From p.j.a.cock at googlemail.com Mon Apr 1 10:28:43 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 1 Apr 2013 15:28:43 +0100 Subject: [BioSQL-l] Google Summer of Code - BioPerl / BioSQL proposal? Message-ID: On 18 March 2013 21:26, Christopher Fields wrote: > Just a heads-up, if there are any students interested in the Google Summer of > Code, the Open Bioinformatics Foundation is planning on participating again > this year! Pjotr Prins will be organizing for OBF; all the Bio* projects are > looking for prospective projects. > > We're open for any project ideas this year, so let us know what you would like > to do! I suggested this last year too, but improving support for BioSQL on SQLite would be great - the schema exists and seems to work fine, but is currently only handled by the Biopython BioSQL bindings. So, the core of a BioSQL/BioPerl GSoC project could tackle: * Adding SQLite support to the BioSQL scripts for loading taxonomies etc https://github.com/biosql/biosql * Adding SQLite support to BioPerl's BioSQL adapter, bioperl-db https://github.com/bioperl/bioperl-db There are a number of things that could be added to this basic idea to make the project more ambitious and to fill out a full summer. One is to extend this to doing BioSQL on SQLite bindings for BioRuby or BioJava (assuming suitable co-mentors are available). One of the nice things about SQLite compared to MySQL or PostgreSQL is the database is just one binary file on disk which is easily portable and can even be checked into source code control for unit tests. This means we can use it to make cross-binding testing far far easier. Thus another part of a GSoC project could be to use the SQlite bindings to establish cross-project testing of the BioSQL implementations for consistency. At that point I'd be interested from the BioSQL and Biopython side, and Biopython may have a few possible co-mentors here. Anyway, to be viable this project would need a Perl mentor with a good knowledge of BioSQL and BioPerl's bindings for it. Is this worth adding to the BioPerl GSoC as a possible idea? http://bioperl.org/wiki/Google_Summer_of_Code#Project_Ideas_for_2013 Regards, Peter (Who doesn't know enough Perl to qualify as a mentor for this) From cjfields at illinois.edu Mon Apr 1 10:35:25 2013 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 1 Apr 2013 14:35:25 +0000 Subject: [BioSQL-l] Google Summer of Code - BioPerl / BioSQL proposal? In-Reply-To: References: Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC9169@CHIMBX5.ad.uillinois.edu> On Apr 1, 2013, at 9:28 AM, Peter Cock wrote: > On 18 March 2013 21:26, Christopher Fields wrote: >> Just a heads-up, if there are any students interested in the Google Summer of >> Code, the Open Bioinformatics Foundation is planning on participating again >> this year! Pjotr Prins will be organizing for OBF; all the Bio* projects are >> looking for prospective projects. >> >> We're open for any project ideas this year, so let us know what you would like >> to do! > > I suggested this last year too, but improving support for BioSQL on > SQLite would be great - the schema exists and seems to work fine, > but is currently only handled by the Biopython BioSQL bindings. ++++1 > So, the core of a BioSQL/BioPerl GSoC project could tackle: > > * Adding SQLite support to the BioSQL scripts for loading taxonomies etc > https://github.com/biosql/biosql > > * Adding SQLite support to BioPerl's BioSQL adapter, bioperl-db > https://github.com/bioperl/bioperl-db > > There are a number of things that could be added to this basic idea > to make the project more ambitious and to fill out a full summer. One > is to extend this to doing BioSQL on SQLite bindings for BioRuby or > BioJava (assuming suitable co-mentors are available). > > One of the nice things about SQLite compared to MySQL or PostgreSQL > is the database is just one binary file on disk which is easily portable and > can even be checked into source code control for unit tests. This means > we can use it to make cross-binding testing far far easier. Thus another > part of a GSoC project could be to use the SQlite bindings to establish > cross-project testing of the BioSQL implementations for consistency. > At that point I'd be interested from the BioSQL and Biopython side, > and Biopython may have a few possible co-mentors here. > > Anyway, to be viable this project would need a Perl mentor with a > good knowledge of BioSQL and BioPerl's bindings for it. > > Is this worth adding to the BioPerl GSoC as a possible idea? > http://bioperl.org/wiki/Google_Summer_of_Code#Project_Ideas_for_2013 Yes. Will add this now. > Regards, > > Peter > (Who doesn't know enough Perl to qualify as a mentor for this) There was a reasonable push for this a while back (BOSC in Boston) but nothing came of