gusdev-gusdev — Topics concerning GUS development

[GUSDEV] Fwd: [WDKDEV] WDK with Postgres?

[Thiago S. <ma...@gm...>]

---------- Forwarded message ----------
From: Thiago Satake <ma...@gm...>
Date: 04/08/2005 11:34
Subject: Re: [WDKDEV] WDK with Postgres?
To: Steve Fischer <sfi...@pc...>


Ok ........

We can list some problems:
1- we had to change all of perl wdk file ... to set te correct driver
to postgres.
2- we had to change  testTables files to change the numeric data type
( number > numeric )
3- and now we are changing  java file to adapt to Postgres ( sequence
manipulation,  Postgres.java - jdbc driver and numeric type )

now we are having problem to use WDKToySite as the log shows:

DEBUG: making a QuestionSetForm
Aug 4, 2005 11:23:14 AM org.apache.struts.action.RequestProcessor
processException
WARNING: Unhandled Exception thrown: class
java.lang.ArrayIndexOutOfBoundsException

and other problems .............

Thanks for the help :-)




2005/8/4, Steve Fischer <sfi...@pc...>:
> Folks-
>
> the production uses of wdk so far are in oracle, so we have not put much
> effort into ensuring the complete functioning of the postgres module.
>
> however, a student did successfully use postgres with the wdk.  he made
> improvements in the PostgreSQL.java file, and a small change in
> ResultFactory that are not yet in the release.
>
> I will incorporate those changes today and test it.   I hope to get  you
> a patch by tomorrow.
>
> can you describe briefly the problems?
>
> steve
>
> Thiago Satake wrote:
>
> >I am having the same problem.........
> >
> >Does Someone have the  wdk working with postgres database ?
> >
> >I would appreciate if someone could help me too !!!!!!!!!!!!!!!!!!! :-)
> >
> >Thanks .............
> >
> >Thiago Seito Satake
> >
> >
> >2005/8/4, fab...@de... <fab...@de...>:
> >
> >
> >>Hello all,
> >>
> >>We have a GUS installation running ok and now we're trying to use WDK 1=
.5 to
> >>explore the postgres schema. We noticed that the WDK code is manipulati=
ng an
> >>Oracle database, due to some type columns, sequence using, etc... that
> >>generates many errors when running wdk programs (wdkCache, wdkQuery,
> >>wdkRecord,...).
> >>
> >>Because of this, we're having a hard work to debug the code and set it =
to work
> >>with the Postgres schema. We would like to know if someone has a WDK wo=
rking
> >>with GUS Postgres perfectly.
> >>
> >>Thanks a lot,
> >>
> >>Fabr=EDcio.
> >>
> >>----------------------------------------------------------------
> >>This message was sent using IMP, the Internet Messaging Program.
> >>_______________________________________________
> >>WDKDev mailing list
> >>WD...@pc...
> >>https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev
> >>
> >>
> >>
> >
> >
> >
> >
>


--
Thiago Seito Satake
!! Tenha um bom dia !!
Tel: (041) 990-55422


--=20
Thiago Seito Satake
!! Tenha um bom dia !!
Tel: (041) 990-55422

[GUSDEV] Re: [WDKDEV] WDK with Postgres?

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

Folks-

the production uses of wdk so far are in oracle, so we have not put much=20
effort into ensuring the complete functioning of the postgres module.

however, a student did successfully use postgres with the wdk.  he made=20
improvements in the PostgreSQL.java file, and a small change in=20
ResultFactory that are not yet in the release.

I will incorporate those changes today and test it.   I hope to get  you=20
a patch by tomorrow.

can you describe briefly the problems?

steve

Thiago Satake wrote:

>I am having the same problem.........=20
>
>Does Someone have the  wdk working with postgres database ?=20
>
>I would appreciate if someone could help me too !!!!!!!!!!!!!!!!!!! :-)
>
>Thanks .............
>
>Thiago Seito Satake=20
> =20
>
>2005/8/4, fab...@de... <fab...@de...>:
> =20
>
>>Hello all,
>>
>>We have a GUS installation running ok and now we're trying to use WDK 1=
.5 to
>>explore the postgres schema. We noticed that the WDK code is manipulati=
ng an
>>Oracle database, due to some type columns, sequence using, etc... that
>>generates many errors when running wdk programs (wdkCache, wdkQuery,
>>wdkRecord,...).
>>
>>Because of this, we're having a hard work to debug the code and set it =
to work
>>with the Postgres schema. We would like to know if someone has a WDK wo=
rking
>>with GUS Postgres perfectly.
>>
>>Thanks a lot,
>>
>>Fabr=EDcio.
>>
>>----------------------------------------------------------------
>>This message was sent using IMP, the Internet Messaging Program.
>>_______________________________________________
>>WDKDev mailing list
>>WD...@pc...
>>https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev
>>
>>   =20
>>
>
>
> =20
>

[GUSDEV] Re: [WDKDEV] WDK with Postgres?

[Thiago S. <ma...@gm...>]

I am having the same problem.........=20

Does Someone have the  wdk working with postgres database ?=20

I would appreciate if someone could help me too !!!!!!!!!!!!!!!!!!! :-)

Thanks .............

Thiago Seito Satake=20
 =20

2005/8/4, fab...@de... <fab...@de...>:
> Hello all,
>=20
> We have a GUS installation running ok and now we're trying to use WDK 1.5=
 to
> explore the postgres schema. We noticed that the WDK code is manipulating=
 an
> Oracle database, due to some type columns, sequence using, etc... that
> generates many errors when running wdk programs (wdkCache, wdkQuery,
> wdkRecord,...).
>=20
> Because of this, we're having a hard work to debug the code and set it to=
 work
> with the Postgres schema. We would like to know if someone has a WDK work=
ing
> with GUS Postgres perfectly.
>=20
> Thanks a lot,
>=20
> Fabr=EDcio.
>=20
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
> _______________________________________________
> WDKDev mailing list
> WD...@pc...
> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev
>=20


--=20
Thiago Seito Satake
!! Tenha um bom dia !!
Tel: (041) 990-55422

[GUSDEV] WDK with Postgres?

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

Hello all,

We have a GUS installation running ok and now we're trying to use WDK 1.5=
 to
explore the postgres schema. We noticed that the WDK code is manipulating=
 an
Oracle database, due to some type columns, sequence using, etc... that
generates many errors when running wdk programs (wdkCache, wdkQuery,
wdkRecord,...).

