From biopython at maubp.freeserve.co.uk Fri Jul 2 11:32:56 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Fri, 2 Jul 2010 16:32:56 +0100 Subject: [BioSQL-l] SQLite support In-Reply-To: References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com> <320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com> <320fb6e00907090529t61239952y1c86963f13c1db78@mail.gmail.com> <320fb6e00907280458q56f74ec6iefa420ac1caab8da@mail.gmail.com> <320fb6e00911240627o49bc1ec9nc0d26065ebc23423@mail.gmail.com> <070E8BA8-B2C1-4E44-AA2D-9934B3742406@illinois.edu> <320fb6e00911240907u32dca751ldb488cbc38f0e035@mail.gmail.com> <320fb6e00912100703g4e2b7068jb4fea67df3ebd8a8@mail.gmail.com> <320fb6e01001130337p1e0a361ci7ea1a5b5a9639731@mail.gmail.com> Message-ID: On Thu, Apr 15, 2010 at 7:23 PM, Peter wrote: > On Wed, Jan 13, 2010 at 6:06 PM, Hilmar Lapp wrote: >> >> Hi Peter, yes, I know I'm remiss on doing that. Will do shortly. Please >> don't stop pestering if I seem to have forgotten :-) >> >> ? ? ? ?-hilmar > > Cough cough ;-) > Hi Hilmar, Do you think the SQLite schema could be reviewed before or during BOSC 2010? Brad will be there so you can go though any queries in person. For anyone interested in the previous posts on the thread, see e.g. http://lists.open-bio.org/pipermail/biosql-l/2010-January/001668.html http://lists.open-bio.org/pipermail/biosql-l/2009-December/001660.html http://lists.open-bio.org/pipermail/biosql-l/2010-March/001692.html Peter From hlapp at gmx.net Fri Jul 2 21:38:23 2010 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 2 Jul 2010 21:38:23 -0400 Subject: [BioSQL-l] SQLite support In-Reply-To: References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com> <320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com> <320fb6e00907090529t61239952y1c86963f13c1db78@mail.gmail.com> <320fb6e00907280458q56f74ec6iefa420ac1caab8da@mail.gmail.com> <320fb6e00911240627o49bc1ec9nc0d26065ebc23423@mail.gmail.com> <070E8BA8-B2C1-4E44-AA2D-9934B3742406@illinois.edu> <320fb6e00911240907u32dca751ldb488cbc38f0e035@mail.gmail.com> <320fb6e00912100703g4e2b7068jb4fea67df3ebd8a8@mail.gmail.com> <320fb6e01001130337p1e0a361ci7ea1a5b5a9639731@mail.gmail.com> Message-ID: On Jul 2, 2010, at 11:32 AM, Peter wrote: > Do you think the SQLite schema could be reviewed before or during > BOSC 2010? That's indeed what I was intending, just didn't get a chance to say it yet :) In fact, I was aiming to do that as part of the Bio* Codefest. Will you be there as well? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From biopython at maubp.freeserve.co.uk Sat Jul 3 06:02:54 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Sat, 3 Jul 2010 11:02:54 +0100 Subject: [BioSQL-l] SQLite support In-Reply-To: References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com> <320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com> <320fb6e00907090529t61239952y1c86963f13c1db78@mail.gmail.com> <320fb6e00907280458q56f74ec6iefa420ac1caab8da@mail.gmail.com> <320fb6e00911240627o49bc1ec9nc0d26065ebc23423@mail.gmail.com> <070E8BA8-B2C1-4E44-AA2D-9934B3742406@illinois.edu> <320fb6e00911240907u32dca751ldb488cbc38f0e035@mail.gmail.com> <320fb6e00912100703g4e2b7068jb4fea67df3ebd8a8@mail.gmail.com> <320fb6e01001130337p1e0a361ci7ea1a5b5a9639731@mail.gmail.com>

