How domyoungetbthe list of public MG IDs?
Sent from my iPad
On May 16, 2013, at 4:45 PM, Folker Meyer <folker.meyer(a)gmail.com> wrote:
> sure. this is quite simple in the API.
>
>
> pseudo code:
> -----------
> for each public_metagenome
>
> do
> # get abundance profile
> curl "http://api.metagenomics.anl.gov/abundanceprofile/ID?type=organism&source=Ge…" | json_xs
>
> # e.g. curl "http://api.metagenomics.anl.gov/abundanceprofile/mgm4440026.3?type=organism…" | json_xs
>
> done
> -----------
> This gives you the taxon info derived from either proteins or 16s using Genbank annotations and NCBI taxon IDs+Names. SEED annotations are also mapped to NCBI taxonomy.
>
> Using Silva (aka SSU) as namespace instead of GenBank above will just give you 16s.
>
> best,
> Folker
>
>
> On May 16, 2013, at 4:19 PM, Matthew Henderson <mhenderson(a)lbl.gov> wrote:
>
>> Hi Folker,
>>
>> Right now we are just building prototypes, so it would still be useful to have the functionality even if it is not optimized.
>>
>> Can we see an example of how to do this with the api? I think that is all we are asking for at this point.
>>
>> Thanks,
>> Matt
>>
>>
>> On Thu, May 16, 2013 at 3:34 PM, Folker Meyer <folker.meyer(a)gmail.com> wrote:
>> this is something that is supported by the API now. But not fast.
>>
>> The query is one of the uses cases we are re-designing the search for MG-RAST for. We expect it to be done in a couple (read 2) of weeks.
>>
>> once that is done, we will implement simple searches in MG-RAST like which taxon is present in which geographic region etc.
>>
>> currently it is very slow. you are going 90 degrees to the way the system is optimized
>>
>> Best,
>> Folker
>>
>> On May 16, 2013, at 3:17 PM, Paramvir Dehal <psdehal(a)lbl.gov> wrote:
>>
>>> Yeah, those methods would work, I just need to know the function call and how to execute it.
>>>
>>>
>>> On Thu, May 16, 2013 at 3:14 PM, Rick stevens <stevens(a)anl.gov> wrote:
>>> For isolate genomes we can use metadata and 16s precomputed mapping.
>>>
>>> For WGS and WGS contigs we need to workout precisely what you mean by assign to a taxon grouping.
>>>
>>>
>>>
>>>
>>> Sent from my iPad
>>>
>>> On May 16, 2013, at 2:58 PM, Rick stevens <stevens(a)anl.gov> wrote:
>>>
>>>> Dylan
>>>>
>>>> I'm trying Ti understand what you want to build.
>>>>
>>>> I think you want some way to have some one select a taxon and bring up in a taxon page all genomes and metagenomes and metagenome derived contigs associated with that taxon..
>>>>
>>>> Is that correct ?
>>>>
>>>> Sent from my iPad
>>>>
>>>> On May 16, 2013, at 2:26 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote:
>>>>
>>>>> I'm confused. Isn't this week a joint hack-a-thon? My guys flew out there to work with your guys. Is that not happening?
>>>>>
>>>>> Thanks,
>>>>> - Dylan
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Thu, May 16, 2013 at 12:21 PM, Folker Meyer <folker(a)mcs.anl.gov> wrote:
>>>>> We are super busy right now. Can we do this next week over the phone. I still need some input on the actual goals of this.
>>>>>
>>>>>
>>>>> --
>>>>> Sent from mobile device
>>>>>
>>>>> On May 16, 2013, at 14:14, Matthew Henderson <mhenderson(a)lbl.gov> wrote:
>>>>>
>>>>>> Paramvir, Mike and I are at Freund Lodge currently, and you guys (Andreas?) are welcome to come over and be part of the excitement of the KBase build and "stuff". Mike and I will also be here tomorrow morning, but will have to leave around lunchtime to get back to the airport for the trip back home.
>>>>>>
>>>>>> Paramvir is less concerned at the moment about thresholding and just wants to see some functionality.
>>>>>>
>>>>>> Alternatively, if you are not feeling Freundlich, an email pointing us in the proper direction would also be appreciated.
>>>>>>
>>>>>> Thanks,
>>>>>> Matt
>>>>>>
>>>>>>
>>>>>> On Thu, May 16, 2013 at 1:28 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote:
>>>>>> Paramvir is a stakeholder here, so we should get his input, including on which identity thresholds he'd like to see.
