From chapmanb at 50mail.com Fri Mar 4 07:38:41 2011 From: chapmanb at 50mail.com (Brad Chapman) Date: Fri, 4 Mar 2011 07:38:41 -0500 Subject: [BioSQL-l] Bioinformatics Open Source Conference (BOSC 2011)--Call for Abstracts Message-ID: <20110304123841.GG27839@sobchak> We invite you to submit an abstract to BOSC 2011! Please forward this message as appropriate, and forgive multiple postings. Call for Abstracts for the 12th Annual Bioinformatics Open Source Conference (BOSC 2011) An ISMB 2011 Special Interest Group (SIG) Dates: July 15-16, 2011 Location: Vienna, Austria Web site: http://www.open-bio.org/wiki/BOSC_2011 Email: bosc at open-bio.org BOSC announcements mailing list: http://lists.open-bio.org/mailman/listinfo/bosc-announce Important Dates: April 18, 2011: Deadline for submitting abstracts to BOSC 2011 May 9, 2011: Notifications of accepted abstracts emailed to corresponding authors July 13-14, 2011: Codefest 2011 programming session (see http://www.open-bio.org/wiki/Codefest_2011 for details) July 15-16, 2011: BOSC 2011 July 17-19, 2011: ISMB 2011 The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form. We invite you to submit abstracts for talks and posters. Sessions include: - Approaches to parallel processing - Cloud-based approaches to improving software and data accessibility - The Semantic Web in open source bioinformatics - Data visualization - Tools for next-generation sequencing - Other Open Source software In addition to the above sessions, there will be a panel discussion about "Meeting the challenges of inter-institutional collaboration". We are also working to arrange a joint session with one of the other ISMB SIGs. Thanks to generous sponsorship from Eagle Genomics and an anonymous donor, we are pleased to announce a competition for three Student Travel Awards for BOSC 2011. Each winner will be awarded $250 to defray the costs of travel to BOSC 2011. For instructions on submitting your abstract, please visit http://www.open-bio.org/wiki/BOSC_2011#Abstract_Submission_Information BOSC 2011 Organizing Committee: Nomi Harris and Peter Rice (co-chairs); Brad Chapman, Peter Cock, Erwin Frise, Darin London, Ron Taylor From hlapp at gmx.net Sun Mar 6 00:45:04 2011 From: hlapp at gmx.net (Hilmar Lapp) Date: Sun, 6 Mar 2011 00:45:04 -0500 Subject: [BioSQL-l] hi Hilmar... re: BIoSQL Phylology module In-Reply-To: References: Message-ID: Hi Richard - sorry, I missed your email among 500 other unread ones that piled up over the past two weeks. One reason why it's always a good idea to post such things to the list :-) (copied here) . Incidentally, someone else pointed out those stale links too just today, and I've fixed them meanwhile. The repository is on Github meanwhile. Let me know if you find one that I've forgotten. It'd be great if we can cross paths again soon - what about your plans for Vienna / BOSC? -hilmar On Feb 28, 2011, at 1:50 AM, Richard Bruskiewich wrote: > Hi Hilmar, > > How are things? We haven't cross paths since the biohackathon in > Tokyo a few years ago... > > I've got a comparative biology project for which I'm wanting to use > the BioSQL schema. Your PhyloDB module would be of interest here, > but the links on the BioSQL wiki at http://www.biosql.org/wiki/Extensions > pointing to http://code.open-bio.org from the BioSQL wiki seem to > be broken. > > Please kindly advise (or, should I be using some other schema?) > > Cheers > Richard > > -- > Richard Bruskiewich, PhD > Senior Scientist, Computational and Systems Biology > Applications Team for Computational Genomics > T.T. Chang Genetic Resources Center > International Rice Research Institute > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From rmb32 at cornell.edu Mon Mar 7 11:38:31 2011 From: rmb32 at cornell.edu (Robert Buels) Date: Mon, 07 Mar 2011 11:38:31 -0500 Subject: [BioSQL-l] Google Summer of Code project ideas Message-ID: <4D750A07.5080704@cornell.edu> Hi all, I'm going to be OBF project admin again this year for Google Summer of code. OBF's application is due later this week, and we need to update our project ideas on the OBF wiki page and on each project's individual wiki pages. So, for each of the OBF projects that wants to do GSoC again this year, please: a.) 