Message-ID: On Sat, Jul 3, 2010 at 2:38 AM, Hilmar Lapp wrote: > > On Jul 2, 2010, at 11:32 AM, Peter wrote: > >> Do you think the SQLite schema could be reviewed before or during >> BOSC 2010? > > That's indeed what I was intending, just didn't get a chance to say it yet > :) In fact, I was aiming to do that as part of the Bio* Codefest. Will you > be there as well? That sounds like a great plan - Brad will be there, but sadly I will not be at BOSC/ISMB this year. Have fun! Peter From biopython at maubp.freeserve.co.uk Tue Jul 20 16:12:06 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Tue, 20 Jul 2010 21:12:06 +0100 Subject: [BioSQL-l] SQLite support In-Reply-To: References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com> <320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com> <320fb6e00907090529t61239952y1c86963f13c1db78@mail.gmail.com> <320fb6e00907280458q56f74ec6iefa420ac1caab8da@mail.gmail.com> <320fb6e00911240627o49bc1ec9nc0d26065ebc23423@mail.gmail.com> <070E8BA8-B2C1-4E44-AA2D-9934B3742406@illinois.edu> <320fb6e00911240907u32dca751ldb488cbc38f0e035@mail.gmail.com> <320fb6e00912100703g4e2b7068jb4fea67df3ebd8a8@mail.gmail.com> <320fb6e01001130337p1e0a361ci7ea1a5b5a9639731@mail.gmail.com>

Message-ID: On Sat, Jul 3, 2010 at 11:02 AM, Peter wrote: > On Sat, Jul 3, 2010 at 2:38 AM, Hilmar Lapp wrote: >> >> On Jul 2, 2010, at 11:32 AM, Peter wrote: >> >>> Do you think the SQLite schema could be reviewed before or during >>> BOSC 2010? >> >> That's indeed what I was intending, just didn't get a chance to say it yet >> :) In fact, I was aiming to do that as part of the Bio* Codefest. Will you >> be there as well? > > That sounds like a great plan - Brad will be there, but sadly I will not > be at BOSC/ISMB this year. Have fun! Did you guys manage to sit down together to look at the BioSQL on SQLite3 schema during BOSC/ISMB? Peter From hlapp at gmx.net Tue Jul 20 17:50:04 2010 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 20 Jul 2010 17:50:04 -0400 Subject: [BioSQL-l] SQLite support In-Reply-To: References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com> <320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com> <320fb6e00907090529t61239952y1c86963f13c1db78@mail.gmail.com> <320fb6e00907280458q56f74ec6iefa420ac1caab8da@mail.gmail.com> <320fb6e00911240627o49bc1ec9nc0d26065ebc23423@mail.gmail.com> <070E8BA8-B2C1-4E44-AA2D-9934B3742406@illinois.edu> <320fb6e00911240907u32dca751ldb488cbc38f0e035@mail.gmail.com> <320fb6e00912100703g4e2b7068jb4fea67df3ebd8a8@mail.gmail.com> <320fb6e01001130337p1e0a361ci7ea1a5b5a9639731@mail.gmail.com>

Message-ID: <8AE63B77-6E24-4A3A-B13E-A5C26043F271@gmx.net> On Jul 20, 2010, at 4:12 PM, Peter wrote: > Did you guys manage to sit down together to look at the BioSQL > on SQLite3 schema during BOSC/ISMB? Yes. I not os much, sadly, but I was lucky enough that one of the participants, Chris Bottoms, volunteered to take on that task, and I believe more or less completed it. I'm indebted to you, Chris! I don't think he has svn write access, so if I'm not mistaken it's not committed yet. Rather than bothering with getting him an account on the open-bio machine, Chris Fields and I were going to migrate BioSQL over to github this week, and then we can go from there. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From biopython at maubp.freeserve.co.uk Wed Jul 21 05:12:08 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Wed, 21 Jul 2010 10:12:08 +0100 Subject: [BioSQL-l] SQLite support In-Reply-To: <8AE63B77-6E24-4A3A-B13E-A5C26043F271@gmx.net> References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com> <320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com> <320fb6e00907090529t61239952y1c86963f13c1db78@mail.gmail.com> <320fb6e00907280458q56f74ec6iefa420ac1caab8da@mail.gmail.com> <320fb6e00911240627o49bc1ec9nc0d26065ebc23423@mail.gmail.com> <070E8BA8-B2C1-4E44-AA2D-9934B3742406@illinois.edu> <320fb6e00911240907u32dca751ldb488cbc38f0e035@mail.gmail.com> <320fb6e00912100703g4e2b7068jb4fea67df3ebd8a8@mail.gmail.com> <320fb6e01001130337p1e0a361ci7ea1a5b5a9639731@mail.gmail.com>

