From hlapp at drycafe.net Tue Jan 14 18:17:43 2014 From: hlapp at drycafe.net (Hilmar Lapp) Date: Tue, 14 Jan 2014 18:17:43 -0500 Subject: [BioSQL-l] Call for Org Admins for OBF's 2014 Google Summer of Code participation Message-ID: The 2014 Google Summer of Code (GSoC) is coming up soon. The published timeline [1] puts the mentoring organization applications from Feb 3 to 14. OBF participated on behalf of our member projects from 2010-2012, and those participations were both important and successful. Through them, our projects gained new contributors, new features, and new community members. The mentors involved from our projects learned as much from the experience as the students, and formed bonds. The mentoring organization payment allowed OBF to sponsor community events and infrastructure. To participate this year, we have to designate 2-3 people as primary and backup organization administrators. This is an important role, and we are looking for people from our community to step forward to serve. An org admin?s role is in many ways that of a cat herder. The whole team of mentors and admins creates the experience for the students, but it falls on the admin to ?keep it together.? Google holds the mentoring organization, not its mentors, accountable for the actions (or non-actions) of its mentors or community, and it falls on the org admin to carry that accountability through to the org?s mentors. The org admin?s responsibilities include: ? Representing our online face to GSoC, in particular to GSoC students. ? Shepherding our mentoring organization application, and submitting it. ? Working out processes and rules for mentors as well as students that promote transparency, fairness, and protect from late-in-the-game surprises. ? Knowing GSoC rules and processes, and making sure ours are consistent with them. ? Reminding participants of rules, and enforcing them in the event it is necessary. ? Mediating, and sometimes arbitrating between students and mentors when needed. ? Ensuring that GSoC timelines are met by everyone. The person we are looking for will genuinely care about the well-being of our communities, is well organized, stays calm in email storms, communicates clearly, has good people skills, and generally is known as a good listener. If you are interested in helping us out in this role, please email us (by Jan 21, 2014) a statement at board at open-bio.org explaining how you would fit well in this role, and what your vision for our GSoC participation is. You need not be a developer or programmer to respond, but for now we do require that you have been active in some capacity in at least one of our project?s communities. Please include in your email a brief summary of such activities even if you are a core developer for one of our projects. We are looking forward to hearing from you! Hilmar Lapp, OBF President, on behalf of the OBF Board of Directors [1] http://www.google-melange.com/gsoc/events/google/gsoc2014 -- Hilmar Lapp -:- lappland.io From trevorgrahambell at gmail.com Wed Jan 15 02:05:25 2014 From: trevorgrahambell at gmail.com (Trevor Bell) Date: Wed, 15 Jan 2014 09:05:25 +0200 Subject: [BioSQL-l] Co-ordinates Message-ID: I worked through the BioSQL tutorial (http://biopython.org/wiki/BioSQL) and then imported a sequence I am interested in. Consider the following section of the full GenBank record of that sequence: ---------- CDS 155..835 /gene="S" /codon_start=1 /product="S protein" /protein_id="AAP79717.1" /db_xref="GI:32330472" ---------- Where in the database schema can I find the co-ordinates of the gene/protein or the genomic region sequenced? I'm interested in the "155..835" in the example above. I can find the other data in the database (S, AAP79717, etc.). With thanks. -- Dr Trevor G. Bell BSc.(Hons), H.Dip.Ed.(PG), MSc., PhD From trevorgrahambell at gmail.com Wed Jan 15 02:09:02 2014 From: trevorgrahambell at gmail.com (Trevor Bell) Date: Wed, 15 Jan 2014 09:09:02 +0200 Subject: [BioSQL-l] NCBI Taxonomy Message-ID: I have worked through the BioSQL tutorial (http://biopython.org/wiki/BioSQL) successfully. I am now interested in importing sequences from one organism only, which I am interested in. Do I need the NCBI taxonomy? It's a very large amount of data, almost all of which will not be used or relevant? Please advise. Thanks. -- Dr Trevor G. Bell BSc.(Hons), H.Dip.Ed.