gusdev-gusdev — Topics concerning GUS development

Re: [Gusdev-gusdev] increasing space for externalaasequence.name

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

Well, As Josef rightly pointed , I guess that can go to description instead 
of name field. Though I don't find a clear demarcation between the two.

For example in this case:

cold inducible similar to other osmotic stress induced gene products 
includin: Tomato abscisic stress ripening protein 1 encoded by GenBank 
Accession Number L08255, Solanum lycopersicum ABA- and ripening-induced 
protein encoded by GenBank Accession Number L20756 and to Solanum chacoense 
abscisic stress ripening protein encoded by GenBank Accession Number U12439 
[Solanum tuberosum]

This happens when I give a --regex_source_id="gi\|(\w+)\|(.*)" 
--regex_secondary_id="gb|emb|dbj|ref|pir|sp\|(\w+)" --regex_name=".*\|(.+)$"
in the insertnewexternalsequence plugin.





At 01:20 PM 11/22/2004 -0500, Steve Fischer wrote:
>can you provide an example of such a name?
>
>steve
>
>Sucheta Tripathy wrote:
>
>>Dear group,
>>
>>I am now uploading data to the externalaasequence, and frequently it gets
>>interrupted because the name has data type varchar2(255), where as some of
>>the names are much longer than that.I was wondering if the table
>>definition can be changed in the distribution to handle this OR is there a
>>reason why this should be kept as varchar2(255)?
>>
>>Thanks
>>
>>Sucheta
>>
>>

Re: [Gusdev-gusdev] increasing space for externalaasequence.name

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

can you provide an example of such a name?

steve

Sucheta Tripathy wrote:

>Dear group,
>
>I am now uploading data to the externalaasequence, and frequently it gets
>interrupted because the name has data type varchar2(255), where as some of
>the names are much longer than that.I was wondering if the table
>definition can be changed in the distribution to handle this OR is there a
>reason why this should be kept as varchar2(255)?
>
>Thanks
>
>Sucheta
>
>  
>

Re: [Gusdev-gusdev] increasing space for externalaasequence.name

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

"Sucheta Tripathy" <su...@vb...> writes:
>
> I am now uploading data to the externalaasequence, and frequently it gets
> interrupted because the name has data type varchar2(255), where as some of
> the names are much longer than that.I was wondering if the table
> definition can be changed in the distribution to handle this OR is there a
> reason why this should be kept as varchar2(255)?

The description column of ExternalNASequence is of type varchar2(2000),
which should be long enough for the full name of your sequence.

A problem we have run into is that the table DoTS.NAFeature
only has the field "name" to describe the feature:

   column          nulls?  type
   name            no      varchar2(30)

and could really use a description field such as:

   description        varchar2(2000)

as the genbank description for many features significantly
exceeds 30 characters.  Sure, the table DoTS.NAFeatureComment
with its "comment_string clob(4000)" column exists, but that
NAFeature lacks a description column is inconsistent with other
GUS tables.


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-gusdev] gus installation

[<fed...@bi...>]

I have other tasks to do and for a while I won't be able to look to the
GUS installation.

If I have good news I'll write you!
Thanks

Federica


> Federica-
>
> Have you had any help yet with these problems?
>
> steve
>
> fed...@bi... wrote:
>
>>Hi folks,
>>I got some problems whit the installation of GUS! I got troubles in 2
>>parts of it!
>>Running the build I have always this problems. Here an
>>exemple (I obtained 12 errors of the same kind):
>>
>>
>>[javac]/opt/projects/GUS/Model/src/java/org/gusdb/model/DoTS/BLATAlignment.java:26:
>> cannot resolve symbol
>>[javac] symbol  : class BLATAlignment_Row
>>[javac] location: class org.gusdb.model.DoTS.BLATAlignment
>>[javac] public class BLATAlignment extends BLATAlignment_Row {
>>[javac]                                    ^
>>
>>
>>
>>And running 'create-db.sh' I always have
>>
>> [root@oracle oracle]# ./create-db.sh
>>
>> SQL*Plus: Release 10.1.0.2.0 - Production on Wed Nov 10 11:59:58 2004
>>
>> Copyright (c) 1982, 2004, Oracle.  All rights reserved.
>>
>> ERROR:
>> ORA-12154: TNS:could not resolve the connect identifier specified
>>
>>
>> Enter user-name: system
>> Enter password:
>> ERROR:
>> ORA-12546: TNS:permission denied
>>
>>Have you got some ideas?
>>thank
>>Federica
>>
>>
>>
>>-------------------------------------------------------
>>This SF.Net email is sponsored by:
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>>
>>
>
>
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[Gusdev-gusdev] increasing space for externalaasequence.name

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

Dear group,

I am now uploading data to the externalaasequence, and frequently it gets
interrupted because the name has data type varchar2(255), where as some of
the names are much longer than that.I was wondering if the table
definition can be changed in the distribution to handle this OR is there a
reason why this should be kept as varchar2(255)?

