January 2013 - Kbase-microcomm - mailman3.cels.anl.gov

Re: [Kbase-MicroComm] plan for tomorrow's call
by Folker Meyer 10 Jan '13

10 Jan '13

Hi Dylan, as discussed in the call, the M5nr currently does not have Pfam directly, but you'd need to use Uniprot (they have Pfam IDs). The FIGfams are only indirectly represented via the SEED subsystem annotations. best, Folker On Jan 10, 2013, at 12:03 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > Great! Can you give us example calls for a Pfam query and a FIGfam query? > > Thanks, > - Dylan > > > On Thu, Jan 10, 2013 at 9:43 AM, Folker Meyer <folker.meyer(a)gmail.com> wrote: > Hi Dylan, > > here is the url in KBase land: > > http://kbase.us/services/communities/sequences/mgm4440036.3?data_type=ontol… > > > On Jan 9, 2013, at 6:59 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > > > hi guys, > > > > for tomorrow, > > > > 1) i'd like to talk about how hard it would be for andreas or jared to add support for FIGfams, Pfam, and TIGRFAM to this method that Jared wrote during the hack-a-thon a year ago: > > > > http://api.metagenomics.anl.gov/sequences/4447970.3/?type=ontology&seq=prot… > > > > also, how hard would it be for andreas / jared to add this method to the KBase CommunitiesAPI? > > > > 2) please give us an update on the processing and access info for the hofmockel data so we can start playing with the biom data for the network analysis with pavel, sergei, and marcin. > > Send an email to Kirsten asking to give you guys access. > > Best, > Folker > > > > > > > > Thu 1/10, 9:30-10:00am PST / 11:30am-12:00pm CST > > 866-740-1260 Code: 4958182# > > > > thanks, > > - dylan > > > > _______________________________________________ > > Kbase-microcomm mailing list > > Kbase-microcomm(a)lists.kbase.us > > https://lists.kbase.us/mailman/listinfo/kbase-microcomm > >

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Re: [Kbase-MicroComm] plan for tomorrow's call
by Dylan Chivian 10 Jan '13

10 Jan '13

Great! Can you give us example calls for a Pfam query and a FIGfam query? Thanks, - Dylan On Thu, Jan 10, 2013 at 9:43 AM, Folker Meyer <folker.meyer(a)gmail.com>wrote: > Hi Dylan, > > here is the url in KBase land: > > > http://kbase.us/services/communities/sequences/mgm4440036.3?data_type=ontol… > > > On Jan 9, 2013, at 6:59 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > > > hi guys, > > > > for tomorrow, > > > > 1) i'd like to talk about how hard it would be for andreas or jared to > add support for FIGfams, Pfam, and TIGRFAM to this method that Jared wrote > during the hack-a-thon a year ago: > > > > > http://api.metagenomics.anl.gov/sequences/4447970.3/?type=ontology&seq=prot… > > > > also, how hard would it be for andreas / jared to add this method to the > KBase CommunitiesAPI? > > > > 2) please give us an update on the processing and access info for the > hofmockel data so we can start playing with the biom data for the network > analysis with pavel, sergei, and marcin. > > Send an email to Kirsten asking to give you guys access. > > Best, > Folker > > > > > > > > Thu 1/10, 9:30-10:00am PST / 11:30am-12:00pm CST > > 866-740-1260 Code: 4958182# > > > > thanks, > > - dylan > > > > _______________________________________________ > > Kbase-microcomm mailing list > > Kbase-microcomm(a)lists.kbase.us > > https://lists.kbase.us/mailman/listinfo/kbase-microcomm > >

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Re: [Kbase-MicroComm] plan for tomorrow's call
by Folker Meyer 10 Jan '13

10 Jan '13

Hi Dylan, here is the url in KBase land: http://kbase.us/services/communities/sequences/mgm4440036.3?data_type=ontol… On Jan 9, 2013, at 6:59 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > hi guys, > > for tomorrow, > > 1) i'd like to talk about how hard it would be for andreas or jared to add support for FIGfams, Pfam, and TIGRFAM to this method that Jared wrote during the hack-a-thon a year ago: > > http://api.metagenomics.anl.gov/sequences/4447970.3/?type=ontology&seq=prot… > > also, how hard would it be for andreas / jared to add this method to the KBase CommunitiesAPI? > > 2) please give us an update on the processing and access info for the hofmockel data so we can start playing with the biom data for the network analysis with pavel, sergei, and marcin. Send an email to Kirsten asking to give you guys access. Best, Folker > > > Thu 1/10, 9:30-10:00am PST / 11:30am-12:00pm CST > 866-740-1260 Code: 4958182# > > thanks, > - dylan > > _______________________________________________ > Kbase-microcomm mailing list > Kbase-microcomm(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/kbase-microcomm