(PG), MSc., PhD From p.j.a.cock at googlemail.com Wed Jan 15 03:02:47 2014 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 15 Jan 2014 08:02:47 +0000 Subject: [BioSQL-l] NCBI Taxonomy In-Reply-To: References: Message-ID: On Wed, Jan 15, 2014 at 7:09 AM, Trevor Bell wrote: > I have worked through the BioSQL tutorial > (http://biopython.org/wiki/BioSQL) successfully. I am now interested > in importing sequences from one organism only, which I am interested > in. Do I need the NCBI taxonomy? It's a very large amount of data, > almost all of which will not be used or relevant? Please advise. > > Thanks. Hi Trevor, You can perhaps skip it, but you may find this means the organism names are effectively lost on import. The details will depend on which bindings you are using - Biopython can query NCBI Entrez to fetch the specific bits of the NCBI taxonomy needed, giving a gradual/incremental population of the taxonomy tables. Peter From p.j.a.cock at googlemail.com Wed Jan 15 03:05:43 2014 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 15 Jan 2014 08:05:43 +0000 Subject: [BioSQL-l] Co-ordinates In-Reply-To: References: Message-ID: On Wed, Jan 15, 2014 at 7:05 AM, Trevor Bell wrote: > I worked through the BioSQL tutorial > (http://biopython.org/wiki/BioSQL) and then imported a sequence I am > interested in. Consider the following section of the full GenBank > record of that sequence: > > ---------- > CDS 155..835 > /gene="S" > /codon_start=1 > /product="S protein" > /protein_id="AAP79717.1" > /db_xref="GI:32330472" > ---------- > > Where in the database schema can I find the co-ordinates of the > gene/protein or the genomic region sequenced? I'm interested in the > "155..835" in the example above. I can find the other data in the > database (S, AAP79717, etc.). The feature location coordinates are in the location table, http://www.biosql.org/wiki/Schema_Overview#LOCATION The protein ID etc should be in the feature annotation bundle. Peter From trevorgrahambell at gmail.com Wed Jan 15 07:09:13 2014 From: trevorgrahambell at gmail.com (Trevor Bell) Date: Wed, 15 Jan 2014 14:09:13 +0200 Subject: [BioSQL-l] NCBI Taxonomy In-Reply-To: References: Message-ID: Thanks for the reply. I created another test case using the tutorial as before, but did not include the steps to import the NCBI Taxonomy. It worked successfully, and the TAXON table contains the name of the organism from the single sequence I added. On 15 January 2014 10:02, Peter Cock wrote: > On Wed, Jan 15, 2014 at 7:09 AM, Trevor Bell > wrote: > > I have worked through the BioSQL tutorial > > (http://biopython.org/wiki/BioSQL) successfully. I am now interested > > in importing sequences from one organism only, which I am interested > > in. Do I need the NCBI taxonomy? It's a very large amount of data, > > almost all of which will not be used or relevant? Please advise. > > > > Thanks. > > Hi Trevor, > > You can perhaps skip it, but you may find this means > the organism names are effectively lost on import. > The details will depend on which bindings you are > using - Biopython can query NCBI Entrez to fetch > the specific bits of the NCBI taxonomy needed, giving > a gradual/incremental population of the taxonomy > tables. > > Peter > -- Dr Trevor G. Bell BSc.(Hons), H.Dip.Ed.(PG), MSc., PhD From trevorgrahambell at gmail.com Wed Jan 15 07:11:25 2014 From: trevorgrahambell at gmail.com (Trevor Bell) Date: Wed, 15 Jan 2014 14:11:25 +0200 Subject: [BioSQL-l] Co-ordinates In-Reply-To: References: Message-ID: > > The feature location coordinates are in the location table, > http://www.biosql.org/wiki/Schema_Overview#LOCATION > > Of course they are :) Thanks. -- Dr Trevor G. Bell BSc.(Hons), H.Dip.Ed.(PG), MSc., PhD From trevorgrahambell at gmail.com Wed Jan 15 07:47:06 2014 From: trevorgrahambell at gmail.com (Trevor Bell) Date: Wed, 15 Jan 2014 14:47:06 +0200 Subject: [BioSQL-l] Download from GenBank to BioSQL Message-ID: I would like to add a few thousand nucleotide sequences, which match a search phrase, to a BioSQL database. There are obviously many different ways of doing this. What is the "best practice" approach? Is it better to search via the website, download al the full records as a single file, parse this file offline and add to the database, rather than querying the entries one by one and adding them? I'm conscious of the overhead/load on the NCBI servers of fetching thousands of sequences individually. -- Dr Trevor G. Bell BSc.(Hons), H.Dip.Ed.