Because of this, we're having a hard work to debug the code and set it to=
 work
with the Postgres schema. We would like to know if someone has a WDK work=
ing
with GUS Postgres perfectly.=20

Thanks a lot,

Fabr=EDcio.=20

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

Re: [GUSDEV] 3.5 install errors: Warning: No JavaType found for 'end_time', type: 'timestamp'

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

Hi Michael,

This is a known bug that has been resolved and the fix will be included in
the next release.  In the meantime, you may wish to review the bug report
and patch available at:

https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=47

--Mike


On 8/3/05 7:15 PM, "michael chaplin" <cha...@vc...> wrote:

> a "fabricio@de..." posted the exact same errors on 7/3/05, but I could
> not see the resolution in any follow up posts.
> 
> when I do a:
> 
>> build GUS install -append -installDBSchema
> 
> I get a schema in postgres, perl objects created, but when it gets to
> generating java objects for tables it throws hundreds of warnings:
> 
> ...
>       [echo] generating java objects
>       [exec] Generating objects for 954 java tables and views
>       [exec] generating java object for Core::Algorithm
>       [exec] (Caching all real table names)
>       [exec] (Caching all parents)
>       [exec] Warning: No JavaType found for 'modification_date', type:
> 'timestamp'
>       [exec] Warning: No JavaType found for 'modification_date', type:
> 'timestamp'
>       [exec] generating java object for Core::AlgorithmImplementation
>       [exec] Warning: No JavaType found for 'modification_date', type:
> 'timestamp'
>       [exec] Warning: No JavaType found for 'modification_date', type:
> 'timestamp'
>       [exec] generating java object for Core::AlgorithmInvocation
>       [exec] Warning: No JavaType found for 'modification_date', type:
> 'timestamp'
>       [exec] Warning: No JavaType found for 'end_time', type: 'timestamp'
>       [exec] Warning: No JavaType found for 'start_time', type: 'timestamp'
>       [exec] (Caching all subclasses)
>       [exec] Warning: No JavaType found for 'start_time', type: 'timestamp'
>       [exec] Warning: No JavaType found for 'modification_date', type:
> 'timestamp'
>       [exec] Warning: No JavaType found for 'end_time', type: 'timestamp'
>       [exec] generating java object for Core::AlgorithmParam
> 
> ...
> 
> and then, when compiling java it gets 100 complilation errors and stops.
> 
> ...
> 
>      [javac] 
> /home/gus/GUS/project_home/GUS/Model/src/java/org/gusdb/model/SRes/AnatomyLine
> age_Row.java:67: 
> cannot resolve symbol
>      [javac] symbol  : class notdefyet
>      [javac] location: class org.gusdb.model.SRes.AnatomyLineage_Row
>      [javac]     public notdefyet getModificationDate () { return
> (notdefyet)get_Attribute("modification_date"); }
>      [javac]            ^
>      [javac] 100 errors
> 
> BUILD FAILED
> /home/gus/GUS/project_home/install/build.xml:28: The following error
> occurred while executing this line:
> /home/gus/GUS/project_home/GUS/build.xml:99: The following error
> occurred while executing this line:
> /home/gus/GUS/project_home/install/build.xml:259: The following error
> occurred while executing this line:
> /home/gus/GUS/project_home/install/build.xml:278: Compile failed; see
> the compiler error output for details.
> 
> Total time: 13 seconds
> 
> I've tried everything, including deleting the database and starting over
> from scratch.
> 
> Can fabricio tell me how he resolved it?
> 
> 
> 
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[GUSDEV] 3.5 install errors: Warning: No JavaType found for 'end_time', type: 'timestamp'

[michael c. <cha...@vc...>]

a "fabricio@de..." posted the exact same errors on 7/3/05, but I could 
not see the resolution in any follow up posts.

when I do a:

 >build GUS install -append -installDBSchema

I get a schema in postgres, perl objects created, but when it gets to
generating java objects for tables it throws hundreds of warnings:

...
      [echo] generating java objects
      [exec] Generating objects for 954 java tables and views
      [exec] generating java object for Core::Algorithm
      [exec] (Caching all real table names)
      [exec] (Caching all parents)
      [exec] Warning: No JavaType found for 'modification_date', type: 
'timestamp'
      [exec] Warning: No JavaType found for 'modification_date', type: 
'timestamp'
      [exec] generating java object for Core::AlgorithmImplementation
      [exec] Warning: No JavaType found for 'modification_date', type: 
'timestamp'
      [exec] Warning: No JavaType found for 'modification_date', type: 
'timestamp'
      [exec] generating java object for Core::AlgorithmInvocation
      [exec] Warning: No JavaType found for 'modification_date', type: 
'timestamp'
      [exec] Warning: No JavaType found for 'end_time', type: 'timestamp'
      [exec] Warning: No JavaType found for 'start_time', type: 'timestamp'
      [exec] (Caching all subclasses)
      [exec] Warning: No JavaType found for 'start_time', type: 'timestamp'
      [exec] Warning: No JavaType found for 'modification_date', type: 
'timestamp'
      [exec] Warning: No JavaType found for 'end_time', type: 'timestamp'
      [exec] generating java object for Core::AlgorithmParam

...

and then, when compiling java it gets 100 complilation errors and stops.

...

     [javac] 
/home/gus/GUS/project_home/GUS/Model/src/java/org/gusdb/model/SRes/AnatomyLineage_Row.java:67: 
cannot resolve symbol
     [javac] symbol  : class notdefyet
     [javac] location: class org.gusdb.model.SRes.AnatomyLineage_Row
     [javac]     public notdefyet getModificationDate () { return 
(notdefyet)get_Attribute("modification_date"); }
     [javac]            ^
     [javac] 100 errors

BUILD FAILED
/home/gus/GUS/project_home/install/build.xml:28: The following error 
occurred while executing this line:
/home/gus/GUS/project_home/GUS/build.xml:99: The following error 
occurred while executing this line:
/home/gus/GUS/project_home/install/build.xml:259: The following error 
occurred while executing this line:
/home/gus/GUS/project_home/install/build.xml:278: Compile failed; see 
the compiler error output for details.

Total time: 13 seconds

I've tried everything, including deleting the database and starting over 
from scratch.

Can fabricio tell me how he resolved it?

RE: [GUSDEV] Loading Prosite DB

[Kumar, S. \(Contr\) <San...@ng...>]

So, The PlugIn which you are writing will not be taking care detail =
Prosite data, right?
If yes then I will write a separate plugin to load detail Prosite master =
data.

Thanks
Sanjeev

-----Original Message-----
From: Aaron J. Mackey [mailto:am...@pc...]
Sent: Tuesday, August 02, 2005 5:01 PM
To: Kumar, Sanjeev (Contr)
Cc: Jian Lu; gus...@li...
Subject: Re: [GUSDEV] Loading Prosite DB


Yes, InterProScan only provides domain analysis results, not the =20
actual domain/pattern/motif databases themselves.

