gusdev-gusdev — Topics concerning GUS development

Re: [Gusdev-gusdev] OrthoMCL procedure

[Arnaud K. <ax...@sa...>]

Steve Fischer wrote:

> Arnaud-
>
> see below.
>
> steve
>
> Arnaud Kerhornou wrote:
>
>> Hi everyone
>>
>> To be able to reproduce the OrthoMCL method, I would like to raise 
>> two issues we've got:
>>
>> * The first issue relates to the view where are stored the protein 
>> sequences. I was thinking to use the TranslatedAASequence view as 
>> this one contains the translated sequences of our gene models. The 
>> problem I have is that it is missing a name attribute so I can not 
>> match the blast output query and subject names with the data into GUS 
>> (I didn't want to use the TranslatedAASequence primary keys as the 
>> identifiers of my proteins of interest).
>> Could we add a name attribute to this view ?
>
>
> hmm.   not quite following.   what would this name be, where would it 
> be derived from?

By default we assign the systematic id of the corresponding CDS to the 
protein name.

>   why not use source_id and/or secondary_identifier? 

We could do that, but in any case that would involve to modify the code 
of the loading BLAST output plugin (LoadBlastSimFast.pm) to get the 
sequences entries. At the moment the match is made on the primary key 
(which I want to avoid) or the name attribute. The source_id attribute 
would do instead of the name attribute. It must work for any blast (DNA 
Vs DNA or Protein Vs Protein) with the various potential GUS sequence 
objects we want to attach similarity data to. As far as I can see the 
source_id attribute is present in all of them (AASequenceImp and 
NASequenceImp tables).

>   or, presumably this translated sequence has a relationship back to 
> its na sequence (although i don't immediately see that in the schema 
> browser), so couldn't you get a name or source_id from there?
>
That would require a more sophisticate query to get the sequence entry.

>>
>> * The second issue relates to the BLAST output parsing, done by a 
>> module called BlastAnal.pm in the CBIL package. This module seems to 
>> parse BLAST output file with only one query sequence. I have more 
>> than one query sequence reported so I had to change the code of this 
>> module to allow more than one query sequence. Can my code be 
>> integrated  to CBIL package ? Note that I didn't change the interface 
>> of this module so it doesn't affect the scripts that are using it, 
>> I'm thinking in particular of parseBlastFilesForSimilarity.pl
>
> this sounds ok.   how about we just take a quick look at this together 
> while you are visiting?   then we can fold it into the code base.   do 
> you want to send it by mail?
>
That's fine, the module is attached.

>>
>> cheers
>> Arnaud
>>
>>
>

Re: [Gusdev-gusdev] OrthoMCL procedure

[Steve F. <sfi...@pc...>]

Arnaud-

see below.

steve

Arnaud Kerhornou wrote:

> Hi everyone
>
> To be able to reproduce the OrthoMCL method, I would like to raise two 
> issues we've got:
>
> * The first issue relates to the view where are stored the protein 
> sequences. I was thinking to use the TranslatedAASequence view as this 
> one contains the translated sequences of our gene models. The problem 
> I have is that it is missing a name attribute so I can not match the 
> blast output query and subject names with the data into GUS (I didn't 
> want to use the TranslatedAASequence primary keys as the identifiers 
> of my proteins of interest).
> Could we add a name attribute to this view ?

hmm.   not quite following.   what would this name be, where would it be 
derived from?   why not use source_id and/or secondary_identifier?    
or, presumably this translated sequence has a relationship back to its 
na sequence (although i don't immediately see that in the schema 
browser), so couldn't you get a name or source_id from there?

>
> * The second issue relates to the BLAST output parsing, done by a 
> module called BlastAnal.pm in the CBIL package. This module seems to 
> parse BLAST output file with only one query sequence. I have more than 
> one query sequence reported so I had to change the code of this module 
> to allow more than one query sequence. Can my code be integrated  to 
> CBIL package ? Note that I didn't change the interface of this module 
> so it doesn't affect the scripts that are using it, I'm thinking in 
> particular of parseBlastFilesForSimilarity.pl

this sounds ok.   how about we just take a quick look at this together 
while you are visiting?   then we can fold it into the code base.   do 
you want to send it by mail?

>
> cheers
> Arnaud
>
>
> -------------------------------------------------------
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[Gusdev-gusdev] GUS Administation & DBA Resources

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

All,

As I mentioned the other day, a working group is forming to explore some 
of the issues around GUS Administration and Manageability.

I've created a new mailing list to support these efforts and to serve as 
a general resource for GUS DBAs.  The list is available at:

https://mail.pcbi.upenn.edu/mailman/listinfo/gusdba

General information about the list:

---
The primary focus of this list is the overall administration and 
manageability of GUS installations, particularly at the intersection 
with RDBMS systems. Thus, the following topics are appropriate: 
installing the GUS schema, GUS/RDBMS compatibility, upgrading the GUS 
schema, managing GUS objects within the RDBMS (i.e. collecting 
statistics, indexes, etc), and so on. The following topics are not 
appropriate: general RDBMS issues, the GUS WDK, Plugins, or other 
components not relating to the database/schema, and questions relating 
to the application of the schema (i.e. biological domain issues).

The list is open to all who are interested. Concurrent membership with 
the GUS-DEV list is highly recommended.
---

The working group is in the process of forming.  Please join the list if 
you're interested in participating.  More details will be posted to 
GUSDBA shortly.

Thanks,

Mike Saffitz
CBIL

[Gusdev-gusdev] OrthoMCL procedure

[Arnaud K. <ax...@sa...>]

Hi everyone

To be able to reproduce the OrthoMCL method, I would like to raise two 
issues we've got:

* The first issue relates to the view where are stored the protein 
sequences. I was thinking to use the TranslatedAASequence view as this 
one contains the translated sequences of our gene models. The problem I 
have is that it is missing a name attribute so I can not match the blast 
output query and subject names with the data into GUS (I didn't want to 
use the TranslatedAASequence primary keys as the identifiers of my 
proteins of interest).
Could we add a name attribute to this view ?

* The second issue relates to the BLAST output parsing, done by a module 
called BlastAnal.pm in the CBIL package. This module seems to parse 
BLAST output file with only one query sequence. I have more than one 
query sequence reported so I had to change the code of this module to 
allow more than one query sequence. Can my code be integrated  to CBIL 
package ? Note that I didn't change the interface of this module so it 
doesn't affect the scripts that are using it, I'm thinking in particular 
of parseBlastFilesForSimilarity.pl

cheers
Arnaud

[Gusdev-gusdev] GUS WDK 1.0

[Steve F. <sfi...@pc...>]

Folks-

We are pleased to announce the first release of the WDK, the successor 
of the "classic" WDK, developed as a collaboration between Computational 
Biology and Informatics Laboratory (CBIL) at the University of 
Pennsylvania and the Pathogen Sequencing Unit at the Wellcome Trust 
Sanger Institute.

The software can be downloaded from http://www.gusdb.org/wdk.  An 
introduction to the package together with detailed documentation can be 
found on http://www.gusdb.org/wiki/index.php/GusWdk

Steve

[Gusdev-gusdev] Re: Re GUS Working Group

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

Copied to the group, and comments inline...

Jinal Jhaveri wrote:
> Mike,
> 
> I would be interested in joining this working group. Extending the idea(s) you 
> have about representing the schema in xml format,  I believe that following 
> will be some immediate questions
> 

Thanks for your interest...

> a) How exactly will the dtd of xml file look like. How will it solve the 
> problems of commonly representing both oracle's and postgresql's data-types
> 

XML won't solve the translation problem alone, but it provides 
programmatic access to the schema and allows for easy access, storage, 
and tracking of the canonical schema.

> b) Will we need to write some of our own tools to convert this xml to pgsql 
> and oracle sql for installing the schema?
> 

I would imagine we will need to write some of our own tools, unless 
someone is aware of an existing tool (commercial or otherwise) that 
meets our needs.

> c) How easy or tough it will be for us to update the xml file whenever any 
> major/minor change is made in the schema
> 

I think that one of the goals of this effort would be to make this task 
easy!

> d) Will we have a consistent documentation system (+ wiki entry) for briefly 
> documenting this changes and announcing it to the newsgroup?
> 

Yes, I think we should!

