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From: Chris H. <che...@cg...> - 2011-05-20 20:45:47
|
ISGA 1.3.2 is now available for download at https://sourceforge.net/projects/isga/ With this release, we have moved our development and downloads to SourceForge. For the time being, installation instructions will still be hosted at the CGB and are available at: https://wiki.cgb.indiana.edu/display/brp/isga-install-1.3 To reiterate the changes in 1.3.2 compared to the previous version of ISGA available for download - New Prokaryotic Annotation Pipeline Release: - All calls to wu-blast programs have been replaced with NCBI blast - We have enabled the pathway image output for Asgard - Reference databases have been updated - Improved validation and auto-correction of Fasta input - Streamline output-generation and include more information in summary files Other New Features: - Pipelines are now modular and can be installed independently of the ISGA installation process - Workbench interface has been standardized to make adding new tools easier - Added PhyloEGGS tool for studying gene clusters across phylogenies of prokaryotes. - Added ability to "upload" files to ISGA by providing a URL - Fixed several instances where large files were read in entirety into memory Cheers, Chris Hemmerich |
|
From: Chris H. <che...@cg...> - 2011-03-05 15:21:39
|
The ISGA demonstration site available at http://isga.cgb.indiana.edu/ has been updated to version 1.3 . In the coming weeks we will integrate any bug fixes and release 1.3 for local installation. New Prokaryotic Annotation Pipeline Release: - All calls to wu-blast programs have been replaced with NCBI blast - We have enabled the pathway image output for Asgard - Reference databases have been updated - Improved validation and auto-correction of Fasta input - Streamline output-generation and include more information in summary files Other New Features: - Pipelines are now modular and can be installed independently of the ISGA installation process - Workbench interface has been standardized to make adding new tools easier - Added PhyloEGGS tool for studying gene clusters across phylogenies of prokaryotes. - Added ability to "upload" files to ISGA by providing a URL - Fixed several instances where large files could be read into memory A full list of new features, and bug fixes will be included in the downloadable release. Cheers, Chris Hemmerich |
|
From: Dave C. <cle...@ne...> - 2011-02-02 06:21:50
|
Hello all, Yesterday, we opened registration for the March 2011 GMOD Meeting (see http://gmod.oicr.on.ca/wiki/March_2011_GMOD_Meeting). *That meeting is part of a larger event, GMOD Americas 2011, that also includes several Satellite Meetings on March 7*, the day after the meeting ends. Satellite meetings are smaller groups of people meeting to discuss a common interest, or work on a common problem (think special interest groups / birds-of-a-feather). Unlike the GMOD Meeting, there is *no registration fee * for the Satellites, and you don't even need to go to any other GMOD Americas events to participate in the Satellites. *If you are in the area, or attending other GMOD Americas events, or are just very interested in the topic, we strongly encourage you to attend.* The current list of Satellites (see http://gmod.oicr.on.ca/wiki/Satellite_Meetings_-_GMOD_Americas_2011) includes: - *GMOD Evo Hackathon Followup*<http://gmod.oicr.on.ca/wiki/GMOD_Evo_Hackathon#March_2011_Satellite>, organized by Duke Leto <http://gmod.oicr.on.ca/wiki/User:Dukeleto>. A followup to the GMOD Evo Hackathon<http://gmod.oicr.on.ca/wiki/GMOD_Evo_Hackathon>held at NESCent in November 2011. You didn't to participate in the original event to participate in this followup. Also, if there is interest, this satellite can extend for more than one day. - *Customizing and Extending JBrowse<http://gmod.oicr.on.ca/wiki/JBrowse> *, organized by Mitch Skinner<http://gmod.oicr.on.ca/wiki/User:MitchSkinner> . JBrowse <http://gmod.oicr.on.ca/wiki/JBrowse> has a few different extension points, but they're not (yet) well-documented or widely used. The GMOD meeting would be a good time to review those APIs<http://gmod.oicr.on.ca/wiki/Glossary#API>, relate them to the things that people want to do with them, discuss any potential changes or new APIs to support specific use cases, and potentially start to implement an extension. - *GMOD Web services toolkit* <http://gmod.oicr.on.ca/wiki/GMOD_RPC_API>, organized by Josh Goodman <http://gmod.oicr.on.ca/wiki/User:Jogoodma>. Come to work on or discuss the GMOD Web services API and the toolkit<http://gmod.oicr.on.ca/wiki/GMOD_RPC_API> . - *GMOD in the Sequencing Center*<http://gmod.oicr.on.ca/wiki/GMOD_in_the_Sequencing_Center>, organized by Chris Hemmerich <http://gmod.oicr.on.ca/wiki/User:Chemmeri>, Dave Clements <http://gmod.oicr.on.ca/wiki/User:Clements>. Sequencing centers have tremendous bioinformatics needs that GMOD can help address. Attend this satellite to find out what other sequencing centers are doing with GMOD, and how GMOD can help you help your researchers. If you are interested in participating in these, please contact the organizers, and/or add your name to the satellite's participants list on the wiki. Satellites can be organized by anyone. If you have a topic you would like to cover, please add it to the list and announce it the appropriate mailing lists. Several previous satellites are written up on the GMOD wiki, if you want an idea of what happens at a satellite. Finally, please let me and Scott know if you have any questions. Thanks, and hope to see you in March! Dave C. -- http://gmod.org/wiki/GMOD_Americas_2011 http://gmod.org/wiki/GMOD_News http://usegalaxy.org/ |