-Aaron

On Aug 2, 2005, at 4:54 PM, Kumar, Sanjeev (Contr) wrote:

> Hi Aaron/Jian,
>    The Interproscan data has only PrositeID and description in it. =20
> But to load other information for a prosite ID, we need to load the =20
> Prosite data which comes in different format than Interpro.
> That is what I found, Do you copy?
>
> Thanks
> Sanjeev
>
> -----Original Message-----
> From: Aaron J. Mackey [mailto:am...@pc...]
> Sent: Tuesday, August 02, 2005 4:43 PM
> To: Jian Lu
> Cc: Kumar, Sanjeev (Contr)
> Subject: Re: [GUSDEV] Loading Prosite DB
>
>
>
>  From http://www.ebi.ac.uk/interpro/README1.html
>
> PROSITE patterns.
>
> Some biologically significant amino acid patterns can be summarised
> in the form of regular expressions.
>
> ScanRegExp (by Wol...@eb...), Ppsearch (Fuchs, R.
> 1994) .
>
> PROSITE profile.
>
> There are a number of protein families as well as functional or
> structural domains that cannot be detected using patterns due to
> their extreme sequence divergence; the use of techniques based on
> weight matrices (also known as profiles) allows the detection of such
> domains.
>
>    pfscan from thePftools package (by Phi...@is...).
>
> PRINTS.
> The PRINTS database houses a collection of protein family
> fingerprints. These are groups of motifs that together are
> diagnostically more potent than single motifs by making use of the
> biological context inherent in a multiple-motif method.
>
>       FingerPRINTScan (Scordis, P. et al. 1999) .
>
>   PFAM.
> Pfam is a database of protein domain families. Pfam contains curated
> multiple sequence alignments for each family and corresponding
> profile hidden Markov models (HMMs).
>
>       hmmpfam from theHMMER2.1 package (by Sean Eddy,
> ed...@ge..., http://hmmer.wustl.edu),
> DeCypher=99 (TimeLogic) implementation of HMM search.
>
>   PRODOM.
> ProDom families are built by an automated process based on a
> recursive use ofPSI-BLAST homology searches.
>
>       BlastProDom.pl (by Florence Servant, fse...@to...)
> =96 a filter on top of theBlast package (Altschul, S. F. et al. 1997) =
.
>
>   SMART.
> SMART domains are extensively annotated with respect to phyletic
> distributions, functional class, tertiary structures and functionally
> important residues. SMART alignments are optimised manually and
> following construction of corresponding hidden Markov models (HMMs).
>
>       hmmpfam from theHMMER2.1 package.
>
> TIGRFAMs.
> TIGRFAMs are a collection of protein families featuring curated
> multiple sequence alignments, Hidden Markov Models (HMMs) and
> associated information designed to support the automated functional
> identification of proteins by sequence homology. Classification by
> equivalog family (see below), where achievable, complements
> classification by orthologs, superfamily, domain or motif. It
> provides the information best suited for automatic assignment of
> specific functions to proteins from large scale genome sequencing
> projects
>
> =D8     hmmpfam from theHMMER2.1 package.
>
> Optionally, predictions for coiled-coil, signal peptide cleavage
> sites (SignalP v2) and TM helices (TMHMM v2) are supported.
>
>
>
> On Aug 2, 2005, at 4:32 PM, Jian Lu wrote:
>
>
>> I don't think so. Here is the data sheet from InterProScan.
>>
>> Kumar, Sanjeev (Contr) wrote:
>>
>>
>>
>>> Hi Aaron/Jian,
>>>   What all types of data we are talking in IterProScan plugin?
>>>  Does it include Prosite data.
>>> Thanks
>>> Sanjeev
>>>
>>> -----Original Message-----
>>> From: Jian Lu [mailto:jl...@vb...]
>>> Sent: Tuesday, August 02, 2005 2:02 PM
>>> To: Aaron J. Mackey
>>> Cc: Kumar, Sanjeev (Contr); gus...@li...
>>> Subject: Re: [GUSDEV] Loading Prosite DB
>>>
>>>
>>> Aaron,
>>>
>>> We are also working on InterProScan and other analysis tools. But
>>> we haven't got a plugin yet. If your plugin is ready, I would like
>>> to play it. Here is the view that we created for InterProScan.
>>> Please comment it. Thanks.
>>>
>>> --
>>> -- VIEW DOTS.INTERPROSCAN
>>> -- used to store outputs from InterProScan
>>> -- June 29, 2005
>>>
>>>
>>>
>>
>>
>> <InterProScan_OUTPUT.pdf>
>>
>>
>
> --
> Aaron J. Mackey, Ph.D.
> Project Manager, ApiDB Bioinformatics Resource Center
> Penn Genomics Institute, University of Pennsylvania
> email:  am...@pc...
> office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI)
> fax:    215-746-6697
> postal: Penn Genomics Institute
>          Goddard Labs 212
>          415 S. University Avenue
>          Philadelphia, PA  19104-6017
>
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
> from IBM. Find simple to follow Roadmaps, straightforward articles,
> informative Webcasts and more! Get everything you need to get up to
> speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=CCk
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

--
Aaron J. Mackey, Ph.D.
Project Manager, ApiDB Bioinformatics Resource Center
Penn Genomics Institute, University of Pennsylvania
email:  am...@pc...
office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI)
fax:    215-746-6697
postal: Penn Genomics Institute
         Goddard Labs 212
         415 S. University Avenue
         Philadelphia, PA  19104-6017

Re: [GUSDEV] Loading Prosite DB

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

Yes, InterProScan only provides domain analysis results, not the =20
actual domain/pattern/motif databases themselves.

-Aaron

On Aug 2, 2005, at 4:54 PM, Kumar, Sanjeev (Contr) wrote:

> Hi Aaron/Jian,
>    The Interproscan data has only PrositeID and description in it. =20
> But to load other information for a prosite ID, we need to load the =20=

