Menu
▾
▴
gusdev-gusdev
|
From: Michael S. <msa...@pc...> - 2005-01-25 16:16:00
|
All, As you may be aware, we've been working towards a GUS 3.5 release for quite some time now. There is now a wiki page, available at: http://gusdb.org/wiki/index.php/Gus3.5RoadMap which outlines the major changes that are planned for GUS 3.5. These items are the result of many conversations here at CBIL and with our collaborators. 3.5 is primarily intended to be a maintenance release, to be eventually followed with 4.0 which will be a major feature release. Having said that, we're interested in feedback on any (high priority) pressing issues that have been omitted from the road map above and should be considered for 3.5. Thanks, Mike Saffitz |
|
From: Sucheta T. <su...@vb...> - 2005-01-26 12:38:12
|
Hi Mike, Its great that you have released GUS 3.5. Will I be able to upgrade my version from 3.0 to 3.5 smoothly? Sucheta > > > All, > > As you may be aware, we've been working towards a GUS 3.5 release for > quite some time now. There is now a wiki page, available at: > > http://gusdb.org/wiki/index.php/Gus3.5RoadMap > > which outlines the major changes that are planned for GUS 3.5. These > items are the result of many conversations here at CBIL and with our > collaborators. > > 3.5 is primarily intended to be a maintenance release, to be eventually > followed with 4.0 which will be a major feature release. Having said > that, we're interested in feedback on any (high priority) pressing > issues that have been omitted from the road map above and should be > considered for 3.5. > > Thanks, > > Mike Saffitz > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting > Tool for open source databases. Create drag-&-drop reports. Save time > by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. > Download a FREE copy at http://www.intelliview.com/go/osdn_nl > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > -- Sucheta Tripathy Virginia Bioinformatics Institute Phase-I Washington street. Virginia Tech. Blacksburg,VA 24061-0447 phone:(540)231-8138 Fax: (540) 231-2606 |
|
From: Michael S. <msa...@pc...> - 2005-01-26 14:28:03
|
Hi Sucheta, First, a quick clarification: GUS 3.5 has _not_ been released yet. This is purely an announcement and solicitation for feedback. We expect to release GUS 3.5 in mid-February. We do plan on providing upgrade scripts to GUS 3.5. The major problem here is that our versioning in the past has not been very strict, so these scripts will need to be manually applied and reviewed. With the GUS 3.5 release, we will be including a XML version of the schema, which will allow for proper upgrading in the future, including the possibility of automated upgrades. --Mike Sucheta Tripathy wrote: > Hi Mike, > > Its great that you have released GUS 3.5. Will I be able to upgrade my > version from 3.0 to 3.5 smoothly? > > Sucheta > > >> >>All, >> >>As you may be aware, we've been working towards a GUS 3.5 release for >>quite some time now. There is now a wiki page, available at: >> >>http://gusdb.org/wiki/index.php/Gus3.5RoadMap >> >>which outlines the major changes that are planned for GUS 3.5. These >>items are the result of many conversations here at CBIL and with our >>collaborators. >> >>3.5 is primarily intended to be a maintenance release, to be eventually >>followed with 4.0 which will be a major feature release. Having said >>that, we're interested in feedback on any (high priority) pressing >>issues that have been omitted from the road map above and should be >>considered for 3.5. >> >>Thanks, >> >>Mike Saffitz >> >> >> >>------------------------------------------------------- >>This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting >>Tool for open source databases. Create drag-&-drop reports. Save time >>by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. >>Download a FREE copy at http://www.intelliview.com/go/osdn_nl >>_______________________________________________ >>Gusdev-gusdev mailing list >>Gus...@li... >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> > > > |
|
From: Alberto D. <da...@io...> - 2005-01-26 13:39:40
|
Hi Mike, I have 3 questions for you: a) Such as Sucheta, I wonder we will be able to move from GUS 3.0 to 3.5 without big problems b) Will 3.5 support (be compatible) with Postgres ? That would be bad to have to debug/port it "again" to Postgres.. c) I went to the wiki site you mentioned, but was unable to enter/open the BrowseSchema, so... will 3.5 support or have tables for phylogeny/evolutionary data (distance, maximum likelihood and bayesian) ? Thanks, Alberto On Tue, 2005-01-25 at 11:15 -0500, Michael Saffitz wrote: > > All, > > As you may be aware, we've been working towards a GUS 3.5 release for > quite some time now. There is now a wiki page, available at: > > http://gusdb.org/wiki/index.php/Gus3.5RoadMap > > which outlines the major changes that are planned for GUS 3.5. These > items are the result of many conversations here at CBIL and with our > collaborators. > > 3.5 is primarily intended to be a maintenance release, to be eventually > followed with 4.0 which will be a major feature release. Having said > that, we're interested in feedback on any (high priority) pressing > issues that have been omitted from the road map above and should be > considered for 3.5. > > Thanks, > > Mike Saffitz |