|
From: Dave C. G. H. D. <he...@gm...> - 2011-01-02 18:34:18
|
Hello all, The application deadline for the 2011 GMOD Spring Training (http://gmod.org/wiki/2011_GMOD_Spring_Training) is the end of this coming Friday, January 7. Admission is competitive, so please apply by Friday to avoid being automatically placed on the waiting list. Details are below. Thanks, and happy new year! Dave C ------- Applications are now being accepted for the 2011 GMOD Spring Training course (http://gmod.org/wiki/2011_GMOD_Spring_Training), 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. These components will be covered: * Apollo - genome annotation editor * Chado - biological database schema * Galaxy - analysis and data integration framework * 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. Links: http://gmod.org/wiki/2011_GMOD_Spring_Training http://gmod.org/wiki/GMOD_Americas_2011 http://www.nescent.org/ |
|
From: Dave C. G. H. D. <he...@gm...> - 2010-12-04 00:46:57
|
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 |
|
From: Julian K. <Kra...@gm...> - 2010-09-10 08:23:20
|
Hello,
thanks for your prompt reply. so i figuered out that the problem has nothing to do with the database conection. the update_run_status.pl works fine and when i try to create a new account from the webinterface with the same email adress it says that the email adress already exists.
When i try to create a new account nothing happens for a couple of minutes, but then
Your account request was successfully processed, and a confirmation email message was sent to the email address you provided. You must follow the link in that message within 48 hours to confirm the request. .
But now i am aware that i need to create an account through the web nterface and need to confirm it through the link sended by ISGA.
I dont know where i have to tell isga how to send these emails(from which account and which password)?
thanks
Julian
-------- Original-Nachricht --------
> Datum: Fri, 10 Sep 2010 00:41:57 -0400 (EDT)
> Von: Chris Hemmerich <che...@cg...>
> An: Julian Krauskopf <Kra...@gm...>
> CC: isg...@li...
> Betreff: Re: [Isga-users] local installation of ISGA
>
> Julian,
>
> When perl loads the ISGA module, quite a few rows are read from the
> database, so if you are not connected to the database you should see
> errors on apache startup. A simple way to test this is to execute one of
> the housekeeping scripts installed in the bin directory
>
> perl update_run_status.pl
>
> If this throws an error, please send it to the list and I'll help you work
> trough it.
>
> The only error that I see in your entry below is that the password needs
> to be run through a MD5 digest:
>
> Digest::MD5::md5_hex($pass)
>
> This will definitely keep you from being able to login until it is fixed
> though.
>
> Have you tried creating an account through the web interface? If that
> doesn't work I would be interested in seeing what errors you receive.
>
> Cheers,
>
> Chris
>
>
> On Wed, 8 Sep 2010, Julian Krauskopf wrote:
>
> > Hello,
> > I allready installed Ergatis and Isga on my System(Debian 5) and it runs
> on apache2. But i can not log in. i created the following records in
> PostgreSQL 8.3.
> >
> > table account
> >
> > party_id | account_email | account_password
> |userclass_id
> >
> ----------+---------------+----------------------------------+--------------
> > 1 | bli@bla.bub | 123 |
> 1
> >
> > party
> >
> > party_id | partypartition_id | party_name | partystatus_id |
> party_createdat | party_institution | party_isprivate |
> party_iswalkthroughdisabled | party_iswalkthroughhidden
> >
> ----------+-------------------+------------+----------------+----------------------------+-------------------+-----------------+-----------------------------+---------------------------
> > 1 | 1 | test | 1 | 2010-09-08
> 17:49:48.949177 | test | f | f
> >
> > groupmembership
> >
> > party_id | partypartition_id | party_name | partystatus_id |
> party_createdat | party_institution | party_isprivate |
> party_iswalkthroughdisabled | party_iswalkthroughhidden
> >
> ----------+-------------------+------------+----------------+----------------------------+-------------------+-----------------+-----------------------------+---------------------------
> > 1 | 1 | test | 1 | 2010-09-08
> 17:49:48.949177 | test | f | f
> >
> > in CONFIG.yaml i entered the following database connection parameters:
> > database: { name: isga_dev, user: isga, type: Pg }
> >
> > Is there a way to check if isga is able to connect to the database at
> all? or did we make some error within the user creation?
