There's been some talk on various Bioinformatic mailing lists of a
>>>>> "hackathon" coinciding with Apple's WWDC this June (see below).
>>>>>
>>>>> Are any GUS users out there thinking about attending either the
>>>>> hackathon or the WWDC, and if so, is there any interest in forming
>>>>> a GUS contingent?
>>>>>
>>>>> Possible topics and areas of development could include plugin work,
>>>>> support for integrating other databases (i.e. tools to load data
>>>>> from chado databases), object layer development/improvements, ????
>>>>> ideas ?
>>>>>
>>>>> --Mike
>>>>>
>>>>>
>>>>>>> From: Suzanna Lewis <su...@fr...>
>>>>>>> Date: April 20, 2005 6:42:29 PM EDT
>>>>>>> To: da...@bi..., bak...@bi...,
>>>>>>> bio...@bi..., "go-...@ge..."
>>>>>>> <go-...@ge...>, go-...@fr...,
>>>>>>> mge...@li...,
>>>>>>> gmo...@li..., bio...@op...,
>>>>>>> bio...@bi..., em...@em...
>>>>>>> Cc: George Hartzell <har...@ke...>, Cyrus Harmon
>>>>>>> <cy...@cy...>, Steve Chervitz
>>>>>>> <Ste...@af...>
>>>>>>> Subject: Hackathon 2005
>>>>>>>
>>>>>>> (sorry for multiple postings, but please do forward to
>>>>>>> anyone else who you think might be interested)
>>>>>>>
>>>>>>> --------------------------------------------------------------------
>>>>>>> --
>>>>>>> ---
>>>>>>> ----------
>>>>>>>
>>>>>>> Dear everyone,
>>>>>>>
>>>>>>> It has been a long time and we Bioinformatics devotees are
>>>>>>> overdue for
>>>>>>> another total-immersion coding-fest (the last hackathon was held in
>>>>>>> Singapore February 2003, more than two years ago).  Apple has
>>>>>>> offered
>>>>>>> to host us this year, and as an added bonus include free
>>>>>>> admission to
>>>>>>> the World-Wide Developers Conference in San Francisco the prior
>>>>>>> week.
>>>>>>> They are also looking for some people to present interesting new
>>>>>>> developments at the WWDC, so if you have something noteworthy please
>>>>>>> let us know. Apple is not attaching any strings, so our work need
>>>>>>> not
>>>>>>> address Apple-specific software or hardware areas. Apple will
>>>>>>> provide
>>>>>>> space and hardware (and access to their engineers if we'd like).
>>>>>>>
>>>>>>> Week 1 (June 6-10) would be spent at the WWDC. Week 2 (June 12-16)
>>>>>>> would be in Cupertino, at Apple's headquarters.  We're free to focus
>>>>>>> on what interests us, our tentative plans include:
>>>>>>>
>>>>>>>   1. Bio-ontologies software
>>>>>>>   2. High-performance computing (e.g. large scale computations,
>>>>>>> optimization)
>>>>>>>   3. Image analysis
>>>>>>>   4. Documentation
>>>>>>>   5. Anything else that may interest you
>>>>>>>
>>>>>>> Our plan is to organize this much as the Aspen Center for Physics
>>>>>>> computational biology workshops were organized (for those old enough
>>>>>>> to
>>>>>>> remember): A couple of presentations to start the day; collaboration
>>>>>>> and coding afterwards; time for a bit of fun (does anyone else
>>>>>>> cycle?), and discussions in the late afternoons and evenings.
>>>>>>>
>>>>>>> Would everyone who is interested in attending please send us a short
>>>>>>> description of what you would like to do, and perhaps other
>>>>>>> people who
>>>>>>> you would like to work with. There is somewhat limited space, so we
>>>>>>> will try to prioritize groups that have a clear focus and a need to
>>>>>>> interact. We now this is very short notice, but we hope that there
>>>>>>> will be enough interest to make it possible.
>>>>>>>
>>>>>>> We are looking into additional funding support, to pay for travel
>>>>>>> expenses, but this is still to be decided.
>>>>>>>
>>>>>>> Looking forward to hearing from everyone.
>>>>>>> George, Cyrus, Steve, and Suzanna (the Bay Area locals)
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> This message is from the GOFriends moderated mailing list.  A
>>>>>>> list of
>>>>>>> public
>>>>>>> announcements and discussion of the Gene Ontology (GO) project.
>>>>>>> Problems with the list?           E-mail:
>>>>>>> own...@ge...
>>>>>>> Subscribing   send   "subscribe"   to
>>>>>>> gof...@ge...
>>>>>>> Unsubscribing send   "unsubscribe"  to
>>>>>>> gof...@ge...
>>>>>>> Web:          http://www.geneontology.org/
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>> -------------------------------------------------------
>>>> This SF.Net email is sponsored by: NEC IT Guy Games.
>>>> Get your fingers limbered up and give it your best shot. 4 great
>>>> events, 4
>>>> opportunities to win big! Highest score wins.NEC IT Guy Games. Play to
>>>> win an NEC 61 plasma display. Visit http://www.necitguy.com/?r=20
>>>> _______________________________________________
>>>> Gusdev-gusdev mailing list
>>>> Gus...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>
>>>
>>>
>>> -------------------------------------------------------
>>> This SF.Net email is sponsored by: NEC IT Guy Games.
>>> Get your fingers limbered up and give it your best shot. 4 great
>>> events, 4
>>> opportunities to win big! Highest score wins.NEC IT Guy Games. Play to
>>> win an NEC 61 plasma display. Visit http://www.necitguy.com/?r=20
>>> _______________________________________________
>>> Gusdev-gusdev mailing list
>>> Gus...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by: NEC IT Guy Games.
>> Get your fingers limbered up and give it your best shot. 4 great events, 4
>> opportunities to win big! Highest score wins.NEC IT Guy Games. Play to
>> win an NEC 61 plasma display. Visit http://www.necitguy.com/?r=20
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
>
> --__--__--
>
> _______________________________________________
> Gusdev-gusdev mailing list
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> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
> End of Gusdev-gusdev Digest
>

