From hlapp at drycafe.net Sun Mar 3 12:54:16 2013 From: hlapp at drycafe.net (Hilmar Lapp) Date: Sun, 3 Mar 2013 12:54:16 -0500 Subject: [BioSQL-l] GSoC 2013 is ON Message-ID: Forwarding on behalf of Pjotr Prins, who just volunteered to serve as OBF's GSoC admin for this year. ~~~ Game on! GSoC 2013 is ON. I am running with the OBF project administration this year for the Google Summer of code (GSoC). First and foremost I want to thank Robert Buels and others for making OBF/GSoC a success in the previous three years! This year, Robert, Chris Fields and Hilmar Lapp will act as backup administrators. The deadline for the OBF application for GSoC2013 as a mentoring organisation is Friday March 29! See http://www.google-melange.com/gsoc/events/google/gsoc2013 Similar to previous years, each Bio* project needs to update and add project ideas on the project's individual OBF wiki page and create links from the main OBF page at http://www.open-bio.org/wiki/Google_Summer_of_Code (we will update the main information on that page soon). So, for each of the OBF projects that wants to do GSoC again this year: 1. Update the list of project ideas on your project's GSoC page (BioPython, BioPerl, BioRuby, etc). Add new ones, remove ones that have already been done or no longer relevant, etc. For an example see http://bioruby.open-bio.org/wiki/Google_Summer_of_Code 2. Update the final list of project ideas on the main OBF GSoC page to match. http://www.open-bio.org/wiki/Google_Summer_of_Code 3. Register with gsoc at lists.open-bio.org 4. Announce it on that list when you are ready :) Anyone can submit a project idea! Former GSoC students are especially encouraged to contribute ideas to the mailing lists. Please have the updates done by Friday March 22nd. The number and quality of the project ideas are part of the evaluation process for whether OBF is accepted as a Summer of Code organisation again this year, so let's come up with some good ones! Pj. (Pjotr Prins) Important dates: * March 22nd: Finalise project ideas * March 29th: Deadline OBF mentoring organisation submission to Google http://www.open-bio.org/wiki/Google_Summer_of_Code From dtomso at agbiome.com Mon Mar 4 11:14:54 2013 From: dtomso at agbiome.com (Dan Tomso) Date: Mon, 4 Mar 2013 11:14:54 -0500 Subject: [BioSQL-l] New to list--hello message Message-ID: <6B9C6089-A172-4710-9FD4-0AC7866BAFCF@agbiome.com> Hello all-- I just want to say 'hi' to the list members. I'm using BioSQL via BioPython, and will certainly have a few questions. I will be working heavily with microbial genomes and will be warehousing lots of sequence data, so I've decided to give BioSQL a try rather than invent my own schema. Best regards, Dan Tomso Chief Science Officer AgBiome Inc. From dtomso at agbiome.com Tue Mar 12 13:51:46 2013 From: dtomso at agbiome.com (Dan Tomso) Date: Tue, 12 Mar 2013 13:51:46 -0400 Subject: [BioSQL-l] Question regarding updating records in a BioSQL database (under Python) Message-ID: Hello all-- This seems trivial, but I'm struggling with how to add SeqFeatures to a BioSQL DBSeqRecord object. I can update the object, but then I can't update the DB. If I delete the original from the db, it kills the updated copy. If I try to deep copy the original, I get lots of errors. If I try to load the modified record without removing the original, I get a collision. I've tried also just updating the entry via the dictionary-like approach. Where am I going wrong? Thanks, Dan Tomso From p.j.a.cock at googlemail.com Tue Mar 12 16:58:07 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 12 Mar 2013 20:58:07 +0000 Subject: [BioSQL-l] Question regarding updating records in a BioSQL database (under Python) In-Reply-To: References: Message-ID: On Tuesday, March 12, 2013, Dan Tomso wrote: > Hello all-- > This seems trivial, but I'm struggling with how to add SeqFeatures to a > BioSQL DBSeqRecord object. > > I can update the object, but then I can't update the DB. If I delete the > original from the db, it kills the updated copy. If I try to deep copy the > original, I get lots of errors. If I try to load the modified record > without removing the original, I get a collision. > > I've