(PG), MSc., PhD From p.j.a.cock at googlemail.com Wed Jan 15 08:45:45 2014 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 15 Jan 2014 13:45:45 +0000 Subject: [BioSQL-l] Download from GenBank to BioSQL In-Reply-To: References: Message-ID: On Wed, Jan 15, 2014 at 12:47 PM, Trevor Bell wrote: > I would like to add a few thousand nucleotide sequences, which match a > search phrase, to a BioSQL database. There are obviously many different > ways of doing this. What is the "best practice" approach? > > Is it better to search via the website, download al the full records as a > single file, parse this file offline and add to the database, rather than > querying the entries one by one and adding them? I'm conscious of the > overhead/load on the NCBI servers of fetching thousands of sequences > individually. Personally I would download GenBank format files from the NCBI using their FTP site if possible (depends on what organism etc you work with) or with the Entrez web API (respecting their usage guidelines, and including a sanity test for complete downloads). If you use Entrez, you can make batch requests (e.g. 100 sequences at a time - adjust depending on the size you're working with, less if whole genomes). Then, separately, I would import the GenBank files into BioSQL. You should be able to do that in BioPerl/Biopython/BioRuby/BioJava. Peter From trevorgrahambell at gmail.com Wed Jan 22 06:42:29 2014 From: trevorgrahambell at gmail.com (Trevor Bell) Date: Wed, 22 Jan 2014 13:42:29 +0200 Subject: [BioSQL-l] Modification Date in LOCUS Message-ID: I've looked through the documentation, but I am unable to determine where the modification date (at the end of the LOCUS) field is imported to into the SQL schema? http://www.biosql.org/wiki/Schema_Overview#BIOENTRY Thanks. -- Dr Trevor G. Bell BSc.(Hons), H.Dip.Ed.(PG), MSc., PhD From roy.chaudhuri at gmail.com Wed Jan 22 06:54:37 2014 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Wed, 22 Jan 2014 11:54:37 +0000 Subject: [BioSQL-l] Modification Date in LOCUS In-Reply-To: References: Message-ID: <52DFB17D.6040108@gmail.com> Hi Trevor, They are in bioentry_qualfier_value with the name "date_changed". Cheers, Roy. On 22/01/14 11:42, Trevor Bell wrote: > I've looked through the documentation, but I am unable to determine where > the modification date (at the end of the LOCUS) field is imported to into > the SQL schema? > > http://www.biosql.org/wiki/Schema_Overview#BIOENTRY > > Thanks. > From trevorgrahambell at gmail.com Wed Jan 22 06:57:45 2014 From: trevorgrahambell at gmail.com (Trevor Bell) Date: Wed, 22 Jan 2014 13:57:45 +0200 Subject: [BioSQL-l] Modification Date in LOCUS In-Reply-To: <52DFB17D.6040108@gmail.com> References: <52DFB17D.6040108@gmail.com> Message-ID: Thanks Roy. On 22 January 2014 13:54, Roy Chaudhuri wrote: > Hi Trevor, > > They are in bioentry_qualfier_value with the name "date_changed". > > Cheers, > Roy. > > > On 22/01/14 11:42, Trevor Bell wrote: > >> I've looked through the documentation, but I am unable to determine where >> the modification date (at the end of the LOCUS) field is imported to into >> the SQL schema? >> >> http://www.biosql.org/wiki/Schema_Overview#BIOENTRY >> >> Thanks. >> >> > -- Dr Trevor G. Bell BSc.(Hons), H.Dip.Ed.(PG), MSc., PhD From hlapp at drycafe.net Wed Jan 22 14:33:40 2014 From: hlapp at drycafe.net (Hilmar Lapp) Date: Wed, 22 Jan 2014 14:33:40 -0500 Subject: [BioSQL-l] Fwd: Call for Org Admins for OBF's 2014 Google Summer of Code participation References: Message-ID: <7F0887E5-482C-4310-A842-68ADD8ED6175@drycafe.net> FYI, we are extending the deadline for responding to this Saturday, January 25. Also, in case this wasn't clear from the text, this isn't a pro forma solicitation. There is no plan B. If we don't receive qualified applications by the deadline, OBF will not apply this year as a mentoring organization. -hilmar Begin forwarded message: From: Hilmar Lapp Subject: Call for Org Admins for OBF's 2014 Google Summer of Code participation Date: January 14, 2014 6:16:02 PM EST To: BioPerl List The 2014 Google Summer of Code (GSoC) is coming up soon. The published timeline [1] puts the mentoring organization applications from Feb 3 to 14. OBF participated on behalf of our member projects from 2010-2012, and those participations were both important and successful. Through them, our projects gained new contributors, new features, and new community members. The mentors involved from our projects learned as much from the experience as the students, and formed bonds. The mentoring organization payment allowed OBF to