|
From: Michael S. <msa...@pc...> - 2005-01-26 14:33:37
|
Hi Alberto, My comments are below... Alberto Davila wrote: > Hi Mike, > > I have 3 questions for you: > > a) Such as Sucheta, I wonder we will be able to move from GUS 3.0 to 3.5 > without big problems > Yes, in short. See my previous email to Sucheta and the list with more details. > b) Will 3.5 support (be compatible) with Postgres ? That would be bad to > have to debug/port it "again" to Postgres.. > Yes, official PostgreSQL support is a major enhancement to GUS in 3.5. It's worth noting: GUS _does not_ currently support Postgres. The work that has been done and released was very preliminary work, provided because there were many groups out there who absolutely needed something ASAP. The Postgres support in 3.5 will be different than what was previously sent by me-- it more closely resembles the last round of scripts sent by Jeetendra. > c) I went to the wiki site you mentioned, but was unable to enter/open > the BrowseSchema, so... will 3.5 support or have tables for > phylogeny/evolutionary data (distance, maximum likelihood and > bayesian) ? Sorry about that-- the SchemaBrowser linked from those pages is now working. I'm not aware of any additional tables for this type of data, perhaps someone more knowledgeable with this can let the list know if tables to support this data already exist? --Mike > > Thanks, Alberto > > On Tue, 2005-01-25 at 11:15 -0500, Michael Saffitz wrote: > >>All, >> >>As you may be aware, we've been working towards a GUS 3.5 release for >>quite some time now. There is now a wiki page, available at: >> >>http://gusdb.org/wiki/index.php/Gus3.5RoadMap >> >>which outlines the major changes that are planned for GUS 3.5. These >>items are the result of many conversations here at CBIL and with our >>collaborators. >> >>3.5 is primarily intended to be a maintenance release, to be eventually >>followed with 4.0 which will be a major feature release. Having said >>that, we're interested in feedback on any (high priority) pressing >>issues that have been omitted from the road map above and should be >>considered for 3.5. >> >>Thanks, >> >>Mike Saffitz > > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting > Tool for open source databases. Create drag-&-drop reports. Save time > by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. > Download a FREE copy at http://www.intelliview.com/go/osdn_nl > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
|
From: Michael S. <msa...@pc...> - 2005-01-26 16:13:55
|
Hi Alberto and all, I'm replying to my own post here, after speaking with Chris and Steve here. GUS doesn't currently support phylogeny/evolutionary data, but are very open to adding it to GUS. Do you have a schema (rough or otherwise) in mind? --Mike Michael Saffitz wrote: > > Hi Alberto, > > My comments are below... > > > Alberto Davila wrote: > >> Hi Mike, >> >> I have 3 questions for you: >> >> a) Such as Sucheta, I wonder we will be able to move from GUS 3.0 to 3.5 >> without big problems >> > > Yes, in short. See my previous email to Sucheta and the list with more > details. > >> b) Will 3.5 support (be compatible) with Postgres ? That would be bad to >> have to debug/port it "again" to Postgres.. >> > > Yes, official PostgreSQL support is a major enhancement to GUS in 3.5. > It's worth noting: GUS _does not_ currently support Postgres. The work > that has been done and released was very preliminary work, provided > because there were many groups out there who absolutely needed something > ASAP. The Postgres support in 3.5 will be different than what was > previously sent by me-- it more closely resembles the last round of > scripts sent by Jeetendra. > >> c) I went to the wiki site you mentioned, but was unable to enter/open >> the BrowseSchema, so... will 3.5 support or have tables for >> phylogeny/evolutionary data (distance, maximum likelihood and >> bayesian) ? > > > Sorry about that-- the SchemaBrowser linked from those pages is now > working. I'm not aware of any additional tables for this type of data, > perhaps someone more knowledgeable with this can let the list know if > tables to support this data already exist? > > --Mike > >> >> Thanks, Alberto >> >> On Tue, 2005-01-25 at 11:15 -0500, Michael Saffitz wrote: >> >>> All, >>> >>> As you may be aware, we've