gmod-ware-users — General list for users of modware

[Gmod-ware-users] Re: Modware status

[Siddhartha B. <bi...@gm...>]

Hi Amelia, 
I am doing a complete rewrite of Modware which is under active
development. It's in github https://github.com/dictyBase/Modware
Currently it has a working version of Publication module that is used at
dictyBase for the past one year. The rest of it getting developed and
my goal is to finished by the start of next year.

The one in sourceforge is no longer being maintained or supported.
Please let me know if you need any other information or anything else to
help you out.

cheers, 
-siddhartha


On Wed, 11 Jul 2012, Amelia Ireland wrote:

> Hello,
> 
> I am writing on behalf of GMOD to check the status of Modware that
> we can update our wiki listings. Is it still being maintained,
> developed, and/or supported?
> 
> Thank you for your help!
> 
> -- 
> Amelia Ireland
> GMOD Community Support Specialist || http://gmod.org
> 
> ------------------------------------------------------------------------------
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> https://lists.sourceforge.net/lists/listinfo/gmod-ware-users

[Gmod-ware-users] Modware status

[Amelia I. <ame...@gm...>]

Hello,

I am writing on behalf of GMOD to check the status of Modware that
we can update our wiki listings. Is it still being maintained,
developed, and/or supported?

Thank you for your help!

-- 
Amelia Ireland
GMOD Community Support Specialist || http://gmod.org

[Gmod-ware-users] 2011 GMOD Spring Training, March 8-12

[Dave C. G. H. D. <he...@gm...>]

Applications are now being accepted for the 2011 GMOD Spring Training
course a five-day hands-on school aimed at teaching new GMOD
administrators how to install, configure and integrate popular GMOD
components. The course will be held March 8-12 at the US National
Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, as
part of GMOD Americas 2011.

Links:
   * http://gmod.org/wiki/2011_GMOD_Spring_Training
   * http://gmod.org/wiki/GMOD_Americas_2011
   * http://www.nescent.org/

These components will be covered:
   * Apollo - genome annotation editor
   * Chado - biological database schema
   * Galaxy - workflow system
   * GBrowse - genome viewer
   * GBrowse_syn - synteny viewer
   * GFF3 - genome annotation file format and tools
   * InterMine - biological data mining system
   * JBrowse - next generation genome browser
   * MAKER - genome annotation pipeline
   * Tripal - web front end to Chado databases

The deadline for applying is the end of Friday, January 7, 2011.
Admission is competitive and is based on the strength of the
application, especially the statement of interest. The 2010 school had
over 60 applicants for the 25 slots. Any application received after
deadline will be automatically placed on the waiting list.

The course requires some knowledge of Linux as a prerequisite. The
registration fee will be $265 (only $53 per day!). There will be a
limited number of scholarships available.

This may be the only GMOD School offered in 2011. If you are
interested, you are strongly encouraged to apply by January 7.

Thanks,

Dave Clements
--
http://gmod.org/wiki/GMOD_Americas_2011
http://gmod.org/wiki/GMOD_News
http://gmod.org/wiki/Help_Desk_Feedback

Re: [Gmod-ware-users] Modware status update

[Robert B. <rm...@co...>]

Congrats Siddhartha!

Rob

Siddhartha Basu wrote:
> Hi folks, 
> Good news and update on the current status of Modware development. Modware is
> is getting back on track and currently being actively developed at
> dictyBase since last few months. It is being written using Moose and
> DBIx-Class(more precisely Bio-Chado-Schema or BCS) ORM. This part of
> development is done in sync with dictyBase's major data migration
> project which includes literature and gene ontology annotations. So,  the
> first release of this new version  is expected to deal with
> publication and ontology datasets in chado. Handling of feature module
> will be added after the first release get settled down. Like any other
> standard Perl module Modware's public release will be available from
> CPAN and the bleeding edge can be grabbed from github. 
> Github link: http://github.com/cybersiddhu/Modware
> Relevant documentations and guidelines will also be added to the GMOD
> wiki. 
> The first CPAN release is expected to be early next year.  
>  
> thanks, 
> -siddhartha
>  
> Siddhartha Basu
> Modware developer,  dictyBase
> www.dictybase.org
> 
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
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> http://p.sf.net/sfu/nokia-dev2dev
> _______________________________________________
> Gmod-ware-users mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ware-users
> 