it code-wise that I have seen. Not sure where it stands now. chris From hlapp at drycafe.net Mon Apr 1 12:38:46 2013 From: hlapp at drycafe.net (Hilmar Lapp) Date: Mon, 1 Apr 2013 12:38:46 -0400 Subject: [BioSQL-l] [Bioperl-l] Google Summer of Code - BioPerl / BioSQL proposal? In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74DC9169@CHIMBX5.ad.uillinois.edu> References: <118F034CF4C3EF48A96F86CE585B94BF74DC9169@CHIMBX5.ad.uillinois.edu> Message-ID: <6B9A2644-9075-486F-977C-86750D88B737@drycafe.net> Just to add another possibility for a summer project here, Bioperl-db (the BioPerl bindings to BioSQL) in essence constitute a self-made ORM, invented at a time when DBIx::Class didn't exist yet. As such, it has some advantages (if you are willing to count overly clever features to be counted in this category), but arguably many more disadvantages, chief among them being the unsustainably small (you could also say non-existent) developer community supporting it, and the fact that DBIx::Class now has existed for years, and is fairly mature. So, rewriting Bioperl-db with a DBIx::Class (or another well-supported generic ORM) would, I think, stand to make a considerable impact on our ability to further develop Bioperl's relational storage capabilities, as well as BioSQL itself. And I'd be willing to help out with such a project in a at least a co-mentoring capacity. (If primary mentor, I'd need a committed co-mentor to make it viable.) -hilmar On Apr 1, 2013, at 10:35 AM, Fields, Christopher J wrote: > On Apr 1, 2013, at 9:28 AM, Peter Cock wrote: > >> On 18 March 2013 21:26, Christopher Fields wrote: >>> Just a heads-up, if there are any students interested in the Google Summer of >>> Code, the Open Bioinformatics Foundation is planning on participating again >>> this year! Pjotr Prins will be organizing for OBF; all the Bio* projects are >>> looking for prospective projects. >>> >>> We're open for any project ideas this year, so let us know what you would like >>> to do! >> >> I suggested this last year too, but improving support for BioSQL on >> SQLite would be great - the schema exists and seems to work fine, >> but is currently only handled by the Biopython BioSQL bindings. > > ++++1 > >> So, the core of a BioSQL/BioPerl GSoC project could tackle: >> >> * Adding SQLite support to the BioSQL scripts for loading taxonomies etc >> https://github.com/biosql/biosql >> >> * Adding SQLite support to BioPerl's BioSQL adapter, bioperl-db >> https://github.com/bioperl/bioperl-db >> >> There are a number of things that could be added to this basic idea >> to make the project more ambitious and to fill out a full summer. One >> is to extend this to doing BioSQL on SQLite bindings for BioRuby or >> BioJava (assuming suitable co-mentors are available). >> >> One of the nice things about SQLite compared to MySQL or PostgreSQL >> is the database is just one binary file on disk which is easily portable and >> can even be checked into source code control for unit tests. This means >> we can use it to make cross-binding testing far far easier. Thus another >> part of a GSoC project could be to use the SQlite bindings to establish >> cross-project testing of the BioSQL implementations for consistency. >> At that point I'd be interested from the BioSQL and Biopython side, >> and Biopython may have a few possible co-mentors here. >> >> Anyway, to be viable this project would need a Perl mentor with a >> good knowledge of BioSQL and BioPerl's bindings for it. >> >> Is this worth adding to the BioPerl GSoC as a possible idea? >> http://bioperl.org/wiki/Google_Summer_of_Code#Project_Ideas_for_2013 > > Yes. Will add this now. > >> Regards, >> >> Peter >> (Who doesn't know enough Perl to qualify as a mentor for this) > > There was a reasonable push for this a while back (BOSC in Boston) but nothing came of it code-wise that I have seen. Not sure where it stands now. > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From cjfields at illinois.edu Mon Apr 1 23:21:16 2013 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 2 Apr 2013 03:21:16 +0000 Subject: [BioSQL-l] [Bioperl-l] Google Summer of Code - BioPerl / BioSQL proposal? In-Reply-To: <6B9A2644-9075-486F-977C-86750D88B737@drycafe.net> References: <118F034CF4C3EF48A96F86CE585B94BF74DC9169@CHIMBX5.ad.uillinois.edu> <6B9A2644-9075-486F-977C-86750D88B737@drycafe.net> Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DCAEAE@CHIMBX5.ad.uillinois.edu> Added! http://bioperl.org/wiki/Google_Summer_of_Code http://www.open-bio.org/wiki/Google_Summer_of_Code#Project_ideas chris On Apr 1, 2013, at 11:38 AM, Hilmar Lapp wrote: > Just to add another possibility for a summer project here, Bioperl-db (the BioPerl bindings to BioSQL) in essence constitute a self-made ORM, invented at a time when DBIx::Class didn't