Re: [GUSDEV] GUS @ BOSC?

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

Oh sure, in Scotland!  Lucky devils.

-Aaron

Haiming Wang wrote:

> I think Steve might have given a talk about GUS at BOSC2004.
> http://open-bio.org/bosc2004/accepted_abstracts.html#abstracts
> 
> -Haiming
> 
> Aaron J. Mackey wrote:
> 
>> As a BOSC organizer this year, I can almost guarantee that if there 
>> was someone who wanted to give a talk on GUS (status, future plans, 
>> etc), that the talk would be accepted (has there ever been a GUS talk 
>> at BOSC?)  Perhaps a lightning talk even?
>>
>> -Aaron
>>
>> Michael Saffitz wrote:
>>
>>>
>>> Since there wasn't any interest in a GUS meetup at the 
>>> Bioinformatics  Hackathon, we'd thought we'd see if there was greater 
>>> interest for a  GUS meeting/hackathon/get together in conjunction 
>>> with BOSC/ISMB:
>>>
>>> http://open-bio.org/bosc2005/
>>>
>>> Anyone out there interested in GUS User group meetings?
>>>
>>> --Mike
>>>
>>>
>>> On Apr 22, 2005, at 6:36 PM, Michael Saffitz wrote:
>>>
>>>>
>>>> There's been some talk on various Bioinformatic mailing lists of a  
>>>> "hackathon" coinciding with Apple's WWDC this June (see below).
>>>>
>>>> Are any GUS users out there thinking about attending either the  
>>>> hackathon or the WWDC, and if so, is there any interest in forming  
>>>> a GUS contingent?
>>>>
>>>> Possible topics and areas of development could include plugin work,  
>>>> support for integrating other databases (i.e. tools to load data  
>>>> from chado databases), object layer development/improvements, ????  
>>>> ideas ?
>>>>
>>>> --Mike
>>>>
>>>>
>>>>>> From: Suzanna Lewis <su...@fr...>
>>>>>> Date: April 20, 2005 6:42:29 PM EDT
>>>>>> To: da...@bi..., bak...@bi...,
>>>>>> bio...@bi..., "go-...@ge..."
>>>>>> <go-...@ge...>, go-...@fr...,
>>>>>> mge...@li...,
>>>>>> gmo...@li..., bio...@op...,
>>>>>> bio...@bi..., em...@em...
>>>>>> Cc: George Hartzell <har...@ke...>, Cyrus Harmon
>>>>>> <cy...@cy...>, Steve Chervitz
>>>>>> <Ste...@af...>
>>>>>> Subject: Hackathon 2005
>>>>>>
>>>>>> (sorry for multiple postings, but please do forward to
>>>>>> anyone else who you think might be interested)
>>>>>>
>>>>>> -------------------------------------------------------------------- 
>>>>>> -- 
>>>>>> ---
>>>>>> ----------
>>>>>>
>>>>>> Dear everyone,
>>>>>>
>>>>>> It has been a long time and we Bioinformatics devotees are  
>>>>>> overdue for
>>>>>> another total-immersion coding-fest (the last hackathon was held in
>>>>>> Singapore February 2003, more than two years ago).  Apple has  
>>>>>> offered
>>>>>> to host us this year, and as an added bonus include free  
>>>>>> admission to
>>>>>> the World-Wide Developers Conference in San Francisco the prior  
>>>>>> week.
>>>>>> They are also looking for some people to present interesting new
>>>>>> developments at the WWDC, so if you have something noteworthy please
>>>>>> let us know. Apple is not attaching any strings, so our work need  
>>>>>> not
>>>>>> address Apple-specific software or hardware areas. Apple will  
>>>>>> provide
>>>>>> space and hardware (and access to their engineers if we'd like).