> 
> 
> Let me know if I understood your suggestion correctly from the above suggested 
> extensions.
> 
> 
> Probably its a good idea to structure this working group before approaching 
> the problem
> 

Yes... we'll see who all is interested and figure out how to proceed.

> ---Jinal

Re: [Gusdev-gusdev] improving GUS install/evolution

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

All,

As Steve mentioned, I've been exploring manageability and administration
of the GUS schema.

As it sits today, the canonical GUS schema is maintained within an
Oracle instance here at CBIL.  The schema is evolved within this
instance-- tables added and removed, etc.  As necessary, the schema is
then "dumped" from this instance to Oracle DDL using a custom script
($GUS_HOME/bin/dumpSchema.pl).  These Oracle DDL scripts comprise the
installation scripts for new GUS installations.

The current approach has several limitations:

* Since the canonical schema is maintained inside an active database, we
have no way of tracking changes, nor do we have any way of validating
the completeness of any given schema.

* All schema changes must be applied in our instance; We cannot support
changes from the community in the same fashion that CVS would allow
(i.e. various contributors checking in changes).

* Our installation is passive in the sense that we generate a large
number of scripts, and a meta-script which calls these scripts, but we
do not detect or attempt to recover from errors.  This has led to
various issues with missed components during installation (i.e. missing
sequences).

* Our schema is represented as database objects (tables, views,
constraints, etc.) and cannot be represented or modeled in an object
orientated fashion (i.e. capturing our subclassing system).

* The generation of a Postgres compatible system is much more
unpleasant, because we first dump the schema from the database, and then
need to parse the dumped schema and translate it to postgres.

In looking to address these limitations, it has become obvious that the
canonical GUS schema should be represented outside of any given
instance, in some file that can be checked into CVS, allowing changes to
be tracked, and serving as the foundation for validation of various GUS
schema installations.

My recent work has led me to believe that his external canonical GUS
schema should be represented as XML, which provides excellent
programmatic access to the schema, and is independent of Oracle or Postgres.

I spent several weeks looking at the SQLFairy
(http://sqlfairy.sourceforge.net/) package, which allows for translation
from many sources (Oracle, Postgres, XML, etc.) to many other sources
(Oracle, Postgres, HTML Documentation, XML, etc.) This would allow us to
generate the GUS XML canonical schema (generally a one-time operation),
maintain the schema in XML, and then transform the XML to Oracle or
Postgres DDL.  Unfortunately, SQLFairy doesn't appear to be ready to
support this task-- it doesn't yet support much of the functionality we
require, the parsers are incomplete.  While I initially thought that
SQLFairy could be modified to add these items, I think that significant
architectural issues prevent it from being a solution to our needs.

I've also examined some of the other packages available, including
Ora2Pg and the Jakarta Sandbox SQL commons project.  No project provides
all of the functionality we require.  As a result, I've begun to
explore implementing our own system to provide this functionality.

I have some early thoughts about how to accomplish these goals, but I'd 
like to solicit feedback and participation from the community.  If 
you're interested on participating in a GUS Management Working Group-- 
at any level-- please let me know.  Once we have a list of interested 
parties, we'll figure out the best way to proceed-- perhaps a conference 
call at some point.

--Mike
CBIL



Steve Fischer wrote:
> folks-
> 
> some people here at cbil and also at uga have begun thinking about how 
> to improve the GUS install, and how to manage schema evolution.
> 
> the two pieces of the gus install are:
>   (1) the database schema and initial data
>   (2) the software
> 
> mike at cbil has made progress on (1), and it seems like alan, ed and 
> haiming at uga have ideas about this.
> 
> mike is promising to write to the group to give a report on his efforts.
> 
> so, maybe that will be a good way to get the discussion rolling....
> 
> if folks have ideas or energy to tackle (2) that would be great.
> 
> steve
> 
> 
> 
> 
> 
> -------------------------------------------------------
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Re: [Gusdev-gusdev] OrthologGroupsMCL plugin

[Arnaud K. <ax...@sa...>]

Hi

I've removed the line and commited the change.

Arnaud

Arnaud Kerhornou wrote:

> Hi Li
>
> There is an extra line in the plugin that doesn't seem necessary.
>
>    use Objects::dbiperl_utils::DbiDatabase;
>
> The plugin doesn't find the DbiDatabase module and stops. Can this 
> line be removed ?
> I ran the plugin without this line and it is working fine.
>
> It that's ok, I can remove it and do the commit
>
> Arnaud
>
>
> -------------------------------------------------------
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> Use IT products in your business? Tell us what you think of them. Give us
> Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out 
> more
> http://productguide.itmanagersjournal.com/guidepromo.tmpl
> _______________________________________________
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> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

[Gusdev-gusdev] OrthologGroupsMCL plugin

[Arnaud K. <ax...@sa...>]

Hi Li

There is an extra line in the plugin that doesn't seem necessary.

    use Objects::dbiperl_utils::DbiDatabase;

The plugin doesn't find the DbiDatabase module and stops. Can this line 
be removed ?
I ran the plugin without this line and it is working fine.

It that's ok, I can remove it and do the commit

Arnaud

Re: [Gusdev-gusdev] improving GUS install/evolution

[Terry C. <tc...@it...>]

Steve-

This does sound like good timing.  

It makes sense to integrate some of these modules, which
comes as no surprise from me :-)

We are using plugins; I said that wrong to distinguish writing 
plugins versus writing descriptions for the "universal" XMLGUS plugin.  
It consists of the engine we talked about where the specifics are 
defined descriptively in the XML and grammar. So we are going 
through the object layer as usual.
XMLGUS.pm is the plugin part of the system; the grammar
drives XMLGUS.pm based on the input from the GUS XML.

Here are some pointers on the web to materials 

I posted the paper at 
    http://flora.ittc.ku.edu/xmlgus/
in pdf and ps formats.


All the code and support systems for XMLGUS are on
the web site. There are some toy examples there.
We also put two production systems online that we are
using for 1) loading annotated arabidipopsis
chromosomes and 2) processing & loading reads cleaned 
of vector sequence using a GUS pipeline. The latter
uses XSLT to transform the BLAST output to GUS XML.


I'll look forward to hearing from you and
others interested in this.

all the best,

Terry

p.s. About the Chicago team - we are still a cohort.
Josef Jurek gives XMLGUS significant workouts in Daphne Preuss' 
lab; Gregory Kettler is now a graduate student at MIT; and 
I am getting setup in my new laboratory at the University of Kansas. 



