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

Re: [Kbase-MicroComm] do we need a call today?
by Folker Meyer 31 Jan '13

31 Jan '13

lets cancel On Jan 31, 2013, at 10:36 AM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > I just need to keep corresponding with Andreas by email. Are there other topics that need a phone call? Otherwise I suggest we cancel the call. > > Thanks, > - Dylan > > _______________________________________________ > Kbase-microcomm mailing list > Kbase-microcomm(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/kbase-microcomm

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do we need a call today?
by Dylan Chivian 31 Jan '13

31 Jan '13

I just need to keep corresponding with Andreas by email. Are there other topics that need a phone call? Otherwise I suggest we cancel the call. Thanks, - Dylan

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Re: [Kbase-MicroComm] call tomorrow?
by Andreas Wilke 24 Jan '13

24 Jan '13

Hi Dylan, ok, but ping me if you have questions. Andreas On Jan 24, 2013, at 1:28 AM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > hi all, > > there's nothing I need to discuss right now that needs the phone. anyone else? otherwise let's cancel the call and use email for any issues that arise. > > thanks, > - dylan > > _______________________________________________ > Kbase-microcomm mailing list > Kbase-microcomm(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/kbase-microcomm

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call tomorrow?
by Dylan Chivian 24 Jan '13

24 Jan '13

hi all, there's nothing I need to discuss right now that needs the phone. anyone else? otherwise let's cancel the call and use email for any issues that arise. thanks, - dylan

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no call tomorrow
by Dylan Chivian 16 Jan '13

16 Jan '13

I have to bring my boys to the pediatrician in the morning. thanks, - dylan

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Re: [Kbase-MicroComm] [Kbase-devel] [Microbe] Blast Services for KBase
by Folker Meyer 10 Jan '13

10 Jan '13

we have >20 TBp of data..... experience shows this is kind of hard to re-analyze..... and takes some time On Jan 10, 2013, at 3:03 PM, Rick stevens <stevens(a)anl.gov> wrote: > Why can it be updated only once a year ? > > Sent from my iPad > > On Jan 10, 2013, at 3:57 PM, Folker Meyer <folker(a)anl.gov> wrote: > >> I see your point, but the underlying requirements for communities are such that we can only update once a year. AND we need to be able to support other namespaces.... >> >> can we subject the other areas to the only one update per year requirement? >> >> Best, >> Folker >> On Jan 10, 2013, at 2:37 PM, Rick stevens <stevens(a)anl.gov> wrote: >> >>> We need a coherent NR for KBase. >>> >>> Not one for microbes and one for communities. >>> >>> >>> Sent from my iPad >>> >>> On Jan 10, 2013, at 3:24 PM, Folker Meyer <folker(a)anl.gov> wrote: >>> >>>> Dylan, >>>> >>>> good idea. actually this is a great service for people wanting to search metagenomes, I encourage you to build it. >>>> >>>> It should do exactly what you suggest: >>>> >>>> - any sequence input is searched against the m5nr >>>> - retrieve md5s for the m5nr entries >>>> - retrieve list of metagenome_IDs that this md5 is present in >>>> - find any sequences matching the md5s in your metagenome(s) of choice with very loose cut-offs >>>> - re-run a BLAST(?) or some other search on the sequence set and return things that hit for real with good (strict) cut-offs. >>>> >>>> We will have to implement an Md5->metagenome_ID function (we can do that if you decide to go for this) >>>> >>>> I think this would be an excellent service to offer, it might be resource constraining, but this is definitely something that a lot of users have asked for in the past. >>>> >>>> Best, >>>> Folker >>>> >>>> >>>> On Jan 10, 2013, at 12:07 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: >>>> >>>>> ... and what about searching metagenomic sequence? (i'd wink, but it's not funny) >>>>> >>>>> since these guys use the m5nr, we could expand any hit from a query sequence to an m5nr sequence into the mg reads that are close to the m5nr exemplar. just a thought. any other ideas? >>>>> >>>>> thanks, >>>>> - dylan >>>>> >>>>> >>>>> On Wed, Jan 9, 2013 at 8:55 PM, Christopher Henry <chrisshenry(a)gmail.com> wrote: >>>>> Well, it's a fair question. >>>>> >>>>> First, we are going to have users, like me, who specifically want to run specific BLAST queries for specific reasons. For that, I think we need a BLAST server. I for one want a blast query to look for specific sequence without having to worry about whether or not the gene callers missed this gene. In particular, this is something we are speculating is a universal gene, and so for the genomes where we don't find it already, we want to do a REALLY thorough search. Does this make sense? So I was thinking TBlastN is what I want… even if it is painfully slow and inefficient… it's to meet this very specific need… and I won't be using it to process a ton of sequence. Just query 10 or so diverse versions for this protein. >>>>> >>>>> I posit… given the increasing drive towards protein speculation and resolving more challenging problems in annotation, this is going to be a common use scenario. >>>>> >>>>> Second, it's completely fair to say we need a service that says "I have a sequence that I want to find what KB knows about". It's a separate use scenario in my mind. It's almost a search query, and the sim service is darn close to being able to handle this particular use scenario. >>>>> >>>>> On Jan 9, 2013, at 2:43 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: >>>>> >>>>>> Do we really mean "BLAST" in particular, or is the problem really "I have sequence that I want to find what KB knows about" ? >>>>>> >>>>>> On Jan 9, 2013, at 2:41 PM, Shreyas Cholia wrote: >>>>>> >>>>>>> OK - that was some serious redundancy, but I think you catch my drift. >>>>>>> >>>>>>> application specific syntactic sugar for specific apps. >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Kbase-devel mailing list >>>>>>> Kbase-devel(a)lists.kbase.us >>>>>>> https://lists.kbase.us/mailman/listinfo/kbase-devel >>>>>> >>>>>> _______________________________________________ >>>>>> Kbase-devel mailing list >>>>>> Kbase-devel(a)lists.kbase.us >>>>>> https://lists.kbase.us/mailman/listinfo/kbase-devel >>>>> >>>>> _______________________________________________ >>>>> Kbase-devel mailing list >>>>> Kbase-devel(a)lists.kbase.us >>>>> https://lists.kbase.us/mailman/listinfo/kbase-devel >>>> >>>> _______________________________________________ >>>> Kbase-microcomm mailing list >>>> Kbase-microcomm(a)lists.kbase.us >>>> https://lists.kbase.us/mailman/listinfo/kbase-microcomm >> > _______________________________________________ > 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] [Kbase-devel] [Microbe] Blast Services for KBase
by Rick stevens 10 Jan '13