Re: [Gmod-ware-users] Modware status update

[Siddhartha B. <sid...@no...>]

Hi folks, 
Good news and update on the current status of Modware development. Modware is
is getting back on track and currently being actively developed at
dictyBase since last few months. It is being written using Moose and
DBIx-Class(more precisely Bio-Chado-Schema or BCS) ORM. This part of
development is done in sync with dictyBase's major data migration
project which includes literature and gene ontology annotations. So,  the
first release of this new version  is expected to deal with
publication and ontology datasets in chado. Handling of feature module
will be added after the first release get settled down. Like any other
standard Perl module Modware's public release will be available from
CPAN and the bleeding edge can be grabbed from github. 
Github link: http://github.com/cybersiddhu/Modware
Relevant documentations and guidelines will also be added to the GMOD
wiki. 
The first CPAN release is expected to be early next year.  
 
thanks, 
-siddhartha
 
Siddhartha Basu
Modware developer,  dictyBase
www.dictybase.org

[Gmod-ware-users] GMOD Europe 2010 Update

[Dave C. G. H. D. <he...@gm...>]

Hello all,

GMOD Europe 2010 (http://gmod.org/wiki/GMOD_Europe_2010) starts in
less than two weeks. If you are planning on attending and haven't yet
registered, then please do so in the next few days. The BioMart
Workshop has only a few slots left, and the registration fee for the
GMOD Meeting goes from £50 to £65 on 6 September. We are encouraging
people to submit topic suggestions for the GMOD Meeting and the GMOD
Satellite Meetings.

We are also pleased to announce that Jason Swedlow of the University
of Dundee will be the guest speaker at the GMOD Meeting. Jason will
speak on "The Open Microscopy Environment: Open Informatics for
Biological Imaging," a particularly timely topic as many researchers
move into image intensive areas such as phenotypes and gene
expression, and as high-throughput imaging platforms become available.

There is still space available at all 4 events, and registration for
the GMOD Satellite Meetings, InterMine Workshop and BioMart Workshop
is free.

Scott Cain and Dave Clements

Links:
http://gmod.org/wiki/GMOD_Europe_2010
http://gmod.org/wiki/September_2010_GMOD_Meeting
http://gmod.org/wiki/Satellite_Meetings_-_GMOD_Europe_2010
http://gmod.org/wiki/InterMine_Workshop_-_GMOD_Europe_2010
http://gmod.org/wiki/BioMart_Workshop_-_GMOD_Europe_2010

[Gmod-ware-users] GMOD Europe 2010 Registration Now Open

[Dave C. G. H. D. <he...@gm...>]

GMOD Europe 2010
================
13-16 September 2010
Cambridge, UK
http://gmod.org/wiki/GMOD_Europe_2010


We are pleased to announce GMOD Europe 2010, four days of GMOD events being
held 13-16 September 2010, at the University of Cambridge. GMOD Europe 2010
includes:

1) GMOD Community Meeting, Monday & Tuesday:  Project updates, developer and
user presentations and best practices, project direction.

2) GMOD Satellite Meetings, Wednesday:  Special interest groups where GMOD
community members meet to discuss specific topics of interest.

3) InterMine Workshop, Wednesday:  A one day workshop on installing,
configuring and using the InterMine biological data warehouse system.

4) BioMart Workshop, Thursday:  A one day workshop on using the BioMart
biological data warehouse system, including accessing data through APIs.

Registration is now open for these events. There is a £50 registration fee
for the GMOD Meeting to cover catered lunches, coffee/tee breaks, and other
expenses. Registration for all other events is free, but still required, as
space is limited.

These events are open to all: GMOD users, developers, prospective users,
biologists, and computer scientists.  For an idea of what goes on at GMOD
meetings, see http://gmod.org/wiki/January_2010_GMOD_Meeting.

See you in Cambridge!

Scott Cain and Dave Clements


PS: If you have topics you want to have covered (or you want to cover) at
the GMOD Meeting, or at the Satellite Meetings, please add them to the wiki
pages, or contact us. We are also asking for guest speaker nominations for
the meeting.
-- 
http://gmod.org/wiki/GMOD_News
<http://gmod.org/wiki/GMOD_News>http://gmod.org/wiki/GMOD_Evo_Hackathon
http://gmod.org/wiki/GMOD_Europe_2010
http://gmod.org/wiki/Help_Desk_Feedback

[Gmod-ware-users] GMOD Evo Hackathon Open Call for Participation

[Dave C. G. H. D. <he...@gm...>]

We are seeking participants for the GMOD Tools for Evolutionary Biology
Hackathon, held November 8-12, 2010 at the US National Evolutionary
Synthesis Center (NESCent) in Durham, NC.