>>>>>>
>>>>>> Week 1 (June 6-10) would be spent at the WWDC. Week 2 (June 12-16)
>>>>>> would be in Cupertino, at Apple's headquarters.  We're free to focus
>>>>>> on what interests us, our tentative plans include:
>>>>>>
>>>>>>   1. Bio-ontologies software
>>>>>>   2. High-performance computing (e.g. large scale computations,
>>>>>> optimization)
>>>>>>   3. Image analysis
>>>>>>   4. Documentation
>>>>>>   5. Anything else that may interest you
>>>>>>
>>>>>> Our plan is to organize this much as the Aspen Center for Physics
>>>>>> computational biology workshops were organized (for those old enough
>>>>>> to
>>>>>> remember): A couple of presentations to start the day; collaboration
>>>>>> and coding afterwards; time for a bit of fun (does anyone else
>>>>>> cycle?), and discussions in the late afternoons and evenings.
>>>>>>
>>>>>> Would everyone who is interested in attending please send us a short
>>>>>> description of what you would like to do, and perhaps other  
>>>>>> people who
>>>>>> you would like to work with. There is somewhat limited space, so we
>>>>>> will try to prioritize groups that have a clear focus and a need to
>>>>>> interact. We now this is very short notice, but we hope that there
>>>>>> will be enough interest to make it possible.
>>>>>>
>>>>>> We are looking into additional funding support, to pay for travel
>>>>>> expenses, but this is still to be decided.
>>>>>>
>>>>>> Looking forward to hearing from everyone.
>>>>>> George, Cyrus, Steve, and Suzanna (the Bay Area locals)
>>>>>>
>>>>>>
>>>>>> -- 
>>>>>> This message is from the GOFriends moderated mailing list.  A  
>>>>>> list of
>>>>>> public
>>>>>> announcements and discussion of the Gene Ontology (GO) project.
>>>>>> Problems with the list?           E-mail:
>>>>>> own...@ge...
>>>>>> Subscribing   send   "subscribe"   to
>>>>>> gof...@ge...
>>>>>> Unsubscribing send   "unsubscribe"  to
>>>>>> gof...@ge...
>>>>>> Web:          http://www.geneontology.org/
>>>>>>
>>>>>
>>>>
>>>
>>>
>>>
>>> -------------------------------------------------------
>>> This SF.Net email is sponsored by: NEC IT Guy Games.
>>> Get your fingers limbered up and give it your best shot. 4 great 
>>> events, 4
>>> opportunities to win big! Highest score wins.NEC IT Guy Games. Play to
>>> win an NEC 61 plasma display. Visit http://www.necitguy.com/?r=20
>>> _______________________________________________
>>> Gusdev-gusdev mailing list
>>> Gus...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by: NEC IT Guy Games.
>> Get your fingers limbered up and give it your best shot. 4 great 
>> events, 4
>> opportunities to win big! Highest score wins.NEC IT Guy Games. Play to
>> win an NEC 61 plasma display. Visit http://www.necitguy.com/?r=20
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by: NEC IT Guy Games.
> Get your fingers limbered up and give it your best shot. 4 great events, 4
> opportunities to win big! Highest score wins.NEC IT Guy Games. Play to
> win an NEC 61 plasma display. Visit http://www.necitguy.com/?r=20
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [GUSDEV] GUS @ BOSC?