<8AE63B77-6E24-4A3A-B13E-A5C26043F271@gmx.net> Message-ID: On Tue, Jul 20, 2010 at 10:50 PM, Hilmar Lapp wrote: > > > On Jul 20, 2010, at 4:12 PM, Peter wrote: > >> Did you guys manage to sit down together to look at the BioSQL >> on SQLite3 schema during BOSC/ISMB? > > > Yes. I not os much, sadly, but I was lucky enough that one of the > participants, Chris Bottoms, volunteered to take on that task, and I believe > more or less completed it. I'm indebted to you, Chris! > > I don't think he has svn write access, so if I'm not mistaken it's not > committed yet. Rather than bothering with getting him an account on the > open-bio machine, Chris Fields and I were going to migrate BioSQL over > to github this week, and then we can go from there. > Excellent - and using github should make it easier for contributions from other Bio* projects since most of them are now on github. Peter From bonnalraoul at ingm.it Wed Jul 21 05:48:52 2010 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Wed, 21 Jul 2010 11:48:52 +0200 Subject: [BioSQL-l] R: SQLite support References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com><320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com><320fb6e00907090529t61239952y1c86963f13c1db78@mail.gmail.com><320fb6e00907280458q56f74ec6iefa420ac1caab8da@mail.gmail.com><320fb6e00911240627o49bc1ec9nc0d26065ebc23423@mail.gmail.com><070E8BA8-B2C1-4E44-AA2D-9934B3742406@illinois.edu><320fb6e00911240907u32dca751ldb488cbc38f0e03 5@mail.gmail.com><320fb6e00912100703g4e2b7068jb4fea67df3ebd8a8@mail.gmail.com><320fb6e01001130337p1e0a361ci7ea1a5b5a9639731@mail.gmail.com>

<8AE63B77-6E24-4A3A-B13E-A5C26043F271@gmx.net> Message-ID: <46f62504-80c1-470f-92d0-87d9c53fee0d@ingm.it> > -----Messaggio originale----- > > I don't think he has svn write access, so if I'm not mistaken it's > not > > committed yet. Rather than bothering with getting him an account on > the > > open-bio machine, Chris Fields and I were going to migrate BioSQL > over > > to github this week, and then we can go from there. > > > > Excellent - and using github should make it easier for contributions > from other Bio* projects since most of them are now on github. This is a great news -- Raoul J.P. Bonnal Life Science Informatics Integrative Biology Program Fondazione INGM Via F. Sforza 28 20122 Milano, IT phone: +39 02 006 623 26 fax: +39 02 006 623 46 http://www.ingm.it From hlapp at gmx.net Wed Jul 21 09:51:26 2010 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 21 Jul 2010 09:51:26 -0400 Subject: [BioSQL-l] SQLite support In-Reply-To: References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com> <320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com> <320fb6e00907090529t61239952y1c86963f13c1db78@mail.gmail.com> <320fb6e00907280458q56f74ec6iefa420ac1caab8da@mail.gmail.com> <320fb6e00911240627o49bc1ec9nc0d26065ebc23423@mail.gmail.com> <070E8BA8-B2C1-4E44-AA2D-9934B3742406@illinois.edu> <320fb6e00911240907u32dca751ldb488cbc38f0e035@mail.gmail.com> <320fb6e00912100703g4e2b7068jb4fea67df3ebd8a8@mail.gmail.com> <320fb6e01001130337p1e0a361ci7ea1a5b5a9639731@mail.gmail.com>