On  0, Steve Fischer <sfi...@pc...> wrote:
> Terry-
> 
> Great to hear that your paper will be in Applied Bioinformatics.
> 
> I just had a visit to UGA where Jessica Kissinger's lab is using GUS.
> 
> We have been discussing the GBParser and the parser of TIGR XML, 
> considering whether they should be re-written/unified.  Ed Robinson 
> there is focusing on this.
> 
> The approach we have been thinking of is to have both of them parse into 
> a common object model (either bioperl, if it turns out they have an 
> appropriate model, or the existing and possibly modified CBIL genbank 
> objects).   They would both share a layer that writes the object model 
> into GUS objects and submits.   They would differ in the layer that 
> parses into the model. 
> 
> Ed has been thinking about the layer to parse into the objects and has 
> mentioned a declarative mapping from the source into the objects.
> 
> I told him about your work, so, this is perfect timing.
> 
> Can we get a pre-print of your paper?
> 
> Also, you mention below that you are not using plugins, and are 
> transforming directly from XML into the schema.   Sounds like you are 
> not using the object layer.   But, the object layer and ga have benefits 
> like handling overhead rows, algorithm tracking and versioning.   How do 
> you handle that stuff?   Would it be possible to modify your approach to 
> fit into the plugin framework so that, instead of going to the schema 
> directly, it goes into the objects?   Or, am did i misinterpret and are 
> you doing this already?
> 
> Thanks,
> steve
> 
> Terry Clark wrote:
> 
> >One component of schema evolution is getting data 
> >into the schema; another side is moving new data 
> >into existing schema. 
> >
> >Folks at UChicago and I have worked out an XML
> >based strategy for incorporating data into GUS. 
> >The idea is around a GUS XML that contains key constraints
> >as attributes, which is interpretted by a byacc
> >parser and processor (together these are a plugin).
> >The data-to-schema routing happens by way of the XML
> >and grammar.
> >
> >There is a paper to appear in Applied Bioinformatics
> >(probably the next issue) about our GUX XML processed
> >by XMLGUS. We find this a useful tool in our production 
> >work. 
> >
> >Now writing plugins is unnecessary for us apart 
> >from occasional special cases, which XMLGUS has hooks for.
> >We now use XML and context free grammars to define the
> >mapping from data to schema, in most of our cases. 
> >There is one case my colleague found it easier to write
> >a plugin from scratch    - I have yet to study this to
> >see what caused this.
> >
> >The GUS install needs a way to incorporate local tables.
> >A GUS table need not be part of the canonical set of 
> >tables; some can be site specific. We add local tables now, 
> >but the process is very ad hoc. 
> >
> >Presently, we are working now on automating the production
> >of the XMLGUS framework, and the table problem. It would
> >be useful to see what people are thinking about and
> >where the needs are.
> >
> >Maybe such ideas could be discussed at a GUS meeting?
> >
> >cheers,
> >
> >Terry
> >
> >
> >
> >
> >
> >On  0, Sucheta Tripathy <su...@vb...> wrote:
> >  
> >
> >>Steve,
> >>
> >>We at VBI welcome the idea of releasing a version with install data.
> >>
> >>This has been the main cause of concern for GUS users who had to spend
> >>lots of time finding the pre-requisite data .
> >>
> >>We can certainly contribute to the initial dataset.
> >>
> >>In addition we would be more interested to initiate a discussion on
> >>functional annotation.
> >>
> >>cheers
> >>
> >>Sucheta
> >>
> >>    
> >>
> >>>folks-
> >>>
> >>>some people here at cbil and also at uga have begun thinking about how
> >>>to improve the GUS install, and how to manage schema evolution.
> >>>
> >>>the two pieces of the gus install are:
> >>>   (1) the database schema and initial data
> >>>   (2) the software
> >>>
> >>>mike at cbil has made progress on (1), and it seems like alan, ed and
> >>>haiming at uga have ideas about this.
> >>>
> >>>mike is promising to write to the group to give a report on his efforts.
> >>>
> >>>so, maybe that will be a good way to get the discussion rolling....
> >>>
> >>>if folks have ideas or energy to tackle (2) that would be great.
> >>>
> >>>steve
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>-------------------------------------------------------
> >>>This SF.net email is sponsored by: IT Product Guide on ITManagersJournal
> >>>Use IT products in your business? Tell us what you think of them. Give us
> >>>Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out
> >>>more
> >>>http://productguide.itmanagersjournal.com/guidepromo.tmpl
> >>>_______________________________________________
> >>>Gusdev-gusdev mailing list
> >>>Gus...@li...
> >>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>
> >>>      
> >>>
> >>-- 
> >>Sucheta Tripathy
> >>Virginia Bioinformatics Institute Phase-I
> >>Washington street.
> >>Virginia Tech.
> >>Blacksburg,VA 24061-0447
> >>phone:(540)231-8138
> >>Fax:  (540) 231-2606
> >>
> >>
> >>-------------------------------------------------------
> >>This SF.net email is sponsored by: IT Product Guide on ITManagersJournal
> >>Use IT products in your business? Tell us what you think of them. Give us
> >>Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more
> >>http://productguide.itmanagersjournal.com/guidepromo.tmpl
> >>_______________________________________________
> >>Gusdev-gusdev mailing list
> >>Gus...@li...
> >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>    
> >>
> >
> >
> >-------------------------------------------------------
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> >Use IT products in your business? Tell us what you think of them. Give us
> >Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more
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> >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >  
> >

Re: [Gusdev-gusdev] improving GUS install/evolution

[Steve F. <sfi...@pc...>]

Terry-

Great to hear that your paper will be in Applied Bioinformatics.

I just had a visit to UGA where Jessica Kissinger's lab is using GUS.

We have been discussing the GBParser and the parser of TIGR XML, 
considering whether they should be re-written/unified.  Ed Robinson 
there is focusing on this.

The approach we have been thinking of is to have both of them parse into 
a common object model (either bioperl, if it turns out they have an 
appropriate model, or the existing and possibly modified CBIL genbank 
objects).   They would both share a layer that writes the object model 
into GUS objects and submits.   They would differ in the layer that 
parses into the model. 

Ed has been thinking about the layer to parse into the objects and has 
mentioned a declarative mapping from the source into the objects.

I told him about your work, so, this is perfect timing.

Can we get a pre-print of your paper?

Also, you mention below that you are not using plugins, and are 
transforming directly from XML into the schema.   Sounds like you are 
not using the object layer.   But, the object layer and ga have benefits 
like handling overhead rows, algorithm tracking and versioning.   How do 
you handle that stuff?   Would it be possible to modify your approach to 
fit into the plugin framework so that, instead of going to the schema 
directly, it goes into the objects?   Or, am did i misinterpret and are 
you doing this already?

Thanks,
steve

Terry Clark wrote:

>One component of schema evolution is getting data 
>into the schema; another side is moving new data 
>into existing schema. 
>
>Folks at UChicago and I have worked out an XML
>based strategy for incorporating data into GUS. 
>The idea is around a GUS XML that contains key constraints
>as attributes, which is interpretted by a byacc
>parser and processor (together these are a plugin).
>The data-to-schema routing happens by way of the XML
>and grammar.
>
>There is a paper to appear in Applied Bioinformatics
>(probably the next issue) about our GUX XML processed
>by XMLGUS. We find this a useful tool in our production 
>work. 
>
>Now writing plugins is unnecessary for us apart 
>from occasional special cases, which XMLGUS has hooks for.
>We now use XML and context free grammars to define the
>mapping from data to schema, in most of our cases. 
>There is one case my colleague found it easier to write
>a plugin from scratch    - I have yet to study this to
>see what caused this.
>
>The GUS install needs a way to incorporate local tables.
>A GUS table need not be part of the canonical set of 
>tables; some can be site specific. We add local tables now, 
>but the process is very ad hoc. 
>
>Presently, we are working now on automating the production
>of the XMLGUS framework, and the table problem. It would
>be useful to see what people are thinking about and
>where the needs are.
>
>Maybe such ideas could be discussed at a GUS meeting?
>
>cheers,
>
>Terry
>
>
>
>
>
>On  0, Sucheta Tripathy <su...@vb...> wrote:
>  
>
>>Steve,
>>
>>We at VBI welcome the idea of releasing a version with install data.
>>
>>This has been the main cause of concern for GUS users who had to spend
>>lots of time finding the pre-requisite data .
>>
>>We can certainly contribute to the initial dataset.
>>
>>In addition we would be more interested to initiate a discussion on
>>functional annotation.
>>
>>cheers
>>
>>Sucheta
>>
>>    
>>
>>>folks-
>>>
>>>some people here at cbil and also at uga have begun thinking about how
>>>to improve the GUS install, and how to manage schema evolution.
>>>
>>>the two pieces of the gus install are:
>>>   (1) the database schema and initial data
>>>   (2) the software
>>>
>>>mike at cbil has made progress on (1), and it seems like alan, ed and
>>>haiming at uga have ideas about this.
>>>
>>>mike is promising to write to the group to give a report on his efforts.
>>>
>>>so, maybe that will be a good way to get the discussion rolling....
>>>
>>>if folks have ideas or energy to tackle (2) that would be great.
>>>
>>>steve
>>>
>>>
>>>
>>>
>>>
>>>-------------------------------------------------------
>>>This SF.net email is sponsored by: IT Product Guide on ITManagersJournal
>>>Use IT products in your business? Tell us what you think of them. Give us
>>>Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out
>>>more
>>>http://productguide.itmanagersjournal.com/guidepromo.tmpl
>>>_______________________________________________
>>>Gusdev-gusdev mailing list
>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>      
>>>
>>-- 
>>Sucheta Tripathy
>>Virginia Bioinformatics Institute Phase-I
>>Washington street.
>>Virginia Tech.
>>Blacksburg,VA 24061-0447
>>phone:(540)231-8138
>>Fax:  (540) 231-2606
>>
>>
>>-------------------------------------------------------
>>This SF.net email is sponsored by: IT Product Guide on ITManagersJournal
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>>Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more
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>>    
>>
>
>
>-------------------------------------------------------
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Re: [Gusdev-gusdev] improving GUS install/evolution

[Terry C. <tc...@it...>]

One component of schema evolution is getting data 
into the schema; another side is moving new data 
into existing schema. 