[Haiming W. <hw...@ug...>]

I think Steve might have given a talk about GUS at BOSC2004.
http://open-bio.org/bosc2004/accepted_abstracts.html#abstracts

-Haiming

Aaron J. Mackey wrote:

> As a BOSC organizer this year, I can almost guarantee that if there 
> was someone who wanted to give a talk on GUS (status, future plans, 
> etc), that the talk would be accepted (has there ever been a GUS talk 
> at BOSC?)  Perhaps a lightning talk even?
>
> -Aaron
>
> Michael Saffitz wrote:
>
>>
>> Since there wasn't any interest in a GUS meetup at the 
>> Bioinformatics  Hackathon, we'd thought we'd see if there was greater 
>> interest for a  GUS meeting/hackathon/get together in conjunction 
>> with BOSC/ISMB:
>>
>> http://open-bio.org/bosc2005/
>>
>> Anyone out there interested in GUS User group meetings?
>>
>> --Mike
>>
>>
>> On Apr 22, 2005, at 6:36 PM, Michael Saffitz wrote:
>>
>>>
>>> There's been some talk on various Bioinformatic mailing lists of a  
>>> "hackathon" coinciding with Apple's WWDC this June (see below).
>>>
>>> Are any GUS users out there thinking about attending either the  
>>> hackathon or the WWDC, and if so, is there any interest in forming  
>>> a GUS contingent?
>>>
>>> Possible topics and areas of development could include plugin work,  
>>> support for integrating other databases (i.e. tools to load data  
>>> from chado databases), object layer development/improvements, ????  
>>> ideas ?
>>>
>>> --Mike
>>>
>>>
>>>>> From: Suzanna Lewis <su...@fr...>
>>>>> Date: April 20, 2005 6:42:29 PM EDT
>>>>> To: da...@bi..., bak...@bi...,
>>>>> bio...@bi..., "go-...@ge..."
>>>>> <go-...@ge...>, go-...@fr...,
>>>>> mge...@li...,
>>>>> gmo...@li..., bio...@op...,
>>>>> bio...@bi..., em...@em...
>>>>> Cc: George Hartzell <har...@ke...>, Cyrus Harmon
>>>>> <cy...@cy...>, Steve Chervitz
>>>>> <Ste...@af...>
>>>>> Subject: Hackathon 2005
>>>>>
>>>>> (sorry for multiple postings, but please do forward to
>>>>> anyone else who you think might be interested)
>>>>>
>>>>> -------------------------------------------------------------------- 
>>>>> -- 
>>>>> ---
>>>>> ----------
>>>>>
>>>>> Dear everyone,
>>>>>
>>>>> It has been a long time and we Bioinformatics devotees are  
>>>>> overdue for
>>>>> another total-immersion coding-fest (the last hackathon was held in
>>>>> Singapore February 2003, more than two years ago).  Apple has  
>>>>> offered
>>>>> to host us this year, and as an added bonus include free  
>>>>> admission to
>>>>> the World-Wide Developers Conference in San Francisco the prior  
>>>>> week.
>>>>> They are also looking for some people to present interesting new
>>>>> developments at the WWDC, so if you have something noteworthy please
>>>>> let us know. Apple is not attaching any strings, so our work need  
>>>>> not
>>>>> address Apple-specific software or hardware areas. Apple will  
>>>>> provide
>>>>> space and hardware (and access to their engineers if we'd like).
>>>>>
>>>>> Week 1 (June 6-10) would be spent at the WWDC. Week 2 (June 12-16)
>>>>> would be in Cupertino, at Apple's headquarters.  We're free to focus
>>>>> on what interests us, our tentative plans include:
>>>>>
>>>>>   1. Bio-ontologies software
>>>>>   2. High-performance computing (e.g. large scale computations,
>>>>> optimization)
>>>>>   3. Image analysis
>>>>>   4. Documentation
>>>>>   5. Anything else that may interest you
>>>>>
>>>>> Our plan is to organize this much as the Aspen Center for Physics
>>>>> computational biology workshops were organized (for those old enough
>>>>> to
>>>>> remember): A couple of presentations to start the day; collaboration
>>>>> and coding afterwards; time for a bit of fun (does anyone else
>>>>> cycle?), and discussions in the late afternoons and evenings.
>>>>>
>>>>> Would everyone who is interested in attending please send us a short
>>>>> description of what you would like to do, and perhaps other  
>>>>> people who
>>>>> you would like to work with. There is somewhat limited space, so we
>>>>> will try to prioritize groups that have a clear focus and a need to
>>>>> interact. We now this is very short notice, but we hope that there
>>>>> will be enough interest to make it possible.
>>>>>
>>>>> We are looking into additional funding support, to pay for travel
>>>>> expenses, but this is still to be decided.
>>>>>
>>>>> Looking forward to hearing from everyone.
>>>>> George, Cyrus, Steve, and Suzanna (the Bay Area locals)
>>>>>
>>>>>
>>>>> -- 
>>>>> This message is from the GOFriends moderated mailing list.  A  
>>>>> list of
>>>>> public
>>>>> announcements and discussion of the Gene Ontology (GO) project.
>>>>> Problems with the list?           E-mail:
>>>>> own...@ge...
>>>>> Subscribing   send   "subscribe"   to
>>>>> gof...@ge...
>>>>> Unsubscribing send   "unsubscribe"  to
>>>>> gof...@ge...
>>>>> Web:          http://www.geneontology.org/
>>>>>
>>>>
>>>
>>
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by: NEC IT Guy Games.
>> Get your fingers limbered up and give it your best shot. 4 great 
>> events, 4
>> opportunities to win big! Highest score wins.NEC IT Guy Games. Play to
>> win an NEC 61 plasma display. Visit http://www.necitguy.com/?r=20
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: NEC IT Guy Games.
> Get your fingers limbered up and give it your best shot. 4 great 
> events, 4
> opportunities to win big! Highest score wins.NEC IT Guy Games. Play to
> win an NEC 61 plasma display. Visit http://www.necitguy.com/?r=20
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