<8AE63B77-6E24-4A3A-B13E-A5C26043F271@gmx.net> Message-ID: <27E4A3B4-5EA0-4971-BD30-19AFBEF6AFAD@gmx.net> On Jul 21, 2010, at 5:12 AM, Peter wrote: > Excellent - and using github should make it easier for contributions > from other Bio* projects since most of them are now on github. That's indeed part of the rationale. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at illinois.edu Wed Jul 21 09:46:12 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jul 2010 08:46:12 -0500 Subject: [BioSQL-l] R: SQLite support In-Reply-To: <46f62504-80c1-470f-92d0-87d9c53fee0d@ingm.it> References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com><320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com><320fb6e00907090529t61239952y1c86963f13c1db78@mail.gmail.com><320fb6e00907280458q56f74ec6iefa420ac1caab8da@mail.gmail.com><320fb6e00911240627o49bc1ec9nc0d26065ebc23423@mail.gmail.com><070E8BA8-B2C1-4E44-AA2D-9934B3742406@illinois.edu><320fb6e00911240907u32dca751ldb488cbc38f0e03 5@mail.gmail.com><320fb6e00912100703g4e2b7068jb4fea67df3ebd8a8@mail.gmail.com><320fb6e01001130337p1e0a361ci7ea1a5b5a9639731@mail.gmail.com>

<8AE63B77-6E24-4A3A-B13E-A5C26043F271@gmx.net> <46f62504-80c1-470f-92d0-87d9c53fee0d@ingm.it> Message-ID: On Jul 21, 2010, at 4:48 AM, Raoul Bonnal wrote: > -----Messaggio originale----- >>> I don't think he has svn write access, so if I'm not mistaken it's >> not >>> committed yet. Rather than bothering with getting him an account on >> the >>> open-bio machine, Chris Fields and I were going to migrate BioSQL >> over >>> to github this week, and then we can go from there. >>> >> >> Excellent - and using github should make it easier for contributions >> from other Bio* projects since most of them are now on github. > This is a great news The move to github should occur pretty soon (maybe by Friday if everything proceeds well). chris From hlapp at drycafe.net Thu Jul 29 19:08:00 2010 From: hlapp at drycafe.net (Hilmar Lapp) Date: Thu, 29 Jul 2010 19:08:00 -0400 Subject: [BioSQL-l] migration to github Message-ID: <22BC0098-7BEB-41E3-9EE6-D8987323CC24@drycafe.net> As mentioned previously, Chris Fields is currently heroically migrating the BioSQL repository to Github. If you have previously contributed to BioSQL through your own svn account on the open-bio.org repository, please 1) create an account on Github, and 2) link your open-bio.org email address to your account (userid at open-bio.org ). That way, your previous svn commits will automatically get mapped to your Github account; otherwise it will simply remain associated your open-bio.org email ID. I have pasted a list of the open-bio.org usernames below (and copied this to the respective @open-bio.org email addresses). Finally, does anyone have a strong feeling about the capitalization of BioSQL on Github? All lowercase (github.com/biosql) or capitalized (github.com/BioSQL)? -hilmar amackey birney bosborne chapmanb cjm elia hartzell jason jerm jestill jhannah savikalpa shawnh thomasd -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From biopython at maubp.freeserve.co.uk Fri Jul 30 04:17:11 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Fri, 30 Jul 2010 09:17:11 +0100 Subject: [BioSQL-l] migration to github In-Reply-To: <22BC0098-7BEB-41E3-9EE6-D8987323CC24@drycafe.net> References: <22BC0098-7BEB-41E3-9EE6-D8987323CC24@drycafe.net> Message-ID: On Fri, Jul 30, 2010 at 12:08 AM, Hilmar Lapp wrote: > > As mentioned previously, Chris Fields is currently heroically migrating the > BioSQL repository to Github. > Great. > > Finally, does anyone have a strong feeling about the capitalization of > BioSQL on Github? All lowercase (github.com/biosql) or capitalized > (github.com/BioSQL)? Personally I'd pick lowercase - it seems more commonly used for repositories and usernames in general. In our case it also avoided Biopython vs BioPython confusion. Curiously most but not all of the BioPerl repositories are in lowercase... Peter From cjfields at illinois.edu Sat Jul 31 19:15:56 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 31 Jul 2010 18:15:56 -0500 Subject: [BioSQL-l] migration to github In-Reply-To: References: <22BC0098-7BEB-41E3-9EE6-D8987323CC24@drycafe.net> Message-ID: <04BBA390-6BC0-4700-8B14-812F6E2E4705@illinois.edu> On Jul 30, 2010, at 3:17 AM, Peter wrote: > On Fri, Jul 30, 2010 at 12:08 AM, Hilmar Lapp wrote: >> >> As mentioned previously, Chris Fields is currently heroically migrating the >> BioSQL repository to Github. >> > > Great. > >> >> Finally, does anyone have a strong feeling about the capitalization of >> BioSQL on Github? All lowercase (github.com/biosql) or capitalized >> (github.com/BioSQL)? > > Personally I'd pick lowercase - it seems more commonly used > for repositories and usernames in general. In our case it also > avoided Biopython vs BioPython confusion. Curiously most but > not all of the BioPerl repositories are in lowercase... > > Peter Okay, organization and repo name are both now 'biosql'. No take-backs! Re: upper case with bioperl repos, do you mean the Bio-* ones? The emphasis there that (1) they aren't part of bioperl core but are still part of the Bio namespace, and (2) the dist will match the actual namespace and the module name (Bio::FeatureIO, for instance), unlike BioPerl and the others, and (3) there is some precedent (Bio::Graphics being one). This simple thing makes it a lot easier for keeping track of names, and the module name can be used for CPAN installation, indexing, and documentation. chris From biopython at maubp.freeserve.co.uk Fri Jul 2 15:32:56 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Fri, 2 Jul 2010 16:32:56 +0100 Subject: [BioSQL-l] SQLite support In-Reply-To: References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com> <320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com> <320fb6e00907090529t61239952y1c86963f13c1db78@mail.gmail.com> <320fb6e00907280458q56f74ec6iefa420ac1caab8da@mail.gmail.com> <320fb6e00911240627o49bc1ec9nc0d26065ebc23423@mail.gmail.com> <070E8BA8-B2C1-4E44-AA2D-9934B3742406@illinois.edu> <320fb6e00911240907u32dca751ldb488cbc38f0e035@mail.gmail.com> <320fb6e00912100703g4e2b7068jb4fea67df3ebd8a8@mail.gmail.com> <320fb6e01001130337p1e0a361ci7ea1a5b5a9639731@mail.gmail.com> Message-ID: On Thu, Apr 15, 2010 at 7:23 PM, Peter wrote: > On Wed, Jan 13, 2010 at 6:06 PM, Hilmar Lapp wrote: >> >> Hi Peter, yes, I know I'm remiss on doing that. Will do shortly. Please >> don't stop pestering if I seem to have forgotten :-) >> >> ? ? ? ?