This hackathon targets three critical gaps in the capabilities of the GMOD
toolbox that currently limit its utility for evolutionary research:
 1. Visualization of comparative genomics data
 2. Visualization of phylogenetic data and trees
 3. Support for population diversity and phenotype data

If you are interested in these areas and have relevant expertise, you are
strongly encouraged to apply.  Relevant areas of expertise include more than
just software development: if you are a GMOD power user, visualization guru,
domain expert (comparative, phylogenetics, population, ...), or
documentation wizard, then your skills are needed!

How To Apply:
Fill out the online application form at http://bit.ly/gmodevohack.
 Applications are due August 25.

About GMOD:
GMOD is an intercompatible suite of open-source software components for
storing, managing, analyzing, and visualizing genome-scale data. GMOD
includes many widely-used software components: GBrowse and JBrowse, both
genome viewers; GBrowse_syn, a comparative genomics viewer; Chado, a generic
and modular database schema; CMap, a comparative map viewer; as well as many
other components including Apollo, MAKER, BioMart, InterMine, and Galaxy.
 We hope to extend the functionality of existing GMOD components, and
integrate new components as well.

About Hackathons:
A hackathon is an intense event at which a group of programmers with
different backgrounds and skills collaborate hands-on and face-to-face to
develop working code that is of utility to the community as a whole. The mix
of people will include domain experts and computer-savvy end-users.

More details about the event, its motivation, organization, procedures, and
attendees, as well as URLs to the hackathon and related websites are
included below.

Sincerely,

The GMOD EvoHack Organizing Committee (and project affiliations as
relevant):

Nicole Washington, Chair (LBNL, modENCODE, Phenote)

Robert Buels (SGN, Chado NatDiv)

Scott Cain (OICR, GMOD)

Dave Clements (NESCent, GMOD)

Hilmar Lapp (NESCent, Phenoscape, Chado NatDiv)

Sheldon McKay (University of Arizona, iPlant, GBrowse_syn)

-----------------------------
About the GMOD Evo HackathonOverviewWe are organizing a hackathon to fill
critical gaps in the capabilities of the Generic Model Organism Database
(GMOD) toolbox that currently limit its utility for evolutionary research.
Specifically, we will focus on tools for 1) viewing comparative genomics
data; 2) visualizing phylogenomic data; and 3) supporting population
diversity data and phenotype annotation.The event will be hosted at NESCent
and bring together a group of about 20+ software developers, end-user
representatives, and documentation experts who would otherwise not meet. The
participants will include key developers of GMOD components that currently
lack features critical for emerging evolutionary biology research,
developers of informatics tools in evolutionary research that lack GMOD
integration, and informatics-savvy biologists who can represent end-user
requirements.

The event will provide a unique opportunity to infuse the GMOD developer
community with a heightened awareness of unmet needs in evolutionary biology
that GMOD components have the potential to fill, and for tool developers in
evolutionary biology to better understand how best to extend or integrate
with already existing GMOD components.
Before the EventDiscussion of ideas and sometimes even design actually
starts well before the hackathon, on mailing lists, wiki pages, and
conference calls set up among accepted attendees.  This advance work lays
the foundation for participants to be productive from the very first day.
 This also means that participants should be willing to contribute some time
in advance of the hackathon itself to participate in this preparatory
discussion.During the EventTypically, hackathon participants use the morning
of the first day of the event to organize themselves into working groups of
between 3 and 6 people, each with a focused implementation objective.  Ideas
and objectives are discussed, and attendees coalesce around the projects in
which they have the most experience or interest.Deliverables / Event ResultsThe
meeting’s attendance, working groups, and outcomes will be fully logged and
documented on the GMOD wiki (http://gmod.org).  Each working group during
the event will typically have its own wiki page, linked from the main
EvoHack page, where it documents its minutes and design notes, and provides
links to the code and documentation it produces.  Also, since GMOD and
NESCent are both committed to open source principles, all code and
documentation produced by participants during the hackathon must be
published under an OSI-approved open source license.  As contributions to
existing GMOD tools, all hackathon products will most likely satisfy this
requirement automatically.NESCentThis event is sponsored by the US National
Evolutionary Synthesis Center (NESCent, http://www.nescent.org) through its
Informatics Whitepapers program (
http://www.nescent.org/informatics/whitepapers.php). NESCent promotes the
synthesis of information, concepts and knowledge to address significant,
emerging, or novel questions in evolutionary science and its applications.
NESCent achieves this by supporting research and education across
disciplinary, institutional, geographic, and demographic boundaries (see
http://www.nescent.org/science/proposals.php).
LinksMain GMOD EvoHack page, and full proposal:
http://gmod.org/wiki/GMOD_Evo_HackathonNESCent: http://www.nescent.org/
GMOD: http://gmod.org
Similar past NESCent events, see: http://hackathon.nescent.org/
GMOD hackathon application:  http://bit.ly/gmodevohack