> Prosite data which comes in different format than Interpro.
> That is what I found, Do you copy?
>
> Thanks
> Sanjeev
>
> -----Original Message-----
> From: Aaron J. Mackey [mailto:am...@pc...]
> Sent: Tuesday, August 02, 2005 4:43 PM
> To: Jian Lu
> Cc: Kumar, Sanjeev (Contr)
> Subject: Re: [GUSDEV] Loading Prosite DB
>
>
>
>  =46rom http://www.ebi.ac.uk/interpro/README1.html
>
> PROSITE patterns.
>
> Some biologically significant amino acid patterns can be summarised
> in the form of regular expressions.
>
> ScanRegExp (by Wol...@eb...), Ppsearch (Fuchs, R.
> 1994) .
>
> PROSITE profile.
>
> There are a number of protein families as well as functional or
> structural domains that cannot be detected using patterns due to
> their extreme sequence divergence; the use of techniques based on
> weight matrices (also known as profiles) allows the detection of such
> domains.
>
>    pfscan from thePftools package (by Phi...@is...).
>
> PRINTS.
> The PRINTS database houses a collection of protein family
> fingerprints. These are groups of motifs that together are
> diagnostically more potent than single motifs by making use of the
> biological context inherent in a multiple-motif method.
>
>       FingerPRINTScan (Scordis, P. et al. 1999) .
>
>   PFAM.
> Pfam is a database of protein domain families. Pfam contains curated
> multiple sequence alignments for each family and corresponding
> profile hidden Markov models (HMMs).
>
>       hmmpfam from theHMMER2.1 package (by Sean Eddy,
> ed...@ge..., http://hmmer.wustl.edu),
> DeCypher=99 (TimeLogic) implementation of HMM search.
>
>   PRODOM.
> ProDom families are built by an automated process based on a
> recursive use ofPSI-BLAST homology searches.
>
>       BlastProDom.pl (by Florence Servant, fse...@to...)
> =96 a filter on top of theBlast package (Altschul, S. F. et al. 1997) =
.
>
>   SMART.
> SMART domains are extensively annotated with respect to phyletic
> distributions, functional class, tertiary structures and functionally
> important residues. SMART alignments are optimised manually and
> following construction of corresponding hidden Markov models (HMMs).
>
>       hmmpfam from theHMMER2.1 package.
>
> TIGRFAMs.
> TIGRFAMs are a collection of protein families featuring curated
> multiple sequence alignments, Hidden Markov Models (HMMs) and
> associated information designed to support the automated functional
> identification of proteins by sequence homology. Classification by
> equivalog family (see below), where achievable, complements
> classification by orthologs, superfamily, domain or motif. It
> provides the information best suited for automatic assignment of
> specific functions to proteins from large scale genome sequencing
> projects
>
> =D8     hmmpfam from theHMMER2.1 package.
>
> Optionally, predictions for coiled-coil, signal peptide cleavage
> sites (SignalP v2) and TM helices (TMHMM v2) are supported.
>
>
>
> On Aug 2, 2005, at 4:32 PM, Jian Lu wrote:
>
>
>> I don't think so. Here is the data sheet from InterProScan.
>>
>> Kumar, Sanjeev (Contr) wrote:
>>
>>
>>
>>> Hi Aaron/Jian,
>>>   What all types of data we are talking in IterProScan plugin?
>>>  Does it include Prosite data.
>>> Thanks
>>> Sanjeev
>>>
>>> -----Original Message-----
>>> From: Jian Lu [mailto:jl...@vb...]
>>> Sent: Tuesday, August 02, 2005 2:02 PM
>>> To: Aaron J. Mackey
>>> Cc: Kumar, Sanjeev (Contr); gus...@li...
>>> Subject: Re: [GUSDEV] Loading Prosite DB
>>>
>>>
>>> Aaron,
>>>
>>> We are also working on InterProScan and other analysis tools. But
>>> we haven't got a plugin yet. If your plugin is ready, I would like
>>> to play it. Here is the view that we created for InterProScan.
>>> Please comment it. Thanks.
>>>
>>> --
>>> -- VIEW DOTS.INTERPROSCAN
>>> -- used to store outputs from InterProScan
>>> -- June 29, 2005
>>>
>>>
>>>
>>
>>
>> <InterProScan_OUTPUT.pdf>
>>
>>
>
> --
> Aaron J. Mackey, Ph.D.
> Project Manager, ApiDB Bioinformatics Resource Center
> Penn Genomics Institute, University of Pennsylvania
> email:  am...@pc...
> office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI)
> fax:    215-746-6697
> postal: Penn Genomics Institute
>          Goddard Labs 212
>          415 S. University Avenue
>          Philadelphia, PA  19104-6017
>
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
> from IBM. Find simple to follow Roadmaps, straightforward articles,
> informative Webcasts and more! Get everything you need to get up to
> speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=CCk
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

--
Aaron J. Mackey, Ph.D.
Project Manager, ApiDB Bioinformatics Resource Center
Penn Genomics Institute, University of Pennsylvania
email:  am...@pc...
office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI)
fax:    215-746-6697
postal: Penn Genomics Institute
         Goddard Labs 212
         415 S. University Avenue
         Philadelphia, PA  19104-6017

RE: [GUSDEV] Loading Prosite DB

[Kumar, S. \(Contr\) <San...@ng...>]

Hi Aaron/Jian,
   The Interproscan data has only PrositeID and description in it. But =
to load other information for a prosite ID, we need to load the Prosite =
data which comes in different format than Interpro.
That is what I found, Do you copy?

Thanks
Sanjeev=20

-----Original Message-----
From: Aaron J. Mackey [mailto:am...@pc...]
Sent: Tuesday, August 02, 2005 4:43 PM
To: Jian Lu
Cc: Kumar, Sanjeev (Contr)
Subject: Re: [GUSDEV] Loading Prosite DB



 From http://www.ebi.ac.uk/interpro/README1.html

PROSITE patterns.

Some biologically significant amino acid patterns can be summarised =20
in the form of regular expressions.

ScanRegExp (by Wol...@eb...), Ppsearch (Fuchs, R. =20
1994) .

PROSITE profile.

There are a number of protein families as well as functional or =20
structural domains that cannot be detected using patterns due to =20
their extreme sequence divergence; the use of techniques based on =20
weight matrices (also known as profiles) allows the detection of such =20
domains.

   pfscan from thePftools package (by Phi...@is...).

PRINTS.
The PRINTS database houses a collection of protein family =20
fingerprints. These are groups of motifs that together are =20
diagnostically more potent than single motifs by making use of the =20
biological context inherent in a multiple-motif method.

      FingerPRINTScan (Scordis, P. et al. 1999) .

  PFAM.
Pfam is a database of protein domain families. Pfam contains curated =20
multiple sequence alignments for each family and corresponding =20
profile hidden Markov models (HMMs).

      hmmpfam from theHMMER2.1 package (by Sean Eddy, =20
ed...@ge..., http://hmmer.wustl.edu),
DeCypher=99 (TimeLogic) implementation of HMM search.

  PRODOM.
ProDom families are built by an automated process based on a =20
recursive use ofPSI-BLAST homology searches.

      BlastProDom.pl (by Florence Servant, fse...@to...) =20
=96 a filter on top of theBlast package (Altschul, S. F. et al. 1997) .

  SMART.
SMART domains are extensively annotated with respect to phyletic =20
distributions, functional class, tertiary structures and functionally =20
important residues. SMART alignments are optimised manually and =20
following construction of corresponding hidden Markov models (HMMs).

      hmmpfam from theHMMER2.1 package.

TIGRFAMs.
TIGRFAMs are a collection of protein families featuring curated =20
multiple sequence alignments, Hidden Markov Models (HMMs) and =20
associated information designed to support the automated functional =20
identification of proteins by sequence homology. Classification by =20
equivalog family (see below), where achievable, complements =20
classification by orthologs, superfamily, domain or motif. It =20
provides the information best suited for automatic assignment of =20
specific functions to proteins from large scale genome sequencing =20
projects

=D8     hmmpfam from theHMMER2.1 package.

Optionally, predictions for coiled-coil, signal peptide cleavage =20
sites (SignalP v2) and TM helices (TMHMM v2) are supported.