Folks at UChicago and I have worked out an XML
based strategy for incorporating data into GUS. 
The idea is around a GUS XML that contains key constraints
as attributes, which is interpretted by a byacc
parser and processor (together these are a plugin).
The data-to-schema routing happens by way of the XML
and grammar.

There is a paper to appear in Applied Bioinformatics
(probably the next issue) about our GUX XML processed
by XMLGUS. We find this a useful tool in our production 
work. 

Now writing plugins is unnecessary for us apart 
from occasional special cases, which XMLGUS has hooks for.
We now use XML and context free grammars to define the
mapping from data to schema, in most of our cases. 
There is one case my colleague found it easier to write
a plugin from scratch    - I have yet to study this to
see what caused this.

The GUS install needs a way to incorporate local tables.
A GUS table need not be part of the canonical set of 
tables; some can be site specific. We add local tables now, 
but the process is very ad hoc. 

Presently, we are working now on automating the production
of the XMLGUS framework, and the table problem. It would
be useful to see what people are thinking about and
where the needs are.

Maybe such ideas could be discussed at a GUS meeting?

cheers,

Terry





On  0, Sucheta Tripathy <su...@vb...> wrote:
> Steve,
> 
> We at VBI welcome the idea of releasing a version with install data.
> 
> This has been the main cause of concern for GUS users who had to spend
> lots of time finding the pre-requisite data .
> 
> We can certainly contribute to the initial dataset.
> 
> In addition we would be more interested to initiate a discussion on
> functional annotation.
> 
> cheers
> 
> Sucheta
> 
> > folks-
> >
> > some people here at cbil and also at uga have begun thinking about how
> > to improve the GUS install, and how to manage schema evolution.
> >
> > the two pieces of the gus install are:
> >    (1) the database schema and initial data
> >    (2) the software
> >
> > mike at cbil has made progress on (1), and it seems like alan, ed and
> > haiming at uga have ideas about this.
> >
> > mike is promising to write to the group to give a report on his efforts.
> >
> > so, maybe that will be a good way to get the discussion rolling....
> >
> > if folks have ideas or energy to tackle (2) that would be great.
> >
> > steve
> >
> >
> >
> >
> >
> > -------------------------------------------------------
> > This SF.net email is sponsored by: IT Product Guide on ITManagersJournal
> > Use IT products in your business? Tell us what you think of them. Give us
> > Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out
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> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
> 
> 
> -- 
> Sucheta Tripathy
> Virginia Bioinformatics Institute Phase-I
> Washington street.
> Virginia Tech.
> Blacksburg,VA 24061-0447
> phone:(540)231-8138
> Fax:  (540) 231-2606
> 
> 
> -------------------------------------------------------
> This SF.net email is sponsored by: IT Product Guide on ITManagersJournal
> Use IT products in your business? Tell us what you think of them. Give us
> Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more
> http://productguide.itmanagersjournal.com/guidepromo.tmpl
> _______________________________________________
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> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [Gusdev-gusdev] improving GUS install/evolution

[Steve F. <sfi...@pc...>]

ok.   great.   lets keep this going as part of the discussion.

steve

Sucheta Tripathy wrote:

>Steve,
>
>We at VBI welcome the idea of releasing a version with install data.
>
>This has been the main cause of concern for GUS users who had to spend
>lots of time finding the pre-requisite data .
>
>We can certainly contribute to the initial dataset.
>
>In addition we would be more interested to initiate a discussion on
>functional annotation.
>
>cheers
>
>Sucheta
>
>  
>
>>folks-
>>
>>some people here at cbil and also at uga have begun thinking about how
>>to improve the GUS install, and how to manage schema evolution.
>>
>>the two pieces of the gus install are:
>>   (1) the database schema and initial data
>>   (2) the software
>>
>>mike at cbil has made progress on (1), and it seems like alan, ed and
>>haiming at uga have ideas about this.
>>
>>mike is promising to write to the group to give a report on his efforts.
>>
>>so, maybe that will be a good way to get the discussion rolling....
>>
>>if folks have ideas or energy to tackle (2) that would be great.
>>
>>steve
>>
>>
>>
>>
>>
>>-------------------------------------------------------
>>This SF.net email is sponsored by: IT Product Guide on ITManagersJournal
>>Use IT products in your business? Tell us what you think of them. Give us
>>Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out
>>more
>>http://productguide.itmanagersjournal.com/guidepromo.tmpl
>>_______________________________________________
>>Gusdev-gusdev mailing list
>>Gus...@li...
>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>    
>>
>
>
>  
>

Re: [Gusdev-gusdev] improving GUS install/evolution

[Sucheta T. <su...@vb...>]

Steve,

We at VBI welcome the idea of releasing a version with install data.

This has been the main cause of concern for GUS users who had to spend
lots of time finding the pre-requisite data .

We can certainly contribute to the initial dataset.

In addition we would be more interested to initiate a discussion on
functional annotation.

cheers

Sucheta

> folks-
>
> some people here at cbil and also at uga have begun thinking about how
> to improve the GUS install, and how to manage schema evolution.
>
> the two pieces of the gus install are:
>    (1) the database schema and initial data
>    (2) the software
>
> mike at cbil has made progress on (1), and it seems like alan, ed and
> haiming at uga have ideas about this.
>
> mike is promising to write to the group to give a report on his efforts.
>
> so, maybe that will be a good way to get the discussion rolling....
>
> if folks have ideas or energy to tackle (2) that would be great.
>
> steve
>
>
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: IT Product Guide on ITManagersJournal
> Use IT products in your business? Tell us what you think of them. Give us
> Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out
> more
> http://productguide.itmanagersjournal.com/guidepromo.tmpl
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>


-- 
Sucheta Tripathy
Virginia Bioinformatics Institute Phase-I
Washington street.
Virginia Tech.
Blacksburg,VA 24061-0447
phone:(540)231-8138
Fax:  (540) 231-2606

Re: [Gusdev-gusdev] improving GUS install/evolution

[Jinal J. <jjh...@vb...>]

Steve,

I would be more than happy to express my views/give suggestions on this. We=
=20
have an interoperability working group at VBI (right now focused on GUS=20
related matters) and I am cc'ing  this message to them as well if they woul=
d=20
like to express their views on this matter.

I will try to send a brief report on this pretty soon.


=2D-Jinal

On Friday 01 October 2004 11:15 am, Steve Fischer wrote:
> some people here at cbil and also at uga have begun thinking about how
> to improve the GUS install, and how to manage schema evolution.
>
> the two pieces of the gus install are:
> =A0 =A0(1) the database schema and initial data
> =A0 =A0(2) the software
>
> mike at cbil has made progress on (1), and it seems like alan, ed and
> haiming at uga have ideas about this.
>
> mike is promising to write to the group to give a report on his efforts.
>
> so, maybe that will be a good way to get the discussion rolling....
>
> if folks have ideas or energy to tackle (2) that would be great.
>
> steve

[Gusdev-gusdev] improving GUS install/evolution

[Steve F. <sfi...@pc...>]

folks-

some people here at cbil and also at uga have begun thinking about how 
to improve the GUS install, and how to manage schema evolution.

the two pieces of the gus install are:
   (1) the database schema and initial data
   (2) the software

mike at cbil has made progress on (1), and it seems like alan, ed and 
haiming at uga have ideas about this.

mike is promising to write to the group to give a report on his efforts.

so, maybe that will be a good way to get the discussion rolling....

if folks have ideas or energy to tackle (2) that would be great.

steve

[Gusdev-gusdev] Oracle version

[Craig A. C. <cr...@st...>]

Hi there,

I am preparing to install GUS and I first need to install Oracle.  Can I
install any versions newer than 9i? Thanks.