Thanks

Sucheta

-- 
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] Adding features to the sequence

[Angel P. <an...@pc...>]

Jeetendra Soneja wrote:

>Steve,
>
>     I'm referring to the last case in the list that Angel mentioned. It
>deletes the feature if it is in Db but not in the file. We have a
>scenario where new features are predicted and uploaded in different
>steps. Thus, while uploading the new features predicted in later
>steps, we don't want the features uploaded during previous steps to
>be deleted.
>
>  --Jeetendra.
>
>  
>
Not that hard to fix. Add this line (assuming $flag is your new option) 
to line 1106

next if ($flag);


This will skip the deletion step in the if {} else{}  block
-angel

>
>  
>
>>Jeetendra-
>>
>>I just talked to Angel who wrote this parser a long time ago.
>>
>>He says that the parser is supposed to:
>>  - match the existing features in the db against the new ones mentioned
>>in the gb file
>>  - if a feature is in the file but not in the db, it adds the feature
>>  - if the feature is in both, it leaves the feature alone
>>  - if the feature is in the db but not in the file, it deletes it.
>>
>>is this not what you are observing?
>>
>>steve
>>
>>Jeetendra Soneja wrote:
>>
>>    
>>
>>>Hi all,
>>>
>>>When we try to upload an existing sequence (and features) using the
>>>GBParser, it updates the features of that sequence, i.e. it removes the
>>>old and inserts the new ones.
>>>
>>>However, is there a way to just ADD features (of any type) to the
>>>existing
>>>sequence in the GUS DB ?
>>>
>>>Thanks a lot for your help,
>>>Jeetendra.
>>>
>>>
>>>
>>>
>>>-------------------------------------------------------
>>>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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>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>
>>>      
>>>
>
>
>  
>

Re: [Gusdev-gusdev] Adding features to the sequence

[Jeetendra S. <so...@vb...>]

Steve,

     I'm referring to the last case in the list that Angel mentioned. It
deletes the feature if it is in Db but not in the file. We have a
scenario where new features are predicted and uploaded in different
steps. Thus, while uploading the new features predicted in later
steps, we don't want the features uploaded during previous steps to
be deleted.

  --Jeetendra.



> Jeetendra-
>
> I just talked to Angel who wrote this parser a long time ago.
>
> He says that the parser is supposed to:
>   - match the existing features in the db against the new ones mentioned
> in the gb file
>   - if a feature is in the file but not in the db, it adds the feature
>   - if the feature is in both, it leaves the feature alone
>   - if the feature is in the db but not in the file, it deletes it.
>
> is this not what you are observing?
>
> steve
>
> Jeetendra Soneja wrote:
>
>>Hi all,
>>
>>When we try to upload an existing sequence (and features) using the
>>GBParser, it updates the features of that sequence, i.e. it removes the
>>old and inserts the new ones.
>>
>>However, is there a way to just ADD features (of any type) to the
>> existing
>>sequence in the GUS DB ?
>>
>>Thanks a lot for your help,
>>Jeetendra.
>>
>>
>>
>>
>>-------------------------------------------------------
>>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
>>
>>
>


-- 
Jeetendra Soneja
Research Associate
Virginia Bioinformatics Institute
1880 Pratt Dr., Building XV
Blacksburg, VA 24060, USA
Phone: (540)-231-2789
http://www.vbi.vt.edu

Re: [Gusdev-gusdev] Adding features to the sequence

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

Jeetendra-

I just talked to Angel who wrote this parser a long time ago.