> > Thanks for any help
> > Julian Krauskopf
> >
> > --
> > GMX DSL SOMMER-SPECIAL: Surf & Phone Flat 16.000 für nur 19,99
> Euro/mtl.!*
> > http://portal.gmx.net/de/go/dsl
> >
> >
> ------------------------------------------------------------------------------
> > Automate Storage Tiering Simply
> > Optimize IT performance and efficiency through flexible, powerful,
> > automated storage tiering capabilities. View this brief to learn how
> > you can reduce costs and improve performance.
> > http://p.sf.net/sfu/dell-sfdev2dev
> > _______________________________________________
> > Isga-users mailing list
> > Isg...@li...
> > https://lists.sourceforge.net/lists/listinfo/isga-users
> >
--
GRATIS: Spider-Man 1-3 sowie 300 weitere Videos!
Jetzt freischalten! http://portal.gmx.net/de/go/maxdome
--
GRATIS: Spider-Man 1-3 sowie 300 weitere Videos!
Jetzt freischalten! http://portal.gmx.net/de/go/maxdome
|
|
From: Chris H. <che...@cg...> - 2010-09-10 04:42:05
|
Julian,
When perl loads the ISGA module, quite a few rows are read from the
database, so if you are not connected to the database you should see
errors on apache startup. A simple way to test this is to execute one of
the housekeeping scripts installed in the bin directory
perl update_run_status.pl
If this throws an error, please send it to the list and I'll help you work
trough it.
The only error that I see in your entry below is that the password needs
to be run through a MD5 digest:
Digest::MD5::md5_hex($pass)
This will definitely keep you from being able to login until it is fixed
though.
Have you tried creating an account through the web interface? If that
doesn't work I would be interested in seeing what errors you receive.
Cheers,
Chris
On Wed, 8 Sep 2010, Julian Krauskopf wrote:
> Hello,
> I allready installed Ergatis and Isga on my System(Debian 5) and it runs on apache2. But i can not log in. i created the following records in PostgreSQL 8.3.
>
> table account
>
> party_id | account_email | account_password |userclass_id
> ----------+---------------+----------------------------------+--------------
> 1 | bli@bla.bub | 123 | 1
>
> party
>
> party_id | partypartition_id | party_name | partystatus_id | party_createdat | party_institution | party_isprivate | party_iswalkthroughdisabled | party_iswalkthroughhidden
> ----------+-------------------+------------+----------------+----------------------------+-------------------+-----------------+-----------------------------+---------------------------
> 1 | 1 | test | 1 | 2010-09-08 17:49:48.949177 | test | f | f
>
> groupmembership
>
> party_id | partypartition_id | party_name | partystatus_id | party_createdat | party_institution | party_isprivate | party_iswalkthroughdisabled | party_iswalkthroughhidden
> ----------+-------------------+------------+----------------+----------------------------+-------------------+-----------------+-----------------------------+---------------------------
> 1 | 1 | test | 1 | 2010-09-08 17:49:48.949177 | test | f | f
>
> in CONFIG.yaml i entered the following database connection parameters:
> database: { name: isga_dev, user: isga, type: Pg }
>
> Is there a way to check if isga is able to connect to the database at all? or did we make some error within the user creation?
> Thanks for any help
> Julian Krauskopf
>
> --
> GMX DSL SOMMER-SPECIAL: Surf & Phone Flat 16.000 für nur 19,99 Euro/mtl.!*
> http://portal.gmx.net/de/go/dsl
>
> ------------------------------------------------------------------------------
> Automate Storage Tiering Simply
> Optimize IT performance and efficiency through flexible, powerful,
> automated storage tiering capabilities. View this brief to learn how
> you can reduce costs and improve performance.
> http://p.sf.net/sfu/dell-sfdev2dev
> _______________________________________________
> Isga-users mailing list
> Isg...@li...
> https://lists.sourceforge.net/lists/listinfo/isga-users
> |
|
From: Julian K. <Kra...@gm...> - 2010-09-08 16:34:08
|
Hello,
I allready installed Ergatis and Isga on my System(Debian 5) and it runs on apache2. But i can not log in. i created the following records in PostgreSQL 8.3.
table account
party_id | account_email | account_password |userclass_id
----------+---------------+----------------------------------+--------------
1 | bli@bla.bub | 123 | 1
party
party_id | partypartition_id | party_name | partystatus_id | party_createdat | party_institution | party_isprivate | party_iswalkthroughdisabled | party_iswalkthroughhidden
----------+-------------------+------------+----------------+----------------------------+-------------------+-----------------+-----------------------------+---------------------------
1 | 1 | test | 1 | 2010-09-08 17:49:48.949177 | test | f | f
groupmembership
party_id | partypartition_id | party_name | partystatus_id | party_createdat | party_institution | party_isprivate | party_iswalkthroughdisabled | party_iswalkthroughhidden
----------+-------------------+------------+----------------+----------------------------+-------------------+-----------------+-----------------------------+---------------------------
1 | 1 | test | 1 | 2010-09-08 17:49:48.949177 | test | f | f
in CONFIG.yaml i entered the following database connection parameters:
database: { name: isga_dev, user: isga, type: Pg }
Is there a way to check if isga is able to connect to the database at all? or did we make some error within the user creation?