>>>>>>
>>>>>> Thanks,
>>>>>> - Dylan
>>>>>>
>>>>>>
>>>>>> On Thu, May 16, 2013 at 11:10 AM, Dylan Chivian <dcchivian(a)lbl.gov> wrote:
>>>>>> Hi guys,
>>>>>>
>>>>>> instead of the call today, probably the time would be best spent with Folker and Andreas working with Matt and Mike directly on the metagenomics species search functionality for the Taxon pages. I expect it is an expensive operation, so it is probably something that should be a one-time compute and stored somewhere associated with each taxon rather than on-the-fly when someone calls up the Taxon page. There should probably also be separate lists for 99% identity and 97% identity (not sure other thresholds make any sense).
>>>>>>
>>>>>> Thoughts? Are there other things to discuss and we should have the call anyway?
>>>>>>
>>>>>> Thanks,
>>>>>> - Dylan
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>
>>> _______________________________________________
>>> 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
>>
>> _______________________________________________
>> 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
>
> _______________________________________________
> Kbase-microcomm mailing list
> Kbase-microcomm(a)lists.kbase.us
> https://lists.kbase.us/mailman/listinfo/kbase-microcomm
sure. this is quite simple in the API.
pseudo code:
-----------
for each public_metagenome
do
# get abundance profile
curl "http://api.metagenomics.anl.gov/abundanceprofile/ID?type=organism&source=Ge…" | json_xs
# e.g. curl "http://api.metagenomics.anl.gov/abundanceprofile/mgm4440026.3?type=organism…" | json_xs
done
-----------
This gives you the taxon info derived from either proteins or 16s using Genbank annotations and NCBI taxon IDs+Names. SEED annotations are also mapped to NCBI taxonomy.
Using Silva (aka SSU) as namespace instead of GenBank above will just give you 16s.
best,
Folker
On May 16, 2013, at 4:19 PM, Matthew Henderson <mhenderson(a)lbl.gov> wrote:
> Hi Folker,
>
> Right now we are just building prototypes, so it would still be useful to have the functionality even if it is not optimized.
>
> Can we see an example of how to do this with the api? I think that is all we are asking for at this point.
>
> Thanks,
> Matt
>
>
> On Thu, May 16, 2013 at 3:34 PM, Folker Meyer <folker.meyer(a)gmail.com> wrote:
> this is something that is supported by the API now. But not fast.
>
> The query is one of the uses cases we are re-designing the search for MG-RAST for. We expect it to be done in a couple (read 2) of weeks.
>
> once that is done, we will implement simple searches in MG-RAST like which taxon is present in which geographic region etc.
>
> currently it is very slow. you are going 90 degrees to the way the system is optimized
>
> Best,
> Folker
>
> On May 16, 2013, at 3:17 PM, Paramvir Dehal <psdehal(a)lbl.gov> wrote:
>
> > Yeah, those methods would work, I just need to know the function call and how to execute it.
> >
> >
> > On Thu, May 16, 2013 at 3:14 PM, Rick stevens <stevens(a)anl.gov> wrote:
> > For isolate genomes we can use metadata and 16s precomputed mapping.
> >
> > For WGS and WGS contigs we need to workout precisely what you mean by assign to a taxon grouping.
> >
> >
> >
> >
> > Sent from my iPad
> >
> > On May 16, 2013, at 2:58 PM, Rick stevens <stevens(a)anl.gov> wrote:
> >
> >> Dylan
> >>
> >> I'm trying Ti understand what you want to build.
> >>
> >> I think you want some way to have some one select a taxon and bring up in a taxon page all genomes and metagenomes and metagenome derived contigs associated with that taxon..
> >>
> >> Is that correct ?
> >>
> >> Sent from my iPad
> >>
> >> On May 16, 2013, at 2:26 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote:
> >>
> >>> I'm confused. Isn't this week a joint hack-a-thon? My guys flew out there to work with your guys. Is that not happening?
> >>>
> >>> Thanks,
> >>> - Dylan
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> On Thu, May 16, 2013 at 12:21 PM, Folker Meyer <folker(a)mcs.anl.gov> wrote:
> >>> We are super busy right now. Can we do this next week over the phone. I still need some input on the actual goals of this.