-Craig

[Gusdev-gusdev] added view for RAD3.ElementResultImp

[Elisabetta M. <man...@pc...>]

We are creating the following new view to accomodate QuantArray results:

CREATE VIEW RAD3.QuantArrayElementResult AS SELECT
  element_result_id,
  element_id,
  composite_element_result_id,
  quantification_id,
  subclass_view,
  foreground AS intensity,
  background,
  foreground_sd AS intensity_sdev,
  background_sd AS background_sdev,
  float1 As x_location,
  float2 AS y_location,
  float3 AS diameter,
  float4 AS area,
  float5 AS footprint,
  float6 AS circularity,
  float7 AS spot_uniformity,
  float8 AS bkg_uniformity,
  float9 AS sn_ratio,
  float10 AS confidence,
  tinyint1 AS diameter_filter
  tinyint2 AS area_filter,
  tinyint3 AS footprint_filter,
  smallint1 AS circularity_filter,
  smallint2 AS spot_uniformity_filter,
  smallint3 AS bkg_uniformity_filter,
  int1 AS sn_ratio_filter,
  int2 AS replicate_filter,
  int3   AS ignore_filter,
  modification_date,
  user_read,
  user_write,
  group_read,
  group_write,
  other_read,
  other_write,
  row_user_id,
  row_group_id,
  row_project_id,
  row_alg_invocation_id
FROM ElementResultImp
WHERE subclass_view = 'QuantArrayElementResult' WITH CHECK OPTION;
--

CREATE OR REPLACE VIEW Rad3ver.QuantArrayElementResultVer AS
  SELECT
  element_result_id,
  element_id,
  composite_element_result_id,
  quantification_id,
  subclass_view,
  foreground AS intensity,
  background,
  foreground_sd AS intensity_sdev,
  background_sd AS background_sdev,
  float1 As x_location,
  float2 AS y_location,
  float3 AS diameter,
  float4 AS area,
  float5 AS footprint,
  float6 AS circularity,
  float7 AS spot_uniformity,
  float8 AS bkg_uniformity,
  float9 AS sn_ratio,
  float10 AS confidence,
  tinyint1 AS diameter_filter
  tinyint2 AS area_filter,
  tinyint3 AS footprint_filter,
  smallint1 AS circularity_filter,
  smallint2 AS spot_uniformity_filter,
  smallint3 AS bkg_uniformity_filter,
  int1 AS sn_ratio_filter,
  int2 AS replicate_filter,
  int3   AS ignore_filter,
  modification_date,
  user_read,
  user_write,
  group_read,
  group_write,
  other_read,
  other_write,
  row_user_id,
  row_group_id,
  row_project_id,
  row_alg_invocation_id,
  version_alg_invocation_id,
  version_date,
  version_transaction_id
FROM RAD3ver.ElementResultImpVer WHERE subclass_view =
'QuantArrayElementResult'
WITH CHECK OPTION
--

[Gusdev-gusdev] two new tables for protein secondary structure predictions

[John I. <io...@pc...>]

All,

Shailesh has generated some secondary-structure predictions.  Below are
proposed GUS tables to store them.

An immediate application for the data is the addition of a new stripe to
the PlasmoDB "Prediction protein features" graphic (which currently
looks like this:
http://plasmodb.org/plasmodb/servlet/sv?page=gene&source_id=PFD0830w&view=proteinset#proteinGraphic
).

The prediction process amounts to assigning a secondary structure, such
as "helix", to each amino acid in the protein, together with a
confidence score for the prediction.  Multiple predictions (each with
low confidence) can be made at the same amino acid.

Thanks in advance for any comments.

John

---------------------------------------------------------
 
create table SecondaryStructure (
 secondary_structure_id NUMBER(10) PRIMARY KEY,
 aa_sequence_id NUMBER(10) NOT NULL,
 algorithm_id NUMBER(10) NOT NULL,
 modification_date DATE NOT NULL,
 user_read NUMBER(1) NOT NULL,
 user_write NUMBER(1) NOT NULL,
 group_read NUMBER(1) NOT NULL,
 group_write NUMBER(1) NOT NULL,
 other_read NUMBER(1) NOT NULL,
 other_write NUMBER(1) NOT NULL,
 row_user_id NUMBER(12) NOT NULL,
 row_group_id NUMBER(3) NOT NULL,
 row_project_id NUMBER(4) NOT NULL,
 row_alg_invocation_id NUMBER(12) NOT NULL,
 CONSTRAINT SecondaryStructure_fk01
   FOREIGN KEY (aa_sequence_id)
   REFERENCES DoTS.AaSequenceImp (aa_sequence_id),
 CONSTRAINT SecondaryStructure_fk02
   FOREIGN KEY (algorithm_id)
   REFERENCES Core.Algorithm (algorithm_id)
);
 
create table SecondaryStructureCall (
 secondary_structure_call_id NUMBER(10) PRIMARY KEY,
 secondary_structure_id NUMBER(10) NOT NULL,
 structure_type varchar(1) NOT NULL,
 call_confidence CLOB,
 CONSTRAINT SecondaryStructureCall_fk01
   FOREIGN KEY (secondary_structure_id)
   REFERENCES SecondaryStructure (secondary_structure_id)
);

Re: [Gusdev-gusdev] (no subject)

[Deborah F. P. <pi...@pc...>]

The parser requires a value for --gbRel which should be a number, the 
release number issued by genbank and generally found in their 
README.genbank file at ftp://ftp.ncbi.nih.gov/genbank/. The parser dies 
otherwise. Could you have given it this source_id like designation, 
AAEE0100000000, as the release number?

                                                     Debbie

On Mon, 27 Sep 2004, Deborah F. Pinney wrote:

> I think the error is actually created_rel_ver which should be a number not a 
> string. This seems to be the source_id. The date is OK. I'm not sure why the 
> parser is using the source_id as the created_rel_ver value.
>
>                                             -Debbie
>
> On Mon, 27 Sep 2004, Ed Robinson wrote:
>
>> Everything is parsing now, but I am still getting a SQL error so nothing 
>> is going in.  Here is the SQL:
>> 
>>  INSERT INTO DoTS.NAEntry (  created_date, row_user_id, user_write, 
>> group_write, created_rel_ver, na_sequence_id, row_project_id, group_read, 
>> row_group_id, other_read, na_entry_id, source_id, modification_date, 
>> user_read, row_alg_invocation_id, other_write, version, division )
>>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? 
>> )
>> Values: 2004-4-05 00:00:00, 1, 1, 1, AAEE0100000000, 43, 1, 1, 1, 1, 43, 
>> AAEE01000001, 1, 104, 0, 1, INV
>> 
>> As far as I can tell, it's all good except for the format of the date. 
>> Here is the full error from the error log.  All 18 chromosomes return the 
>> same error:
>> 
>> Again, thanks for everyone's help on this.
>> 
>> 
>> -Ed
>> 
>> ----
>> 
>> ------------------ entry number 1 -----------------
>> 
>> SQL ERROR!! involving
>> 
>>    INSERT INTO DoTS.NAEntry (  created_date, row_user_id, user_write, 
>> group_write, created_rel_ver, na_sequence_id, row_project_id, group_read, 
>> row_group_id, other_read, na_entry_id, source_id, modification_date, 
>> user_read, row_alg_invocation_id, other_write, version, division )
>>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? 
>> )
>> Values: 2004-4-05 00:00:00, 1, 1, 1, AAEE0100000000, 43, 1, 1, 1, 1, 43, 
>> AAEE01000001, 1, 104, 0, 1, INV at 
>> /var/local/GUSTest/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 185
>>        GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x8ab7b78)', 
>> '^J SQL ERROR!! involving^J ^J    INSERT INTO DoTS.NAEntry (  create...') 
>> called at /var/local/GUSTest/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm 
>> line 148
>>        GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x8ab7b78)', 
>> 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x9ce0958)', 'ARRAY(0x9ce0808)', '^J 
>> INSERT INTO DoTS.NAEntry (  created_date, row_user_id, user...') called at 
>> /var/local/GUSTest/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 681
>>        GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::DoTS::NAEntry=HASH(0x949ea18)', 
>> 'HASH(0x9cc906c)') called at 
>> /var/local/GUSTest/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 628
>>        GUS::ObjRelP::DbiRow::insert('GUS::Model::DoTS::NAEntry=HASH(0x949ea18)') 
>> called at /var/local/GUSTest/gus_home/lib/perl/GUS/Model/GusRow.pm line 
>> 1677
>>        GUS::Model::GusRow::submit('GUS::Model::DoTS::NAEntry=HASH(0x949ea18)', 
>> undef, 1) called at 
>> /var/local/GUSTest/gus_home/lib/perl/GUS/Model/GusRow.pm line 1764
>>        GUS::Model::GusRow::submitChildrenInClass('GUS::Model::DoTS::ExternalNASequence=HASH(0x94a084c)', 
>> 'GUS::Model::DoTS::NAEntry') called at 
>> /var/local/GUSTest/gus_home/lib/perl/GUS/Model/GusRow.pm line 1745
>>        GUS::Model::GusRow::submitAllChildren('GUS::Model::DoTS::ExternalNASequence=HASH(0x94a084c)') 
>> called at /var/local/GUSTest/gus_home/lib/perl/GUS/Model/GusRow.pm line 
>> 1684
>>        GUS::Model::GusRow::submit('GUS::Model::DoTS::ExternalNASequence=HASH(0x94a084c)') 
>> called at 
>> /var/local/GUSTest/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 
>> 284
>>        GUS::Common::Plugin::GBParser::processEntry('GUS::Common::Plugin::GBParser=HASH(0x8106d54)', 
>> 'CBIL::Bio::GenBank::ArrayStream=HASH(0x90e130c)') called at 
>> /var/local/GUSTest/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 
>> 185
>>        eval {...} called at 
>> /var/local/GUSTest/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 
>> 184
>>        GUS::Common::Plugin::GBParser::run('GUS::Common::Plugin::GBParser=HASH(0x8106d54)', 
>> 'HASH(0x8d0a8f8)') called at 
>> /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 
>> 453
>>        eval {...} called at 
>> /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 
>> 450
>>        GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 
>> 'GUS::Common::Plugin::GBParser', 1) called at 
>> /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 
>> 383
>>        GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 
>> 'GUS::Common::Plugin::GBParser') called at 
>> /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 
>> 289
>>        GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 
>> 'GUS::Common::Plugin::GBParser') called at 
>> /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 
>> 198
>> 
>>        GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 
>> 'ARRAY(0x8102dec)') called at /var/local/GUSTest/gus_home/bin/ga line 11
>> 
>> 
>> Ed Robinson
>> 255 Deerfield Rd
>> Bogart, GA 30622
>> (706)425-9181
>> http://www.electedrobinson.com
>> 
>> --Learn more about the face of your neighbor, and less about your own.
>>         -Sargent Shriver
>> 
>> 
>> 
>> 
>> 
>> -------------------------------------------------------
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>> 
>
>
> -------------------------------------------------------
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Re: [Gusdev-gusdev] (no subject)