exist yet. As such, it has some advantages (if you are willing to count overly clever features to be counted in this category), but arguably many more disadvantages, chief among them being the unsustainably small (you could also say non-existent) developer community supporting it, and the fact that DBIx::Class now has existed for years, and is fairly mature. > > So, rewriting Bioperl-db with a DBIx::Class (or another well-supported generic ORM) would, I think, stand to make a considerable impact on our ability to further develop Bioperl's relational storage capabilities, as well as BioSQL itself. > > And I'd be willing to help out with such a project in a at least a co-mentoring capacity. (If primary mentor, I'd need a committed co-mentor to make it viable.) > > -hilmar > > On Apr 1, 2013, at 10:35 AM, Fields, Christopher J wrote: > >> On Apr 1, 2013, at 9:28 AM, Peter Cock wrote: >> >>> On 18 March 2013 21:26, Christopher Fields wrote: >>>> Just a heads-up, if there are any students interested in the Google Summer of >>>> Code, the Open Bioinformatics Foundation is planning on participating again >>>> this year! Pjotr Prins will be organizing for OBF; all the Bio* projects are >>>> looking for prospective projects. >>>> >>>> We're open for any project ideas this year, so let us know what you would like >>>> to do! >>> >>> I suggested this last year too, but improving support for BioSQL on >>> SQLite would be great - the schema exists and seems to work fine, >>> but is currently only handled by the Biopython BioSQL bindings. >> >> ++++1 >> >>> So, the core of a BioSQL/BioPerl GSoC project could tackle: >>> >>> * Adding SQLite support to the BioSQL scripts for loading taxonomies etc >>> https://github.com/biosql/biosql >>> >>> * Adding SQLite support to BioPerl's BioSQL adapter, bioperl-db >>> https://github.com/bioperl/bioperl-db >>> >>> There are a number of things that could be added to this basic idea >>> to make the project more ambitious and to fill out a full summer. One >>> is to extend this to doing BioSQL on SQLite bindings for BioRuby or >>> BioJava (assuming suitable co-mentors are available). >>> >>> One of the nice things about SQLite compared to MySQL or PostgreSQL >>> is the database is just one binary file on disk which is easily portable and >>> can even be checked into source code control for unit tests. This means >>> we can use it to make cross-binding testing far far easier. Thus another >>> part of a GSoC project could be to use the SQlite bindings to establish >>> cross-project testing of the BioSQL implementations for consistency. >>> At that point I'd be interested from the BioSQL and Biopython side, >>> and Biopython may have a few possible co-mentors here. >>> >>> Anyway, to be viable this project would need a Perl mentor with a >>> good knowledge of BioSQL and BioPerl's bindings for it. >>> >>> Is this worth adding to the BioPerl GSoC as a possible idea? >>> http://bioperl.org/wiki/Google_Summer_of_Code#Project_Ideas_for_2013 >> >> Yes. Will add this now. >> >>> Regards, >>> >>> Peter >>> (Who doesn't know enough Perl to qualify as a mentor for this) >> >> There was a reasonable push for this a while back (BOSC in Boston) but nothing came of it code-wise that I have seen. Not sure where it stands now. >> >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : > =========================================================== > > > > From p.j.a.cock at googlemail.com Tue Apr 9 06:20:43 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 9 Apr 2013 11:20:43 +0100 Subject: [BioSQL-l] OBF not accepted for GSoC 2013 Message-ID: Dear all, Unfortunately this year we have not been accepted on the Google Summer of Code scheme: I'm sure the rest of the OBF board and the other Bio* developers will join me in thanking Pjotr Prins for his efforts as the OBF GSoC administrator co-ordinating our application this year, as well as last year's administrator Rob Bruels and the other mentors for their efforts. For those of you not subscribed to the OBF's GSoC mailing list, I am forwarding Pjotr's email from last night (also below): http://lists.open-bio.org/pipermail/gsoc/2013/000211.html In all 177 organisations were accepted (about the same as the last few years), and they will be listed here (once they have filled out their profile information): https://google-melange.appspot.com/gsoc/accepted_orgs/google/gsoc2013 To potential students this summer, the good news is that some related organisations have been accepted, such as NESCent, the National Resource for Network Biology (NRNB - known for Cytoscape), SciRuby (Ruby Science Foundation), so there is still some scope for doing a bioinformatics related project in GSoC 2013, perhaps even with a Bio* developer as a co-mentor. Thank you all, Peter (Biopython developer, OBF