tried also just updating the entry via the dictionary-like approach. > > Where am I going wrong? > > Thanks, > Dan Tomso > > Hi Dan, It sounds like you are using Biopython, right? Clearly our docs need a little more clarification - the dictionary like interface (and the whole DBSeqRecord) uses a read only lazy loading approach (for example neither the sequence nor the features are loaded from the database into objects in memory until accessed). You could try creating a separate namespace (e.g. Old and New) within the same database to allow you to save the modified record into a new namespace and so avoid the clashes... but basically the problem is you are trying to do something the API was never designed to cater to. If you want to discuss possible enhancements, then the Biopython-dev mailing list might be more relevant. Regards, Peter From dtomso at agbiome.com Wed Mar 13 09:47:27 2013 From: dtomso at agbiome.com (Dan Tomso) Date: Wed, 13 Mar 2013 09:47:27 -0400 Subject: [BioSQL-l] Question regarding updating records in a BioSQL database (under Python) In-Reply-To: References: Message-ID: Thanks, Peter. I arrived at the same solution (new/old DB namespace). I will soldier on with some combination of new entry creation/old entry destruction and using files for 'holding' sequences at various stages of annotation. I'll take further discussion to the Dev list as suggested. Best regards, Dan T. On Mar 12, 2013, at 4:58 PM, Peter Cock wrote: > > > On Tuesday, March 12, 2013, Dan Tomso wrote: > Hello all-- > This seems trivial, but I'm struggling with how to add SeqFeatures to a BioSQL DBSeqRecord object. > > I can update the object, but then I can't update the DB. If I delete the original from the db, it kills the updated copy. If I try to deep copy the original, I get lots of errors. If I try to load the modified record without removing the original, I get a collision. > > I've tried also just updating the entry via the dictionary-like approach. > > Where am I going wrong? > > Thanks, > Dan Tomso > > > Hi Dan, > > It sounds like you are using Biopython, right? Clearly our > docs need a little more clarification - the dictionary like > interface (and the whole DBSeqRecord) uses a read only > lazy loading approach (for example neither the sequence > nor the features are loaded from the database into objects > in memory until accessed). > > You could try creating a separate namespace (e.g. Old > and New) within the same database to allow you to > save the modified record into a new namespace and > so avoid the clashes... but basically the problem is you > are trying to do something the API was never designed > to cater to. > > If you want to discuss possible enhancements, then > the Biopython-dev mailing list might be more relevant. > > Regards, > > Peter From hlapp at drycafe.net Sat Mar 23 15:14:43 2013 From: hlapp at drycafe.net (Hilmar Lapp) Date: Sat, 23 Mar 2013 15:14:43 -0400 Subject: [BioSQL-l] Fwd: GSoC 2013 is ON References: <20130320211932.GA23848@thebird.nl> Message-ID: FYI - reminder from Pjotr about project ideas for GSoC 2013. -hilmar Begin forwarded message: > From: Pjotr Prins > Subject: Re: GSoC 2013 is ON > Date: March 20, 2013 5:19:32 PM EDT > To: OBF GSoC > > Heads up! One more week to go for project ideas! Please update > > https://github.com/OBF/GSoC/wiki/Google-Summer-of-Code-2013 > > with the latest links. And maybe a wakeup call to your lists? > > If you are not on the Internet you don't exist. If you are not making > use of GSoC, you might as well be dead ;). > > Kidding. But, the more ideas, the better. > > Pj. > > * March 22nd: Finalise project ideas > * March 29th: Deadline OBF mentoring organisation submission to Google > > On Sun, Mar 03, 2013 at 12:23:26PM +0100, Pjotr Prins wrote: >> Dear project leaders. >> >> I am sending below announcement to you, to have it forwarded by you to >> your mailing lists. Please do so. Also pass this message on to anyone >> who might be in some way interested in the OBF/GSoC initiative. To >> participate, start by signing up to the soc mailing list at >> http://lists.open-bio.org/mailman/listinfo/gsoc >> >> Spread the word! >> >> ~~~ >> >> Game on! GSoC 2013 is