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. b.) Update the list of project ideas on the main OBF GSoC page (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match. c.) Let me know via email that you have done so and it's ready for Google to peruse. Please have the updates done, if possible, by this Friday (March 11). The number and quality of the project ideas are part of the evaluation process for whether OBF is accepted as a Summer of Code organization again this year, so let's come up with some good ones. :-) Rob ---- Robert Buels (prospective) 2011 OBF GSoC Organization Admin From rmb32 at cornell.edu Fri Mar 18 15:25:37 2011 From: rmb32 at cornell.edu (Robert Buels) Date: Fri, 18 Mar 2011 15:25:37 -0400 Subject: [BioSQL-l] Google Summer of Code is *ON* for OBF projects! Message-ID: <4D83B1B1.6070509@cornell.edu> Hi all, Great news: Google announced today that the Open Bioinformatics Foundation has been accepted as a mentoring organization for this summer's Google Summer of Code! GSoC is a Google-sponsored student internship program for open-source projects, open to students from around the world (not just US residents). Students are paid a $5000 USD stipend to work as a developer on an open-source project for the summer. For more on GSoC, see GSoC 2011 FAQ at http://bit.ly/hpoz8W Student applications are due April 8, 2011 at 19:00 UTC. Students who are interested in participating should look at the OBF's GSoC page at http://open-bio.org/wiki/Google_Summer_of_Code, which lists project ideas, and whom to contact about applying. For current developers on OBF projects, please consider volunteering to be a mentor if you have not already, and contribute project ideas. Just list your name and project ideas on OBF wiki and on the relevant project's GSoC wiki page. Thanks to all who helped make OBF's application to GSoC a success, and let's have a great, productive summer of code! Rob Buels OBF GSoC 2011 Administrator From rmb32 at cornell.edu Tue Mar 29 17:20:41 2011 From: rmb32 at cornell.edu (Robert Buels) Date: Tue, 29 Mar 2011 14:20:41 -0700 Subject: [BioSQL-l] Announcing OBF Summer of Code - please forward! Message-ID: <4D924D29.3020707@cornell.edu> Hi all, Here's an advertising-ready announcement for OBF's Summer of Code, thanks to Christian Zmasek and Hilmar Lapp for their excellent writing. Student applications are due April 8! Please spread it widely, we need to reach lots of students with it! Rob Buels OBF GSoC 2011 Admin ============================================================ *** Please disseminate widely at your local institutions *** *** including posting to message and job boards, so that *** *** we reach as many students as possible. *** ============================================================ OPEN BIOINFORMATICS FOUNDATION SUMMER OF CODE 2011 Applications due 19:00 UTC, April 8, 2010. http://www.open-bio.org/wiki/Google_Summer_of_Code The Open Bioinformatics Foundation Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for bioinformatics under the mentorship of experienced developers from around the world. The program is the participation of the Open Bioinformatics Foundation (OBF) as a mentoring organization in the Google Summer of Code(tm) (http://code.google.com/soc/). Students successfully completing the 3 month program receive a $5,000 USD stipend, and may work entirely from their home or home institution. Participation is open to students from any country in the world except countries subject to US trade restrictions. Each student will have at least one dedicated mentor to show them the ropes and help them complete their project. The Open Bioinformatics Foundation is particularly seeking students interested in both bioinformatics (computational biology) and software development. Some initial project ideas are listed on the website. These range from Galaxy phylogenetics pipeline development in Biopython to lightweight sequence objects and lazy parsing in BioPerl, a DAS Server for large files on local filesystems, and mapping Java libraries to Perl/Ruby/Python using Biolib+SWIG+JNI. All project ideas are flexible and many can be adjusted in scope to match the skills of the student. We also welcome and encourage students proposing their own project ideas; historically some of the most successful Summer of Code projects are ones proposed by the students themselves. TO APPLY: Apply online at the Google Summer of Code website (http://socghop.appspot.com/), where you will also find GSoC program rules and eligibility requirements. The 12-day application period for students runs from Monday, March 28 through Friday, April 8th, 2011. INQUIRIES: We strongly encourage all interested students to get in touch with us with their ideas as early on as possible. See the OBF GSoC page for contact details. 