board member) ---------- Forwarded message ---------- From: Pjotr Prins Date: Mon, Apr 8, 2013 at 9:13 PM Subject: Re: GSoC 2013 is ON To: Pjotr Prins Cc: ..., OBF GSoC Sadly, our application got rejected by GSoC this year. I am not sure what the reason was, but I am convinced our application was similar to that of other years. Maybe the project ideas could have been better presented. I am not sure at this stage. I'll make a list of successful projects to see if we can digest some truths. The upside is that FOSS is going strong! And that the field is getting increasingly competitive. As an open source geezer I can only be happy, even if it hurts our own application. Sorry everyone, and many thanks for the trouble you took getting projects written up. Let's not feel discouraged for next year. Pj. From scott at scottcain.net Tue Apr 9 06:57:40 2013 From: scott at scottcain.net (Scott Cain) Date: Tue, 9 Apr 2013 11:57:40 +0100 Subject: [BioSQL-l] [Bioperl-l] OBF not accepted for GSoC 2013 In-Reply-To: References: Message-ID: <3155B235-4068-491C-B611-1117EF1B5C50@scottcain.net> Hi all, I was certainly surprised the the openbio application wasn't accepted; completion must be very tight. I just want to point out another bio project for inclined students: the Genome Informatics project is a GSoC collaboration of several well known projects, including GMOD (chado, gbrowse, jbrowse), Reactome, and Galaxy. For more information, see: http://gmod.org/wiki/GSoC Thanks, Scott Sent from my iPhone On Apr 9, 2013, at 11:20 AM, Peter Cock wrote: > Dear all, > > Unfortunately this year we have not been accepted on the Google > Summer of Code scheme: > > I'm sure the rest of the OBF board and the other Bio* developers > will join me in thanking Pjotr Prins for his efforts as the OBF > GSoC administrator co-ordinating our application this year, as > well as last year's administrator Rob Bruels and the other mentors > for their efforts. > > For those of you not subscribed to the OBF's GSoC mailing list, > I am forwarding Pjotr's email from last night (also below): > http://lists.open-bio.org/pipermail/gsoc/2013/000211.html > > In all 177 organisations were accepted (about the same as the > last few years), and they will be listed here (once they have filled > out their profile information): > https://google-melange.appspot.com/gsoc/accepted_orgs/google/gsoc2013 > > To potential students this summer, the good news is that some > related organisations have been accepted, such as NESCent, > the National Resource for Network Biology (NRNB - known for > Cytoscape), SciRuby (Ruby Science Foundation), so there is > still some scope for doing a bioinformatics related project in > GSoC 2013, perhaps even with a Bio* developer as a co-mentor. > > Thank you all, > > Peter > (Biopython developer, OBF board member) > > ---------- Forwarded message ---------- > From: Pjotr Prins > Date: Mon, Apr 8, 2013 at 9:13 PM > Subject: Re: GSoC 2013 is ON > To: Pjotr Prins > Cc: ..., OBF GSoC > > > Sadly, our application got rejected by GSoC this year. I am not sure > what the reason was, but I am convinced our application was similar to > that of other years. Maybe the project ideas could have been better > presented. I am not sure at this stage. I'll make a list of successful > projects to see if we can digest some truths. > > The upside is that FOSS is going strong! And that the field is getting > increasingly competitive. As an open source geezer I can only be > happy, even if it hurts our own application. > > Sorry everyone, and many thanks for the trouble you took getting > projects written up. Let's not feel discouraged for next year. > > Pj. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From l.m.timmermans at students.uu.nl Tue Apr 9 08:24:24 2013 From: l.m.timmermans at students.uu.nl (Leon Timmermans) Date: Tue, 9 Apr 2013 14:24:24 +0200 Subject: [BioSQL-l] [Bioperl-l] OBF not accepted for GSoC 2013 In-Reply-To: References: Message-ID: On Tue, Apr 9, 2013 at 12:20 PM, Peter Cock wrote: > Sadly, our application got rejected by GSoC this year. I am not sure > what the reason was, but I am convinced our application was similar to > that of other years. Maybe the project ideas could have been better > presented. I am not sure at this stage. I'll make a list of successful > projects to see if we can digest some truths. Something similar happened to The Perl Foundation last year, so we asked them why? We had been a well-performing organization (100% success rate in the preceding year) that put a lot of effort in our submission and had a solid community behind us. The answer was not quite what we expected. It had little to do with the quality of the application, but everything with them wanting new blood in the SOC. The same had happened to other projects I'm told. Leon