sponsor community events and infrastructure. To participate this year, we have to designate 2-3 people as primary and backup organization administrators. This is an important role, and we are looking for people from our community to step forward to serve. An org admin?s role is in many ways that of a cat herder. The whole team of mentors and admins creates the experience for the students, but it falls on the admin to ?keep it together.? Google holds the mentoring organization, not its mentors, accountable for the actions (or non-actions) of its mentors or community, and it falls on the org admin to carry that accountability through to the org?s mentors. The org admin?s responsibilities include: ? Representing our online face to GSoC, in particular to GSoC students. ? Shepherding our mentoring organization application, and submitting it. ? Working out processes and rules for mentors as well as students that promote transparency, fairness, and protect from late-in-the-game surprises. ? Knowing GSoC rules and processes, and making sure ours are consistent with them. ? Reminding participants of rules, and enforcing them in the event it is necessary. ? Mediating, and sometimes arbitrating between students and mentors when needed. ? Ensuring that GSoC timelines are met by everyone. The person we are looking for will genuinely care about the well-being of our communities, is well organized, stays calm in email storms, communicates clearly, has good people skills, and generally is known as a good listener. If you are interested in helping us out in this role, please email us (by Jan 21, 2014) a statement at board at open-bio.org explaining how you would fit well in this role, and what your vision for our GSoC participation is. You need not be a developer or programmer to respond, but for now we do require that you have been active in some capacity in at least one of our project?s communities. Please include in your email a brief summary of such activities even if you are a core developer for one of our projects. We are looking forward to hearing from you! Hilmar Lapp, OBF President, on behalf of the OBF Board of Directors [1] http://www.google-melange.com/gsoc/events/google/gsoc2014 -- Hilmar Lapp -:- lappland.io From hlapp at drycafe.net Tue Jan 14 23:17:43 2014 From: hlapp at drycafe.net (Hilmar Lapp) Date: Tue, 14 Jan 2014 18:17:43 -0500 Subject: [BioSQL-l] Call for Org Admins for OBF's 2014 Google Summer of Code participation Message-ID: The 2014 Google Summer of Code (GSoC) is coming up soon. The published timeline [1] puts the mentoring organization applications from Feb 3 to 14. OBF participated on behalf of our member projects from 2010-2012, and those participations were both important and successful. Through them, our projects gained new contributors, new features, and new community members. The mentors involved from our projects learned as much from the experience as the students, and formed bonds. The mentoring organization payment allowed OBF to sponsor community events and infrastructure. To participate this year, we have to designate 2-3 people as primary and backup organization administrators. This is an important role, and we are looking for people from our community to step forward to serve. An org admin?s role is in many ways that of a cat herder. The whole team of mentors and admins creates the experience for the students, but it falls on the admin to ?keep it together.? Google holds the mentoring organization, not its mentors, accountable for the actions (or non-actions) of its mentors or community, and it falls on the org admin to carry that accountability through to the org?s mentors. The org admin?s responsibilities include: ? Representing our online face to GSoC, in particular to GSoC students. ? Shepherding our mentoring organization application, and submitting it. ? Working out processes and rules for mentors as well as students that promote transparency, fairness, and protect from late-in-the-game surprises. ? Knowing GSoC rules and processes, and making sure ours are consistent with them. ? Reminding participants of rules, and enforcing them in the event it is necessary. ? Mediating, and sometimes arbitrating between students and mentors when needed. ? Ensuring that GSoC timelines are met by everyone. The person we are looking for will genuinely care about the well-being of our communities, is well organized, stays calm in email storms, communicates clearly, has good people skills, and