10 Jan '13

Why can it be updated only once a year ? Sent from my iPad On Jan 10, 2013, at 3:57 PM, Folker Meyer <folker(a)anl.gov> wrote: > I see your point, but the underlying requirements for communities are such that we can only update once a year. AND we need to be able to support other namespaces.... > > can we subject the other areas to the only one update per year requirement? > > Best, > Folker > On Jan 10, 2013, at 2:37 PM, Rick stevens <stevens(a)anl.gov> wrote: > >> We need a coherent NR for KBase. >> >> Not one for microbes and one for communities. >> >> >> Sent from my iPad >> >> On Jan 10, 2013, at 3:24 PM, Folker Meyer <folker(a)anl.gov> wrote: >> >>> Dylan, >>> >>> good idea. actually this is a great service for people wanting to search metagenomes, I encourage you to build it. >>> >>> It should do exactly what you suggest: >>> >>> - any sequence input is searched against the m5nr >>> - retrieve md5s for the m5nr entries >>> - retrieve list of metagenome_IDs that this md5 is present in >>> - find any sequences matching the md5s in your metagenome(s) of choice with very loose cut-offs >>> - re-run a BLAST(?) or some other search on the sequence set and return things that hit for real with good (strict) cut-offs. >>> >>> We will have to implement an Md5->metagenome_ID function (we can do that if you decide to go for this) >>> >>> I think this would be an excellent service to offer, it might be resource constraining, but this is definitely something that a lot of users have asked for in the past. >>> >>> Best, >>> Folker >>> >>> >>> On Jan 10, 2013, at 12:07 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: >>> >>>> ... and what about searching metagenomic sequence? (i'd wink, but it's not funny) >>>> >>>> since these guys use the m5nr, we could expand any hit from a query sequence to an m5nr sequence into the mg reads that are close to the m5nr exemplar. just a thought. any other ideas? >>>> >>>> thanks, >>>> - dylan >>>> >>>> >>>> On Wed, Jan 9, 2013 at 8:55 PM, Christopher Henry <chrisshenry(a)gmail.com> wrote: >>>> Well, it's a fair question. >>>> >>>> First, we are going to have users, like me, who specifically want to run specific BLAST queries for specific reasons. For that, I think we need a BLAST server. I for one want a blast query to look for specific sequence without having to worry about whether or not the gene callers missed this gene. In particular, this is something we are speculating is a universal gene, and so for the genomes where we don't find it already, we want to do a REALLY thorough search. Does this make sense? So I was thinking TBlastN is what I want… even if it is painfully slow and inefficient… it's to meet this very specific need… and I won't be using it to process a ton of sequence. Just query 10 or so diverse versions for this protein. >>>> >>>> I posit… given the increasing drive towards protein speculation and resolving more challenging problems in annotation, this is going to be a common use scenario. >>>> >>>> Second, it's completely fair to say we need a service that says "I have a sequence that I want to find what KB knows about". It's a separate use scenario in my mind. It's almost a search query, and the sim service is darn close to being able to handle this particular use scenario. >>>> >>>> On Jan 9, 2013, at 2:43 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: >>>> >>>>> Do we really mean "BLAST" in particular, or is the problem really "I have sequence that I want to find what KB knows about" ? >>>>> >>>>> On Jan 9, 2013, at 2:41 PM, Shreyas Cholia wrote: >>>>> >>>>>> OK - that was some serious redundancy, but I think you catch my drift. >>>>>> >>>>>> application specific syntactic sugar for specific apps. >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Kbase-devel mailing list >>>>>> Kbase-devel(a)lists.kbase.us >>>>>> https://lists.kbase.us/mailman/listinfo/kbase-devel >>>>> >>>>> _______________________________________________ >>>>> Kbase-devel mailing list >>>>> Kbase-devel(a)lists.kbase.us >>>>> https://lists.kbase.us/mailman/listinfo/kbase-devel >>>> >>>> _______________________________________________ >>>> Kbase-devel mailing list >>>> Kbase-devel(a)lists.kbase.us >>>> https://lists.kbase.us/mailman/listinfo/kbase-devel >>> >>> _______________________________________________ >>> 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] [Kbase-devel] [Microbe] Blast Services for KBase
by Folker Meyer 10 Jan '13