2011 OBF Summer of Code: http://www.open-bio.org/wiki/Google_Summer_of_Code Google Summer of Code FAQ: http://www.google-melange.com/document/show/gsoc_program/google/gsoc2011/faqs From hlapp at drycafe.net Wed Mar 30 11:55:16 2011 From: hlapp at drycafe.net (Hilmar Lapp) Date: Wed, 30 Mar 2011 11:55:16 -0400 Subject: [BioSQL-l] [Bioperl-l] Difficulty downloading biosql schema In-Reply-To: References: Message-ID: Hi Josh, there is a separate list for BioSQL (copied). Sorry for this mistake in the documentation - the svn server on open-bio.org is no longer active. You can simply download the code (including schema) from GitHub (using "git clone git://github.com/biosql/biosql.git"), or you can download one of the releases (http://www.biosql.org/wiki/Downloads). Let me know if you need more information. -hilmar On Mar 30, 2011, at 11:23 AM, Josh Earl wrote: > > Hello all, > > I'm trying to download the schema for biosql, however, when I run > the command: > svn co svn://code.open-bio.org/biosql/biosql-schema/trunk biosql- > schema > > (as per the instructions @ https://github.com/biosql/biosql/blob/master/INSTALL) > I either get no response, or it times out. I've tried this a couple > of times, the last time was a few weeks ago. Anyone know what's > going on? > > Here's an example error: > svn: Can't connect to host 'code.open-bio.org': Connection timed out > > thanks, > ~josh > > Center for Genomic Sciences > (412)-359-8341 > > > _______________________________________________ > 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 Wed Mar 30 11:54:00 2011 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 30 Mar 2011 10:54:00 -0500 Subject: [BioSQL-l] [Bioperl-l] Difficulty downloading biosql schema In-Reply-To: References: Message-ID: <87CBA000-B964-40DA-BF35-BC229CF24BB6@illinois.edu> BioSQL moved to github a while back: https://github.com/biosql/biosql (this might be better asked on the biosql-l list, which I've cc'd) chris On Mar 30, 2011, at 10:23 AM, Josh Earl wrote: > > Hello all, > > I'm trying to download the schema for biosql, however, when I run the command: > svn co svn://code.open-bio.org/biosql/biosql-schema/trunk biosql-schema > > (as per the instructions @ https://github.com/biosql/biosql/blob/master/INSTALL) > I either get no response, or it times out. I've tried this a couple of times, the last time was a few weeks ago. Anyone know what's going on? > > Here's an example error: > svn: Can't connect to host 'code.open-bio.org': Connection timed out > > thanks, > ~josh > > Center for Genomic Sciences > (412)-359-8341 > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From p.j.a.cock at googlemail.com Wed Mar 30 12:05:08 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 30 Mar 2011 17:05:08 +0100 Subject: [BioSQL-l] [Bioperl-l] Difficulty downloading biosql schema In-Reply-To: References: Message-ID: On Wed, Mar 30, 2011 at 4:55 PM, Peter Cock wrote: > Secondly, the instructions you pointed to are out of date, we'll have to > fix that. Just use git: > > git clone git://github.com/biosql/biosql.git > > Thanks for the heads up! This should work too - just in case the git protocol is blocked by a firewall: git clone https://github.com/bioperl/bioperl-db.git Documentation fixed now, https://github.com/biosql/biosql/commit/253b86f159a812edebd6827a26f162e6bd0d46dc Cheers, Peter From hlapp at drycafe.net Wed Mar 30 12:07:45 2011 From: hlapp at drycafe.net (Hilmar Lapp) Date: Wed, 30 Mar 2011 12:07:45 -0400 Subject: [BioSQL-l] [Bioperl-l] Difficulty downloading biosql schema In-Reply-To: References: Message-ID: <286B0E94-E607-4F7C-AE0C-48374C70CF79@drycafe.net> On Mar 30, 2011, at 12:05 PM, Peter Cock wrote: > Documentation fixed now, > https://github.com/biosql/biosql/commit/253b86f159a812edebd6827a26f162e6bd0d46dc Thanks Peter! -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From chapmanb at 50mail.com Fri