ON. I am running with the OBF project >> administration this year for the Google Summer of code (GSoC). >> First and foremost I want to thank Robert Buels and others for making >> OBF/GSoC a success in the previous three years! This year, Robert, Chris >> Fields and Hilmar Lapp will act as backup administrators. >> >> The deadline for the OBF application for GSoC2013 as a mentoring >> organisation is Friday March 29! See >> >> http://www.google-melange.com/gsoc/events/google/gsoc2013 >> >> Similar to previous years, each Bio* project needs to update and add project >> ideas on the project's individual OBF wiki page and create links from the main >> OBF page at >> >> http://www.open-bio.org/wiki/Google_Summer_of_Code >> >> (we will update the main information on that page soon). >> >> So, for each of the OBF projects that wants to do GSoC again this >> year: >> >> 1. Update the list of project ideas on your project's GSoC page (BioPython, >> BioPerl, BioRuby, etc). Add new ones, remove ones that have already been done >> or no longer relevant, etc. For an example see >> >> http://bioruby.open-bio.org/wiki/Google_Summer_of_Code >> >> 2. Update the final list of project ideas on the main OBF GSoC page >> to match. >> >> http://www.open-bio.org/wiki/Google_Summer_of_Code >> >> 3. Register with gsoc at lists.open-bio.org >> >> 4. Announce it on that list when you are ready :) >> >> Anyone can submit a project idea! Former GSoC students are especially >> encouraged to contribute ideas to the mailing lists. >> >> Please have the updates done by Friday March 22nd. The number and quality of >> the project ideas are part of the evaluation process for whether OBF is >> accepted as a Summer of Code organisation again this year, so let's come up >> with some good ones! >> >> Pj. (Pjotr Prins) >> >> Important dates: >> >> * March 22nd: Finalise project ideas >> * March 29th: Deadline OBF mentoring organisation submission to Google >> >> http://www.open-bio.org/wiki/Google_Summer_of_Code >> -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From hlapp at drycafe.net Sun Mar 3 17:54:16 2013 From: hlapp at drycafe.net (Hilmar Lapp) Date: Sun, 3 Mar 2013 12:54:16 -0500 Subject: [BioSQL-l] GSoC 2013 is ON Message-ID: Forwarding on behalf of Pjotr Prins, who just volunteered to serve as OBF's GSoC admin for this year. ~~~ Game on! GSoC 2013 is ON. I am running with the OBF project administration this year for the Google Summer of code (GSoC). First and foremost I want to thank Robert Buels and others for making OBF/GSoC a success in the previous three years! This year, Robert, Chris Fields and Hilmar Lapp will act as backup administrators. The deadline for the OBF application for GSoC2013 as a mentoring organisation is Friday March 29! See http://www.google-melange.com/gsoc/events/google/gsoc2013 Similar to previous years, each Bio* project needs to update and add project ideas on the project's individual OBF wiki page and create links from the main OBF page at http://www.open-bio.org/wiki/Google_Summer_of_Code (we will update the main information on that page soon). So, for each of the OBF projects that wants to do GSoC again this year: 1. Update the list of project ideas on your project's GSoC page (BioPython, BioPerl, BioRuby, etc). Add new ones, remove ones that have already been done or no longer relevant, etc. For an example see http://bioruby.open-bio.org/wiki/Google_Summer_of_Code 2. Update the final list of project ideas on the main OBF GSoC page to match. http://www.open-bio.org/wiki/Google_Summer_of_Code 3. Register with gsoc at lists.open-bio.org 4. Announce it on that list when you are ready :) Anyone can submit a project idea! Former GSoC students are especially encouraged to contribute ideas to the mailing lists. Please have the updates done by Friday March 22nd. The number and quality of the project ideas are part of the evaluation process for whether OBF is accepted as a Summer of Code organisation again this year, so let's come up with some good ones! Pj. (Pjotr Prins) Important dates: * March 22nd: Finalise project ideas * March 29th: Deadline OBF mentoring organisation submission to Google