He says that the parser is supposed to:
  - match the existing features in the db against the new ones mentioned 
in the gb file
  - if a feature is in the file but not in the db, it adds the feature
  - if the feature is in both, it leaves the feature alone
  - if the feature is in the db but not in the file, it deletes it.

is this not what you are observing?

steve

Jeetendra Soneja wrote:

>Hi all,
>
>When we try to upload an existing sequence (and features) using the
>GBParser, it updates the features of that sequence, i.e. it removes the
>old and inserts the new ones.
>
>However, is there a way to just ADD features (of any type) to the existing
>sequence in the GUS DB ?
>
>Thanks a lot for your help,
>Jeetendra.
>
>
>
>
>-------------------------------------------------------
>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] Adding features to the sequence

[Jeetendra S. <so...@vb...>]

Hi Steve,
        Since this requirement would be mandatory for our project, I
decided to try and modify the plugin myself. I am trying to add a
command-line option --addFeatures, which would tell GBParser to
just add the features (rather than delete and reinsert). However,
I haven't had a chance to test it.
        I would appreciate your comments on the same.

Thank you,
Jeetendra.



> Jeetendra-
>
> Did you get any help for this question yet?
>
> steve
>
> Jeetendra Soneja wrote:
>
>>Hi all,
>>
>>When we try to upload an existing sequence (and features) using the
>>GBParser, it updates the features of that sequence, i.e. it removes the
>>old and inserts the new ones.
>>
>>However, is there a way to just ADD features (of any type) to the
>> existing
>>sequence in the GUS DB ?
>>
>>Thanks a lot for your help,
>>Jeetendra.
>>
>>
>>
>>
>>-------------------------------------------------------
>>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
>>
>>
>


-- 
Jeetendra Soneja
Research Associate
Virginia Bioinformatics Institute
1880 Pratt Dr., Building XV
Blacksburg, VA 24060, USA
Phone: (540)-231-2789
http://www.vbi.vt.edu

Re: [Gusdev-gusdev] Adding features to the sequence

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

Jeetendra-

Did you get any help for this question yet?

steve

Jeetendra Soneja wrote:

>Hi all,
>
>When we try to upload an existing sequence (and features) using the
>GBParser, it updates the features of that sequence, i.e. it removes the
>old and inserts the new ones.
>
>However, is there a way to just ADD features (of any type) to the existing
>sequence in the GUS DB ?
>
>Thanks a lot for your help,
>Jeetendra.
>
>
>
>
>-------------------------------------------------------
>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] gus installation

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

Federica-

Have you had any help yet with these problems?

steve

fed...@bi... wrote:

>Hi folks,
>I got some problems whit the installation of GUS! I got troubles in 2
>parts of it!
>Running the build I have always this problems. Here an
>exemple (I obtained 12 errors of the same kind):
>
>
>[javac]/opt/projects/GUS/Model/src/java/org/gusdb/model/DoTS/BLATAlignment.java:26:
> cannot resolve symbol
>[javac] symbol  : class BLATAlignment_Row
>[javac] location: class org.gusdb.model.DoTS.BLATAlignment
>[javac] public class BLATAlignment extends BLATAlignment_Row {
>[javac]                                    ^
>
>
>
>And running 'create-db.sh' I always have
>
> [root@oracle oracle]# ./create-db.sh
>
> SQL*Plus: Release 10.1.0.2.0 - Production on Wed Nov 10 11:59:58 2004
>
> Copyright (c) 1982, 2004, Oracle.  All rights reserved.
>
> ERROR:
> ORA-12154: TNS:could not resolve the connect identifier specified
>
>
> Enter user-name: system
> Enter password:
> ERROR:
> ORA-12546: TNS:permission denied
>
>Have you got some ideas?
>thank
>Federica
>
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by:
>Sybase ASE Linux Express Edition - download now for FREE
>LinuxWorld Reader's Choice Award Winner for best database on Linux.
>http://ads.osdn.com/?ad_id=5588&alloc_id=12065&op=click
>_______________________________________________
>Gusdev-gusdev mailing list
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>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

[Gusdev-gusdev] new version of MAS5StudyModuleILoader plugin now available

[Shailesh D. <sv...@pc...>]

an updated version the MAS5StudyModuleILoader plugin, the associated 
sample config file, and documentation is now available in via the sanger 
cvs. please update your copies accordingly.

Multiple changes:

- Method changes:
   1. The plugin had memory problems due to the very large number of
   objects created and stored before submission. This is now changed, the
   plugin creates and submits each assay.

- Bug fixes:
   1. Bug related to date/time modification (12pm was not being
   represented).

- Enhancements:
   1. Users may/may not use trailing slashes '/' for file paths.
   2. Users can now specify file extensions for each type of file: EXP,
   RPT, CEL, DAT and Metrics files

similar changes are being planned for GenePixStudyModuleILoader plugin, 
and will be announced in due time.