On Aug 2, 2005, at 4:32 PM, Jian Lu wrote:

> I don't think so. Here is the data sheet from InterProScan.
>
> Kumar, Sanjeev (Contr) wrote:
>
>
>> Hi Aaron/Jian,
>>   What all types of data we are talking in IterProScan plugin?
>>  Does it include Prosite data.
>> Thanks
>> Sanjeev
>>
>> -----Original Message-----
>> From: Jian Lu [mailto:jl...@vb...]
>> Sent: Tuesday, August 02, 2005 2:02 PM
>> To: Aaron J. Mackey
>> Cc: Kumar, Sanjeev (Contr); gus...@li...
>> Subject: Re: [GUSDEV] Loading Prosite DB
>>
>>
>> Aaron,
>>
>> We are also working on InterProScan and other analysis tools. But =20
>> we haven't got a plugin yet. If your plugin is ready, I would like =20
>> to play it. Here is the view that we created for InterProScan. =20
>> Please comment it. Thanks.
>>
>> --
>> -- VIEW DOTS.INTERPROSCAN
>> -- used to store outputs from InterProScan
>> -- June 29, 2005
>>
>>
>
>
> <InterProScan_OUTPUT.pdf>
>

--
Aaron J. Mackey, Ph.D.
Project Manager, ApiDB Bioinformatics Resource Center
Penn Genomics Institute, University of Pennsylvania
email:  am...@pc...
office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI)
fax:    215-746-6697
postal: Penn Genomics Institute
         Goddard Labs 212
         415 S. University Avenue
         Philadelphia, PA  19104-6017

RE: [GUSDEV] Loading Prosite DB

[Kumar, S. \(Contr\) <San...@ng...>]

Hi Aaron/Jian,
   What all types of data we are talking in IterProScan plugin?
  Does it include Prosite data.
Thanks
Sanjeev

-----Original Message-----
From: Jian Lu [mailto:jl...@vb...]
Sent: Tuesday, August 02, 2005 2:02 PM
To: Aaron J. Mackey
Cc: Kumar, Sanjeev (Contr); gus...@li...
Subject: Re: [GUSDEV] Loading Prosite DB


Aaron,

We are also working on InterProScan and other analysis tools. But we=20
haven't got a plugin yet. If your plugin is ready, I would like to play=20
it. Here is the view that we created for InterProScan. Please comment=20
it. Thanks.

--
-- VIEW DOTS.INTERPROSCAN
-- used to store outputs from InterProScan
-- June 29, 2005
--=20
-- For GUS 3.0
CREATE VIEW DOTS.INTERPROSCAN AS SELECT
    AA_FEATURE_ID,
    AA_SEQUENCE_ID,
    FEATURE_NAME_ID,
    PARENT_ID,
    NA_FEATURE_ID,
    SUBCLASS_VIEW,
    SEQUENCE_ONTOLOGY_ID,
    DESCRIPTION,
    PFAM_ENTRY_ID,
    MOTIF_AA_SEQUENCE_ID,
    REPEAT_TYPE_ID,
    EXTERNAL_DATABASE_RELEASE_ID,
    SOURCE_ID AS INTERPROSCAN_ID,
    PREDICTION_ALGORITHM_ID,
    IS_PREDICTED,
    REVIEW_STATUS_ID,
    INT1 AS PVALUE_EXP,
    FLOAT1  as PVALUE_MANT,
    FLOAT2  as SCORE,
    STRING1 AS MEMBER_ID,
    STRING2 AS MEMBER_DESCRIPTION,
    MODIFICATION_DATE, USER_READ, USER_WRITE, GROUP_READ, GROUP_WRITE,=20
OTHER_READ, OTHER_WRITE, ROW_USER_ID, ROW_GROUP_ID, ROW_PROJECT_ID,=20
ROW_ALG_INVOCATION_ID
    FROM DOTS.AAFEATUREIMP
    WHERE SUBCLASS_VIEW=3D'InterProScan';

-- For GUS 3.5
CREATE VIEW DOTS.INTERPROSCAN AS SELECT
    AA_FEATURE_ID,
    AA_SEQUENCE_ID,
    FEATURE_NAME_ID,
    PARENT_ID,
    NA_FEATURE_ID,
    SUBCLASS_VIEW,
    SEQUENCE_ONTOLOGY_ID,
    DESCRIPTION,
    PFAM_ENTRY_ID,
    MOTIF_AA_SEQUENCE_ID,
    REPEAT_TYPE_ID,
    EXTERNAL_DATABASE_RELEASE_ID,
    SOURCE_ID AS INTERPROSCAN_ID,
    PREDICTION_ALGORITHM_ID,
    IS_PREDICTED,
    REVIEW_STATUS_ID,
    NUMBER1 as PVALUE_EXP,
    FLOAT1  as PVALUE_MANT,
    FLOAT2  as SCORE,
    STRING1 as MEMBER_ID,
    STRING2 as MEMBER_DESCRIPTION,
    MODIFICATION_DATE, USER_READ, USER_WRITE, GROUP_READ, GROUP_WRITE,=20
OTHER_READ, OTHER_WRITE, ROW_USER_ID, ROW_GROUP_ID, ROW_PROJECT_ID,=20
ROW_ALG_INVOCATION_ID
    FROM DOTS.AAFEATUREIMP
    WHERE SUBCLASS_VIEW=3D'InterProScan';

Aaron J. Mackey wrote:

> FYI, we are currently developing a plugin to load such data from =20
> InterProScan ... we're happy to collaborate with interested parties.
>
> -Aaron
>
> On Aug 2, 2005, at 11:21 AM, Chris Stoeckert wrote:
>
>> Hi Sanjeev,
>> I don't think we have a loader at CBIL for Prosite. We load Prodom =20
>> and CDD (pfam, SMART).
>> Cheers,
>> Chris
>>
>> On Aug 1, 2005, at 4:49 PM, Kumar, Sanjeev (Contr) wrote:
>>
>>
>>> Hi,
>>>   Do we have Plugin to load PrositeDB data related to Protein =20
>>> motif? The data is available
>>>   at url address : http://ca.expasy.org/prosite/
>>>
>>> Thanks
>>> Sanjeev
>>>
>>>
>>> -------------------------------------------------------
>>> SF.Net email is sponsored by: Discover Easy Linux Migration  =
Strategies
>>> from IBM. Find simple to follow Roadmaps, straightforward articles,
>>> informative Webcasts and more! Get everything you need to get up to
>>> speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=CCk
>>> _______________________________________________
>>> Gusdev-gusdev mailing list
>>> Gus...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>
>>
>>
>>
>> -------------------------------------------------------
>> SF.Net email is sponsored by: Discover Easy Linux Migration =
Strategies
>> from IBM. Find simple to follow Roadmaps, straightforward articles,
>> informative Webcasts and more! Get everything you need to get up to
>> speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=CCk
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>
> --=20
> Aaron J. Mackey, Ph.D.
> Project Manager, ApiDB Bioinformatics Resource Center
> Penn Genomics Institute, University of Pennsylvania
> email:  am...@pc...
> office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI)
> fax:    215-746-6697
> postal: Penn Genomics Institute
>         Goddard Labs 212
>         415 S. University Avenue
>         Philadelphia, PA  19104-6017
>
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
> from IBM. Find simple to follow Roadmaps, straightforward articles,
> informative Webcasts and more! Get everything you need to get up to
> speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=CCk
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [GUSDEV] Loading Prosite DB

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

Why could you not use DoTS.DomainFeature?

In general, our group is trying not to create new views whenever  
possible.