-hilmar > > Cough cough ;-) > Hi Hilmar, Do you think the SQLite schema could be reviewed before or during BOSC 2010? Brad will be there so you can go though any queries in person. For anyone interested in the previous posts on the thread, see e.g. http://lists.open-bio.org/pipermail/biosql-l/2010-January/001668.html http://lists.open-bio.org/pipermail/biosql-l/2009-December/001660.html http://lists.open-bio.org/pipermail/biosql-l/2010-March/001692.html Peter From hlapp at gmx.net Sat Jul 3 01:38:23 2010 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 2 Jul 2010 21:38:23 -0400 Subject: [BioSQL-l] SQLite support In-Reply-To: References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com> <320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com> <320fb6e00907090529t61239952y1c86963f13c1db78@mail.gmail.com> <320fb6e00907280458q56f74ec6iefa420ac1caab8da@mail.gmail.com> <320fb6e00911240627o49bc1ec9nc0d26065ebc23423@mail.gmail.com> <070E8BA8-B2C1-4E44-AA2D-9934B3742406@illinois.edu> <320fb6e00911240907u32dca751ldb488cbc38f0e035@mail.gmail.com> <320fb6e00912100703g4e2b7068jb4fea67df3ebd8a8@mail.gmail.com> <320fb6e01001130337p1e0a361ci7ea1a5b5a9639731@mail.gmail.com> Message-ID: On Jul 2, 2010, at 11:32 AM, Peter wrote: > Do you think the SQLite schema could be reviewed before or during > BOSC 2010? That's indeed what I was intending, just didn't get a chance to say it yet :) In fact, I was aiming to do that as part of the Bio* Codefest. Will you be there as well? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From biopython at maubp.freeserve.co.uk Sat Jul 3 10:02:54 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Sat, 3 Jul 2010 11:02:54 +0100 Subject: [BioSQL-l] SQLite support In-Reply-To: References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com> <320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com> <320fb6e00907090529t61239952y1c86963f13c1db78@mail.gmail.com> <320fb6e00907280458q56f74ec6iefa420ac1caab8da@mail.gmail.com> <320fb6e00911240627o49bc1ec9nc0d26065ebc23423@mail.gmail.com> <070E8BA8-B2C1-4E44-AA2D-9934B3742406@illinois.edu> <320fb6e00911240907u32dca751ldb488cbc38f0e035@mail.gmail.com> <320fb6e00912100703g4e2b7068jb4fea67df3ebd8a8@mail.gmail.com> <320fb6e01001130337p1e0a361ci7ea1a5b5a9639731@mail.gmail.com>

Message-ID: On Sat, Jul 3, 2010 at 2:38 AM, Hilmar Lapp wrote: > > On Jul 2, 2010, at 11:32 AM, Peter wrote: > >> Do you think the SQLite schema could be reviewed before or during >> BOSC 2010? > > That's indeed what I was intending, just didn't get a chance to say it yet > :) In fact, I was aiming to do that as part of the Bio* Codefest. Will you > be there as well? That sounds like a great plan - Brad will be there, but sadly I will not be at BOSC/ISMB this year. Have fun! Peter From biopython at maubp.freeserve.co.uk Tue Jul 20 20:12:06 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Tue, 20 Jul 2010 21:12:06 +0100 Subject: [BioSQL-l] SQLite support In-Reply-To: References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com> <320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com> <320fb6e00907090529t61239952y1c86963f13c1db78@mail.gmail.com> <320fb6e00907280458q56f74ec6iefa420ac1caab8da@mail.gmail.com> <320fb6e00911240627o49bc1ec9nc0d26065ebc23423@mail.gmail.com> <070E8BA8-B2C1-4E44-AA2D-9934B3742406@illinois.edu> <320fb6e00911240907u32dca751ldb488cbc38f0e035@mail.gmail.com> <320fb6e00912100703g4e2b7068jb4fea67df3ebd8a8@mail.gmail.com> <320fb6e01001130337p1e0a361ci7ea1a5b5a9639731@mail.gmail.com>

