From holland at eaglegenomics.com Wed Dec 9 07:07:16 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Wed, 9 Dec 2009 12:07:16 +0000 Subject: [BioSQL-l] Job vacancies Message-ID: Hi there, Apologies for posting job ads to the lists but I think this one is relevant to the members so please forgive me. If you know of anyone that might be interested, could you forward them this job ad? Also if you have any local resources for posting job ads, it would be great if you could put the ad up there as well. Sorry to intrude - I'll leave you in peace again now. :) thanks! Richard 1. Senior Bioinformatics Software Developer (Perl/Ensembl) 2. Senior Bioinformatics Software Developer (Java/Taverna) Eagle Genomics Ltd., Cambridge, UK http://www.eaglegenomics.com/ We are a young and exciting bioinformatics company looking to revolutionise the way in which industry and academia work together. We are based at the heart of Europe's largest biotech cluster in Cambridge, UK. As we expand our client base, we're looking to build a talented and committed team of experts. We are currently looking for TWO top-class developers to work on a wide range of complex projects. Both these roles involve a large element of customer support and so you'll need to be friendly, communicative, and happy to work face-to-face with our customers on a daily basis. You will have had substantial prior experience working in a life science company or research institute. For the Perl/Ensembl role, you will have had extensive experience as a Perl developer and ideally you will have written code or plugins for the Ensembl Genome Browser or used its APIs in your own progams. For the Java/Taverna role you will be an expert Java developer with the ability to rapidly analyse and understand complex systems. Ideally you will have written code or plugins for the Taverna project or written code that makes use of it. For both roles, in addition to your superb technical and customer service skills, you will also: ? be able to communicate clearly and proactively, ? have the ability to quickly translate scientific problems into real software solutions, ? be able to put technical concepts into simple language for end users to understand, ? be able to pick up new skills and techniques in record time, ? work well in a collaborative team environment, ? be creative, innovative, and forward-thinking. You will also have had hands-on experience in at least two of the following: ? SQL query design, ? Open-source bioinformatics toolkits such as BioPerl, BioJava, BioSQL, etc., ? Amazon EC2, ? Workflow/pipeline design, ? System and user documentation, ? Developing user training courses. The successful candidate would be expected to work from our offices near Cambridge, however remote working in the UK/Europe may be considered for exceptional candidates (depending on exact location). We offer a competitive salary and a range of company benefits. To apply, please send your CV and cover letter as PDF documents to jobs @eaglegenomics.com . We are only able to offer positions to EEA citizens and permanent residents, or existing holders of UK Tier 1 migrant visas. No agencies please. Closing date: 8th JANUARY 2010. -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From biopython at maubp.freeserve.co.uk Thu Dec 10 10:03:21 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 10 Dec 2009 15:03:21 +0000 Subject: [BioSQL-l] SQLite support In-Reply-To: <320fb6e00911240907u32dca751ldb488cbc38f0e035@mail.gmail.com> References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com> <320fb6e00812150243w4b0dc223g40abcf684af1ccf5@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> Message-ID: <320fb6e00912100703g4e2b7068jb4fea67df3ebd8a8@mail.gmail.com> On Tue, Nov 24, 2009 at 5:07 PM, Peter wrote: > On Tue, Nov 24, 2009 at 4:36 PM, Chris Fields wrote: >> >> Just want to add that I would like to see SQLite support as well >> (I might even feel the need to implement the necessary bioperl-db bits). > > Excellent :) > Brad and I are hoping to include BioSQL on SQLite support in the imminent release of Biopython 1.53, although we will stress in the release notes that this (and the schema) is still experimental. For this initial release, the user probably still have to manually create the SQLite database - this is something I hope we can make much more user friendly in the subsequent releases of Biopython (taking advantage of the fact the SQLite is included with Python 2.5 onwards, so we can do this without any external dependencies). Peter See also: http://bugzilla.open-bio.org/show_bug.cgi?id=2870 http://bugzilla.open-bio.org/show_bug.cgi?id=2866 