> >>>
> >>>
> >>> --
> >>> Sent from mobile device
> >>>
> >>> On May 16, 2013, at 14:14, Matthew Henderson <mhenderson(a)lbl.gov> wrote:
> >>>
> >>>> Paramvir, Mike and I are at Freund Lodge currently, and you guys (Andreas?) are welcome to come over and be part of the excitement of the KBase build and "stuff". Mike and I will also be here tomorrow morning, but will have to leave around lunchtime to get back to the airport for the trip back home.
> >>>>
> >>>> Paramvir is less concerned at the moment about thresholding and just wants to see some functionality.
> >>>>
> >>>> Alternatively, if you are not feeling Freundlich, an email pointing us in the proper direction would also be appreciated.
> >>>>
> >>>> Thanks,
> >>>> Matt
> >>>>
> >>>>
> >>>> On Thu, May 16, 2013 at 1:28 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote:
> >>>> Paramvir is a stakeholder here, so we should get his input, including on which identity thresholds he'd like to see.
> >>>>
> >>>> Thanks,
> >>>> - Dylan
> >>>>
> >>>>
> >>>> On Thu, May 16, 2013 at 11:10 AM, Dylan Chivian <dcchivian(a)lbl.gov> wrote:
> >>>> Hi guys,
> >>>>
> >>>> instead of the call today, probably the time would be best spent with Folker and Andreas working with Matt and Mike directly on the metagenomics species search functionality for the Taxon pages. I expect it is an expensive operation, so it is probably something that should be a one-time compute and stored somewhere associated with each taxon rather than on-the-fly when someone calls up the Taxon page. There should probably also be separate lists for 99% identity and 97% identity (not sure other thresholds make any sense).
> >>>>
> >>>> Thoughts? Are there other things to discuss and we should have the call anyway?
> >>>>
> >>>> Thanks,
> >>>> - Dylan
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> 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
> >>>
> >>> _______________________________________________
> >>> 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
> >
> > _______________________________________________
> > 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
>
> _______________________________________________
> 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
It doesn't have to be fast, we'll use whatever is there. I looked through
the communities api doc on the website and couldn't figure out what
function call to use. It would be great if you could point me to the doc
explaining the functionality assuming I've got a 16s and will set the
threshold.
I'm not going to be at the build tomorrow, but Mike, Matt and Bill will be
there.
this is something that is supported by the API now. But not fast.
The query is one of the uses cases we are re-designing the search for
MG-RAST for. We expect it to be done in a couple (read 2) of weeks.
once that is done, we will implement simple searches in MG-RAST like which
taxon is present in which geographic region etc.
currently it is very slow. you are going 90 degrees to the way the system
is optimized
Best,
Folker
On May 16, 2013, at 3:17 PM, Paramvir Dehal <psdehal(a)lbl.gov> wrote:
> Yeah, those methods would work, I just need to know the function call and
how to execute it.
>
>
> On Thu, May 16, 2013 at 3:14 PM, Rick stevens <stevens(a)anl.gov> wrote:
> For isolate genomes we can use metadata and 16s precomputed mapping.
>
> For WGS and WGS contigs we need to workout precisely what you mean by
assign to a taxon grouping.
>
>
>
>
> Sent from my iPad
>
> On May 16, 2013, at 2:58 PM, Rick stevens <stevens(a)anl.gov> wrote:
>
>> Dylan
>>
>> I'm trying Ti understand what you want to build.
>>
>> I think you want some way to have some one select a taxon and bring up
in a taxon page all genomes and metagenomes and metagenome derived contigs
associated with that taxon..
>>
>> Is that correct ?
>>
>> Sent from my iPad
>>
>> On May 16, 2013, at 2:26 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote:
>>
>>> I'm confused. Isn't this week a joint hack-a-thon? My guys flew out
there to work with your guys. Is that not happening?
>>>
>>> Thanks,
>>> - Dylan
>>>
>>>
>>>
>>>
>>>
>>> On Thu, May 16, 2013 at 12:21 PM, Folker Meyer <folker(a)mcs.anl.gov>
wrote:
>>> We are super busy right now. Can we do this next week over the phone. I
still need some input on the actual goals of this.