------------------------------------------------
  SHAILESH DATE, Postdoctoral Fellow
  1423 Blockley Hall, Center for Bioinformatics,
  423 Guardian Dr., University of Pennsylvania,
  Philadelphia, PA 19104
  Phone: 215-746-7020 | FAX: 215-573-3111
------------------------------------------------

Re: [Gusdev-gusdev] prerequisites for RAD ArrayLoader

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

Kevin,

> So, for instance, in an array load data file I got from CBIL 
> (HG-U133A.forRAD.txt), the ext_db_rel_id column is 2 for all rows, where 2 
> refers to a release id in CBIL's database that indirectly links to an 
> SRES.ExternalDatabase record that might represent GenBank?  (Is it Genbank, 
> in this case?) And the source_id column might contain the accession number of 
> a Genbank sequence (e.g. U48705) to which this probe row is related?

Yes, it's Genbank.

> Our GUS instance does not have GenBank loaded yet.

What do you mean by loaded? You do not have to have the actual data from 
Genbank in your database. You only need to have one entry in 
SRes.ExternalDatabase denoting the Genbank database and then one or more 
entries in SRes.ExternalDatabaseRelease pointing to the latter. (In our 
instance we only keep one general ExternalDatabaseRelease entry for 
Genbank.)

> Is it OK just to put in a placeholder record for GenBank in 
> SRES.ExternalDatabase and then replace '2' 
> with whatever our release id winds up being in the corresponding 
> SRES.ExternalDatabaseRelease record?

Yes, that's what you need to do.
Elisabetta

Re: [Gusdev-gusdev] prerequisites for RAD ArrayLoader

[Kevin M. <mu...@ge...>]

On Nov 15, 2004, at 12:54 PM, Elisabetta Manduchi wrote:
> yes you'll need to have the relevant entry in 
> SRes.ExternalDatabaseRelease if you want to enter 
> (external_database_release_id, source_id) in any given GUS table and 
> you create this in the order you outline.

Pardon my thickness.

So, for instance, in an array load data file I got from CBIL 
(HG-U133A.forRAD.txt), the ext_db_rel_id column is 2 for all rows, 
where 2 refers to a release id in CBIL's database that indirectly links 
to an SRES.ExternalDatabase record that might represent GenBank?  (Is 
it Genbank, in this case?) And the source_id column might contain the 
accession number of  a Genbank sequence (e.g. U48705) to which this 
probe row is related?

Our GUS instance does not have GenBank loaded yet.  Is it OK just to 
put in a placeholder record for GenBank in SRES.ExternalDatabase and 
then replace '2' with whatever our release id winds up being in the 
corresponding SRES.ExternalDatabaseRelease record?

Thanks,
Kevin Murphy

Re: Re: [Gusdev-gusdev] PostgreSQL version

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

As an FYI: I will be helping 4 groups in Brazil set-up and run GUS on their own the first couple of weeks in December.  Two of these groups will be using Postgres SQL as their database.   The more I can see of the Postgres version, the better.  I would like to practice with it a couple times before I have to present it.

Thanks for all the work you are putting into this.

-Ed



> 
> From: Michael Saffitz <msa...@pc...>
> Date: 2004/11/10 Wed PM 01:17:17 EST
> To: Jeetendra Soneja <so...@vb...>
> CC: gus...@li...
> Subject: Re: [Gusdev-gusdev] PostgreSQL version
> 
> 
> Hello Jeetendra,
> 
> The PostgreSQL version of GUS is my responsibility, and it's release is 
> part of the recent GUS Administrative Toolkit which is under development 
> (see the GUSDBA mailing list for more).  The short answer to your 
> question is that I hope to release beta SQL scripts for PostgreSQL 
> before Thanksgiving, and an official release by the end of the year (and 
> I expect little to change in the actual SQL scripts between these 
> releases-- the primary differences will be tool that generates the scripts).
> 
> As you plan to use PostgreSQL, please remember that there's a large code 
> base that will have been built against Oracle, and while we've done 
> preliminary evaluations, some amount of issues are expected and extra 
> time planned should be scheduled to address them.
> 
> Thanks,
> 
> --Mike
> 
> Jeetendra Soneja wrote:
> > Hello all,
> > 
> >       Our group is eagerly waiting on the PostgreSQL version of GUS. I
> > would greatly appreciate if someone could comment on when it is
> > expected to be released.
> >        This would help us plan our research.
> > 
> > Thanks a lot,
> > Jeetendra.
> > 
> > 
> > -------------------------------------------------------
> > This SF.Net email is sponsored by:
> > Sybase ASE Linux Express Edition - download now for FREE
> > LinuxWorld Reader's Choice Award Winner for best database on Linux.
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> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> 
> 
> -------------------------------------------------------
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> _______________________________________________
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> 