Thanks,

-Aaron

On Aug 2, 2005, at 2:01 PM, Jian Lu wrote:

> Here is the view that we created for InterProScan. Please comment  
> it. Thanks.
>

--
Aaron J. Mackey, Ph.D.
Project Manager, ApiDB Bioinformatics Resource Center
Penn Genomics Institute, University of Pennsylvania
email:  am...@pc...
office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI)
fax:    215-746-6697
postal: Penn Genomics Institute
         Goddard Labs 212
         415 S. University Avenue
         Philadelphia, PA  19104-6017

Re: [GUSDEV] Loading Prosite DB

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

Aaron,

We are also working on InterProScan and other analysis tools. But we=20
haven't got a plugin yet. If your plugin is ready, I would like to play=20
it. Here is the view that we created for InterProScan. Please comment=20
it. Thanks.

--
-- VIEW DOTS.INTERPROSCAN
-- used to store outputs from InterProScan
-- June 29, 2005
--=20
-- For GUS 3.0
CREATE VIEW DOTS.INTERPROSCAN AS SELECT
    AA_FEATURE_ID,
    AA_SEQUENCE_ID,
    FEATURE_NAME_ID,
    PARENT_ID,
    NA_FEATURE_ID,
    SUBCLASS_VIEW,
    SEQUENCE_ONTOLOGY_ID,
    DESCRIPTION,
    PFAM_ENTRY_ID,
    MOTIF_AA_SEQUENCE_ID,
    REPEAT_TYPE_ID,
    EXTERNAL_DATABASE_RELEASE_ID,
    SOURCE_ID AS INTERPROSCAN_ID,
    PREDICTION_ALGORITHM_ID,
    IS_PREDICTED,
    REVIEW_STATUS_ID,
    INT1 AS PVALUE_EXP,
    FLOAT1  as PVALUE_MANT,
    FLOAT2  as SCORE,
    STRING1 AS MEMBER_ID,
    STRING2 AS MEMBER_DESCRIPTION,
    MODIFICATION_DATE, USER_READ, USER_WRITE, GROUP_READ, GROUP_WRITE,=20
OTHER_READ, OTHER_WRITE, ROW_USER_ID, ROW_GROUP_ID, ROW_PROJECT_ID,=20
ROW_ALG_INVOCATION_ID
    FROM DOTS.AAFEATUREIMP
    WHERE SUBCLASS_VIEW=3D'InterProScan';

-- For GUS 3.5
CREATE VIEW DOTS.INTERPROSCAN AS SELECT
    AA_FEATURE_ID,
    AA_SEQUENCE_ID,
    FEATURE_NAME_ID,
    PARENT_ID,
    NA_FEATURE_ID,
    SUBCLASS_VIEW,
    SEQUENCE_ONTOLOGY_ID,
    DESCRIPTION,
    PFAM_ENTRY_ID,
    MOTIF_AA_SEQUENCE_ID,
    REPEAT_TYPE_ID,
    EXTERNAL_DATABASE_RELEASE_ID,
    SOURCE_ID AS INTERPROSCAN_ID,
    PREDICTION_ALGORITHM_ID,
    IS_PREDICTED,
    REVIEW_STATUS_ID,
    NUMBER1 as PVALUE_EXP,
    FLOAT1  as PVALUE_MANT,
    FLOAT2  as SCORE,
    STRING1 as MEMBER_ID,
    STRING2 as MEMBER_DESCRIPTION,
    MODIFICATION_DATE, USER_READ, USER_WRITE, GROUP_READ, GROUP_WRITE,=20
OTHER_READ, OTHER_WRITE, ROW_USER_ID, ROW_GROUP_ID, ROW_PROJECT_ID,=20
ROW_ALG_INVOCATION_ID
    FROM DOTS.AAFEATUREIMP
    WHERE SUBCLASS_VIEW=3D'InterProScan';

Aaron J. Mackey wrote:

> FYI, we are currently developing a plugin to load such data from =20
> InterProScan ... we're happy to collaborate with interested parties.
>
> -Aaron
>
> On Aug 2, 2005, at 11:21 AM, Chris Stoeckert wrote:
>
>> Hi Sanjeev,
>> I don't think we have a loader at CBIL for Prosite. We load Prodom =20
>> and CDD (pfam, SMART).
>> Cheers,
>> Chris
>>
>> On Aug 1, 2005, at 4:49 PM, Kumar, Sanjeev (Contr) wrote:
>>
>>
>>> Hi,
>>>   Do we have Plugin to load PrositeDB data related to Protein =20
>>> motif? The data is available
>>>   at url address : http://ca.expasy.org/prosite/
>>>
>>> Thanks
>>> Sanjeev
>>>
>>>
>>> -------------------------------------------------------
>>> SF.Net email is sponsored by: Discover Easy Linux Migration  Strategi=
es
>>> from IBM. Find simple to follow Roadmaps, straightforward articles,
>>> informative Webcasts and more! Get everything you need to get up to
>>> speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=CCk
>>> _______________________________________________
>>> Gusdev-gusdev mailing list
>>> Gus...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>
>>
>>
>>
>> -------------------------------------------------------
>> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
>> from IBM. Find simple to follow Roadmaps, straightforward articles,
>> informative Webcasts and more! Get everything you need to get up to
>> speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=CCk
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>
> --=20
> Aaron J. Mackey, Ph.D.
> Project Manager, ApiDB Bioinformatics Resource Center
> Penn Genomics Institute, University of Pennsylvania
> email:  am...@pc...
> office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI)
> fax:    215-746-6697
> postal: Penn Genomics Institute
>         Goddard Labs 212
>         415 S. University Avenue
>         Philadelphia, PA  19104-6017
>
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
> from IBM. Find simple to follow Roadmaps, straightforward articles,
> informative Webcasts and more! Get everything you need to get up to
> speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=CCk
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

RE: [GUSDEV] Loading Prosite DB

[Kumar, S. \(Contr\) <San...@ng...>]

Hi Aaron,
   Definetly we are interested in this as well.In the mean while I will =
start writing Plugin for the "ProSite data", which is in the format =
mentioed in below given url.
I don't know whether you have already decided the tables and columns =
where you are going to store such data. If yes then could you pl. share =
that with me.

Thanks
Sanjeev

-----Original Message-----
From: Aaron J. Mackey [mailto:am...@pc...]
Sent: Tuesday, August 02, 2005 11:25 AM
Cc: Kumar, Sanjeev (Contr); gus...@li...
Subject: Re: [GUSDEV] Loading Prosite DB


FYI, we are currently developing a plugin to load such data from =20
InterProScan ... we're happy to collaborate with interested parties.