Mar 4 12:38:41 2011 From: chapmanb at 50mail.com (Brad Chapman) Date: Fri, 4 Mar 2011 07:38:41 -0500 Subject: [BioSQL-l] Bioinformatics Open Source Conference (BOSC 2011)--Call for Abstracts Message-ID: <20110304123841.GG27839@sobchak> We invite you to submit an abstract to BOSC 2011! Please forward this message as appropriate, and forgive multiple postings. Call for Abstracts for the 12th Annual Bioinformatics Open Source Conference (BOSC 2011) An ISMB 2011 Special Interest Group (SIG) Dates: July 15-16, 2011 Location: Vienna, Austria Web site: http://www.open-bio.org/wiki/BOSC_2011 Email: bosc at open-bio.org BOSC announcements mailing list: http://lists.open-bio.org/mailman/listinfo/bosc-announce Important Dates: April 18, 2011: Deadline for submitting abstracts to BOSC 2011 May 9, 2011: Notifications of accepted abstracts emailed to corresponding authors July 13-14, 2011: Codefest 2011 programming session (see http://www.open-bio.org/wiki/Codefest_2011 for details) July 15-16, 2011: BOSC 2011 July 17-19, 2011: ISMB 2011 The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form. We invite you to submit abstracts for talks and posters. Sessions include: - Approaches to parallel processing - Cloud-based approaches to improving software and data accessibility - The Semantic Web in open source bioinformatics - Data visualization - Tools for next-generation sequencing - Other Open Source software In addition to the above sessions, there will be a panel discussion about "Meeting the challenges of inter-institutional collaboration". We are also working to arrange a joint session with one of the other ISMB SIGs. Thanks to generous sponsorship from Eagle Genomics and an anonymous donor, we are pleased to announce a competition for three Student Travel Awards for BOSC 2011. Each winner will be awarded $250 to defray the costs of travel to BOSC 2011. For instructions on submitting your abstract, please visit http://www.open-bio.org/wiki/BOSC_2011#Abstract_Submission_Information BOSC 2011 Organizing Committee: Nomi Harris and Peter Rice (co-chairs); Brad Chapman, Peter Cock, Erwin Frise, Darin London, Ron Taylor From hlapp at gmx.net Sun Mar 6 05:45:04 2011 From: hlapp at gmx.net (Hilmar Lapp) Date: Sun, 6 Mar 2011 00:45:04 -0500 Subject: [BioSQL-l] hi Hilmar... re: BIoSQL Phylology module In-Reply-To: References: Message-ID: Hi Richard - sorry, I missed your email among 500 other unread ones that piled up over the past two weeks. One reason why it's always a good idea to post such things to the list :-) (copied here) . Incidentally, someone else pointed out those stale links too just today, and I've fixed them meanwhile. The repository is on Github meanwhile. Let me know if you find one that I've forgotten. It'd be great if we can cross paths again soon - what about your plans for Vienna / BOSC? -hilmar On Feb 28, 2011, at 1:50 AM, Richard Bruskiewich wrote: > Hi Hilmar, > > How are things? We haven't cross paths since the biohackathon in > Tokyo a few years ago... > > I've got a comparative biology project for which I'm wanting to use > the BioSQL schema. Your PhyloDB module would be of interest here, > but the links on the BioSQL wiki at http://www.biosql.org/wiki/Extensions > pointing to http://code.open-bio.org from the BioSQL wiki seem to > be broken. > > Please kindly advise (or, should I be using some other schema?) > > Cheers > Richard > > -- > Richard Bruskiewich, PhD > Senior Scientist, Computational and Systems Biology > Applications Team for Computational Genomics > T.T. Chang Genetic Resources Center > International Rice Research Institute > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From rmb32 at cornell.edu Mon Mar 7 16:38:31 2011 From: rmb32 at cornell.edu (Robert Buels) Date: Mon, 07 Mar 2011 11:38:31 -0500 Subject: [BioSQL-l] Google Summer of Code project ideas Message-ID: <4D750A07.5080704@cornell.edu> Hi all, I'm going to be OBF project admin again this year for Google Summer of code. OBF's application is due later this week, and we need to update our project ideas on the OBF wiki page and on each project's individual wiki pages. So, for each of the OBF projects that wants to do GSoC again this year, please: a.) 