From p.j.a.cock at googlemail.com Mon Apr 1 14:28:43 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 1 Apr 2013 15:28:43 +0100 Subject: [BioSQL-l] Google Summer of Code - BioPerl / BioSQL proposal? Message-ID: On 18 March 2013 21:26, Christopher Fields wrote: > Just a heads-up, if there are any students interested in the Google Summer of > Code, the Open Bioinformatics Foundation is planning on participating again > this year! Pjotr Prins will be organizing for OBF; all the Bio* projects are > looking for prospective projects. > > We're open for any project ideas this year, so let us know what you would like > to do! I suggested this last year too, but improving support for BioSQL on SQLite would be great - the schema exists and seems to work fine, but is currently only handled by the Biopython BioSQL bindings. So, the core of a BioSQL/BioPerl GSoC project could tackle: * Adding SQLite support to the BioSQL scripts for loading taxonomies etc https://github.com/biosql/biosql * Adding SQLite support to BioPerl's BioSQL adapter, bioperl-db https://github.com/bioperl/bioperl-db There are a number of things that could be added to this basic idea to make the project more ambitious and to fill out a full summer. One is to extend this to doing BioSQL on SQLite bindings for BioRuby or BioJava (assuming suitable co-mentors are available). One of the nice things about SQLite compared to MySQL or PostgreSQL is the database is just one binary file on disk which is easily portable and can even be checked into source code control for unit tests. This means we can use it to make cross-binding testing far far easier. Thus another part of a GSoC project could be to use the SQlite bindings to establish cross-project testing of the BioSQL implementations for consistency. At that point I'd be interested from the BioSQL and Biopython side, and Biopython may have a few possible co-mentors here. Anyway, to be viable this project would need a Perl mentor with a good knowledge of BioSQL and BioPerl's bindings for it. Is this worth adding to the BioPerl GSoC as a possible idea? http://bioperl.org/wiki/Google_Summer_of_Code#Project_Ideas_for_2013 Regards, Peter (Who doesn't know enough Perl to qualify as a mentor for this) From cjfields at illinois.edu Mon Apr 1 14:35:25 2013 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 1 Apr 2013 14:35:25 +0000 Subject: [BioSQL-l] Google Summer of Code - BioPerl / BioSQL proposal? In-Reply-To: References: Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DC9169@CHIMBX5.ad.uillinois.edu> On Apr 1, 2013, at 9:28 AM, Peter Cock wrote: > On 18 March 2013 21:26, Christopher Fields wrote: >> Just a heads-up, if there are any students interested in the Google Summer of >> Code, the Open Bioinformatics Foundation is planning on participating again >> this year! Pjotr Prins will be organizing for OBF; all the Bio* projects are >> looking for prospective projects. >> >> We're open for any project ideas this year, so let us know what you would like >> to do! > > I suggested this last year too, but improving support for BioSQL on > SQLite would be great - the schema exists and seems to work fine, > but is currently only handled by the Biopython BioSQL bindings. ++++1 > So, the core of a BioSQL/BioPerl GSoC project could tackle: > > * Adding SQLite support to the BioSQL scripts for loading taxonomies etc > https://github.com/biosql/biosql > > * Adding SQLite support to BioPerl's BioSQL adapter, bioperl-db > https://github.com/bioperl/bioperl-db > > There are a number of things that could be added to this basic idea > to make the project more ambitious and to fill out a full summer. One > is to extend this to doing BioSQL on SQLite bindings for BioRuby or > BioJava (assuming suitable co-mentors are available). > > One of the nice things about SQLite compared to MySQL or PostgreSQL > is the database is just one binary file on disk which is easily portable and > can even be checked into source code control for unit tests. This means > we can use it to make cross-binding testing far far easier. Thus another > part of a GSoC project could be to use the SQlite bindings to establish > cross-project testing of the BioSQL implementations for consistency. > At that point I'd be interested from the BioSQL and Biopython side, > and Biopython may have a few possible co-mentors here. > > Anyway, to be viable this project would need a Perl mentor with a > good knowledge of BioSQL and BioPerl's bindings for it. > > Is this worth adding to the BioPerl GSoC as a possible idea? > http://bioperl.org/wiki/Google_Summer_of_Code#Project_Ideas_for_2013 Yes. Will add this now. > Regards, > > Peter > (Who doesn't know enough Perl to qualify as a mentor for this) There was a reasonable push for this a while back (BOSC in Boston) but nothing came of