http://www.open-bio.org/wiki/Google_Summer_of_Code From dtomso at agbiome.com Mon Mar 4 16:14:54 2013 From: dtomso at agbiome.com (Dan Tomso) Date: Mon, 4 Mar 2013 11:14:54 -0500 Subject: [BioSQL-l] New to list--hello message Message-ID: <6B9C6089-A172-4710-9FD4-0AC7866BAFCF@agbiome.com> Hello all-- I just want to say 'hi' to the list members. I'm using BioSQL via BioPython, and will certainly have a few questions. I will be working heavily with microbial genomes and will be warehousing lots of sequence data, so I've decided to give BioSQL a try rather than invent my own schema. Best regards, Dan Tomso Chief Science Officer AgBiome Inc. From dtomso at agbiome.com Tue Mar 12 17:51:46 2013 From: dtomso at agbiome.com (Dan Tomso) Date: Tue, 12 Mar 2013 13:51:46 -0400 Subject: [BioSQL-l] Question regarding updating records in a BioSQL database (under Python) Message-ID: Hello all-- This seems trivial, but I'm struggling with how to add SeqFeatures to a BioSQL DBSeqRecord object. I can update the object, but then I can't update the DB. If I delete the original from the db, it kills the updated copy. If I try to deep copy the original, I get lots of errors. If I try to load the modified record without removing the original, I get a collision. I've tried also just updating the entry via the dictionary-like approach. Where am I going wrong? Thanks, Dan Tomso From p.j.a.cock at googlemail.com Tue Mar 12 20:58:07 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 12 Mar 2013 20:58:07 +0000 Subject: [BioSQL-l] Question regarding updating records in a BioSQL database (under Python) In-Reply-To: References: Message-ID: On Tuesday, March 12, 2013, Dan Tomso wrote: > Hello all-- > This seems trivial, but I'm struggling with how to add SeqFeatures to a > BioSQL DBSeqRecord object. > > I can update the object, but then I can't update the DB. If I delete the > original from the db, it kills the updated copy. If I try to deep copy the > original, I get lots of errors. If I try to load the modified record > without removing the original, I get a collision. > > I've tried also just updating the entry via the dictionary-like approach. > > Where am I going wrong? > > Thanks, > Dan Tomso > > Hi Dan, It sounds like you are using Biopython, right? Clearly our docs need a little more clarification - the dictionary like interface (and the whole DBSeqRecord) uses a read only lazy loading approach (for example neither the sequence nor the features are loaded from the database into objects in memory until accessed). You could try creating a separate namespace (e.g. Old and New) within the same database to allow you to save the modified record into a new namespace and so avoid the clashes... but basically the problem is you are trying to do something the API was never designed to cater to. If you want to discuss possible enhancements, then the Biopython-dev mailing list might be more relevant. Regards, Peter From dtomso at agbiome.com Wed Mar 13 13:47:27 2013 From: dtomso at agbiome.com (Dan Tomso) Date: Wed, 13 Mar 2013 09:47:27 -0400 Subject: [BioSQL-l] Question regarding updating records in a BioSQL database (under Python) In-Reply-To: References: Message-ID: Thanks, Peter. I arrived at the same solution (new/old DB namespace). I will soldier on with some combination of new entry creation/old entry destruction and using files for 'holding' sequences at various stages of annotation. I'll take further discussion to the Dev list as suggested. Best regards, Dan T. On Mar 12, 2013, at 4:58 PM, Peter Cock wrote: > > > On Tuesday, March 12, 2013, Dan Tomso wrote: > Hello all-- > This seems trivial, but I'm struggling with how to add SeqFeatures to a BioSQL DBSeqRecord object. > > I can update the object, but then I can't update the DB. If I delete the original from the db, it kills the updated copy. If I try to deep copy the original, I get lots of errors. If I try to load the modified record without removing the original, I get a collision. > > I've tried also just updating the entry via the dictionary-like approach. > > Where am I going wrong? > > Thanks, > Dan Tomso > > > Hi Dan, > > It sounds like you are using Biopython, right? Clearly our > docs need a little more