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. b.) Update the list of project ideas on the main OBF GSoC page (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match. c.) Let me know via email that you have done so and it's ready for Google to peruse. Please have the updates done, if possible, by this Friday (March 11). The number and quality of the project ideas are part of the evaluation process for whether OBF is accepted as a Summer of Code organization again this year, so let's come up with some good ones. :-) Rob ---- Robert Buels (prospective) 2011 OBF GSoC Organization Admin From rmb32 at cornell.edu Fri Mar 18 19:25:37 2011 From: rmb32 at cornell.edu (Robert Buels) Date: Fri, 18 Mar 2011 15:25:37 -0400 Subject: [BioSQL-l] Google Summer of Code is *ON* for OBF projects! Message-ID: <4D83B1B1.6070509@cornell.edu> Hi all, Great news: Google announced today that the Open Bioinformatics Foundation has been accepted as a mentoring organization for this summer's Google Summer of Code! GSoC is a Google-sponsored student internship program for open-source projects, open to students from around the world (not just US residents). Students are paid a $5000 USD stipend to work as a developer on an open-source project for the summer. For more on GSoC, see GSoC 2011 FAQ at http://bit.ly/hpoz8W Student applications are due April 8, 2011 at 19:00 UTC. Students who are interested in participating should look at the OBF's GSoC page at http://open-bio.org/wiki/Google_Summer_of_Code, which lists project ideas, and whom to contact about applying. For current developers on OBF projects, please consider volunteering to be a mentor if you have not already, and contribute project ideas. Just list your name and project ideas on OBF wiki and on the relevant project's GSoC wiki page. Thanks to all who helped make OBF's application to GSoC a success, and let's have a great, productive summer of code! Rob Buels OBF GSoC 2011 Administrator From rmb32 at cornell.edu Tue Mar 29 21:20:41 2011 From: rmb32 at cornell.edu (Robert Buels) Date: Tue, 29 Mar 2011 14:20:41 -0700 Subject: [BioSQL-l] Announcing OBF Summer of Code - please forward! Message-ID: <4D924D29.3020707@cornell.edu> Hi all, Here's an advertising-ready announcement for OBF's Summer of Code, thanks to Christian Zmasek and Hilmar Lapp for their excellent writing. Student applications are due April 8! Please spread it widely, we need to reach lots of students with it! Rob Buels OBF GSoC 2011 Admin ============================================================ *** Please disseminate widely at your local institutions *** *** including posting to message and job boards, so that *** *** we reach as many students as possible. *** ============================================================ OPEN BIOINFORMATICS FOUNDATION SUMMER OF CODE 2011 Applications due 19:00 UTC, April 8, 2010. http://www.open-bio.org/wiki/Google_Summer_of_Code The Open Bioinformatics Foundation Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for bioinformatics under the mentorship of experienced developers from around the world. The program is the participation of the Open Bioinformatics Foundation (OBF) as a mentoring organization in the Google Summer of Code(tm) (http://code.google.com/soc/). Students successfully completing the 3 month program receive a $5,000 USD stipend, and may work entirely from their home or home institution. Participation is open to students from any country in the world except countries subject to US trade restrictions. Each student will have at least one dedicated mentor to show them the ropes and help them complete their project. The Open Bioinformatics Foundation is particularly seeking students interested in both bioinformatics (computational biology) and software development. Some initial project ideas are listed on the website. These range from Galaxy phylogenetics pipeline development in Biopython to lightweight sequence objects and lazy parsing in BioPerl, a DAS Server for large files on local filesystems, and mapping Java libraries to Perl/Ruby/Python using Biolib+SWIG+JNI. All project ideas are flexible and many can be adjusted in scope to match the skills of the student. We also welcome and encourage students proposing their own project ideas; historically some of the most successful Summer of Code projects are ones proposed by the students themselves. TO APPLY: Apply online at the Google Summer of Code website (http://socghop.appspot.com/), where you will also find GSoC program rules and eligibility requirements. The 12-day application period for students runs from Monday, March 28 through Friday, April 8th, 2011. INQUIRIES: We strongly encourage all interested students to get in touch with us with their ideas as early on as possible. See the OBF GSoC page for contact details. 