it code-wise that I have seen. Not sure where it stands now. chris From hlapp at drycafe.net Mon Apr 1 16:38:46 2013 From: hlapp at drycafe.net (Hilmar Lapp) Date: Mon, 1 Apr 2013 12:38:46 -0400 Subject: [BioSQL-l] [Bioperl-l] Google Summer of Code - BioPerl / BioSQL proposal? In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74DC9169@CHIMBX5.ad.uillinois.edu> References: <118F034CF4C3EF48A96F86CE585B94BF74DC9169@CHIMBX5.ad.uillinois.edu> Message-ID: <6B9A2644-9075-486F-977C-86750D88B737@drycafe.net> Just to add another possibility for a summer project here, Bioperl-db (the BioPerl bindings to BioSQL) in essence constitute a self-made ORM, invented at a time when DBIx::Class didn't exist yet. As such, it has some advantages (if you are willing to count overly clever features to be counted in this category), but arguably many more disadvantages, chief among them being the unsustainably small (you could also say non-existent) developer community supporting it, and the fact that DBIx::Class now has existed for years, and is fairly mature. So, rewriting Bioperl-db with a DBIx::Class (or another well-supported generic ORM) would, I think, stand to make a considerable impact on our ability to further develop Bioperl's relational storage capabilities, as well as BioSQL itself. And I'd be willing to help out with such a project in a at least a co-mentoring capacity. (If primary mentor, I'd need a committed co-mentor to make it viable.) -hilmar On Apr 1, 2013, at 10:35 AM, Fields, Christopher J wrote: > On Apr 1, 2013, at 9:28 AM, Peter Cock wrote: > >> On 18 March 2013 21:26, Christopher Fields wrote: >>> Just a heads-up, if there are any students interested in the Google Summer of >>> Code, the Open Bioinformatics Foundation is planning on participating again >>> this year! Pjotr Prins will be organizing for OBF; all the Bio* projects are >>> looking for prospective projects. >>> >>> We're open for any project ideas this year, so let us know what you would like >>> to do! >> >> I suggested this last year too, but improving support for BioSQL on >> SQLite would be great - the schema exists and seems to work fine, >> but is currently only handled by the Biopython BioSQL bindings. > > ++++1 > >> So, the core of a BioSQL/BioPerl GSoC project could tackle: >> >> * Adding SQLite support to the BioSQL scripts for loading taxonomies etc >> https://github.com/biosql/biosql >> >> * Adding SQLite support to BioPerl's BioSQL adapter, bioperl-db >> https://github.com/bioperl/bioperl-db >> >> There are a number of things that could be added to this basic idea >> to make the project more ambitious and to fill out a full summer. One >> is to extend this to doing BioSQL on SQLite bindings for BioRuby or >> BioJava (assuming suitable co-mentors are available). >> >> One of the nice things about SQLite compared to MySQL or PostgreSQL >> is the database is just one binary file on disk which is easily portable and >> can even be checked into source code control for unit tests. This means >> we can use it to make cross-binding testing far far easier. Thus another >> part of a GSoC project could be to use the SQlite bindings to establish >> cross-project testing of the BioSQL implementations for consistency. >> At that point I'd be interested from the BioSQL and Biopython side, >> and Biopython may have a few possible co-mentors here. >> >> Anyway, to be viable this project would need a Perl mentor with a >> good knowledge of BioSQL and BioPerl's bindings for it. >> >> Is this worth adding to the BioPerl GSoC as a possible idea? >> http://bioperl.org/wiki/Google_Summer_of_Code#Project_Ideas_for_2013 > > Yes. Will add this now. > >> Regards, >> >> Peter >> (Who doesn't know enough Perl to qualify as a mentor for this) > > There was a reasonable push for this a while back (BOSC in Boston) but nothing came of it code-wise that I have seen. Not sure where it stands now. > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From cjfields at illinois.edu Tue Apr 2 03:21:16 2013 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 2 Apr 2013 03:21:16 +0000 Subject: [BioSQL-l] [Bioperl-l] Google Summer of Code - BioPerl / BioSQL proposal? In-Reply-To: <6B9A2644-9075-486F-977C-86750D88B737@drycafe.net> References: <118F034CF4C3EF48A96F86CE585B94BF74DC9169@CHIMBX5.ad.uillinois.edu> <6B9A2644-9075-486F-977C-86750D88B737@drycafe.net> Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74DCAEAE@CHIMBX5.ad.uillinois.edu> Added! http://bioperl.org/wiki/Google_Summer_of_Code http://www.open-bio.org/wiki/Google_Summer_of_Code#Project_ideas chris On Apr 1, 2013, at 11:38 AM, Hilmar Lapp wrote: > Just to add another possibility for a summer project here, Bioperl-db (the BioPerl bindings to BioSQL) in essence constitute a self-made ORM, invented at a time when DBIx::Class