clarification - the dictionary like > interface (and the whole DBSeqRecord) uses a read only > lazy loading approach (for example neither the sequence > nor the features are loaded from the database into objects > in memory until accessed). > > You could try creating a separate namespace (e.g. Old > and New) within the same database to allow you to > save the modified record into a new namespace and > so avoid the clashes... but basically the problem is you > are trying to do something the API was never designed > to cater to. > > If you want to discuss possible enhancements, then > the Biopython-dev mailing list might be more relevant. > > Regards, > > Peter From hlapp at drycafe.net Sat Mar 23 19:14:43 2013 From: hlapp at drycafe.net (Hilmar Lapp) Date: Sat, 23 Mar 2013 15:14:43 -0400 Subject: [BioSQL-l] Fwd: GSoC 2013 is ON References: <20130320211932.GA23848@thebird.nl> Message-ID: FYI - reminder from Pjotr about project ideas for GSoC 2013. -hilmar Begin forwarded message: > From: Pjotr Prins > Subject: Re: GSoC 2013 is ON > Date: March 20, 2013 5:19:32 PM EDT > To: OBF GSoC > > Heads up! One more week to go for project ideas! Please update > > https://github.com/OBF/GSoC/wiki/Google-Summer-of-Code-2013 > > with the latest links. And maybe a wakeup call to your lists? > > If you are not on the Internet you don't exist. If you are not making > use of GSoC, you might as well be dead ;). > > Kidding. But, the more ideas, the better. > > Pj. > > * March 22nd: Finalise project ideas > * March 29th: Deadline OBF mentoring organisation submission to Google > > On Sun, Mar 03, 2013 at 12:23:26PM +0100, Pjotr Prins wrote: >> Dear project leaders. >> >> I am sending below announcement to you, to have it forwarded by you to >> your mailing lists. Please do so. Also pass this message on to anyone >> who might be in some way interested in the OBF/GSoC initiative. To >> participate, start by signing up to the soc mailing list at >> http://lists.open-bio.org/mailman/listinfo/gsoc >> >> Spread the word! >> >> ~~~ >> >> Game on! GSoC 2013 is ON. I am running with the OBF project >> administration this year for the Google Summer of code (GSoC). >> First and foremost I want to thank Robert Buels and others for making >> OBF/GSoC a success in the previous three years! This year, Robert, Chris >> Fields and Hilmar Lapp will act as backup administrators. >> >> The deadline for the OBF application for GSoC2013 as a mentoring >> organisation is Friday March 29! See >> >> http://www.google-melange.com/gsoc/events/google/gsoc2013 >> >> Similar to previous years, each Bio* project needs to update and add project >> ideas on the project's individual OBF wiki page and create links from the main >> OBF page at >> >> http://www.open-bio.org/wiki/Google_Summer_of_Code >> >> (we will update the main information on that page soon). >> >> So, for each of the OBF projects that wants to do GSoC again this >> year: >> >> 1. Update the list of project ideas on your project's GSoC page (BioPython, >> BioPerl, BioRuby, etc). Add new ones, remove ones that have already been done >> or no longer relevant, etc. For an example see >> >> http://bioruby.open-bio.org/wiki/Google_Summer_of_Code >> >> 2. Update the final list of project ideas on the main OBF GSoC page >> to match. >> >> http://www.open-bio.org/wiki/Google_Summer_of_Code >> >> 3. Register with gsoc at lists.open-bio.org >> >> 4. Announce it on that list when you are ready :) >> >> Anyone can submit a project idea! Former GSoC students are especially >> encouraged to contribute ideas to the mailing lists. >> >> Please have the updates done by Friday March 22nd. The number and quality of >> the project ideas are part of the evaluation process for whether OBF is >> accepted as a Summer of Code organisation again this year, so let's come up >> with some good ones! >> >> Pj. (Pjotr Prins) >> >> Important dates: >> >> * March 22nd: Finalise project ideas >> * March 29th: Deadline OBF mentoring organisation submission to Google >> >> http://www.open-bio.org/wiki/Google_Summer_of_Code >> -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : ===========================================================