10 Jan '13

I see your point, but the underlying requirements for communities are such that we can only update once a year. AND we need to be able to support other namespaces.... can we subject the other areas to the only one update per year requirement? Best, Folker On Jan 10, 2013, at 2:37 PM, Rick stevens <stevens(a)anl.gov> wrote: > We need a coherent NR for KBase. > > Not one for microbes and one for communities. > > > Sent from my iPad > > On Jan 10, 2013, at 3:24 PM, Folker Meyer <folker(a)anl.gov> wrote: > >> Dylan, >> >> good idea. actually this is a great service for people wanting to search metagenomes, I encourage you to build it. >> >> It should do exactly what you suggest: >> >> - any sequence input is searched against the m5nr >> - retrieve md5s for the m5nr entries >> - retrieve list of metagenome_IDs that this md5 is present in >> - find any sequences matching the md5s in your metagenome(s) of choice with very loose cut-offs >> - re-run a BLAST(?) or some other search on the sequence set and return things that hit for real with good (strict) cut-offs. >> >> We will have to implement an Md5->metagenome_ID function (we can do that if you decide to go for this) >> >> I think this would be an excellent service to offer, it might be resource constraining, but this is definitely something that a lot of users have asked for in the past. >> >> Best, >> Folker >> >> >> On Jan 10, 2013, at 12:07 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: >> >>> ... and what about searching metagenomic sequence? (i'd wink, but it's not funny) >>> >>> since these guys use the m5nr, we could expand any hit from a query sequence to an m5nr sequence into the mg reads that are close to the m5nr exemplar. just a thought. any other ideas? >>> >>> thanks, >>> - dylan >>> >>> >>> On Wed, Jan 9, 2013 at 8:55 PM, Christopher Henry <chrisshenry(a)gmail.com> wrote: >>> Well, it's a fair question. >>> >>> First, we are going to have users, like me, who specifically want to run specific BLAST queries for specific reasons. For that, I think we need a BLAST server. I for one want a blast query to look for specific sequence without having to worry about whether or not the gene callers missed this gene. In particular, this is something we are speculating is a universal gene, and so for the genomes where we don't find it already, we want to do a REALLY thorough search. Does this make sense? So I was thinking TBlastN is what I want… even if it is painfully slow and inefficient… it's to meet this very specific need… and I won't be using it to process a ton of sequence. Just query 10 or so diverse versions for this protein. >>> >>> I posit… given the increasing drive towards protein speculation and resolving more challenging problems in annotation, this is going to be a common use scenario. >>> >>> Second, it's completely fair to say we need a service that says "I have a sequence that I want to find what KB knows about". It's a separate use scenario in my mind. It's almost a search query, and the sim service is darn close to being able to handle this particular use scenario. >>> >>> On Jan 9, 2013, at 2:43 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: >>> >>>> Do we really mean "BLAST" in particular, or is the problem really "I have sequence that I want to find what KB knows about" ? >>>> >>>> On Jan 9, 2013, at 2:41 PM, Shreyas Cholia wrote: >>>> >>>>> OK - that was some serious redundancy, but I think you catch my drift. >>>>> >>>>> application specific syntactic sugar for specific apps. >>>>> >>>>> >>>>> _______________________________________________ >>>>> Kbase-devel mailing list >>>>> Kbase-devel(a)lists.kbase.us >>>>> https://lists.kbase.us/mailman/listinfo/kbase-devel >>>> >>>> _______________________________________________ >>>> Kbase-devel mailing list >>>> Kbase-devel(a)lists.kbase.us >>>> https://lists.kbase.us/mailman/listinfo/kbase-devel >>> >>> _______________________________________________ >>> Kbase-devel mailing list >>> Kbase-devel(a)lists.kbase.us >>> https://lists.kbase.us/mailman/listinfo/kbase-devel >> >> _______________________________________________ >> 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] [Kbase-devel] [Microbe] Blast Services for KBase