didn't exist yet. As such, it has some advantages (if you are willing to count overly clever features to be counted in this category), but arguably many more disadvantages, chief among them being the unsustainably small (you could also say non-existent) developer community supporting it, and the fact that DBIx::Class now has existed for years, and is fairly mature. > > So, rewriting Bioperl-db with a DBIx::Class (or another well-supported generic ORM) would, I think, stand to make a considerable impact on our ability to further develop Bioperl's relational storage capabilities, as well as BioSQL itself. > > And I'd be willing to help out with such a project in a at least a co-mentoring capacity. (If primary mentor, I'd need a committed co-mentor to make it viable.) > > -hilmar > > On Apr 1, 2013, at 10:35 AM, Fields, Christopher J wrote: > >> On Apr 1, 2013, at 9:28 AM, Peter Cock wrote: >> >>> On 18 March 2013 21:26, Christopher Fields wrote: >>>> Just a heads-up, if there are any students interested in the Google Summer of >>>> Code, the Open Bioinformatics Foundation is planning on participating again >>>> this year! Pjotr Prins will be organizing for OBF; all the Bio* projects are >>>> looking for prospective projects. >>>> >>>> We're open for any project ideas this year, so let us know what you would like >>>> to do! >>> >>> I suggested this last year too, but improving support for BioSQL on >>> SQLite would be great - the schema exists and seems to work fine, >>> but is currently only handled by the Biopython BioSQL bindings. >> >> ++++1 >> >>> So, the core of a BioSQL/BioPerl GSoC project could tackle: >>> >>> * Adding SQLite support to the BioSQL scripts for loading taxonomies etc >>> https://github.com/biosql/biosql >>> >>> * Adding SQLite support to BioPerl's BioSQL adapter, bioperl-db >>> https://github.com/bioperl/bioperl-db >>> >>> There are a number of things that could be added to this basic idea >>> to make the project more ambitious and to fill out a full summer. One >>> is to extend this to doing BioSQL on SQLite bindings for BioRuby or >>> BioJava (assuming suitable co-mentors are available). >>> >>> One of the nice things about SQLite compared to MySQL or PostgreSQL >>> is the database is just one binary file on disk which is easily portable and >>> can even be checked into source code control for unit tests. This means >>> we can use it to make cross-binding testing far far easier. Thus another >>> part of a GSoC project could be to use the SQlite bindings to establish >>> cross-project testing of the BioSQL implementations for consistency. >>> At that point I'd be interested from the BioSQL and Biopython side, >>> and Biopython may have a few possible co-mentors here. >>> >>> Anyway, to be viable this project would need a Perl mentor with a >>> good knowledge of BioSQL and BioPerl's bindings for it. >>> >>> Is this worth adding to the BioPerl GSoC as a possible idea? >>> http://bioperl.org/wiki/Google_Summer_of_Code#Project_Ideas_for_2013 >> >> Yes. Will add this now. >> >>> Regards, >>> >>> Peter >>> (Who doesn't know enough Perl to qualify as a mentor for this) >> >> There was a reasonable push for this a while back (BOSC in Boston) but nothing came of it code-wise that I have seen. Not sure where it stands now. >> >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : > =========================================================== > > > > From p.j.a.cock at googlemail.com Tue Apr 9 10:20:43 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 9 Apr 2013 11:20:43 +0100 Subject: [BioSQL-l] OBF not accepted for GSoC 2013 Message-ID: Dear all, Unfortunately this year we have not been accepted on the Google Summer of Code scheme: I'm sure the rest of the OBF board and the other Bio* developers will join me in thanking Pjotr Prins for his efforts as the OBF GSoC administrator co-ordinating our application this year, as well as last year's administrator Rob Bruels and the other mentors for their efforts. For those of you not subscribed to the OBF's GSoC mailing list, I am forwarding Pjotr's email from last night (also below): http://lists.open-bio.org/pipermail/gsoc/2013/000211.html In all 177 organisations were accepted (about the same as the last few years), and they will be listed here (once they have filled out their profile information): https://google-melange.appspot.com/gsoc/accepted_orgs/google/gsoc2013 To potential students this summer, the good news is that some related organisations have been accepted, such as NESCent, the National Resource for Network Biology (NRNB - known for Cytoscape), SciRuby (Ruby Science Foundation), so there is still some scope for doing a bioinformatics related project in GSoC 2013, perhaps even with a Bio* developer as a co-mentor. Thank you all, Peter (Biopython developer, OBF