[Deborah F. P. <pi...@pc...>]

I think the error is actually created_rel_ver which should be a number not 
a string. This seems to be the source_id. The date is OK. I'm not sure why 
the parser is using the source_id as the created_rel_ver value.

                                              -Debbie

On Mon, 27 Sep 2004, Ed Robinson wrote:

> Everything is parsing now, but I am still getting a SQL error so nothing is going in.  Here is the SQL:
>
>  INSERT INTO DoTS.NAEntry (  created_date, row_user_id, user_write, group_write, created_rel_ver, na_sequence_id, row_project_id, group_read, row_group_id, other_read, na_entry_id, source_id, modification_date, user_read, row_alg_invocation_id, other_write, version, division )
>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> Values: 2004-4-05 00:00:00, 1, 1, 1, AAEE0100000000, 43, 1, 1, 1, 1, 43, AAEE01000001, 1, 104, 0, 1, INV
>
> As far as I can tell, it's all good except for the format of the date.  Here is the full error from the error log.  All 18 chromosomes return the same error:
>
> Again, thanks for everyone's help on this.
>
>
> -Ed
>
> ----
>
> ------------------ entry number 1 -----------------
>
> SQL ERROR!! involving
>
>    INSERT INTO DoTS.NAEntry (  created_date, row_user_id, user_write, group_write, created_rel_ver, na_sequence_id, row_project_id, group_read, row_group_id, other_read, na_entry_id, source_id, modification_date, user_read, row_alg_invocation_id, other_write, version, division )
>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> Values: 2004-4-05 00:00:00, 1, 1, 1, AAEE0100000000, 43, 1, 1, 1, 1, 43, AAEE01000001, 1, 104, 0, 1, INV at /var/local/GUSTest/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 185
>        GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x8ab7b78)', '^J SQL ERROR!! involving^J ^J    INSERT INTO DoTS.NAEntry (  create...') called at /var/local/GUSTest/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 148
>        GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x8ab7b78)', 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x9ce0958)', 'ARRAY(0x9ce0808)', '^J    INSERT INTO DoTS.NAEntry (  created_date, row_user_id, user...') called at /var/local/GUSTest/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 681
>        GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::DoTS::NAEntry=HASH(0x949ea18)', 'HASH(0x9cc906c)') called at /var/local/GUSTest/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 628
>        GUS::ObjRelP::DbiRow::insert('GUS::Model::DoTS::NAEntry=HASH(0x949ea18)') called at /var/local/GUSTest/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
>        GUS::Model::GusRow::submit('GUS::Model::DoTS::NAEntry=HASH(0x949ea18)', undef, 1) called at /var/local/GUSTest/gus_home/lib/perl/GUS/Model/GusRow.pm line 1764
>        GUS::Model::GusRow::submitChildrenInClass('GUS::Model::DoTS::ExternalNASequence=HASH(0x94a084c)', 'GUS::Model::DoTS::NAEntry') called at /var/local/GUSTest/gus_home/lib/perl/GUS/Model/GusRow.pm line 1745
>        GUS::Model::GusRow::submitAllChildren('GUS::Model::DoTS::ExternalNASequence=HASH(0x94a084c)') called at /var/local/GUSTest/gus_home/lib/perl/GUS/Model/GusRow.pm line 1684
>        GUS::Model::GusRow::submit('GUS::Model::DoTS::ExternalNASequence=HASH(0x94a084c)') called at /var/local/GUSTest/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 284
>        GUS::Common::Plugin::GBParser::processEntry('GUS::Common::Plugin::GBParser=HASH(0x8106d54)', 'CBIL::Bio::GenBank::ArrayStream=HASH(0x90e130c)') called at /var/local/GUSTest/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 185
>        eval {...} called at /var/local/GUSTest/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 184
>        GUS::Common::Plugin::GBParser::run('GUS::Common::Plugin::GBParser=HASH(0x8106d54)', 'HASH(0x8d0a8f8)') called at /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 453
>        eval {...} called at /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 450
>        GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::GBParser', 1) called at /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
>        GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::GBParser') called at /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 289
>        GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::GBParser') called at /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 198
>
>        GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'ARRAY(0x8102dec)') called at /var/local/GUSTest/gus_home/bin/ga line 11
>
>
> Ed Robinson
> 255 Deerfield Rd
> Bogart, GA 30622
> (706)425-9181
> http://www.electedrobinson.com
>
> --Learn more about the face of your neighbor, and less about your own.
>         -Sargent Shriver
>
>
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
> Project Admins to receive an Apple iPod Mini FREE for your judgement on
> who ports your project to Linux PPC the best. Sponsored by IBM.
> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

[Gusdev-gusdev] (no subject)

[Ed R. <ed_...@be...>]

Everything is parsing now, but I am still getting a SQL error so nothing is going in.  Here is the SQL:

  INSERT INTO DoTS.NAEntry (  created_date, row_user_id, user_write, group_write, created_rel_ver, na_sequence_id, row_project_id, group_read, row_group_id, other_read, na_entry_id, source_id, modification_date, user_read, row_alg_invocation_id, other_write, version, division )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
 Values: 2004-4-05 00:00:00, 1, 1, 1, AAEE0100000000, 43, 1, 1, 1, 1, 43, AAEE01000001, 1, 104, 0, 1, INV 

As far as I can tell, it's all good except for the format of the date.  Here is the full error from the error log.  All 18 chromosomes return the same error:

Again, thanks for everyone's help on this. 