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good times never seemed so good.
I've been inclined
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     --Neil Diamond


We're just a bunch of idiots.
      --Johnny Damon

Re: [Gusdev-gusdev] prerequisites for RAD ArrayLoader

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

Kevin,
yes you'll need to have the relevant entry in SRes.ExternalDatabaseRelease 
if you want to enter (external_database_release_id, source_id) in any 
given GUS table and you create this in the order you outline.
For the specific case of the ArrayLoader, this pair of fields is present 
both in RAD3.Array and in views of RAD3.ElementImp and 
RAD3.CompositeElementImp.
An example of an external_database for a RAD3.Array entry might be 
ArrayExpress, if you want to indicate an identifier (through source_id) 
for the same array in another database. In our instance of RAD our arrays 
are typically pointed to an ArrayExpress array (if they are also in there) 
or to nothing, but of course you can point to anything you like.
In views of ElementImp and CompositeElementImp the external database is 
typically important as it enables to identify what the element or 
composite element on the array represent. Examples of databases that are 
of relevance here might be GenBank, IMAGE, etc. For the same array 
different elements (composite elements) on that array might point to 
different databases. For examples, for some of the non-commercial arrays 
stored in our instance of RAD, some of the spots on that array are 
identified through an image clone id, others through a GenBank, etc. 
depending on available information.
The source_id always refer to the main identifier in the db pointed to by 
external database id, which identifies the specific entry. For example it 
would be the accession_num for GenBank, the image clone_id for IMAGE, etc. 
Elisabetta
P.S. When you send emails to the GUS list that are of particular 
interest to RAD, could you please also cc the rad-issues source forge 
list, here copied? If you have not subscribed to the latter, I recommend 
you do.

---

On Mon, 15 Nov 2004, Kevin Murphy wrote:

> When loading a new array using GUS/RAD/Plugin/ArrayLoader.pm, what are the 
> database prerequisites for the external_database_release_id and source_id 
> columns in the input data file?
>
> Are you supposed to create an SRES.ExternalDatabase record with, e.g. a 
> 'name' column value of 'FooArray123', then create a corresponding 
> SRES.ExternalDatabaseRelease record, and use that 
> external_database_release_id in the data file?
>
> And what of the source_id column?
>
> Thanks,
> Kevin Murphy
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: InterSystems CACHE
> FREE OODBMS DOWNLOAD - A multidimensional database that combines
> robust object and relational technologies, making it a perfect match
> for Java, C++,COM, XML, ODBC and JDBC. www.intersystems.com/match8
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

[Gusdev-gusdev] prerequisites for RAD ArrayLoader

[Kevin M. <mu...@ge...>]

When loading a new array using GUS/RAD/Plugin/ArrayLoader.pm, what are 
the database prerequisites for the external_database_release_id and 
source_id columns in the input data file?

Are you supposed to create an SRES.ExternalDatabase record with, e.g. a 
'name' column value of 'FooArray123', then create a corresponding 
SRES.ExternalDatabaseRelease record, and use that 
external_database_release_id in the data file?

And what of the source_id column?

Thanks,
Kevin Murphy

Re: [Gusdev-gusdev] PostgreSQL version

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

Hello Jeetendra,

The PostgreSQL version of GUS is my responsibility, and it's release is 
part of the recent GUS Administrative Toolkit which is under development 
(see the GUSDBA mailing list for more).  The short answer to your 
question is that I hope to release beta SQL scripts for PostgreSQL 
before Thanksgiving, and an official release by the end of the year (and 
I expect little to change in the actual SQL scripts between these 
releases-- the primary differences will be tool that generates the scripts).

As you plan to use PostgreSQL, please remember that there's a large code 
base that will have been built against Oracle, and while we've done 
preliminary evaluations, some amount of issues are expected and extra 
time planned should be scheduled to address them.

Thanks,

--Mike

Jeetendra Soneja wrote:
> Hello all,
> 
>       Our group is eagerly waiting on the PostgreSQL version of GUS. I
> would greatly appreciate if someone could comment on when it is
> expected to be released.
>        This would help us plan our research.
> 
> Thanks a lot,
> Jeetendra.
> 
> 
> -------------------------------------------------------
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[Gusdev-gusdev] PostgreSQL version

[Jeetendra S. <so...@vb...>]

Hello all,

      Our group is eagerly waiting on the PostgreSQL version of GUS. I
would greatly appreciate if someone could comment on when it is
expected to be released.
       This would help us plan our research.