generally is known as a good listener. If you are interested in helping us out in this role, please email us (by Jan 21, 2014) a statement at board at open-bio.org explaining how you would fit well in this role, and what your vision for our GSoC participation is. You need not be a developer or programmer to respond, but for now we do require that you have been active in some capacity in at least one of our project?s communities. Please include in your email a brief summary of such activities even if you are a core developer for one of our projects. We are looking forward to hearing from you! Hilmar Lapp, OBF President, on behalf of the OBF Board of Directors [1] http://www.google-melange.com/gsoc/events/google/gsoc2014 -- Hilmar Lapp -:- lappland.io From trevorgrahambell at gmail.com Wed Jan 15 07:05:25 2014 From: trevorgrahambell at gmail.com (Trevor Bell) Date: Wed, 15 Jan 2014 09:05:25 +0200 Subject: [BioSQL-l] Co-ordinates Message-ID: I worked through the BioSQL tutorial (http://biopython.org/wiki/BioSQL) and then imported a sequence I am interested in. Consider the following section of the full GenBank record of that sequence: ---------- CDS 155..835 /gene="S" /codon_start=1 /product="S protein" /protein_id="AAP79717.1" /db_xref="GI:32330472" ---------- Where in the database schema can I find the co-ordinates of the gene/protein or the genomic region sequenced? I'm interested in the "155..835" in the example above. I can find the other data in the database (S, AAP79717, etc.). With thanks. -- Dr Trevor G. Bell BSc.(Hons), H.Dip.Ed.(PG), MSc., PhD From trevorgrahambell at gmail.com Wed Jan 15 07:09:02 2014 From: trevorgrahambell at gmail.com (Trevor Bell) Date: Wed, 15 Jan 2014 09:09:02 +0200 Subject: [BioSQL-l] NCBI Taxonomy Message-ID: I have worked through the BioSQL tutorial (http://biopython.org/wiki/BioSQL) successfully. I am now interested in importing sequences from one organism only, which I am interested in. Do I need the NCBI taxonomy? It's a very large amount of data, almost all of which will not be used or relevant? Please advise. Thanks. -- Dr Trevor G. Bell BSc.(Hons), H.Dip.Ed.(PG), MSc., PhD From p.j.a.cock at googlemail.com Wed Jan 15 08:02:47 2014 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 15 Jan 2014 08:02:47 +0000 Subject: [BioSQL-l] NCBI Taxonomy In-Reply-To: References: Message-ID: On Wed, Jan 15, 2014 at 7:09 AM, Trevor Bell wrote: > I have worked through the BioSQL tutorial > (http://biopython.org/wiki/BioSQL) successfully. I am now interested > in importing sequences from one organism only, which I am interested > in. Do I need the NCBI taxonomy? It's a very large amount of data, > almost all of which will not be used or relevant? Please advise. > > Thanks. Hi Trevor, You can perhaps skip it, but you may find this means the organism names are effectively lost on import. The details will depend on which bindings you are using - Biopython can query NCBI Entrez to fetch the specific bits of the NCBI taxonomy needed, giving a gradual/incremental population of the taxonomy tables. Peter From p.j.a.cock at googlemail.com Wed Jan 15 08:05:43 2014 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 15 Jan 2014 08:05:43 +0000 Subject: [BioSQL-l] Co-ordinates In-Reply-To: References: Message-ID: On Wed, Jan 15, 2014 at 7:05 AM, Trevor Bell wrote: > I worked through the BioSQL tutorial > (http://biopython.org/wiki/BioSQL) and then imported a sequence I am > interested in. Consider the following section of the full GenBank > record of that sequence: > > ---------- > CDS 155..835 > /gene="S" > /codon_start=1 > /product="S protein" > /protein_id="AAP79717.1" > /db_xref="GI:32330472" > ---------- > > Where in the database schema can I find the co-ordinates of the > gene/protein or the genomic region sequenced? I'm interested in the > "155..835" in the example above. I can find the other data in the > database (S, AAP79717, etc.). The feature location coordinates are in the location table, http://www.biosql.org/wiki/Schema_Overview#LOCATION The protein ID etc should be in the feature annotation bundle. Peter From trevorgrahambell at gmail.com Wed Jan 15 12:09:13 2014 From: trevorgrahambell at gmail.com (Trevor Bell) Date: Wed, 15 Jan 2014 14:09:13 +0200 Subject: [BioSQL-l] NCBI Taxonomy In-Reply-To: References: Message-ID: Thanks for the reply. I created another test case using the tutorial as before, but did not include the steps to import the NCBI Taxonomy. It worked successfully, and