Message-ID: On Sat, Jul 3, 2010 at 11:02 AM, Peter wrote: > On Sat, Jul 3, 2010 at 2:38 AM, Hilmar Lapp wrote: >> >> On Jul 2, 2010, at 11:32 AM, Peter wrote: >> >>> Do you think the SQLite schema could be reviewed before or during >>> BOSC 2010? >> >> That's indeed what I was intending, just didn't get a chance to say it yet >> :) In fact, I was aiming to do that as part of the Bio* Codefest. Will you >> be there as well? > > That sounds like a great plan - Brad will be there, but sadly I will not > be at BOSC/ISMB this year. Have fun! Did you guys manage to sit down together to look at the BioSQL on SQLite3 schema during BOSC/ISMB? Peter From hlapp at gmx.net Tue Jul 20 21:50:04 2010 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 20 Jul 2010 17:50:04 -0400 Subject: [BioSQL-l] SQLite support In-Reply-To: References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com> <320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com> <320fb6e00907090529t61239952y1c86963f13c1db78@mail.gmail.com> <320fb6e00907280458q56f74ec6iefa420ac1caab8da@mail.gmail.com> <320fb6e00911240627o49bc1ec9nc0d26065ebc23423@mail.gmail.com> <070E8BA8-B2C1-4E44-AA2D-9934B3742406@illinois.edu> <320fb6e00911240907u32dca751ldb488cbc38f0e035@mail.gmail.com> <320fb6e00912100703g4e2b7068jb4fea67df3ebd8a8@mail.gmail.com> <320fb6e01001130337p1e0a361ci7ea1a5b5a9639731@mail.gmail.com>

Message-ID: <8AE63B77-6E24-4A3A-B13E-A5C26043F271@gmx.net> On Jul 20, 2010, at 4:12 PM, Peter wrote: > Did you guys manage to sit down together to look at the BioSQL > on SQLite3 schema during BOSC/ISMB? Yes. I not os much, sadly, but I was lucky enough that one of the participants, Chris Bottoms, volunteered to take on that task, and I believe more or less completed it. I'm indebted to you, Chris! I don't think he has svn write access, so if I'm not mistaken it's not committed yet. Rather than bothering with getting him an account on the open-bio machine, Chris Fields and I were going to migrate BioSQL over to github this week, and then we can go from there. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From biopython at maubp.freeserve.co.uk Wed Jul 21 09:12:08 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Wed, 21 Jul 2010 10:12:08 +0100 Subject: [BioSQL-l] SQLite support In-Reply-To: <8AE63B77-6E24-4A3A-B13E-A5C26043F271@gmx.net> References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com> <320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com> <320fb6e00907090529t61239952y1c86963f13c1db78@mail.gmail.com> <320fb6e00907280458q56f74ec6iefa420ac1caab8da@mail.gmail.com> <320fb6e00911240627o49bc1ec9nc0d26065ebc23423@mail.gmail.com> <070E8BA8-B2C1-4E44-AA2D-9934B3742406@illinois.edu> <320fb6e00911240907u32dca751ldb488cbc38f0e035@mail.gmail.com> <320fb6e00912100703g4e2b7068jb4fea67df3ebd8a8@mail.gmail.com> <320fb6e01001130337p1e0a361ci7ea1a5b5a9639731@mail.gmail.com>

<8AE63B77-6E24-4A3A-B13E-A5C26043F271@gmx.net> Message-ID: On Tue, Jul 20, 2010 at 10:50 PM, Hilmar Lapp wrote: > > > On Jul 20, 2010, at 4:12 PM, Peter wrote: > >> Did you guys manage to sit down together to look at the BioSQL >> on SQLite3 schema during BOSC/ISMB? > > > Yes. I not os much, sadly, but I was lucky enough that one of the > participants, Chris Bottoms, volunteered to take on that task, and I believe > more or less completed it. I'm indebted to you, Chris! > > I don't think he has svn write access, so if I'm not mistaken it's not > committed yet. Rather than bothering with getting him an account on the > open-bio machine, Chris Fields and I were going to migrate BioSQL over > to github this week, and then we can go from there. > Excellent - and using github