-Aaron

On Aug 2, 2005, at 11:21 AM, Chris Stoeckert wrote:

> Hi Sanjeev,
> I don't think we have a loader at CBIL for Prosite. We load Prodom =20
> and CDD (pfam, SMART).
> Cheers,
> Chris
>
> On Aug 1, 2005, at 4:49 PM, Kumar, Sanjeev (Contr) wrote:
>
>
>> Hi,
>>   Do we have Plugin to load PrositeDB data related to Protein =20
>> motif? The data is available
>>   at url address : http://ca.expasy.org/prosite/
>>
>> Thanks
>> Sanjeev
>>
>>
>> -------------------------------------------------------
>> SF.Net email is sponsored by: Discover Easy Linux Migration =20
>> Strategies
>> from IBM. Find simple to follow Roadmaps, straightforward articles,
>> informative Webcasts and more! Get everything you need to get up to
>> speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=CCk
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
> from IBM. Find simple to follow Roadmaps, straightforward articles,
> informative Webcasts and more! Get everything you need to get up to
> speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=CCk
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

--
Aaron J. Mackey, Ph.D.
Project Manager, ApiDB Bioinformatics Resource Center
Penn Genomics Institute, University of Pennsylvania
email:  am...@pc...
office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI)
fax:    215-746-6697
postal: Penn Genomics Institute
         Goddard Labs 212
         415 S. University Avenue
         Philadelphia, PA  19104-6017

Re: [GUSDEV] Loading Prosite DB

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

FYI, we are currently developing a plugin to load such data from =20
InterProScan ... we're happy to collaborate with interested parties.

-Aaron

On Aug 2, 2005, at 11:21 AM, Chris Stoeckert wrote:

> Hi Sanjeev,
> I don't think we have a loader at CBIL for Prosite. We load Prodom =20
> and CDD (pfam, SMART).
> Cheers,
> Chris
>
> On Aug 1, 2005, at 4:49 PM, Kumar, Sanjeev (Contr) wrote:
>
>
>> Hi,
>>   Do we have Plugin to load PrositeDB data related to Protein =20
>> motif? The data is available
>>   at url address : http://ca.expasy.org/prosite/
>>
>> Thanks
>> Sanjeev
>>
>>
>> -------------------------------------------------------
>> SF.Net email is sponsored by: Discover Easy Linux Migration =20
>> Strategies
>> from IBM. Find simple to follow Roadmaps, straightforward articles,
>> informative Webcasts and more! Get everything you need to get up to
>> speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=CCk
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
> from IBM. Find simple to follow Roadmaps, straightforward articles,
> informative Webcasts and more! Get everything you need to get up to
> speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=CCk
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

--
Aaron J. Mackey, Ph.D.
Project Manager, ApiDB Bioinformatics Resource Center
Penn Genomics Institute, University of Pennsylvania
email:  am...@pc...
office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI)
fax:    215-746-6697
postal: Penn Genomics Institute
         Goddard Labs 212
         415 S. University Avenue
         Philadelphia, PA  19104-6017

Re: [GUSDEV] Loading Prosite DB

[Chris S. <sto...@pc...>]

Hi Sanjeev,
I don't think we have a loader at CBIL for Prosite. We load Prodom =20
and CDD (pfam, SMART).
Cheers,
Chris

On Aug 1, 2005, at 4:49 PM, Kumar, Sanjeev (Contr) wrote:

> Hi,
>   Do we have Plugin to load PrositeDB data related to Protein =20
> motif? The data is available
>   at url address : http://ca.expasy.org/prosite/
>
> Thanks
> Sanjeev
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
> from IBM. Find simple to follow Roadmaps, straightforward articles,
> informative Webcasts and more! Get everything you need to get up to
> speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=CCk
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

Re: [GUSDEV] Postgres Vs. Oracle

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

Hi Juan,

GUS *should* be stable and full featured in Postgres.  It is, of course much
younger code and thus there are likely to be more issues in Postgres than
Oracle.  As these issues come up, they're getting the same attention and
priority that Oracle bugs would get.

Out of the box, Postgres is much slower than Oracle, but you should be able
to optimize to eliminate much, if not all, of the difference.  I'm not sure
who has the largest pg GUS instance running (anyone?), but I can tell you
that GUS on Oracle has scaled for us easily past 500GB (although we've seen
some localized performance problems as we approach 700GB).

Oracle is, as you know, fairly expensive.  We have a site license and a DBA
(me) so for us it's the obvious choice.  Without one or both of these, and
knowing that your data will stay relatively small (under 2-3GB), Postgres is
probably a very good choice.

Ultimately, it comes down to performance needs v. costs and local
preferences.

Hope this helps some.

Mike



On 8/1/05 11:08 AM, "Juan Carlos Perin" <bi...@ge...> wrote:

> I apologize in advance if this topic has been discussed.  We are in the
> process of re-installing GUS and using RAD, but cannot decide on Postgres or
> Oracle.  We used Oracle for our previous installation, which we did on a
> learn as we go method...  We are starting from scratch, and have access to
> Oracle 9i if needed, although fear possibly being charged for it in the near
> future.
> 
> Our fist inclination is to go with Postgres to avoid costs in the future,
> but also because it is more familiar to us, and seems easier to work with in
> general.  Oracle is a bit more foreign to us, but seems like it probably has
> more use in the GUS community, and probably runs with more stability.  We're
> wondering whether Oracle really is more robust for 3.5?  Also, we plan on
> customizing a few components, so our initial assumption is that the oracle
> implementation is probably more familiar to the GUS community, so questions
> may be more easily approached with Oracle.
> 
> Really we're just looking for some reasons to go with one rather then the
> other;  whether Oracle is worth the price, when compared to the simplicity
> and cost efficiency of Postgres?  Thanks in advance!
> 
> Juan Perin
>   
> 
> 
> 
> 
> -------------------------------------------------------
> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
> from IBM. Find simple to follow Roadmaps, straightforward articles,
> informative Webcasts and more! Get everything you need to get up to
> speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

[GUSDEV] Loading Prosite DB

[Kumar, S. \(Contr\) <San...@ng...>]

Hi,
  Do we have Plugin to load PrositeDB data related to Protein motif? The =
data is available
  at url address : http://ca.expasy.org/prosite/

Thanks
Sanjeev

[GUSDEV] Postgres Vs. Oracle

[Juan C. P. <bi...@ge...>]

I apologize in advance if this topic has been discussed.  We are in the
process of re-installing GUS and using RAD, but cannot decide on Postgres or
Oracle.  We used Oracle for our previous installation, which we did on a
learn as we go method...  We are starting from scratch, and have access to
Oracle 9i if needed, although fear possibly being charged for it in the near
future.

Our fist inclination is to go with Postgres to avoid costs in the future,
but also because it is more familiar to us, and seems easier to work with in
general.  Oracle is a bit more foreign to us, but seems like it probably has
more use in the GUS community, and probably runs with more stability.  We're
wondering whether Oracle really is more robust for 3.5?  Also, we plan on
customizing a few components, so our initial assumption is that the oracle
implementation is probably more familiar to the GUS community, so questions
may be more easily approached with Oracle.

Really we're just looking for some reasons to go with one rather then the
other;  whether Oracle is worth the price, when compared to the simplicity
and cost efficiency of Postgres?  Thanks in advance!

Juan Perin
  

Re: [GUSDEV] setting nasequenceimp.sequence_version in 3.5

[Chris S. <sto...@pc...>]

After conferring with Mike, it appears that this happens for only a  
couple tables. Our choices are:
- set default values (which can be done for Oracle or Postgres)
- make the Plugins handle this.
- make these nullable

My inclination is to make the plugins handle this because it  
eliminates special cases (i.e. default values for a couple tables)  
and can be implemented immediately.
Unless I hear a strong argument to convince me otherwise in the next  
week this will be considered resolved.