Thanks a lot,
Jeetendra.

Re: [Gusdev-gusdev] java compilation problems

[Dave B. <db...@pc...>]

Hey Federica,

This sounds a lot like the problem you mentioned last week.  Here was my 
suggestion to handle the java compile problem; let me know if you've tried 
either of these and what the result was. (scroll down for that email).

From your latest email, it also seems as though you are having problems 
connecting to the database 
after installation.  If you have a database administrator on your end, you 
might want to ask them if they can help.  I'm not too familiar with 
solving database connection problems, so unless someone else on the gusdev 
list has any insight, your DBA would be the best option.

Good luck,
Dave

On Fri, 5 Nov 2004, Dave Barkan wrote:

> Hey Federica,
>
> Can you do two things for me to help me discover the source of your problem:
>
> % cd /opt/GUS/projects/GUS/Model/src/java/org/gusdb/model/DoTS
>
> and let me know what is in that directory.
>
> Also, in the database itself, run this query:
>
> 'select count(*) from core.tableinfo where name = 'BLATAlignment'
>
> and let me know if it returns 0 or 1.
>
> Other GUS folks;  I think the problem is that Federica's TableInfo is not 
> populated, as the only objects that are getting compiled are the hand-edited 
> objects.  The rest all depend on having entries in TableInfo, and I don't 
> think that is the case.  I am not that familiar with the GUS installation 
> process; does TableInfo come prepopulated, or is there a step one has to do 
> in order to get it there?
>
> Dave
>
> On Fri, 5 Nov 2004 fed...@bi... wrote:
>
>> Hi!
>> I'm new to linux and to Gus; I've got some problem whit the installation.
>> I modified build.xml and sample.prop as the protocol suggets but while
>> compiling GUS/Model component javac doesn't find BLATAlignement class. It
>> tells me:
>> Installing GUS/Model
>>     [copy] Copying 20 files to /opt/GUS/lib/perl/GUS/Model
>>    [javac] Compiling 3 source files to /opt/GUS/projects/GUS/Model/classes
>>    [javac]
>> /opt/GUS/projects/GUS/Model/src/java/org/gusdb/model/DoTS/BLATAlignment.java:26:
>> cannot resolve symbol
>>    [javac] symbol  : class BLATAlignment_Row
>>    [javac] location: class org.gusdb.model.DoTS.BLATAlignment
>>    [javac] public class BLATAlignment extends BLATAlignment_Row {
>> 
>> 
>> I got the same problems also whit other classes.
>> 
>> Can anyone help me?
>> Thank you very much, it's a long time I try to solve this problem!
>> Federica
>> 
>> 
>> 
>> -------------------------------------------------------
>> This SF.Net email is sponsored by:
>> Sybase ASE Linux Express Edition - download now for FREE
>> LinuxWorld Reader's Choice Award Winner for best database on Linux.
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>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>> 
>

[Gusdev-gusdev] gus installation

[<fed...@bi...>]

Hi folks,
I got some problems whit the installation of GUS! I got troubles in 2
parts of it!
Running the build I have always this problems. Here an
exemple (I obtained 12 errors of the same kind):


[javac]/opt/projects/GUS/Model/src/java/org/gusdb/model/DoTS/BLATAlignment.java:26:
 cannot resolve symbol
[javac] symbol  : class BLATAlignment_Row
[javac] location: class org.gusdb.model.DoTS.BLATAlignment
[javac] public class BLATAlignment extends BLATAlignment_Row {
[javac]                                    ^



And running 'create-db.sh' I always have

 [root@oracle oracle]# ./create-db.sh

 SQL*Plus: Release 10.1.0.2.0 - Production on Wed Nov 10 11:59:58 2004

 Copyright (c) 1982, 2004, Oracle.  All rights reserved.

 ERROR:
 ORA-12154: TNS:could not resolve the connect identifier specified


 Enter user-name: system
 Enter password:
 ERROR:
 ORA-12546: TNS:permission denied

Have you got some ideas?
thank
Federica

[Gusdev-gusdev] BioPerl and GUS

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

A quick google search reveals that efforts to make GUS more 
BioPerl-aware have (seemingly) been attempted since (at least) 2002.  I 
wonder then why everyone on the mailing lists sounds so startled to 
hear about BioPerl's capabilities, and where the previous efforts have 
lead ...