should make it easier for contributions from other Bio* projects since most of them are now on github. Peter From bonnalraoul at ingm.it Wed Jul 21 09:48:52 2010 From: bonnalraoul at ingm.it (Raoul Bonnal) Date: Wed, 21 Jul 2010 11:48:52 +0200 Subject: [BioSQL-l] R: SQLite support References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com><320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com><320fb6e00907090529t61239952y1c86963f13c1db78@mail.gmail.com><320fb6e00907280458q56f74ec6iefa420ac1caab8da@mail.gmail.com><320fb6e00911240627o49bc1ec9nc0d26065ebc23423@mail.gmail.com><070E8BA8-B2C1-4E44-AA2D-9934B3742406@illinois.edu><320fb6e00911240907u32dca751ldb488cbc38f0e03 5@mail.gmail.com><320fb6e00912100703g4e2b7068jb4fea67df3ebd8a8@mail.gmail.com><320fb6e01001130337p1e0a361ci7ea1a5b5a9639731@mail.gmail.com>

<8AE63B77-6E24-4A3A-B13E-A5C26043F271@gmx.net> Message-ID: <46f62504-80c1-470f-92d0-87d9c53fee0d@ingm.it> > -----Messaggio originale----- > > I don't think he has svn write access, so if I'm not mistaken it's > not > > committed yet. Rather than bothering with getting him an account on > the > > open-bio machine, Chris Fields and I were going to migrate BioSQL > over > > to github this week, and then we can go from there. > > > > Excellent - and using github should make it easier for contributions > from other Bio* projects since most of them are now on github. This is a great news -- Raoul J.P. Bonnal Life Science Informatics Integrative Biology Program Fondazione INGM Via F. Sforza 28 20122 Milano, IT phone: +39 02 006 623 26 fax: +39 02 006 623 46 http://www.ingm.it From hlapp at gmx.net Wed Jul 21 13:51:26 2010 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 21 Jul 2010 09:51:26 -0400 Subject: [BioSQL-l] SQLite support In-Reply-To: References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com> <320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com> <320fb6e00907090529t61239952y1c86963f13c1db78@mail.gmail.com> <320fb6e00907280458q56f74ec6iefa420ac1caab8da@mail.gmail.com> <320fb6e00911240627o49bc1ec9nc0d26065ebc23423@mail.gmail.com> <070E8BA8-B2C1-4E44-AA2D-9934B3742406@illinois.edu> <320fb6e00911240907u32dca751ldb488cbc38f0e035@mail.gmail.com> <320fb6e00912100703g4e2b7068jb4fea67df3ebd8a8@mail.gmail.com> <320fb6e01001130337p1e0a361ci7ea1a5b5a9639731@mail.gmail.com>

<8AE63B77-6E24-4A3A-B13E-A5C26043F271@gmx.net> Message-ID: <27E4A3B4-5EA0-4971-BD30-19AFBEF6AFAD@gmx.net> On Jul 21, 2010, at 5:12 AM, Peter wrote: > Excellent - and using github should make it easier for contributions > from other Bio* projects since most of them are now on github. That's indeed part of the rationale. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at illinois.edu Wed Jul 21 13:46:12 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jul 2010 08:46:12 -0500 Subject: [BioSQL-l] R: SQLite support In-Reply-To: <46f62504-80c1-470f-92d0-87d9c53fee0d@ingm.it> References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com><320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com><320fb6e00907090529t61239952y1c86963f13c1db78@mail.gmail.com><320fb6e00907280458q56f74ec6iefa420ac1caab8da@mail.gmail.com><320fb6e00911240627o49bc1ec9nc0d26065ebc23423@mail.gmail.com><070E8BA8-B2C1-4E44-AA2D-9934B3742406@illinois.edu><320fb6e00911240907u32dca751ldb488cbc38f0e03 5@mail.gmail.com><320fb6e00912100703g4e2b7068jb4fea67df3ebd8a8@mail.gmail.com><320fb6e01001130337p1e0a361ci7ea1a5b5a9639731@mail.gmail.com>