>>>
>>>
>>> --
>>> Sent from mobile device
>>>
>>> On May 16, 2013, at 14:14, Matthew Henderson <mhenderson(a)lbl.gov> wrote:
>>>
>>>> Paramvir, Mike and I are at Freund Lodge currently, and you guys
(Andreas?) are welcome to come over and be part of the excitement of the
KBase build and "stuff". Mike and I will also be here tomorrow morning,
but will have to leave around lunchtime to get back to the airport for the
trip back home.
>>>>
>>>> Paramvir is less concerned at the moment about thresholding and just
wants to see some functionality.
>>>>
>>>> Alternatively, if you are not feeling Freundlich, an email pointing us
in the proper direction would also be appreciated.
>>>>
>>>> Thanks,
>>>> Matt
>>>>
>>>>
>>>> On Thu, May 16, 2013 at 1:28 PM, Dylan Chivian <dcchivian(a)lbl.gov>
wrote:
>>>> Paramvir is a stakeholder here, so we should get his input, including
on which identity thresholds he'd like to see.
>>>>
>>>> Thanks,
>>>> - Dylan
>>>>
>>>>
>>>> On Thu, May 16, 2013 at 11:10 AM, Dylan Chivian <dcchivian(a)lbl.gov>
wrote:
>>>> Hi guys,
>>>>
>>>> instead of the call today, probably the time would be best spent with
Folker and Andreas working with Matt and Mike directly on the metagenomics
species search functionality for the Taxon pages. I expect it is an
expensive operation, so it is probably something that should be a one-time
compute and stored somewhere associated with each taxon rather than
on-the-fly when someone calls up the Taxon page. There should probably
also be separate lists for 99% identity and 97% identity (not sure other
thresholds make any sense).
>>>>
>>>> Thoughts? Are there other things to discuss and we should have the
call anyway?
>>>>
>>>> Thanks,
>>>> - Dylan
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> 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
>>>
>>> _______________________________________________
>>> 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
>
> _______________________________________________
> 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
Hi Folker,
Right now we are just building prototypes, so it would still be useful to
have the functionality even if it is not optimized.
Can we see an example of how to do this with the api? I think that is all
we are asking for at this point.
Thanks,
Matt
On Thu, May 16, 2013 at 3:34 PM, Folker Meyer <folker.meyer(a)gmail.com>wrote:
> this is something that is supported by the API now. But not fast.
>
> The query is one of the uses cases we are re-designing the search for
> MG-RAST for. We expect it to be done in a couple (read 2) of weeks.
>
> once that is done, we will implement simple searches in MG-RAST like which
> taxon is present in which geographic region etc.
>
> currently it is very slow. you are going 90 degrees to the way the system
> is optimized
>
> Best,
> Folker
>
> On May 16, 2013, at 3:17 PM, Paramvir Dehal <psdehal(a)lbl.gov> wrote:
>
> > Yeah, those methods would work, I just need to know the function call
> and how to execute it.
> >
> >
> > On Thu, May 16, 2013 at 3:14 PM, Rick stevens <stevens(a)anl.gov> wrote:
> > For isolate genomes we can use metadata and 16s precomputed mapping.
> >
> > For WGS and WGS contigs we need to workout precisely what you mean by
> assign to a taxon grouping.
> >
> >
> >
> >
> > Sent from my iPad
> >
> > On May 16, 2013, at 2:58 PM, Rick stevens <stevens(a)anl.gov> wrote:
> >
> >> Dylan
> >>
> >> I'm trying Ti understand what you want to build.
> >>
> >> I think you want some way to have some one select a taxon and bring up
> in a taxon page all genomes and metagenomes and metagenome derived contigs
> associated with that taxon..
> >>
> >> Is that correct ?
> >>
> >> Sent from my iPad
> >>
> >> On May 16, 2013, at 2:26 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote:
> >>
> >>> I'm confused. Isn't this week a joint hack-a-thon? My guys flew out
> there to work with your guys. Is that not happening?
> >>>
> >>> Thanks,
> >>> - Dylan
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> On Thu, May 16, 2013 at 12:21 PM, Folker Meyer <folker(a)mcs.anl.gov>
> wrote:
> >>> We are super busy right now. Can we do this next week over the phone.
> I still need some input on the actual goals of this.
> >>>
> >>>
> >>> --
> >>> Sent from mobile device
> >>>
> >>> On May 16, 2013, at 14:14, Matthew Henderson <mhenderson(a)lbl.gov>
> wrote:
> >>>
> >>>> Paramvir, Mike and I are at Freund Lodge currently, and you guys
> (Andreas?) are welcome to come over and be part of the excitement of the
> KBase build and "stuff". Mike and I will also be here tomorrow morning,
> but will have to leave around lunchtime to get back to the airport for the
> trip back home.