-Ed

----

 ------------------ entry number 1 -----------------
                                                                                                                             
 SQL ERROR!! involving
                                                                                                                             
    INSERT INTO DoTS.NAEntry (  created_date, row_user_id, user_write, group_write, created_rel_ver, na_sequence_id, row_project_id, group_read, row_group_id, other_read, na_entry_id, source_id, modification_date, user_read, row_alg_invocation_id, other_write, version, division )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
 Values: 2004-4-05 00:00:00, 1, 1, 1, AAEE0100000000, 43, 1, 1, 1, 1, 43, AAEE01000001, 1, 104, 0, 1, INV at /var/local/GUSTest/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 185
        GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x8ab7b78)', '^J SQL ERROR!! involving^J ^J    INSERT INTO DoTS.NAEntry (  create...') called at /var/local/GUSTest/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 148
        GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x8ab7b78)', 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x9ce0958)', 'ARRAY(0x9ce0808)', '^J    INSERT INTO DoTS.NAEntry (  created_date, row_user_id, user...') called at /var/local/GUSTest/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 681
        GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::DoTS::NAEntry=HASH(0x949ea18)', 'HASH(0x9cc906c)') called at /var/local/GUSTest/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 628
        GUS::ObjRelP::DbiRow::insert('GUS::Model::DoTS::NAEntry=HASH(0x949ea18)') called at /var/local/GUSTest/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
        GUS::Model::GusRow::submit('GUS::Model::DoTS::NAEntry=HASH(0x949ea18)', undef, 1) called at /var/local/GUSTest/gus_home/lib/perl/GUS/Model/GusRow.pm line 1764
        GUS::Model::GusRow::submitChildrenInClass('GUS::Model::DoTS::ExternalNASequence=HASH(0x94a084c)', 'GUS::Model::DoTS::NAEntry') called at /var/local/GUSTest/gus_home/lib/perl/GUS/Model/GusRow.pm line 1745
        GUS::Model::GusRow::submitAllChildren('GUS::Model::DoTS::ExternalNASequence=HASH(0x94a084c)') called at /var/local/GUSTest/gus_home/lib/perl/GUS/Model/GusRow.pm line 1684
        GUS::Model::GusRow::submit('GUS::Model::DoTS::ExternalNASequence=HASH(0x94a084c)') called at /var/local/GUSTest/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 284
        GUS::Common::Plugin::GBParser::processEntry('GUS::Common::Plugin::GBParser=HASH(0x8106d54)', 'CBIL::Bio::GenBank::ArrayStream=HASH(0x90e130c)') called at /var/local/GUSTest/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 185
        eval {...} called at /var/local/GUSTest/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 184
        GUS::Common::Plugin::GBParser::run('GUS::Common::Plugin::GBParser=HASH(0x8106d54)', 'HASH(0x8d0a8f8)') called at /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 453
        eval {...} called at /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 450
        GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::GBParser', 1) called at /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
        GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::GBParser') called at /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 289
        GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::GBParser') called at /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 198

        GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'ARRAY(0x8102dec)') called at /var/local/GUSTest/gus_home/bin/ga line 11


Ed Robinson
255 Deerfield Rd
Bogart, GA 30622
(706)425-9181
http://www.electedrobinson.com

--Learn more about the face of your neighbor, and less about your own.
         -Sargent Shriver

Re: [Gusdev-gusdev] GI Number

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

Hi,

because we are alreaday talking about the GBParser.

I wrote a genbank file with all possible features...(hope it is so)... 
the result of missing stuff is attached... I do not know if it makes 
sense to include all, or maybe try to do it automatically...

Cheers,
Thomas

Re: [Gusdev-gusdev] GI Number

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

Hi,

instead of doing
touch $PROJECT_HOME/GUS/Model/schema/VERSION
build GUS/Model install -append # in the $PROJECT_HOME directory...
-- important is the touch

you can also just use the programm
generateGusObjects
to just build the pm's (perl-modul) for this view

I wrote a little bash file, attached, that already (chmod 755 generate.sh)
./generate.sh DoTS GeneFeatureJinal

Cheers,
Thomas


Jhaveri wrote:

>They are created automatically when you compile or build gus
>
>On Monday 27 September 2004 12:50 pm, you wrote:
>  
>
>>What about the PERL objects in Model/ ?  Do we need to modify any of those
>>so they will work with the modified views?
>>
>>-Ed
>>
>>    
>>
>>>From: "Deborah F. Pinney" <pi...@pc...>
>>>Date: 2004/09/27 Mon PM 12:28:38 EDT
>>>To: Angel Pizarro <an...@pc...>
>>>CC: Ed Robinson <ed_...@be...>,
>>>        Jinal Jhaveri <jjh...@vb...>,
>>>        gus...@li...
>>>Subject: Re: [Gusdev-gusdev] GI Number
>>>
>>>Angel is correct. locus_tag is a relatively new (new to the GBParser)
>>>qualifier for existing features, including gene which is already mapped
>>>to dots.GeneFeature. Therefore, my advise was wrong, it should not be
>>>added to the mapping list in the perl module. Adding this field to the
>>>view should fix the problem for "gene" features.
>>>
>>>As genbank adds features and qualifiers and since the parser was tailored
>>>for genbank records, we are going to encounter this problem again. A
>>>compounding problem is that a qualifier is generally not exclusive to a
>>>single feature. In this case, locus_id really should be added to many
>>>views.
>>>
>>>                                                   -Debbie
>>>
>>>On Mon, 27 Sep 2004, Angel Pizarro wrote:
>>>      
>>>
>>>>Deborah F. Pinney wrote:
>>>>        
>>>>
>>>>>locus_tag is not in the list of features in the GBParser. It will have
>>>>>to be added with a table(actually view) destination. Which view is
>>>>>appropriate for this feature? What are the attributes (from the
>>>>>Genbank feature table) for this feature? I'll gladly add this and you
>>>>>can test it or you can add it and test and then commit to cvs.
>>>>>          
>>>>>
>>>>Let me clarify. "locus_tag" is not a GenBank feature, it is a feature
>>>>attribute of the GenBank "gene" feature. The feature is belongs to is
>>>>being mapped to DoTS::GeneFeature. Here is the example from the GB
>>>>record for this feature attribute, available here :
>>>>http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=462293
>>>>67
>>>>
>>>>gene
>>>><http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=46229367&itemID=819
>>>>&view=gbwithparts> complement(<6844..>9270)
>>>>                   /locus_tag="cgd7_10"
>>>>
>>>>
>>>>Thomas' suggestion of adding the attribute "locus_tag" to the
>>>>GeneFeature view and recompiling the objects will work in this case,
>>>>but be a problem for anyone else trying to capture this feature
>>>>attribute.
>>>>
>>>>The GBParser has several known problems, this being one of them. Maybe
>>>>we should start up a wiki for it to aid in development and
>>>>documentation.
>>>>
>>>>Angel
>>>>
>>>>        
>>>>
>>>>>It should be added  >line 808, following my %featureNameTableMapping =
>>>>>(
>>>>>
>>>>>If the attributes are correct in the mapped table (match the genbank
>>>>>attributes), this should work. If this table is not in the
>>>>>%classChildList, it should also be added to the appropriate line also.
>>>>>
>>>>>                                               -Deborah
>>>>>
>>>>>On Mon, 27 Sep 2004, Ed Robinson wrote:
>>>>>          
>>>>>
>>>>>>So far, down here, I can tell that it is parsing the files for crypto
>>>>>>correctly, but I is giving me the following error:
>>>>>>
>>>>>>
>>>>>>********GEtting loc below6844
>>>>>>
>>>>>>Mon Sep 27 10:13:09 2004        INVALID QUALIFIER
>>>>>>GUS::Model::DoTS::GeneFeature   ::      locus_tag       ::     
>>>>>>cgd7_10
>>>>>>
>>>>>>Mon Sep 27 10:13:09 2004        INVALID QUALIFIER
>>>>>>GUS::Model::DoTS::Transcript    ::      locus_tag       ::     
>>>>>>cgd7_10
>>>>>>
>>>>>>Do you have any ideas why it is disliking my locus_tags?  I am
>>>>>>running this without the commit on, if it is looking for this again
>>>>>>in the database.
>>>>>>
>>>>>>Thanks for all the help on this.  I don't want to change anything
>>>>>>that is working, just figure out how to use it.
>>>>>>
>>>>>>-Ed
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>Ed Robinson
>>>>>>255 Deerfield Rd
>>>>>>Bogart, GA 30622
>>>>>>(706)425-9181
>>>>>>http://www.electedrobinson.com
>>>>>>
>>>>>>--Learn more about the face of your neighbor, and less about your
>>>>>>own. -Sargent Shriver
>>>>>>            
>>>>>>
>>>>>-------------------------------------------------------
>>>>>This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
>>>>>Project Admins to receive an Apple iPod Mini FREE for your judgement
>>>>>on who ports your project to Linux PPC the best. Sponsored by IBM.
>>>>>Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
>>>>>_______________________________________________
>>>>>Gusdev-gusdev mailing list
>>>>>Gus...@li...
>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>          
>>>>>
>>Ed Robinson
>>255 Deerfield Rd
>>Bogart, GA 30622
>>(706)425-9181
>>http://www.electedrobinson.com
>>
>>--Learn more about the face of your neighbor, and less about your own.
>>         -Sargent Shriver
>>    
>>
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
>Project Admins to receive an Apple iPod Mini FREE for your judgement on
>who ports your project to Linux PPC the best. Sponsored by IBM.
>Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>  
>