been working towards a GUS 3.5 release for >>> quite some time now. There is now a wiki page, available at: >>> >>> http://gusdb.org/wiki/index.php/Gus3.5RoadMap >>> >>> which outlines the major changes that are planned for GUS 3.5. These >>> items are the result of many conversations here at CBIL and with our >>> collaborators. >>> >>> 3.5 is primarily intended to be a maintenance release, to be >>> eventually followed with 4.0 which will be a major feature release. >>> Having said that, we're interested in feedback on any (high priority) >>> pressing issues that have been omitted from the road map above and >>> should be considered for 3.5. >>> >>> Thanks, >>> >>> Mike Saffitz >> >> >> >> >> >> >> ------------------------------------------------------- >> This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting >> Tool for open source databases. Create drag-&-drop reports. Save time >> by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. >> Download a FREE copy at http://www.intelliview.com/go/osdn_nl >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting > Tool for open source databases. Create drag-&-drop reports. Save time > by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. > Download a FREE copy at http://www.intelliview.com/go/osdn_nl > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
|
From: Aaron J. M. <am...@pc...> - 2005-01-26 16:22:36
|
On Jan 26, 2005, at 11:13 AM, Michael Saffitz wrote: > GUS doesn't currently support phylogeny/evolutionary data, but are > very open to adding it to GUS. Do you have a schema (rough or > otherwise) in mind? I think the upcoming comparative genomics efforts here (and elsewhere) will certainly require support for evolutionary analyses. I would encourage those doing the schema design to consider both multiple sequence alignments and trees (including associated bootstraps, likelihood, branch lengths, etc) as experimental results that may be computed in many different fashions. I.e. don't fall into the trap of the "one true tree", because it doesn't exist. I'd be very interested to be involved in this effort, and to give a talk on my own phylogenetic sequence database (CDAT) for consideration as one possible schema to mimic. -Aaron -- Aaron J. Mackey, Ph.D. Dept. of Biology, Goddard 212 University of Pennsylvania email: am...@pc... 415 S. University Avenue office: 215-898-1205 Philadelphia, PA 19104-6017 fax: 215-746-6697 |
|
From: Chris S. <sto...@pc...> - 2005-01-26 16:37:00
|
Aaron, Sounds good. Can you post the CDAT schema? Do you think we should be thinking of a phylo/evo schema (in the sense of DoTS, RAD, etc.) instead of just adding tables. views to DoTS? Mind you, we don't want to derail GUS3.5 release with major changes. That's for 4.0. I'm thinking of either sliding in a table or two if that works for 3.5 but keeping an eye out for needed changes for 4.0. Cheers, Chris On Jan 26, 2005, at 11:22 AM, Aaron J. Mackey wrote: > > On Jan 26, 2005, at 11:13 AM, Michael Saffitz wrote: > >> GUS doesn't currently support phylogeny/evolutionary data, but are >> very open to adding it to GUS. Do you have a schema (rough or >> otherwise) in mind? > > I think the upcoming comparative genomics efforts here (and elsewhere) > will certainly require support for evolutionary analyses. I would > encourage those doing the schema design to consider both multiple > sequence alignments and trees (including associated bootstraps, > likelihood, branch lengths, etc) as experimental results that may be > computed in many different fashions. I.e. don't fall into the trap of > the "one true tree", because it doesn't exist. > > I'd be very interested to be involved in this effort, and to give a > talk on my own phylogenetic sequence database (CDAT) for consideration > as one possible schema to mimic. > > -Aaron > > -- > Aaron J. Mackey, Ph.D. > Dept. of Biology, Goddard 212 > University of Pennsylvania email: am...@pc... > 415 S. University Avenue office: 215-898-1205 > Philadelphia, PA 19104-6017 fax: 215-746-6697 > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting > Tool for open source databases. Create drag-&-drop reports. Save time > by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. > Download a FREE copy at http://www.intelliview.com/go/osdn_nl > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
|
From: Aaron J. M. <am...@pc...> - 2005-01-26 17:09:56
Attachments:
schema.pdf
|
On Jan 26, 2005, at 11:36 AM, Chris Stoeckert wrote: > Can you post the CDAT schema? Happy to, although it will make more sense in the context of a presentation on it's specific design goals and use cases. |
×
Want the latest updates on software, tech news, and AI?
Get latest updates about software, tech news, and AI from SourceForge directly in your inbox once a month.
Thanks for helping keep SourceForge clean.
X