Steve, you mention that you're afraid BioPerl won't be capable of 
capturing all the information contained in a GUS deployment; though I 
have only a passing acquaintance with GUS, I believe the only aspect of 
GUS that BioPerl would not be able to represent (in some meaningful 
form) is the RAD schema.  BioPerl has both strongly-typed and 
weakly-typed feature/annotation systems, and includes facilities for 
such data related to (in no particular order) Sequences, Assemblies, 
Alignments, Trees, Graphs, Ontologies, Pedigrees, Analyses, Coordinate 
Systems, Databases, Events, Matrices, Phenotypes, Species, Symbols, 
SNPs, etc.  For instance, I would argue that using even just a 
weakly-typed sequence feature system, one can successfully represent 
all sequence-related data (although the prior post about semantic 
difficulties remains relevant; BioPerl may not share the same semantics 
[or be missing it entirely] as GUS, and this will have to be 
programmed).

Also, I don't see GenBank locations as a big issue ("fuzzy locations"), 
since you're only talking about exposing GUS data to BioPerl (which 
doesn't have fuzzy locations) or importing GUS-capable data (which 
presumably will also not have fuzzy locations).  That said, BioPerl has 
an entire suite of location/coordinate handling modules (including 
support for split and/or fuzzy locations, representing the entire 
GenBank location moddel), and mechanisms/policies for "focussing" fuzzy 
locations into exact locations.  You're not the first group to ever 
face such problems.

Now, you will certainly find as you get more into BioPerl that there 
are particularly dusty corners (or ill-documented, but in active use); 
I would argue that these are areas where your developers might spend 
some other their valuable time that was saved by using BioPerl in the 
first place to make improvements to BioPerl, rather than backing away 
and saying "Oh look, the last 5% of the functionality we need isn't 
there, I guess we'll have to do it all ourselves" (cf: the Ensembl 
project).

BioPerl is becoming the lingua-franca of wet-bench biologists who are 
picking up Perl programming for their own lightweight bioinformatics 
tasks.  In 2003, various members of the BioPerl team gave many short 
lectures and workshops are their various host institutions, and at 
national meetings; in 2004, week-long BioPerl workshops were held for 
biologist/programmers at the University of Montreal, CSHL and the NIH.  
Requests for BioPerl training in 2005 are numerous and growing.  
Leaders of the NCI's caBIO and EBI's EnsEMBL projects recognize this, 
and are currently designing their own "bridges" between their code 
bases and BioPerl.  As such, there is much chatter on the BioPerl 
lissts about ways to improve the interoperability of BioPerl objects 
while maintaining current "ease of use" (arguable, of course, but there 
are even plans to make that better as well).  It would be great to have 
more GUS developers as part of the BioPerl community (and, frankly, it 
boggles my mind that there are professional bioinformatics Perl 
programmers who have little or no exposure to, or awareness of, 
BioPerl; remind me to buy more GoogleAds for bioperl.org).

Finally, I won't speak for Lincoln Stein, but I know that the GMOD 
project does want to include GUS in its effort to assimilate existing 
tools, but the current GMOD developers find GUS unapproachable.  I 
would guess that Lincoln and friends would be willing to help out an 
intrepid GUS aficionado get GUS at least talking to the GMOD toolkit 
(presumably leveraging BioPerl to talk ChadoXML; which isn't probably 
as straightforward as it sounds; cf. semantic issues raised earlier).

I'll keep listening ...

Best wishes,

-Aaron

--
Aaron J. Mackey, Ph.D.
Dept. of Biology, Goddard 212
University of Pennsylvania       email:  am...@pc...
415 S. University Avenue         office: 215-898-1205
Philadelphia, PA  19104-6017     fax:    215-746-6697

[Gusdev-gusdev] Re: [ApiDB] Storing Genbank data in GUS

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

This particular plugin, at least as I understand it, will only
load sequence and gene feature information.  The pipeline we
are discussing will manage a number of other plugins which
will load other kinds of information including GO annotations.