Re: [GUSDEV] GUS @ BOSC?

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

As a BOSC organizer this year, I can almost guarantee that if there was 
someone who wanted to give a talk on GUS (status, future plans, etc), 
that the talk would be accepted (has there ever been a GUS talk at 
BOSC?)  Perhaps a lightning talk even?

-Aaron

Michael Saffitz wrote:

> 
> Since there wasn't any interest in a GUS meetup at the Bioinformatics  
> Hackathon, we'd thought we'd see if there was greater interest for a  
> GUS meeting/hackathon/get together in conjunction with BOSC/ISMB:
> 
> http://open-bio.org/bosc2005/
> 
> Anyone out there interested in GUS User group meetings?
> 
> --Mike
> 
> 
> On Apr 22, 2005, at 6:36 PM, Michael Saffitz wrote:
> 
>>
>> There's been some talk on various Bioinformatic mailing lists of a  
>> "hackathon" coinciding with Apple's WWDC this June (see below).
>>
>> Are any GUS users out there thinking about attending either the  
>> hackathon or the WWDC, and if so, is there any interest in forming  a 
>> GUS contingent?
>>
>> Possible topics and areas of development could include plugin work,  
>> support for integrating other databases (i.e. tools to load data  from 
>> chado databases), object layer development/improvements, ????  ideas ?
>>
>> --Mike
>>
>>
>>>> From: Suzanna Lewis <su...@fr...>
>>>> Date: April 20, 2005 6:42:29 PM EDT
>>>> To: da...@bi..., bak...@bi...,
>>>> bio...@bi..., "go-...@ge..."
>>>> <go-...@ge...>, go-...@fr...,
>>>> mge...@li...,
>>>> gmo...@li..., bio...@op...,
>>>> bio...@bi..., em...@em...
>>>> Cc: George Hartzell <har...@ke...>, Cyrus Harmon
>>>> <cy...@cy...>, Steve Chervitz
>>>> <Ste...@af...>
>>>> Subject: Hackathon 2005
>>>>
>>>> (sorry for multiple postings, but please do forward to
>>>> anyone else who you think might be interested)
>>>>
>>>> -------------------------------------------------------------------- --
>>>> ---
>>>> ----------
>>>>
>>>> Dear everyone,
>>>>
>>>> It has been a long time and we Bioinformatics devotees are  overdue for
>>>> another total-immersion coding-fest (the last hackathon was held in
>>>> Singapore February 2003, more than two years ago).  Apple has  offered
>>>> to host us this year, and as an added bonus include free  admission to
>>>> the World-Wide Developers Conference in San Francisco the prior  week.
>>>> They are also looking for some people to present interesting new
>>>> developments at the WWDC, so if you have something noteworthy please
>>>> let us know. Apple is not attaching any strings, so our work need  not
>>>> address Apple-specific software or hardware areas. Apple will  provide
>>>> space and hardware (and access to their engineers if we'd like).
>>>>
>>>> Week 1 (June 6-10) would be spent at the WWDC. Week 2 (June 12-16)
>>>> would be in Cupertino, at Apple's headquarters.  We're free to focus
>>>> on what interests us, our tentative plans include:
>>>>
>>>>   1. Bio-ontologies software
>>>>   2. High-performance computing (e.g. large scale computations,
>>>> optimization)
>>>>   3. Image analysis
>>>>   4. Documentation
>>>>   5. Anything else that may interest you
>>>>
>>>> Our plan is to organize this much as the Aspen Center for Physics
>>>> computational biology workshops were organized (for those old enough
>>>> to
>>>> remember): A couple of presentations to start the day; collaboration
>>>> and coding afterwards; time for a bit of fun (does anyone else