the TAXON table contains the name of the organism from the single sequence I added. On 15 January 2014 10:02, Peter Cock wrote: > On Wed, Jan 15, 2014 at 7:09 AM, Trevor Bell > wrote: > > I have worked through the BioSQL tutorial > > (http://biopython.org/wiki/BioSQL) successfully. I am now interested > > in importing sequences from one organism only, which I am interested > > in. Do I need the NCBI taxonomy? It's a very large amount of data, > > almost all of which will not be used or relevant? Please advise. > > > > Thanks. > > Hi Trevor, > > You can perhaps skip it, but you may find this means > the organism names are effectively lost on import. > The details will depend on which bindings you are > using - Biopython can query NCBI Entrez to fetch > the specific bits of the NCBI taxonomy needed, giving > a gradual/incremental population of the taxonomy > tables. > > Peter > -- Dr Trevor G. Bell BSc.(Hons), H.Dip.Ed.(PG), MSc., PhD From trevorgrahambell at gmail.com Wed Jan 15 12:11:25 2014 From: trevorgrahambell at gmail.com (Trevor Bell) Date: Wed, 15 Jan 2014 14:11:25 +0200 Subject: [BioSQL-l] Co-ordinates In-Reply-To: References: Message-ID: > > The feature location coordinates are in the location table, > http://www.biosql.org/wiki/Schema_Overview#LOCATION > > Of course they are :) Thanks. -- Dr Trevor G. Bell BSc.(Hons), H.Dip.Ed.(PG), MSc., PhD From trevorgrahambell at gmail.com Wed Jan 15 12:47:06 2014 From: trevorgrahambell at gmail.com (Trevor Bell) Date: Wed, 15 Jan 2014 14:47:06 +0200 Subject: [BioSQL-l] Download from GenBank to BioSQL Message-ID: I would like to add a few thousand nucleotide sequences, which match a search phrase, to a BioSQL database. There are obviously many different ways of doing this. What is the "best practice" approach? Is it better to search via the website, download al the full records as a single file, parse this file offline and add to the database, rather than querying the entries one by one and adding them? I'm conscious of the overhead/load on the NCBI servers of fetching thousands of sequences individually. -- Dr Trevor G. Bell BSc.(Hons), H.Dip.Ed.(PG), MSc., PhD From p.j.a.cock at googlemail.com Wed Jan 15 13:45:45 2014 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 15 Jan 2014 13:45:45 +0000 Subject: [BioSQL-l] Download from GenBank to BioSQL In-Reply-To: References: Message-ID: On Wed, Jan 15, 2014 at 12:47 PM, Trevor Bell wrote: > I would like to add a few thousand nucleotide sequences, which match a > search phrase, to a BioSQL database. There are obviously many different > ways of doing this. What is the "best practice" approach? > > Is it better to search via the website, download al the full records as a > single file, parse this file offline and add to the database, rather than > querying the entries one by one and adding them? I'm conscious of the > overhead/load on the NCBI servers of fetching thousands of sequences > individually. Personally I would download GenBank format files from the NCBI using their FTP site if possible (depends on what organism etc you work with) or with the Entrez web API (respecting their usage guidelines, and including a sanity test for complete downloads). If you use Entrez, you can make batch requests (e.g. 100 sequences at a time - adjust depending on the size you're working with, less if whole genomes). Then, separately, I would import the GenBank files into BioSQL. You should be able to do that in BioPerl/Biopython/BioRuby/BioJava. Peter From trevorgrahambell at gmail.com Wed Jan 22 11:42:29 2014 From: trevorgrahambell at gmail.com (Trevor Bell) Date: Wed, 22 Jan 2014 13:42:29 +0200 Subject: [BioSQL-l] Modification Date in LOCUS Message-ID: I've looked through the documentation, but I am unable to determine where the modification date (at the end of the LOCUS) field is imported to into the SQL schema? http://www.biosql.org/wiki/Schema_Overview#BIOENTRY Thanks. -- Dr Trevor G. Bell BSc.(Hons), H.Dip.Ed.