-ed



---- Original message ----
>Date: Tue, 9 Nov 2004 14:05:35 -0500 (EST)
>From: Trish Whetzel <wh...@pc...>  
>Subject: Re: [ApiDB] Storing Genbank data in GUS  
>To: ap...@pc...
>Cc: gus...@li...
>
>I wanted to follow-up on what the plugin is going to load -
sequence
>information only OR will it also load the annotations (GO,
EC) as well.
>The response I heard back from Ed was that the plugin was
only going to
>load the sequence information.  Is that the game plan?
>
>This annotation information is in both the embl and TIGR
files so I was 
>wondering why it would be loaded by two separate plugins.
>
>Trish
>
>
>
>---------- Forwarded message ----------
>Date: Mon, 8 Nov 2004 11:51:49 -0500
>From: Ed Robinson <ero...@ug...>
>To: Trish Whetzel <wh...@pc...>
>Subject: Re: [ApiDB] LoadGeneFeaturesFromXML
>
>The plugin I am writing won't load anything more than sequence
>and gene-feature information.  Other parts of the pipeline we
>are working on will handle go annotations, etc.  Atleast, that
>is how I understand that this is going to work.
>
>-ed
>
>
>
>
>---- Original message ----
>>Date: Mon, 8 Nov 2004 11:37:34 -0500 (EST)
>>From: Trish Whetzel <wh...@pc...>
>>Subject: [ApiDB] LoadGeneFeaturesFromXML
>>To: Ed Robinson <ero...@ug...>
>>Cc: ap...@pc...
>>
>>Hi Ed,
>>
>>Thanks for the docs mapping the TIGR XML file to GUS.  I've
had a quick
>>look through them and it looks like only the sequence
related parts are
>>mentioned.  Was there a decision to NOT include the other
tasks such as
>>GOAnnotation, ECAnnotation?  These are also present in the
embl files and
>>are handled by this plugin.  Will the future version of this
plugin still
>>load this information as well?
>>
>>Trish
>-----------------
>Ed Robinson
>Program Specialist
>Center for Tropical and Emerging Global Diseases
>and Dept. of Genetics
>University of Georgia, Athens, GA 30602
>ero...@ug.../(706) 542.1447
>_______________________________________________
>ApiDB mailing list
>Ap...@pc...
>https://mail.pcbi.upenn.edu/mailman/listinfo/apidb
-----------------
Ed Robinson
Program Specialist
Center for Tropical and Emerging Global Diseases
and Dept. of Genetics
University of Georgia, Athens, GA 30602
ero...@ug.../(706) 542.1447

[Gusdev-gusdev] Re: [ApiDB] Storing Genbank data in GUS

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

I wanted to follow-up on what the plugin is going to load - sequence
information only OR will it also load the annotations (GO, EC) as well.
The response I heard back from Ed was that the plugin was only going to
load the sequence information.  Is that the game plan?

This annotation information is in both the embl and TIGR files so I was 
wondering why it would be loaded by two separate plugins.

Trish



---------- Forwarded message ----------
Date: Mon, 8 Nov 2004 11:51:49 -0500
From: Ed Robinson <ero...@ug...>
To: Trish Whetzel <wh...@pc...>
Subject: Re: [ApiDB] LoadGeneFeaturesFromXML

The plugin I am writing won't load anything more than sequence
and gene-feature information.  Other parts of the pipeline we
are working on will handle go annotations, etc.  Atleast, that
is how I understand that this is going to work.

-ed




---- Original message ----
>Date: Mon, 8 Nov 2004 11:37:34 -0500 (EST)
>From: Trish Whetzel <wh...@pc...>
>Subject: [ApiDB] LoadGeneFeaturesFromXML
>To: Ed Robinson <ero...@ug...>
>Cc: ap...@pc...
>
>Hi Ed,
>
>Thanks for the docs mapping the TIGR XML file to GUS.  I've had a quick
>look through them and it looks like only the sequence related parts are
>mentioned.  Was there a decision to NOT include the other tasks such as
>GOAnnotation, ECAnnotation?  These are also present in the embl files and
>are handled by this plugin.  Will the future version of this plugin still
>load this information as well?
>
>Trish
-----------------
Ed Robinson
Program Specialist
Center for Tropical and Emerging Global Diseases
and Dept. of Genetics
University of Georgia, Athens, GA 30602
ero...@ug.../(706) 542.1447

Re: [Gusdev-gusdev] GUS & bioperl

[Paul M. <pj...@sa...>]

Here is an internal document showing the mapping of my departments EMBL 
qualifiers to GUS tables/fields.
Some of the qualifiers are non EMBL standard as the data we store is, 
well, not non standard :)

Annotation in Bioperl is in the form of a key/value pair, hence the 
name of the key and the representation of the value is crucial if it is 
to be used by others.