-- 
http://gmod.org/wiki/GMOD_News
http://gmod.org/wiki/GMOD_Europe_2010
http://gmod.org/wiki/Help_Desk_Feedback

Re: [Gmod-ware-users] August 2009 GMOD Meeting

[Dave C. G. H. D. <gmo...@go...>]

Hello all,

Just a reminder that the August 2009 GMOD Meeting is being held 6-7
August, in Oxford, UK.  With a little over 3 weeks to go, the meeting
is now 40% full.  All remaining space is available on a first come
first served basis, and I encourage you to register now, before all
open slots are taken.  (The January meeting was completely full.)

You can register at http://gmod.org/wiki/August_2009_GMOD_Meeting.

Please let me know if you have any questions.

Cheers,

Dave C.


On Wed, Jul 1, 2009 at 1:48 PM, Dave Clements, GMOD Help
Desk<gmo...@go...> wrote:
> Hello all,
>
> The next GMOD meeting will be held 6-7 August, at the University of
> Oxford, in Oxford, United Kingdom. Registration is now open. Space is
> available on a first come, first served basis and there is room for 55
> attendees. The meeting cost is £50.  See
> http://gmod.org/wiki/August_2009_GMOD_Meeting to register
>
> As with previous GMOD meetings, this meeting will have a mixture of
> project, component, and user talks. The agenda is driven by attendee
> suggestions, and you are encouraged to add your suggestions now (see
> http://gmod.org/wiki/August_2009_GMOD_Meeting#Agenda_Suggestions).
>
> For examples of what happens at a GMOD meeting, see the writeups of
> the January 2009, July 2008, or any other previous meeting (see
> http://gmod.org/wiki/Meetings). GMOD meetings are an excellent way to
> meet other GMOD developers and users and to learn (and affect) what's
> coming in the project.
>
> Please join us in Oxford this August,
>
> Dave Clements
> GMOD Help Desk
>
> Note: Unless you have applied to and been admitted to the Summer
> School, don't you dare register for it. The registration web site will
> let you do this, but bureaucratic hellishness will ensue.
>
> --
> * Learn more about GMOD at: ISMB/ECCB: http://www.iscb.org/ismbeccb2009/
>   (BioMart, Chado, Galaxy, InterMine)
> * Please keep responses on the list!
> * Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback
>



-- 
* Register now for the August GMOD Meeting:
http://gmod.org/wiki/August_2009_GMOD_Meeting
* Please keep responses on the list!
* Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback

[Gmod-ware-users] August 2009 GMOD Meeting

[Dave C. G. H. D. <gmo...@go...>]

Hello all,

The next GMOD meeting will be held 6-7 August, at the University of
Oxford, in Oxford, United Kingdom. Registration is now open. Space is
available on a first come, first served basis and there is room for 55
attendees. The meeting cost is £50.  See
http://gmod.org/wiki/August_2009_GMOD_Meeting to register

As with previous GMOD meetings, this meeting will have a mixture of
project, component, and user talks. The agenda is driven by attendee
suggestions, and you are encouraged to add your suggestions now (see
http://gmod.org/wiki/August_2009_GMOD_Meeting#Agenda_Suggestions).

For examples of what happens at a GMOD meeting, see the writeups of
the January 2009, July 2008, or any other previous meeting (see
http://gmod.org/wiki/Meetings). GMOD meetings are an excellent way to
meet other GMOD developers and users and to learn (and affect) what's
coming in the project.