Re: [Gusdev-gusdev] GI Number

[Jinal J. <jjh...@vb...>]

Just rebuild gus by using following commands:

touch $PROJECT_HOME/GUS/Model/schema/VERSION
build GUS install -append

or refer this document of wiki!
http://www.gusdb.org/wiki/index.php/Installing%20GUS


On Monday 27 September 2004 01:11 pm, Ed Robinson wrote:
> I modified the views using Oracle Enterprise Manager.  I did not make the
> modifications through a GUS Build.  I have only done a straight GUS
> install, so I am not sure where to make the modifications in the
> project_home to make these changes correctly.
>
> Sorry, I'm still a newbie to GUS, and there isn't much documentation beyond
> he straight-forward installation docs.
>
> -Ed
>
> > From: Jinal Jhaveri <jjh...@vb...>
> > Date: 2004/09/27 Mon PM 01:00:14 EDT
> > To: Ed Robinson <ed_...@be...>
> > CC: gus...@li...
> > Subject: Re: [Gusdev-gusdev] GI Number
> >
> > They are created automatically when you compile or build gus
> >
> > On Monday 27 September 2004 12:50 pm, you wrote:
> > > What about the PERL objects in Model/ ?  Do we need to modify any of
> > > those so they will work with the modified views?
> > >
> > > -Ed
> > >
> > > > From: "Deborah F. Pinney" <pi...@pc...>
> > > > Date: 2004/09/27 Mon PM 12:28:38 EDT
> > > > To: Angel Pizarro <an...@pc...>
> > > > CC: Ed Robinson <ed_...@be...>,
> > > >         Jinal Jhaveri <jjh...@vb...>,
> > > >         gus...@li...
> > > > Subject: Re: [Gusdev-gusdev] GI Number
> > > >
> > > > Angel is correct. locus_tag is a relatively new (new to the GBParser)
> > > > qualifier for existing features, including gene which is already
> > > > mapped to dots.GeneFeature. Therefore, my advise was wrong, it should
> > > > not be added to the mapping list in the perl module. Adding this
> > > > field to the view should fix the problem for "gene" features.
> > > >
> > > > As genbank adds features and qualifiers and since the parser was
> > > > tailored for genbank records, we are going to encounter this problem
> > > > again. A compounding problem is that a qualifier is generally not
> > > > exclusive to a single feature. In this case, locus_id really should
> > > > be added to many views.
> > > >
> > > >                                                    -Debbie
> > > >
> > > > On Mon, 27 Sep 2004, Angel Pizarro wrote:
> > > > > Deborah F. Pinney wrote:
> > > > >> locus_tag is not in the list of features in the GBParser. It will
> > > > >> have to be added with a table(actually view) destination. Which
> > > > >> view is appropriate for this feature? What are the attributes
> > > > >> (from the Genbank feature table) for this feature? I'll gladly add
> > > > >> this and you can test it or you can add it and test and then
> > > > >> commit to cvs.
> > > > >
> > > > > Let me clarify. "locus_tag" is not a GenBank feature, it is a
> > > > > feature attribute of the GenBank "gene" feature. The feature is
> > > > > belongs to is being mapped to DoTS::GeneFeature. Here is the
> > > > > example from the GB record for this feature attribute, available
> > > > > here :
> > > > > http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=46
> > > > >2293 67
> > > > >
> > > > > gene
> > > > > <http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=46229367&itemID
> > > > >=819 &view=gbwithparts> complement(<6844..>9270)
> > > > >                    /locus_tag="cgd7_10"
> > > > >
> > > > >
> > > > > Thomas' suggestion of adding the attribute "locus_tag" to the
> > > > > GeneFeature view and recompiling the objects will work in this
> > > > > case, but be a problem for anyone else trying to capture this
> > > > > feature attribute.
> > > > >
> > > > > The GBParser has several known problems, this being one of them.
> > > > > Maybe we should start up a wiki for it to aid in development and
> > > > > documentation.
> > > > >
> > > > > Angel
> > > > >
> > > > >> It should be added  >line 808, following my
> > > > >> %featureNameTableMapping = (
> > > > >>
> > > > >> If the attributes are correct in the mapped table (match the
> > > > >> genbank attributes), this should work. If this table is not in the
> > > > >> %classChildList, it should also be added to the appropriate line
> > > > >> also.
> > > > >>
> > > > >>                                                -Deborah
> > > > >>
> > > > >> On Mon, 27 Sep 2004, Ed Robinson wrote:
> > > > >>> So far, down here, I can tell that it is parsing the files for
> > > > >>> crypto correctly, but I is giving me the following error:
> > > > >>>
> > > > >>>
> > > > >>> ********GEtting loc below6844
> > > > >>>
> > > > >>> Mon Sep 27 10:13:09 2004        INVALID QUALIFIER
> > > > >>> GUS::Model::DoTS::GeneFeature   ::      locus_tag       ::
> > > > >>> cgd7_10
> > > > >>>
> > > > >>> Mon Sep 27 10:13:09 2004        INVALID QUALIFIER
> > > > >>> GUS::Model::DoTS::Transcript    ::      locus_tag       ::
> > > > >>> cgd7_10
> > > > >>>
> > > > >>> Do you have any ideas why it is disliking my locus_tags?  I am
> > > > >>> running this without the commit on, if it is looking for this
> > > > >>> again in the database.
> > > > >>>
> > > > >>> Thanks for all the help on this.  I don't want to change anything
> > > > >>> that is working, just figure out how to use it.
> > > > >>>
> > > > >>> -Ed
> > > > >>>
> > > > >>>
> > > > >>>
> > > > >>>
> > > > >>>
> > > > >>> Ed Robinson
> > > > >>> 255 Deerfield Rd
> > > > >>> Bogart, GA 30622
> > > > >>> (706)425-9181
> > > > >>> http://www.electedrobinson.com
> > > > >>>
> > > > >>> --Learn more about the face of your neighbor, and less about your
> > > > >>> own. -Sargent Shriver
> > > > >>
> > > > >> -------------------------------------------------------
> > > > >> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
> > > > >> Project Admins to receive an Apple iPod Mini FREE for your
> > > > >> judgement on who ports your project to Linux PPC the best.
> > > > >> Sponsored by IBM. Deadline: Sept. 24. Go here:
> > > > >> http://sf.net/ppc_contest.php
> > > > >> _______________________________________________
> > > > >> Gusdev-gusdev mailing list
> > > > >> Gus...@li...
> > > > >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > >
> > > Ed Robinson
> > > 255 Deerfield Rd
> > > Bogart, GA 30622
> > > (706)425-9181
> > > http://www.electedrobinson.com
> > >
> > > --Learn more about the face of your neighbor, and less about your own.
> > >          -Sargent Shriver
> >
> > -------------------------------------------------------
> > This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
> > Project Admins to receive an Apple iPod Mini FREE for your judgement on
> > who ports your project to Linux PPC the best. Sponsored by IBM.
> > Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
> Ed Robinson
> 255 Deerfield Rd
> Bogart, GA 30622
> (706)425-9181
> http://www.electedrobinson.com
>
> --Learn more about the face of your neighbor, and less about your own.
>          -Sargent Shriver