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plan for tomorrow's call
by Dylan Chivian 09 Jan '13

09 Jan '13

hi guys, for tomorrow, 1) i'd like to talk about how hard it would be for andreas or jared to add support for FIGfams, Pfam, and TIGRFAM to this method that Jared wrote during the hack-a-thon a year ago: http://api.metagenomics.anl.gov/sequences/4447970.3/?type=ontology&seq=prot… also, how hard would it be for andreas / jared to add this method to the KBase CommunitiesAPI? 2) please give us an update on the processing and access info for the hofmockel data so we can start playing with the biom data for the network analysis with pavel, sergei, and marcin. Thu 1/10, 9:30-10:00am PST / 11:30am-12:00pm CST 866-740-1260 Code: 4958182# thanks, - dylan

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Re: [Kbase-MicroComm] agenda for tomorrow's call
by marcinjoachimiak＠gmail.com 03 Jan '13

03 Jan '13

Hey Dylan, I'm still out (and now Ania too) but would it be possible for the communities meetings show up on my calendar? I'll send an email about the demo plan later today. marcin On Jan 3, 2013, at 7:59 AM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > i have a bad sore throat so can't participate today. if nothing else, andi and mike, can you talk with one another about gene sequence retrieval by gene family? the leader code is *8074 if you want to use the readytalk line. > > thanks, > - dylan > > > On Wed, Jan 2, 2013 at 2:44 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: >> hi guys, >> >> other than keith (who is not available), who is going to be able to participate in the communities call tomorrow? i'd like to talk about reimplementing the service that determines gene tree subfamily abundance from metagenome reads. there was a method that jared (i believe) wrote at the hack-a-thon last year that we could retrieve read sequences using args metagenome id and gene family id (which gene family types are supported?). does that still exist somewhere, and better yet, how hard would it be to port to andi's communities api? >> >> also, can you send us any 16S and/or WGS metagenomes that have been loaded from the hofmockel runs? be nice to build our methods around those data. >> >> Thu Jan 3rd, 9:30-10:00am PST / 11:30-12:00pm CST >> Readytalk: 866-740-1260 Code: 4958182# >> >> thanks, >> - dylan > > _______________________________________________ > Kbase-microcomm mailing list > Kbase-microcomm(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/kbase-microcomm

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Re: [Kbase-MicroComm] agenda for tomorrow's call
by Michael Sneddon 03 Jan '13

03 Jan '13

Sure. I just logged in to skype, and my id is m.sneddon. On Thu, Jan 3, 2013 at 9:30 AM, Andreas Wilke <wilke(a)mcs.anl.gov> wrote: > Hi Michael, > > I am around but for some reason it does not accept the code. > > Can you try to reach me via Skype? > > Andreas > > Sent en route > > Am Jan 3, 2013 um 11:20 AM schrieb Michael Sneddon <mwsneddon(a)lbl.gov>: > > I'm still thankfully not sick, so I can talk at 9:30 pst. Anyone else > around this morning? > > As Dylan mentioned, the key thing we wanted to discuss is simply how to > use the communities api to retrieve sequences by experiment and gene > family, so perhaps it would be easier if I just discuss this with Andreas > today. > > -michael > > > On Thu, Jan 3, 2013 at 7:59 AM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > >> i have a bad sore throat so can't participate today. if nothing else, >> andi and mike, can you talk with one another about gene sequence retrieval >> by gene family? the leader code is *8074 if you want to use the readytalk >> line. >> >> thanks, >> - dylan >> >> >> On Wed, Jan 2, 2013 at 2:44 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: >> >>> hi guys, >>> >>> other than keith (who is not available), who is going to be able to >>> participate in the communities call tomorrow? i'd like to talk about >>> reimplementing the service that determines gene tree subfamily abundance >>> from metagenome reads. there was a method that jared (i believe) wrote at >>> the hack-a-thon last year that we could retrieve read sequences using args >>> metagenome id and gene family id (which gene family types are supported?). >>> does that still exist somewhere, and better yet, how hard would it be to >>> port to andi's communities api? >>> >>> also, can you send us any 16S and/or WGS metagenomes that have been >>> loaded from the hofmockel runs? be nice to build our methods around those >>> data. >>> >>> Thu Jan 3rd, 9:30-10:00am PST / 11:30-12:00pm CST >>> Readytalk: 866-740-1260 Code: 4958182# >>> >>> thanks, >>> - dylan >>> >>> >> >