Please join us in Oxford this August,

Dave Clements
GMOD Help Desk

Note: Unless you have applied to and been admitted to the Summer
School, don't you dare register for it. The registration web site will
let you do this, but bureaucratic hellishness will ensue.

--
* Learn more about GMOD at: ISMB/ECCB: http://www.iscb.org/ismbeccb2009/
  (BioMart, Chado, Galaxy, InterMine)
* Please keep responses on the list!
* Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback

Re: [Gmod-ware-users] 2009 GMOD Summer Schools - Americas and Europe

[Dave C. G. H. D. <gmo...@go...>]

Hello all,

***The application deadline for both GMOD summer schools is April 6,
one week from now.***

GMOD Summer School - Americas will be held 16-19 July at the National
Evolutionary Synthesis Center (NESCent), in Durham, NC, USA.  Student
tuition is free.  See
http://gmod.org/wiki/2009_GMOD_Summer_School_-_Americas

GMOD Summer School - Europe will be held 3-6 August at the University
of Oxford, in Oxford, UK.  This is a part of GMOD Europe 2009, which
includes the next GMOD Meeting.  Student tuition is £95.  See
http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe

Please contact the GMOD Help Desk (he...@gm...) if you have questions.

We hope to see you in Durham or Oxford,

Dave C.

On Mon, Mar 16, 2009 at 10:55 AM, Dave Clements, GMOD Help Desk
<gmo...@go...> wrote:
> Hello all,
>
> GMOD is offering two Summer Schools in 2009, one on each side of the
> Atlantic. GMOD Summer Schools
> (http://gmod.org/wiki/GMOD_Summer_School) introduce new GMOD users to
> the GMOD project and include several days of hands-on training on how
> to install, configure and administer GMOD tools.  The 2008 GMOD Summer
> School was a great success with 25 students from 4 countries in
> attendance.
>
> Americas, 16-19 July
> - at the National Evolutionary Synthesis Center (NESCent), Durham, NC, USA
> - Student tuition is free, thanks to NIH grant 1R01HG004483-01.
>  - http://gmod.org/wiki/2009_GMOD_Summer_School_-_Americas
>
> Europe, 3-6 August
>  - at the University of Oxford, Oxford, United Kingdom
>  - Part of GMOD Europe 2009, which includes the next GMOD Meeting
>  - Student tuition is £75
>  - http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe
>
> The schools will feature training on these GMOD components:
> * GBrowse - the most widely installed genome viewer on the web
> * Chado - a modular and extensible database schema
> * Apollo - genome annotation editor
> * BioMart - biological data warehouse system
> * GBrowse_syn - a GBrowse based synteny viewer
> * JBrowse - a brand new Web 2.0 genome browser
> * Artemis-Chado Integration (Europe only)
> * MAKER - Genome annotation pipeline (Americas only)
> * Tripal - Web front end for Chado (Americas only)
>
> Applications for the 2009 GMOD Summer Schools are now being accepted.
>
> ***The deadline for applications is the end of the day, April 6.***
>
> Enrollment is limited to 25 participants in each course.  If
> applications exceed capacity (and we expect they will) then applicants
> will be picked based on the strength of their application.  Applicants
> will be notified of their admission status by mid April.
>
> Please contact the GMOD Help Desk if you have any questions.
>
> Thanks,
>
> Dave Clements
> GMOD Help Desk
> he...@gm...
>
> http://gmod.org/wiki/2009_GMOD_Summer_School_-_Americas
> http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe
> http://gmod.org/wiki/GMOD_Europe_2009
>

[Gmod-ware-users] Polypeptide support and others

[Lionel G. <guy...@gm...>]

(sorry if double-posting)

Hi Siddhartha,

Thanks for your quick answer... I'm definitely going to use modware,  
but I think I will have to either wait or write a couple of functions  
myself. I checked out the latest cvs version, and I've seen the last  
commits are already 10 months old. Do you plan to make any release  
soon (yeah, I know, eternal question...)?