by Rick stevens 10 Jan '13

10 Jan '13

We need a coherent NR for KBase. Not one for microbes and one for communities. Sent from my iPad On Jan 10, 2013, at 3:24 PM, Folker Meyer <folker(a)anl.gov> wrote: > Dylan, > > good idea. actually this is a great service for people wanting to search metagenomes, I encourage you to build it. > > It should do exactly what you suggest: > > - any sequence input is searched against the m5nr > - retrieve md5s for the m5nr entries > - retrieve list of metagenome_IDs that this md5 is present in > - find any sequences matching the md5s in your metagenome(s) of choice with very loose cut-offs > - re-run a BLAST(?) or some other search on the sequence set and return things that hit for real with good (strict) cut-offs. > > We will have to implement an Md5->metagenome_ID function (we can do that if you decide to go for this) > > I think this would be an excellent service to offer, it might be resource constraining, but this is definitely something that a lot of users have asked for in the past. > > Best, > Folker > > > On Jan 10, 2013, at 12:07 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > >> ... and what about searching metagenomic sequence? (i'd wink, but it's not funny) >> >> since these guys use the m5nr, we could expand any hit from a query sequence to an m5nr sequence into the mg reads that are close to the m5nr exemplar. just a thought. any other ideas? >> >> thanks, >> - dylan >> >> >> On Wed, Jan 9, 2013 at 8:55 PM, Christopher Henry <chrisshenry(a)gmail.com> wrote: >> Well, it's a fair question. >> >> First, we are going to have users, like me, who specifically want to run specific BLAST queries for specific reasons. For that, I think we need a BLAST server. I for one want a blast query to look for specific sequence without having to worry about whether or not the gene callers missed this gene. In particular, this is something we are speculating is a universal gene, and so for the genomes where we don't find it already, we want to do a REALLY thorough search. Does this make sense? So I was thinking TBlastN is what I want… even if it is painfully slow and inefficient… it's to meet this very specific need… and I won't be using it to process a ton of sequence. Just query 10 or so diverse versions for this protein. >> >> I posit… given the increasing drive towards protein speculation and resolving more challenging problems in annotation, this is going to be a common use scenario. >> >> Second, it's completely fair to say we need a service that says "I have a sequence that I want to find what KB knows about". It's a separate use scenario in my mind. It's almost a search query, and the sim service is darn close to being able to handle this particular use scenario. >> >> On Jan 9, 2013, at 2:43 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: >> >>> Do we really mean "BLAST" in particular, or is the problem really "I have sequence that I want to find what KB knows about" ? >>> >>> On Jan 9, 2013, at 2:41 PM, Shreyas Cholia wrote: >>> >>>> OK - that was some serious redundancy, but I think you catch my drift. >>>> >>>> application specific syntactic sugar for specific apps. >>>> >>>> >>>> _______________________________________________ >>>> Kbase-devel mailing list >>>> Kbase-devel(a)lists.kbase.us >>>> https://lists.kbase.us/mailman/listinfo/kbase-devel >>> >>> _______________________________________________ >>> Kbase-devel mailing list >>> Kbase-devel(a)lists.kbase.us >>> https://lists.kbase.us/mailman/listinfo/kbase-devel >> >> _______________________________________________ >> Kbase-devel mailing list >> Kbase-devel(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/kbase-devel > > _______________________________________________ > 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] [Kbase-devel] [Microbe] Blast Services for KBase
by Folker Meyer 10 Jan '13