board member) ---------- Forwarded message ---------- From: Pjotr Prins Date: Mon, Apr 8, 2013 at 9:13 PM Subject: Re: GSoC 2013 is ON To: Pjotr Prins Cc: ..., OBF GSoC Sadly, our application got rejected by GSoC this year. I am not sure what the reason was, but I am convinced our application was similar to that of other years. Maybe the project ideas could have been better presented. I am not sure at this stage. I'll make a list of successful projects to see if we can digest some truths. The upside is that FOSS is going strong! And that the field is getting increasingly competitive. As an open source geezer I can only be happy, even if it hurts our own application. Sorry everyone, and many thanks for the trouble you took getting projects written up. Let's not feel discouraged for next year. Pj. From scott at scottcain.net Tue Apr 9 10:57:40 2013 From: scott at scottcain.net (Scott Cain) Date: Tue, 9 Apr 2013 11:57:40 +0100 Subject: [BioSQL-l] [Bioperl-l] OBF not accepted for GSoC 2013 In-Reply-To: References: Message-ID: <3155B235-4068-491C-B611-1117EF1B5C50@scottcain.net> Hi all, I was certainly surprised the the openbio application wasn't accepted; completion must be very tight. I just want to point out another bio project for inclined students: the Genome Informatics project is a GSoC collaboration of several well known projects, including GMOD (chado, gbrowse, jbrowse), Reactome, and Galaxy. For more information, see: http://gmod.org/wiki/GSoC Thanks, Scott Sent from my iPhone On Apr 9, 2013, at 11:20 AM, Peter Cock wrote: > Dear all, > > Unfortunately this year we have not been accepted on the Google > Summer of Code scheme: > > I'm sure the rest of the OBF board and the other Bio* developers > will join me in thanking Pjotr Prins for his efforts as the OBF > GSoC administrator co-ordinating our application this year, as > well as last year's administrator Rob Bruels and the other mentors > for their efforts. > > For those of you not subscribed to the OBF's GSoC mailing list, > I am forwarding Pjotr's email from last night (also below): > http://lists.open-bio.org/pipermail/gsoc/2013/000211.html > > In all 177 organisations were accepted (about the same as the > last few years), and they will be listed here (once they have filled > out their profile information): > https://google-melange.appspot.com/gsoc/accepted_orgs/google/gsoc2013 > > To potential students this summer, the good news is that some > related organisations have been accepted, such as NESCent, > the National Resource for Network Biology (NRNB - known for > Cytoscape), SciRuby (Ruby Science Foundation), so there is > still some scope for doing a bioinformatics related project in > GSoC 2013, perhaps even with a Bio* developer as a co-mentor. > > Thank you all, > > Peter > (Biopython developer, OBF board member) > > ---------- Forwarded message ---------- > From: Pjotr Prins > Date: Mon, Apr 8, 2013 at 9:13 PM > Subject: Re: GSoC 2013 is ON > To: Pjotr Prins > Cc: ..., OBF GSoC > > > Sadly, our application got rejected by GSoC this year. I am not sure > what the reason was, but I am convinced our application was similar to > that of other years. Maybe the project ideas could have been better > presented. I am not sure at this stage. I'll make a list of successful > projects to see if we can digest some truths. > > The upside is that FOSS is going strong! And that the field is getting > increasingly competitive. As an open source geezer I can only be > happy, even if it hurts our own application. > > Sorry everyone, and many thanks for the trouble you took getting > projects written up. Let's not feel discouraged for next year. > > Pj. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From l.m.timmermans at students.uu.nl Tue Apr 9 12:24:24 2013 From: l.m.timmermans at students.uu.nl (Leon Timmermans) Date: Tue, 9 Apr 2013 14:24:24 +0200 Subject: [BioSQL-l] [Bioperl-l] OBF not accepted for GSoC 2013 In-Reply-To: References: Message-ID: On Tue, Apr 9, 2013 at 12:20 PM, Peter Cock wrote: > Sadly, our application got rejected by GSoC this year. I am not sure > what the reason was, but I am convinced our application was similar to > that of other years. Maybe the project ideas could have been better > presented. I am not sure at this stage. I'll make a list of successful > projects to see if we can digest some truths. Something similar happened to The Perl Foundation last year, so we asked them why? We had been a well-performing organization (100% success rate in the preceding year) that put a lot of effort in our submission and had a solid community behind us. The answer was not quite what we expected. It had little to do with the quality of the application, but everything with them wanting new blood in the SOC. The same had happened to other projects I'm told. Leon