From holland at eaglegenomics.com Wed Dec 9 12:07:16 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Wed, 9 Dec 2009 12:07:16 +0000 Subject: [BioSQL-l] Job vacancies Message-ID: Hi there, Apologies for posting job ads to the lists but I think this one is relevant to the members so please forgive me. If you know of anyone that might be interested, could you forward them this job ad? Also if you have any local resources for posting job ads, it would be great if you could put the ad up there as well. Sorry to intrude - I'll leave you in peace again now. :) thanks! Richard 1. Senior Bioinformatics Software Developer (Perl/Ensembl) 2. Senior Bioinformatics Software Developer (Java/Taverna) Eagle Genomics Ltd., Cambridge, UK http://www.eaglegenomics.com/ We are a young and exciting bioinformatics company looking to revolutionise the way in which industry and academia work together. We are based at the heart of Europe's largest biotech cluster in Cambridge, UK. As we expand our client base, we're looking to build a talented and committed team of experts. We are currently looking for TWO top-class developers to work on a wide range of complex projects. Both these roles involve a large element of customer support and so you'll need to be friendly, communicative, and happy to work face-to-face with our customers on a daily basis. You will have had substantial prior experience working in a life science company or research institute. For the Perl/Ensembl role, you will have had extensive experience as a Perl developer and ideally you will have written code or plugins for the Ensembl Genome Browser or used its APIs in your own progams. For the Java/Taverna role you will be an expert Java developer with the ability to rapidly analyse and understand complex systems. Ideally you will have written code or plugins for the Taverna project or written code that makes use of it. For both roles, in addition to your superb technical and customer service skills, you will also: ? be able to communicate clearly and proactively, ? have the ability to quickly translate scientific problems into real software solutions, ? be able to put technical concepts into simple language for end users to understand, ? be able to pick up new skills and techniques in record time, ? work well in a collaborative team environment, ? be creative, innovative, and forward-thinking. You will also have had hands-on experience in at least two of the following: ? SQL query design, ? Open-source bioinformatics toolkits such as BioPerl, BioJava, BioSQL, etc., ? Amazon EC2, ? Workflow/pipeline design, ? System and user documentation, ? Developing user training courses. The successful candidate would be expected to work from our offices near Cambridge, however remote working in the UK/Europe may be considered for exceptional candidates (depending on exact location). We offer a competitive salary and a range of company benefits. To apply, please send your CV and cover letter as PDF documents to jobs @eaglegenomics.com . We are only able to offer positions to EEA citizens and permanent residents, or existing holders of UK Tier 1 migrant visas. No agencies please. Closing date: 8th JANUARY 2010. -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From biopython at maubp.freeserve.co.uk Thu Dec 10 15:03:21 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 10 Dec 2009 15:03:21 +0000 Subject: [BioSQL-l] SQLite support In-Reply-To: <320fb6e00911240907u32dca751ldb488cbc38f0e035@mail.gmail.com> References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com> <320fb6e00812150243w4b0dc223g40abcf684af1ccf5@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> Message-ID: <320fb6e00912100703g4e2b7068jb4fea67df3ebd8a8@mail.gmail.com> On Tue, Nov 24, 2009 at 5:07 PM, Peter wrote: > On Tue, Nov 24, 2009 at 4:36 PM, Chris Fields wrote: >> >> Just want to add that I would like to see SQLite support as well >> (I might even feel the need to implement the necessary bioperl-db bits). > > Excellent :) > Brad and I are hoping to include BioSQL on SQLite support in the imminent release of Biopython 1.53, although we will stress in the release notes that this (and the schema) is still experimental. For this initial release, the user probably still have to manually create the SQLite database - this is something I hope we can make much more user friendly in the subsequent releases of Biopython (taking advantage of the fact the SQLite is included with Python 2.5 onwards, so we can do this without any external dependencies). Peter See also: http://bugzilla.open-bio.org/show_bug.cgi?id=2870 http://bugzilla.open-bio.org/show_bug.cgi?id=2866