>>>> cycle?), and discussions in the late afternoons and evenings.
>>>>
>>>> Would everyone who is interested in attending please send us a short
>>>> description of what you would like to do, and perhaps other  people who
>>>> you would like to work with. There is somewhat limited space, so we
>>>> will try to prioritize groups that have a clear focus and a need to
>>>> interact. We now this is very short notice, but we hope that there
>>>> will be enough interest to make it possible.
>>>>
>>>> We are looking into additional funding support, to pay for travel
>>>> expenses, but this is still to be decided.
>>>>
>>>> Looking forward to hearing from everyone.
>>>> George, Cyrus, Steve, and Suzanna (the Bay Area locals)
>>>>
>>>>
>>>> -- 
>>>> This message is from the GOFriends moderated mailing list.  A  list of
>>>> public
>>>> announcements and discussion of the Gene Ontology (GO) project.
>>>> Problems with the list?           E-mail:
>>>> own...@ge...
>>>> Subscribing   send   "subscribe"   to
>>>> gof...@ge...
>>>> Unsubscribing send   "unsubscribe"  to
>>>> gof...@ge...
>>>> Web:          http://www.geneontology.org/
>>>>
>>>
>>
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by: NEC IT Guy Games.
> Get your fingers limbered up and give it your best shot. 4 great events, 4
> opportunities to win big! Highest score wins.NEC IT Guy Games. Play to
> win an NEC 61 plasma display. Visit http://www.necitguy.com/?r=20
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [GUSDEV] GUS @ BOSC?

[Ed R. <ero...@ug...>]

Yes, very much so.  Especially with everything that is going
on with the Api Project, and now a postgress version, and the
delayed version 4.0 schema talks.......

This conference is a much better venue for GUS.  

-Ed



---- Original message ----
>Date: Wed, 4 May 2005 16:35:16 -0400
>From: Michael Saffitz <msa...@pc...>  
>Subject: [GUSDEV] GUS @ BOSC?  
>To: Gusdev gusdev-gusdev <gus...@li...>
>
>
>Since there wasn't any interest in a GUS meetup at the
Bioinformatics  
>Hackathon, we'd thought we'd see if there was greater
interest for a  
>GUS meeting/hackathon/get together in conjunction with BOSC/ISMB:
>
>http://open-bio.org/bosc2005/
>
>Anyone out there interested in GUS User group meetings?
>
>--Mike
>
>
>On Apr 22, 2005, at 6:36 PM, Michael Saffitz wrote:
>
>>
>> There's been some talk on various Bioinformatic mailing
lists of a  
>> "hackathon" coinciding with Apple's WWDC this June (see below).
>>
>> Are any GUS users out there thinking about attending either
the  
>> hackathon or the WWDC, and if so, is there any interest in
forming  
>> a GUS contingent?
>>
>> Possible topics and areas of development could include
plugin work,  
>> support for integrating other databases (i.e. tools to load
data  
>> from chado databases), object layer
development/improvements, ????  
>> ideas ?
>>
>> --Mike
>>
>>
>>>> From: Suzanna Lewis <su...@fr...>
>>>> Date: April 20, 2005 6:42:29 PM EDT
>>>> To: da...@bi..., bak...@bi...,
>>>> bio...@bi..., "go-...@ge..."
>>>> <go-...@ge...>, go-...@fr...,
>>>> mge...@li...,
>>>> gmo...@li..., bio...@op...,
>>>> bio...@bi..., em...@em...
>>>> Cc: George Hartzell <har...@ke...>, Cyrus
Harmon
>>>> <cy...@cy...>, Steve Chervitz
>>>> <Ste...@af...>
>>>> Subject: Hackathon 2005
>>>>
>>>> (sorry for multiple postings, but please do forward to
>>>> anyone else who you think might be interested)
>>>>
>>>>
--------------------------------------------------------------------