10 Jan '13

Dylan, good idea. actually this is a great service for people wanting to search metagenomes, I encourage you to build it. It should do exactly what you suggest: - any sequence input is searched against the m5nr - retrieve md5s for the m5nr entries - retrieve list of metagenome_IDs that this md5 is present in - find any sequences matching the md5s in your metagenome(s) of choice with very loose cut-offs - re-run a BLAST(?) or some other search on the sequence set and return things that hit for real with good (strict) cut-offs. We will have to implement an Md5->metagenome_ID function (we can do that if you decide to go for this) I think this would be an excellent service to offer, it might be resource constraining, but this is definitely something that a lot of users have asked for in the past. Best, Folker On Jan 10, 2013, at 12:07 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > ... and what about searching metagenomic sequence? (i'd wink, but it's not funny) > > since these guys use the m5nr, we could expand any hit from a query sequence to an m5nr sequence into the mg reads that are close to the m5nr exemplar. just a thought. any other ideas? > > thanks, > - dylan > > > On Wed, Jan 9, 2013 at 8:55 PM, Christopher Henry <chrisshenry(a)gmail.com> wrote: > Well, it's a fair question. > > First, we are going to have users, like me, who specifically want to run specific BLAST queries for specific reasons. For that, I think we need a BLAST server. I for one want a blast query to look for specific sequence without having to worry about whether or not the gene callers missed this gene. In particular, this is something we are speculating is a universal gene, and so for the genomes where we don't find it already, we want to do a REALLY thorough search. Does this make sense? So I was thinking TBlastN is what I want… even if it is painfully slow and inefficient… it's to meet this very specific need… and I won't be using it to process a ton of sequence. Just query 10 or so diverse versions for this protein. > > I posit… given the increasing drive towards protein speculation and resolving more challenging problems in annotation, this is going to be a common use scenario. > > Second, it's completely fair to say we need a service that says "I have a sequence that I want to find what KB knows about". It's a separate use scenario in my mind. It's almost a search query, and the sim service is darn close to being able to handle this particular use scenario. > > On Jan 9, 2013, at 2:43 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: > > > Do we really mean "BLAST" in particular, or is the problem really "I have sequence that I want to find what KB knows about" ? > > > > On Jan 9, 2013, at 2:41 PM, Shreyas Cholia wrote: > > > >> OK - that was some serious redundancy, but I think you catch my drift. > >> > >> application specific syntactic sugar for specific apps. > >> > >> > >> _______________________________________________ > >> Kbase-devel mailing list > >> Kbase-devel(a)lists.kbase.us > >> https://lists.kbase.us/mailman/listinfo/kbase-devel > > > > _______________________________________________ > > Kbase-devel mailing list > > Kbase-devel(a)lists.kbase.us > > https://lists.kbase.us/mailman/listinfo/kbase-devel > > _______________________________________________ > Kbase-devel mailing list > Kbase-devel(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/kbase-devel >

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