For the moment, I need the following features, and I'm going to try to  
code them myself (unless you plan a release in a close future):
- Ability to work with more than one organism. we currently have 4  
genomes in the pipeline. I guess it's possible to have a workaround re- 
setting $ENV{DATABASE_NAME} and the other constants, but it would be  
better to be able to set them when an object is created, e.g. by  
passing an extra argument at that time. I guess it would be possible  
to keep the defaults set in $ENV
- An "richer" polypeptide object. In our database (and this is  
generally the case if you fill it with genbank files, for example), a  
lot of information is kept in the polypeptide object (with "tags"  
note, product, eC_number, etc). It is hard, if not impossible to  
retrieve them for the moment (unless I misread the code). I think I  
read somewhere than you planned to produce Bioperl objects other than  
Bio::Seq in future. Is it still ongoing? What kind of objects do you  
plan to use? How should these "tags" mapped to a Bioperl object?

Best, and thanks for your help!

Lionel

On 16 Mar 2009, at 18:09 , Siddhartha Basu wrote:

> Hi Lionel,
> Thanks a lot for feeback with modware,  we are doing our best to  
> keep it
> current and active. Regarding the error with MRNA object,  we will try
> to address the issue in our next release which are planning to do it  
> on
> gmod-1.0.
> Now about deleting features,  currently the modware codebase assumes
> that once inserted the features should stays in the database for
> archival purpose,  so it does not delete it rather mark it as  
> 'deleted'.
> And then those features get screened through our api. Now to explicity
> purge a feature from database you have to use low level Class::DBI api
> like this ...
>
> # include Chado::AutoDBI module
> use Chado::AutoDBI;
>
> my ($db_obj) = Chado::Feature->search(feature_id => $id);
> $db_obj->delete() if $db_obj;
>
> Here $db_obj is a row level Class::DBI object.
>
> The other option is to use _database_object() method in  
> Modware::Feature
> class,  have a look at it. Let me know if it helps.
>
>
> There is a dedicated mailing list for modware in gmod
> gmo...@li...
> You can subscribe and put all of your questions over there.
>
> Thanks,
> -siddhartha
>
> On Fri, 13 Mar 2009, Lionel Guy wrote:
>
>> Hi Eric and Siddhartha,
>>
>> Great news that Modware is still under development! Thanks for all  
>> the
>> work, it's really what we were looking for. We are still testing  
>> things
>> but it seems really promising.
>>
>> Here is my problem:
>> I have a test database, that I filled with a bacterial chromosome,  
>> under
>> the form of a gbk file downloaded from NCBI RefSeq. I used something
>> like:
>>
>> cat NC_008783.gbk | bp_genbank2gff3.pl -noCDS -in stdin -out stdout >
>> NC_008783.gff
>> cat NC_008783.gff | gmod_bulk_load_gff3.pl -dbname annotation - 
>> organism
>> "BB" -dbuser <user> -dbport 5432 -dbpass <password> -recreate_cache
>>
>> Everything seems fine, I can "plug" artemis on it, see the genes,  
>> etc.
>>
>> Now I tried to use the sample scripts that you provide with  
>> Modware. I
>> tried to run something like:
>>
>> my $gene = new Modware::Gene( -name => "polA" );
>> GMODWriter->Write_gene_report( $gene );
>>
>> And I got the following error:
>>
>> Can't call method "featureloc_feature_id" on an undefined value
>> at /usr/lib/perl5/site_perl/5.10.0/Modware/Feature/MRNA.pm line 245.
>>
>> After some debugging, I found that the error comes from the following
>> function (in Modware::Feature::MRNA.pm):
>>
>> sub _get_bioperl {
>> my ($self, @args) = @_;
>> my $bioperl  = new Bio::SeqFeature::Gene::Transcript();
>> my @subfeatures = $self->subfeatures();
>> my @exons       = grep{ $_->type_id->name eq $self->_exon_type() }
>> @subfeatures;
>> my @bp_exons;
>>
>> foreach my $exon ( @exons ) {
>>    my $locs     = $exon->featureloc_feature_id(); <=
>>    my $location = $locs->next();
>>
>> The program crashes at <=, because $exon is undef... I can't figure  
>> out
>> why, but it seems that the object is "emptied" at some point. For
>> example, if I go into debugging mode and watch @subfeatures, it  
>> contains
>> something when the grep takes place, and nothing after... then,  
>> @exons
>> is undef, but it still enters the foreach loop... Weird!
>>
>> I tried to get rid of the grep command, and made a horrible hack, and
>> now it works:
>>
>> sub _get_bioperl {
>> my ($self, @args) = @_;
>> my $bioperl  = new Bio::SeqFeature::Gene::Transcript();
>> # Ugly hack
>> my @exons = $self->subfeatures();
>> my @bp_exons;
>>
>> foreach my $exon ( @exons ) {
>>    # part of the above ugly hack
>>    next unless $exon->type_id->name eq $self->_exon_type;
>>    # end of ugly hack
>>    my $locs     = $exon->featureloc_feature_id();
>>    my $location = $locs->next();
>>
>> So, it seems that it's working now, but I have no idea why...
>>
>>
>> Nothing to do with this, but another thing that I noticed, is that  
>> when
>> you delete a chromosome with $chromosome->is_deleted(1) and
>> $chromosome->update, the feature actually remains in the database  
>> with
>> is_obsolete = true. Is there a way to actually delete it from the
>> database?
>>
>> Thanks for your help, and sorry for the lengthy email! BTW, should I
>> write directly to you (both?) or write on the gmod-ware mailing list?
>> What do you prefer?
>>
>> Kind regards,
>>
>> Lionel
>>