Thanks for any help
Julian Krauskopf
--
GMX DSL SOMMER-SPECIAL: Surf & Phone Flat 16.000 für nur 19,99 Euro/mtl.!*
http://portal.gmx.net/de/go/dsl
|
|
From: Dave C. G. H. D. <he...@gm...> - 2010-09-07 18:36:09
|
Hello all, GMOD Europe 2010 (http://gmod.org/wiki/GMOD_Europe_2010) starts on Monday, 13 September, less than a week from now. This event runs for 4 days and includes: * September 2010 GMOD Meeting - has openings * GMOD Satellite Meetings - has openings * InterMine Workshop - has openings * BioMart Workshop - full (but you can get on the short waiting list) If you haven't already registered, please do so as soon as possible. This will assure you a seat and help us plan meeting logistics. See http://gmod.org/wiki/GMOD_Europe_2010 for details and a registration link. This is the last broadcast reminder I'll send out. Please let me know if you have any questions. Thanks, Dave C. -- http://gmod.org/wiki/GMOD_News http://gmod.org/wiki/GMOD_Europe_2010 http://hinv.jp/biocuration2010/ http://gmod.org/wiki/Help_Desk_Feedback |
|
From: Dave C. G. H. D. <he...@gm...> - 2010-08-26 18:11:50
|
Hello all, I am pleased to announce that ISGA, Integrative Services for Genomic Analysis, is now a part of GMOD. ISGA is a biologist-friendly web interface for running and customizing Ergatis bioinformaitics pipelines with integrated tools for visualizing and searching results. ISGA was originally built for prokaryotic genome annotation and now includes a prokaryotic assembly pipeline. Transcriptome annotation and functional genomics pipelines are under development. A public instance of ISGA is available at Indiana Univeristy. ISGA is also available for download and has a mailing listand development blog]. You can read the ISGA manuscript] in Bioinformatics. See links below. ISGA (pronounced "I-S-G-A") was created at Indiana University's Center for Genomics and Bioinformatics (CGB) by Chris Hemmerich, Aaron Buechlein, Ram Podicheti, Kashi Revanna, and Qunfeng Dong, and remains under active development at the CGB. Developers amd other community members interested in contributing should join the mailing list. Please join me in welcoming ISGA and the ISGA team to GMOD. Dave C. Links: http://gmod.org/wiki/ISGA http://isga.cgb.indiana.edu - public instance http://cgb.indiana.edu/downloads/6 - download http://wiki.cgb.indiana.edu/display/brp/Development+Blog http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/8/1122 - ISGA manuscript -- ===> PLEASE KEEP RESPONSES ON THE LIST <=== http://gmod.org/wiki/GMOD_News http://gmod.org/wiki/GMOD_Europe_2010 http://hinv.jp/biocuration2010/ http://gmod.org/wiki/Help_Desk_Feedback |
|
From: Dave C. <cle...@ne...> - 2010-08-25 21:10:26
|
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 |
|
From: Chris H. <che...@cg...> - 2010-08-11 18:04:43
|
ISGA 1.2 Released Version 1.2 adds new output to the prokaryotic annotation pipeline - fasta formatted files for cds and translated cds sequences with annotation information as the sequence header. We are in the process of retroactively building these files for existing pipelines. We also added validation tools for fasta uploads, if you believe your fasta file was incorrectly blocked, please contact us at bi...@cg.... Other changes include several small bug fixes, form validation improvements and more helpful error messages in places we noticed users experiencing problems. |
|
From: Chris H. <che...@cg...> - 2010-06-03 21:45:24
|
Version 1.1 adds a prokaryotic assembly pipeline using Celera and tools for processing assembly output for use with the Hawkeye visualization tool. The new version also adds a new page to make your previous toolbox jobs more accessible. It also brings many small interface improvements and bug fixes to make ISGA a more reliable service. Finally, we have also added a running pipeline quota to ensure that all users have fair access to our computing resources. ISGA 1.1 is also available for download and local installation at http://isga-dev.cgb.indiana.edu/Help/DownloadISGA Chris Hemmerich Center for Genomics and Bioinformatics Indiana University |
2 messages has been excluded from this view by a project administrator.