>>>> --
>>>> ---
>>>> ----------
>>>>
>>>> Dear everyone,
>>>>
>>>> It has been a long time and we Bioinformatics devotees are  
>>>> overdue for
>>>> another total-immersion coding-fest (the last hackathon
was held in
>>>> Singapore February 2003, more than two years ago).  Apple
has  
>>>> offered
>>>> to host us this year, and as an added bonus include free  
>>>> admission to
>>>> the World-Wide Developers Conference in San Francisco the
prior  
>>>> week.
>>>> They are also looking for some people to present
interesting new
>>>> developments at the WWDC, so if you have something
noteworthy please
>>>> let us know. Apple is not attaching any strings, so our
work need  
>>>> not
>>>> address Apple-specific software or hardware areas. Apple
will  
>>>> provide
>>>> space and hardware (and access to their engineers if we'd
like).
>>>>
>>>> Week 1 (June 6-10) would be spent at the WWDC. Week 2
(June 12-16)
>>>> would be in Cupertino, at Apple's headquarters.  We're
free to focus
>>>> on what interests us, our tentative plans include:
>>>>
>>>>   1. Bio-ontologies software
>>>>   2. High-performance computing (e.g. large scale
computations,
>>>> optimization)
>>>>   3. Image analysis
>>>>   4. Documentation
>>>>   5. Anything else that may interest you
>>>>
>>>> Our plan is to organize this much as the Aspen Center for
Physics
>>>> computational biology workshops were organized (for those
old enough
>>>> to
>>>> remember): A couple of presentations to start the day;
collaboration
>>>> and coding afterwards; time for a bit of fun (does anyone
else
>>>> cycle?), and discussions in the late afternoons and evenings.
>>>>
>>>> Would everyone who is interested in attending please send
us a short
>>>> description of what you would like to do, and perhaps other  
>>>> people who
>>>> you would like to work with. There is somewhat limited
space, so we
>>>> will try to prioritize groups that have a clear focus and
a need to
>>>> interact. We now this is very short notice, but we hope
that there
>>>> will be enough interest to make it possible.
>>>>
>>>> We are looking into additional funding support, to pay
for travel
>>>> expenses, but this is still to be decided.
>>>>
>>>> Looking forward to hearing from everyone.
>>>> George, Cyrus, Steve, and Suzanna (the Bay Area locals)
>>>>
>>>>
>>>> --
>>>> This message is from the GOFriends moderated mailing
list.  A  
>>>> list of
>>>> public
>>>> announcements and discussion of the Gene Ontology (GO)
project.
>>>> Problems with the list?           E-mail:
>>>> own...@ge...
>>>> Subscribing   send   "subscribe"   to
>>>> gof...@ge...
>>>> Unsubscribing send   "unsubscribe"  to
>>>> gof...@ge...
>>>> Web:          http://www.geneontology.org/
>>>>
>>>
>>
>
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by: NEC IT Guy Games.
>Get your fingers limbered up and give it your best shot. 4
great events, 4
>opportunities to win big! Highest score wins.NEC IT Guy
Games. Play to
>win an NEC 61 plasma display. Visit http://www.necitguy.com/?r=20
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
-----------------
Ed Robinson
Center for Tropical and Emerging Global Diseases
University of Georgia, Athens, GA 30602
ero...@ug.../(706)542.1447/254.8883