============================================
Lionel Guy
Thunmansgatan 25, SE-75421 Uppsala

phone: +46 (0)18 245596
mobile: +46 (0)73 9760618
email: guy...@gm...
============================================

[Gmod-ware-users] 2009 GMOD Summer Schools - Americas and Europe

[Dave C. G. H. D. <gmo...@go...>]

Hello all,

GMOD is offering two Summer Schools in 2009, one on each side of the
Atlantic. GMOD Summer Schools
(http://gmod.org/wiki/GMOD_Summer_School) introduce new GMOD users to
the GMOD project and include several days of hands-on training on how
to install, configure and administer GMOD tools.  The 2008 GMOD Summer
School was a great success with 25 students from 4 countries in
attendance.

Americas, 16-19 July
- at the National Evolutionary Synthesis Center (NESCent), Durham, NC, USA
- Student tuition is free, thanks to NIH grant 1R01HG004483-01.
 - http://gmod.org/wiki/2009_GMOD_Summer_School_-_Americas

Europe, 3-6 August
 - at the University of Oxford, Oxford, United Kingdom
 - Part of GMOD Europe 2009, which includes the next GMOD Meeting
 - Student tuition is £75
 - http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe

The schools will feature training on these GMOD components:
* GBrowse - the most widely installed genome viewer on the web
* Chado - a modular and extensible database schema
* Apollo - genome annotation editor
* BioMart - biological data warehouse system
* GBrowse_syn - a GBrowse based synteny viewer
* JBrowse - a brand new Web 2.0 genome browser
* Artemis-Chado Integration (Europe only)
* MAKER - Genome annotation pipeline (Americas only)
* Tripal - Web front end for Chado (Americas only)

Applications for the 2009 GMOD Summer Schools are now being accepted.

***The deadline for applications is the end of the day, April 6.***

Enrollment is limited to 25 participants in each course.  If
applications exceed capacity (and we expect they will) then applicants
will be picked based on the strength of their application.  Applicants
will be notified of their admission status by mid April.

Please contact the GMOD Help Desk if you have any questions.

Thanks,

Dave Clements
GMOD Help Desk
he...@gm...

http://gmod.org/wiki/2009_GMOD_Summer_School_-_Americas
http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe
http://gmod.org/wiki/GMOD_Europe_2009

[Gmod-ware-users] GMOD Meeting, January 15-16, 2009

[Dave C. G. H. D. <gmo...@go...>]

Hello all,

The next GMOD Community Meeting (
http://gmod.org/wiki/January_2009_GMOD_Meeting) will be held January 15-16,
2009, in San Diego, California, immediately following the Plant and Animal
Genome (PAG 2009) conference.  If you are a GMOD user and/or developer, or
just want to learn more about GMOD then you are encouraged to attend.  See
the July 2008 GMOD Meeting page (http://gmod.org/wiki/July_2008_GMOD_Meeting)
for an idea of what goes on at a GMOD meeting.

You can register for the meeting at
http://gmod.org/wiki/January_2009_GMOD_Meeting_Registration.  Thanks to the
generous support of Doreen Ware and USDA-ARS, registration is *free*.  Space
is limited, so please register early (and it helps us plan).  Details on
lodging and other logistics will be forthcoming as the meeting gets closer.

If you have topics that you want covered at the meeting please add them to
the meeting page.

Please let the Help Desk know if you have any questions.