2011 OBF Summer of Code: http://www.open-bio.org/wiki/Google_Summer_of_Code Google Summer of Code FAQ: http://www.google-melange.com/document/show/gsoc_program/google/gsoc2011/faqs From hlapp at drycafe.net Wed Mar 30 15:55:16 2011 From: hlapp at drycafe.net (Hilmar Lapp) Date: Wed, 30 Mar 2011 11:55:16 -0400 Subject: [BioSQL-l] [Bioperl-l] Difficulty downloading biosql schema In-Reply-To: References: Message-ID: Hi Josh, there is a separate list for BioSQL (copied). Sorry for this mistake in the documentation - the svn server on open-bio.org is no longer active. You can simply download the code (including schema) from GitHub (using "git clone git://github.com/biosql/biosql.git"), or you can download one of the releases (http://www.biosql.org/wiki/Downloads). Let me know if you need more information. -hilmar On Mar 30, 2011, at 11:23 AM, Josh Earl wrote: > > Hello all, > > I'm trying to download the schema for biosql, however, when I run > the command: > svn co svn://code.open-bio.org/biosql/biosql-schema/trunk biosql- > schema > > (as per the instructions @ https://github.com/biosql/biosql/blob/master/INSTALL) > I either get no response, or it times out. I've tried this a couple > of times, the last time was a few weeks ago. Anyone know what's > going on? > > Here's an example error: > svn: Can't connect to host 'code.open-bio.org': Connection timed out > > thanks, > ~josh > > Center for Genomic Sciences > (412)-359-8341 > > > _______________________________________________ > 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 Wed Mar 30 15:54:00 2011 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 30 Mar 2011 10:54:00 -0500 Subject: [BioSQL-l] [Bioperl-l] Difficulty downloading biosql schema In-Reply-To: References: Message-ID: <87CBA000-B964-40DA-BF35-BC229CF24BB6@illinois.edu> BioSQL moved to github a while back: https://github.com/biosql/biosql (this might be better asked on the biosql-l list, which I've cc'd) chris On Mar 30, 2011, at 10:23 AM, Josh Earl wrote: > > Hello all, > > I'm trying to download the schema for biosql, however, when I run the command: > svn co svn://code.open-bio.org/biosql/biosql-schema/trunk biosql-schema > > (as per the instructions @ https://github.com/biosql/biosql/blob/master/INSTALL) > I either get no response, or it times out. I've tried this a couple of times, the last time was a few weeks ago. Anyone know what's going on? > > Here's an example error: > svn: Can't connect to host 'code.open-bio.org': Connection timed out > > thanks, > ~josh > > Center for Genomic Sciences > (412)-359-8341 > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From p.j.a.cock at googlemail.com Wed Mar 30 16:05:08 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 30 Mar 2011 17:05:08 +0100 Subject: [BioSQL-l] [Bioperl-l] Difficulty downloading biosql schema In-Reply-To: References: Message-ID: On Wed, Mar 30, 2011 at 4:55 PM, Peter Cock wrote: > Secondly, the instructions you pointed to are out of date, we'll have to > fix that. Just use git: > > git clone git://github.com/biosql/biosql.git > > Thanks for the heads up! This should work too - just in case the git protocol is blocked by a firewall: git clone https://github.com/bioperl/bioperl-db.git Documentation fixed now, https://github.com/biosql/biosql/commit/253b86f159a812edebd6827a26f162e6bd0d46dc Cheers, Peter From hlapp at drycafe.net Wed Mar 30 16:07:45 2011 From: hlapp at drycafe.net (Hilmar Lapp) Date: Wed, 30 Mar 2011 12:07:45 -0400 Subject: [BioSQL-l] [Bioperl-l] Difficulty downloading biosql schema In-Reply-To: References: Message-ID: <286B0E94-E607-4F7C-AE0C-48374C70CF79@drycafe.net> On Mar 30, 2011, at 12:05 PM, Peter Cock wrote: > Documentation fixed now, > https://github.com/biosql/biosql/commit/253b86f159a812edebd6827a26f162e6bd0d46dc Thanks Peter! -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : ===========================================================