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Re: [Kbase-MicroComm] agenda for tomorrow's call
by Andreas Wilke 03 Jan '13

03 Jan '13

Hi Michael, I am around but for some reason it does not accept the code. Can you try to reach me via Skype? Andreas Sent en route Am Jan 3, 2013 um 11:20 AM schrieb Michael Sneddon <mwsneddon(a)lbl.gov>: > I'm still thankfully not sick, so I can talk at 9:30 pst. Anyone else around this morning? > > As Dylan mentioned, the key thing we wanted to discuss is simply how to use the communities api to retrieve sequences by experiment and gene family, so perhaps it would be easier if I just discuss this with Andreas today. > > -michael > > > On Thu, Jan 3, 2013 at 7:59 AM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: >> i have a bad sore throat so can't participate today. if nothing else, andi and mike, can you talk with one another about gene sequence retrieval by gene family? the leader code is *8074 if you want to use the readytalk line. >> >> thanks, >> - dylan >> >> >> On Wed, Jan 2, 2013 at 2:44 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: >>> hi guys, >>> >>> other than keith (who is not available), who is going to be able to participate in the communities call tomorrow? i'd like to talk about reimplementing the service that determines gene tree subfamily abundance from metagenome reads. there was a method that jared (i believe) wrote at the hack-a-thon last year that we could retrieve read sequences using args metagenome id and gene family id (which gene family types are supported?). does that still exist somewhere, and better yet, how hard would it be to port to andi's communities api? >>> >>> also, can you send us any 16S and/or WGS metagenomes that have been loaded from the hofmockel runs? be nice to build our methods around those data. >>> >>> Thu Jan 3rd, 9:30-10:00am PST / 11:30-12:00pm CST >>> Readytalk: 866-740-1260 Code: 4958182# >>> >>> thanks, >>> - dylan >

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Re: [Kbase-MicroComm] agenda for tomorrow's call
by Michael Sneddon 03 Jan '13

03 Jan '13

I'm still thankfully not sick, so I can talk at 9:30 pst. Anyone else around this morning? As Dylan mentioned, the key thing we wanted to discuss is simply how to use the communities api to retrieve sequences by experiment and gene family, so perhaps it would be easier if I just discuss this with Andreas today. -michael On Thu, Jan 3, 2013 at 7:59 AM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > i have a bad sore throat so can't participate today. if nothing else, > andi and mike, can you talk with one another about gene sequence retrieval > by gene family? the leader code is *8074 if you want to use the readytalk > line. > > thanks, > - dylan > > > On Wed, Jan 2, 2013 at 2:44 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > >> hi guys, >> >> other than keith (who is not available), who is going to be able to >> participate in the communities call tomorrow? i'd like to talk about >> reimplementing the service that determines gene tree subfamily abundance >> from metagenome reads. there was a method that jared (i believe) wrote at >> the hack-a-thon last year that we could retrieve read sequences using args >> metagenome id and gene family id (which gene family types are supported?). >> does that still exist somewhere, and better yet, how hard would it be to >> port to andi's communities api? >> >> also, can you send us any 16S and/or WGS metagenomes that have been >> loaded from the hofmockel runs? be nice to build our methods around those >> data. >> >> Thu Jan 3rd, 9:30-10:00am PST / 11:30-12:00pm CST >> Readytalk: 866-740-1260 Code: 4958182# >> >> thanks, >> - dylan >> >> >

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Re: [Kbase-MicroComm] agenda for tomorrow's call
by Dylan Chivian 03 Jan '13

03 Jan '13

i have a bad sore throat so can't participate today. if nothing else, andi and mike, can you talk with one another about gene sequence retrieval by gene family? the leader code is *8074 if you want to use the readytalk line. thanks, - dylan On Wed, Jan 2, 2013 at 2:44 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > hi guys, > > other than keith (who is not available), who is going to be able to > participate in the communities call tomorrow? i'd like to talk about > reimplementing the service that determines gene tree subfamily abundance > from metagenome reads. there was a method that jared (i believe) wrote at > the hack-a-thon last year that we could retrieve read sequences using args > metagenome id and gene family id (which gene family types are supported?). > does that still exist somewhere, and better yet, how hard would it be to > port to andi's communities api? > > also, can you send us any 16S and/or WGS metagenomes that have been loaded > from the hofmockel runs? be nice to build our methods around those data. > > Thu Jan 3rd, 9:30-10:00am PST / 11:30-12:00pm CST > Readytalk: 866-740-1260 Code: 4958182# > > thanks, > - dylan > >

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