Thanks,

Dave C
GMOD Help Desk

Useful URLs:
http://gmod.org/wiki/January_2009_GMOD_Meeting
http://gmod.org/wiki/January_2009_GMOD_Meeting_Registration
http://gmod.org/wiki/PAG_2009 - GMOD @ PAG 2009
http://www.intl-pag.org/ - Plant and Animal Genome Meeting
http://gmod.org/wiki/July_2008_GMOD_Meeting - notes from prior meeting
http://gmod.org/wiki/2008_GMOD_Community_Survey#GMOD_Meetings

[Gmod-ware-users] 2008 GMOD Community Survery: One Week Left!

[Dave C. G. H. D. <gmo...@go...>]

Hello all,

If you haven't already done so, please take a few minutes to fill out
the first annual GMOD Community Survey:
 http://survey.oit.duke.edu/ViewsFlash/servlet/viewsflash?cmd=page&pollid=NESCent!GMODUserSurvey2008

We'll be running the survey for one more week, until the end of
Friday, October 31.  If you are in the first 100 responders then you
will be enterred to win one of three GMOD T-shirts or mugs.

PLEASE NOTE:
1. There are *not* 50 pages of questions in the survey.  There are
only 38!  (I feel 24% better already!  ;-)  You'll be happy to know
that you will see only 8 pages, plus a page for each component you
use.
2. Your answers are not recorded until you hit "Submit" on the last
page, so please follow through to the last page.

Please take a few minutes to help improve and guide GMOD.  We really
do appreciate and welcome your feedback.

Thanks,

Dave C
GMOD Help Desk
--
Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback
Fill out the the GMOD Community Survey NOW and win some GMOD Gear:
 http://gmod.org/wiki/GMOD_News#2008_GMOD_Community_Survey

[Gmod-ware-users] 2008 GMOD Community Survery, or, Win a GMOD T-Shirt or Mug!

[Dave C. G. H. D. <gmo...@go...>]

Hello all,

Please take a few minutes to fill out the first annual GMOD Community Survey:

  http://survey.oit.duke.edu/ViewsFlash/servlet/viewsflash?cmd=page&pollid=NESCent!GMODUserSurvey2008

We are asking all GMOD users and developers to provide input on how
GMOD is doing, and how it can be improved.  All questions are
optional, but please provide as much information as you can.  The
survey covers GMOD in general, and any GMOD components that you use
(and it only asks about components that you indicate you use).

*** Three randomly selected survey participants will receive the GMOD
T-shirt or mug of their choice (see
http://www.cafepress.com/GenericMOD/).  Names will be drawn from the
first 100 responses we receive, so get your response in early ***

Please contact the GMOD Help Desk <he...@gm...> if you have any questions.

Thank you,

The GMOD Team
http://gmod.org

-- 
Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback

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[Gmod-ware-users] Modware Update

[Dave C. G. H. D. <gmo...@go...>]

Hello all,

The status of Modware came up at the July 2008 GMOD meeting (see
http://gmod.org/July_2008_GMOD_Meeting).  I've since traded e-mails
with Eric Just at Northwestern, and I thought I would pass on the
details to the list.

In general, only a few things have changed since Eric's response to
Kevin Greer's post (on the same topic) in February.  First, Eric has a
new position at Northwestern, but he still works part-time for
DictyBase.  There are also two new programmers at DictyBase,
Siddhartha Basu and Yulia Bushmanova.

>From Eric:
----
We were hoping to get funding for Modware, and we applied for a grant
through the (now apparently defunct) NSF Biological Databases an
Informatics program.  We were very disappointed that it took them
nearly a year to tell us that we did not get funding for the project.
We were planning on having a Modware full time programmer, but because
of the lack of funding, we could not dedicate this resource.
Siddhartha has shown great interest in continuing the project, and
has, in fact added some functionality to it on the CVS HEAD.  Our
immediate plans are to build a new version on top of GMOD 1.0 and
create a new release in the near future.
----
They also have long term plans to secure specific funding for Modware.

The new GMOD 1.0-based release will be announced here and on the GMOD
web site when it comes out.  Also, keep your eyes open for an upcoming
Chado API page on the web site.  It will describe all known Chado API
packages.  (This was suggested at the July GMOD Meeting.)

If you have any questions, please post them to this list.

Thanks,

Dave Clements
GMOD Help Desk
-- 
Was this helpful? Let us know at http://gmod.org/Help_Desk_Feedback

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