Chris

On Jul 19, 2005, at 12:24 AM, Mark S. Heiges wrote:

> ApiComplexa::DataLoad::Plugin::dbEST is the same as  
> GUS::Community::Plugin::dbEST (recently renamed to  
> LoadFromdbESTMirror.pm) except it reads from a remote database link  
> to Penn's dbEST mirror.
>
> With GUS 3.5 it throws the error
>     cannot insert NULL into  
> ("DOTS"."NASEQUENCEIMP"."SEQUENCE_VERSION")
>
> This error is clear enough but this was not a problem in GUS 3.0  
> where sequence_version would always get set to '1'.
> Sequence_version doesn't seem to get set by dbEST so apparently  
> there is some default assignment elsewhere. Checking a GUS3.0  
> Oracle instance, there appears to be a default value defined in the  
> NaSequenceImp table definition that I don't have in my 3.5 instance.
>
> Does sequence_version need to be explicitly set by plugins for 3.5  
> or is my  3.5 NaSequenceImp table erroneously missing a default  
> value for that column?
>
>
> -M
>
>
>
>
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Re: [GUSDEV] Re: [ApiDB] correctly using the tracker

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

Heh, did I hit "reply all"?  Silly me.  Oh well.

-Aaron

Aaron J. Mackey wrote:
> 
> 
> steve wrote:
> 
>> 2 It is assigned by default to the appropriate "User Representative" 
>> for the product. The User Representative is a person on the 
>> development team that best understands the needs of the product's users.
> 
> 
> This is the bit that is slightly worrisome; shouldn't this always, by 
> definition, be me?  If there's someone else who better understands the 
> needs of our developers, then I'm not doing my job.
> 
> Said another way, shouldn't I be the one setting priorities, not (e.g.) 
> Mark?
> 
> Like I said to Mike, I'm willing to give it a whirl, but I wont be 
> surprised by gross noncompliance (or possibly just uncompliance, i.e. no 
> usage).  Hopefully I'll be wrong.
> 
> -Aaron
> 
> 
> -------------------------------------------------------
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[GUSDEV] Re: [ApiDB] correctly using the tracker

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

steve wrote:
> 2 It is assigned by default to the appropriate "User Representative" for 
> the product. The User Representative is a person on the development team 
> that best understands the needs of the product's users.

This is the bit that is slightly worrisome; shouldn't this always, by 
definition, be me?  If there's someone else who better understands the 
needs of our developers, then I'm not doing my job.

Said another way, shouldn't I be the one setting priorities, not (e.g.) 
Mark?

Like I said to Mike, I'm willing to give it a whirl, but I wont be 
surprised by gross noncompliance (or possibly just uncompliance, i.e. no 
usage).  Hopefully I'll be wrong.

-Aaron

[GUSDEV] correctly using the tracker

[steve <sfi...@pc...>]

The correct way to use the tracker is described in the wiki at:

http://www.gusdb.org/wiki/index.php/UsingTheTracker


Here it is for your convenience:

Using the Tracker (correctly)

The Lifecycle of a Request
1 A request originates from a user.
2 It is assigned by default to the appropriate "User Representative" for=20
the product. The User Representative is a person on the development team=20
that best understands the needs of the product's users.
3 The User Representative sets the request's Target (when it should be=20
released). He or she takes into consideration the Priority given to the=20
request by the user, and the scheduling of other requests for the product.
4 The User Representative then assigns the request to the "Engineering=20
Representative" for the product.
5 The Engineering Representative evaluates whether his or her=20
engineering team can deliver the request by the target the User=20
Representative specified.
6 If not, the Engineering Representative and the User Representative=20
discuss, and either
=E2=97=A6 move the request to a further off target
=E2=97=A6 remove one or more request for the specified target to make roo=
m for=20
the new request
=E2=97=A6 move back the time the targeted release is expected by
7 The Engineering Representative modifies the Target as agreed upon.

Adding a New Feature or Bug

Following is a description of the fields you must fill in.

Product

You must chose a product. If you don't know which, guess. The person=20
assigned to the request will sort it out.

Component

You must chose a component. If you don't know, guess. The person=20
assigned to the request will sort it out.

Severity

Chose between
Bug
something broken in the product.
Feature
something new to include in the product

If you aren't sure, guess.

Version

If you are submitting a
bug
this is the version in which you found the bug.
feature
this is the version in which you do not find the feature. It is not the=20
version in which you would like to find the new feature

Priority

This field is set by users only (not by members of the development=20
team). It indicates the user's sense of the importance of the request

Target
This field is set by the development team.

[GUSDEV] RE: [ApiDB] *always* use the tracker

[Y. T. G. <yg...@pc...>]

Also please create an account for yourself on the tracker
so that your can be notified of changes to bugs/features relevant to
you.

I had trouble including some people in the cc box while reporting
issues.

-Thomas

> -----Original Message-----
> From: api...@pc... 
> [mailto:api...@pc...] On Behalf Of steve
> Sent: Monday, July 25, 2005 2:49 PM
> To: Gusdev gusdev-gusdev; ApiDB Project Mailing List
> Subject: [ApiDB] *always* use the tracker
> 
> 
> folks-
> 
> i am seeing a lot of bugs and features being communicated by mail.
> 
> bugs and features *must* be in the tracker for them to be 
> taken care of.
> 
> no exceptions.
> 
> the reasons are:
>   - it is too much to juggle if there isn't a single place 
> for all requests
>   - we can get reports to help us prioritize our work
>   - we can get reports to make release notes from
> 
> thanks,
> steve
> _______________________________________________
> ApiDB mailing list
> Ap...@pc... 
> https://mail.pcbi.upenn.edu/mailman/listinfo/apidb
> 

[GUSDEV] *always* use the tracker

[steve <sfi...@pc...>]

folks-

i am seeing a lot of bugs and features being communicated by mail.

bugs and features *must* be in the tracker for them to be taken care of.

no exceptions.

the reasons are:
  - it is too much to juggle if there isn't a single place for all requests
  - we can get reports to help us prioritize our work
  - we can get reports to make release notes from

thanks,
steve

Re: [GUSDEV] RNAFeature versus RNAType

[Chris S. <sto...@pc...>]

An addendum after further discussion with Steve, Debbie, and Ed.

DoTS.Transcript: This view is for mRNAs (protein coding RNAs) that  
require GenBank-type attributes.
RNAFeature: This view is also for EST assemblies that may or may be  
protein-coding.

Chris

On Jul 19, 2005, at 5:01 PM, Chris Stoeckert wrote:

> Hi,
> There has been some discussion as to the history, semantics, and  
> usage of RNAType versus RNAFeature. After digging into old emails a  
> bit more and with helpful prodding from Steve, I believe that I can  
> define the usage of these NAFeature views.
>
> RNAFeature: This view is for mRNAs (protein coding RNAs). This is  
> why it has attributes referring to translation.
> RNAType: This view is for non-coding RNAs. In the CBIL instance of  
> GUS, we have rRNA, tRNA, snRNA, snoRNA, and scRNA.
>
> Chris
>
>
>
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