(PG), MSc., PhD From roy.chaudhuri at gmail.com Wed Jan 22 11:54:37 2014 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Wed, 22 Jan 2014 11:54:37 +0000 Subject: [BioSQL-l] Modification Date in LOCUS In-Reply-To: References: Message-ID: <52DFB17D.6040108@gmail.com> Hi Trevor, They are in bioentry_qualfier_value with the name "date_changed". Cheers, Roy. On 22/01/14 11:42, Trevor Bell wrote: > I've looked through the documentation, but I am unable to determine where > the modification date (at the end of the LOCUS) field is imported to into > the SQL schema? > > http://www.biosql.org/wiki/Schema_Overview#BIOENTRY > > Thanks. > From trevorgrahambell at gmail.com Wed Jan 22 11:57:45 2014 From: trevorgrahambell at gmail.com (Trevor Bell) Date: Wed, 22 Jan 2014 13:57:45 +0200 Subject: [BioSQL-l] Modification Date in LOCUS In-Reply-To: <52DFB17D.6040108@gmail.com> References: <52DFB17D.6040108@gmail.com> Message-ID: Thanks Roy. On 22 January 2014 13:54, Roy Chaudhuri wrote: > Hi Trevor, > > They are in bioentry_qualfier_value with the name "date_changed". > > Cheers, > Roy. > > > On 22/01/14 11:42, Trevor Bell wrote: > >> I've looked through the documentation, but I am unable to determine where >> the modification date (at the end of the LOCUS) field is imported to into >> the SQL schema? >> >> http://www.biosql.org/wiki/Schema_Overview#BIOENTRY >> >> Thanks. >> >> > -- Dr Trevor G. Bell BSc.(Hons), H.Dip.Ed.(PG), MSc., PhD From hlapp at drycafe.net Wed Jan 22 19:33:40 2014 From: hlapp at drycafe.net (Hilmar Lapp) Date: Wed, 22 Jan 2014 14:33:40 -0500 Subject: [BioSQL-l] Fwd: Call for Org Admins for OBF's 2014 Google Summer of Code participation References: Message-ID: <7F0887E5-482C-4310-A842-68ADD8ED6175@drycafe.net> FYI, we are extending the deadline for responding to this Saturday, January 25. Also, in case this wasn't clear from the text, this isn't a pro forma solicitation. There is no plan B. If we don't receive qualified applications by the deadline, OBF will not apply this year as a mentoring organization. -hilmar Begin forwarded message: From: Hilmar Lapp Subject: Call for Org Admins for OBF's 2014 Google Summer of Code participation Date: January 14, 2014 6:16:02 PM EST To: BioPerl List The 2014 Google Summer of Code (GSoC) is coming up soon. The published timeline [1] puts the mentoring organization applications from Feb 3 to 14. OBF participated on behalf of our member projects from 2010-2012, and those participations were both important and successful. Through them, our projects gained new contributors, new features, and new community members. The mentors involved from our projects learned as much from the experience as the students, and formed bonds. The mentoring organization payment allowed OBF to sponsor community events and infrastructure. To participate this year, we have to designate 2-3 people as primary and backup organization administrators. This is an important role, and we are looking for people from our community to step forward to serve. An org admin?s role is in many ways that of a cat herder. The whole team of mentors and admins creates the experience for the students, but it falls on the admin to ?keep it together.? Google holds the mentoring organization, not its mentors, accountable for the actions (or non-actions) of its mentors or community, and it falls on the org admin to carry that accountability through to the org?s mentors. The org admin?s responsibilities include: ? Representing our online face to GSoC, in particular to GSoC students. ? Shepherding our mentoring organization application, and submitting it. ? Working out processes and rules for mentors as well as students that promote transparency, fairness, and protect from late-in-the-game surprises. ? Knowing GSoC rules and processes, and making sure ours are consistent with them. ? Reminding participants of rules, and enforcing them in the event it is necessary. ? Mediating, and sometimes arbitrating between students and mentors when needed. ? Ensuring that GSoC timelines are met by everyone. The person we are looking for will genuinely care about the well-being of our communities, is well organized, stays calm in email storms, communicates clearly, has good people skills, and generally is known as a good listener. If you are interested in helping us out in this role, please email us (by Jan 21, 2014) a statement at board at open-bio.org explaining how you would fit well in this role, and what your vision for our GSoC participation is. You need not be a developer or programmer to respond, but for now we do require that you have been active in some capacity in at least one of our project?s communities. Please include in your email a brief summary of such activities even if you are a core developer for one of our projects. We are looking forward to hearing from you! Hilmar Lapp, OBF President, on behalf of the OBF Board of Directors [1] http://www.google-melange.com/gsoc/events/google/gsoc2014 -- Hilmar Lapp -:- lappland.io