> >>>>
> >>>> Paramvir is less concerned at the moment about thresholding and just
> wants to see some functionality.
> >>>>
> >>>> Alternatively, if you are not feeling Freundlich, an email pointing
> us in the proper direction would also be appreciated.
> >>>>
> >>>> Thanks,
> >>>> Matt
> >>>>
> >>>>
> >>>> On Thu, May 16, 2013 at 1:28 PM, Dylan Chivian <dcchivian(a)lbl.gov>
> wrote:
> >>>> Paramvir is a stakeholder here, so we should get his input, including
> on which identity thresholds he'd like to see.
> >>>>
> >>>> Thanks,
> >>>> - Dylan
> >>>>
> >>>>
> >>>> On Thu, May 16, 2013 at 11:10 AM, Dylan Chivian <dcchivian(a)lbl.gov>
> wrote:
> >>>> Hi guys,
> >>>>
> >>>> instead of the call today, probably the time would be best spent with
> Folker and Andreas working with Matt and Mike directly on the metagenomics
> species search functionality for the Taxon pages. I expect it is an
> expensive operation, so it is probably something that should be a one-time
> compute and stored somewhere associated with each taxon rather than
> on-the-fly when someone calls up the Taxon page. There should probably
> also be separate lists for 99% identity and 97% identity (not sure other
> thresholds make any sense).
> >>>>
> >>>> Thoughts? Are there other things to discuss and we should have the
> call anyway?
> >>>>
> >>>> Thanks,
> >>>> - Dylan
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> 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
> >>>
> >>> _______________________________________________
> >>> 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
> >
> > _______________________________________________
> > 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
>
> _______________________________________________
> Kbase-microcomm mailing list
> Kbase-microcomm(a)lists.kbase.us
> https://lists.kbase.us/mailman/listinfo/kbase-microcomm
>
On May 16, 2013, at 3:43 PM, Rick Stevens <stevens(a)anl.gov> wrote:
> in the WGS Metagenome contig example in most cases you don't have 16s .so you would need to do some kind of best guess from
> the protein sequences and probably not just one protein but some kind of voting or perhaps a classifier specially designed for this.
we have a naive scheme for inferring taxonomic origin. Actually 3 schemes. Described in the FAQ. all of them rely on using similarities. The LCA probably gives you the most reliable answers, but it is classifying to varying levels.
A good way forward would be a filter that uses the ~50 ribosomal proteins instead/in addition to the 16s. That could be a good thing to implement.
>
> It clearly could be and would be computed when the MG is processed .. but then you would need to work out how to decide what
> to call something if the match is not great or you have hits with no clear consensus (which is what we see sometimes).
Yes. deciding which thresholds to use is the hard part. MG-RAST defers that decision to the user. The user sets parameters at query time.
>
> Also many of the 16s entries are not valid names but simply point to another environmental sample?
valid names... hah. For MG-RAST we have them computed against SILVA. to the names are probably as good as it gets.
>
> It would be nice to have though.
THis is one of the areas where a lot of improvement could be made. Better ways of using the pre-computed similarity information e.g.
However as good contigs are rare and short reads abound. this has not been where we invested the most energy.
Hope this helps
Best,
Folker
>
>
>
>
> On May 16, 2013, at 3:14 PM, Rick stevens <stevens(a)anl.gov> wrote:
>
>> For isolate genomes we can use metadata and 16s precomputed mapping.
>>
>> For WGS and WGS contigs we need to workout precisely what you mean by assign to a taxon grouping.
>>
>>
>>
>>
>> Sent from my iPad
>>
>> On May 16, 2013, at 2:58 PM, Rick stevens <stevens(a)anl.gov> wrote:
>>
>>> Dylan
>>>
>>> I'm trying Ti understand what you want to build.
>>>
>>> I think you want some way to have some one select a taxon and bring up in a taxon page all genomes and metagenomes and metagenome derived contigs associated with that taxon..
>>>
>>> Is that correct ?
>>>
>>> Sent from my iPad
>>>
>>> On May 16, 2013, at 2:26 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote:
>>>
>>>> I'm confused. Isn't this week a joint hack-a-thon? My guys flew out there to work with your guys. Is that not happening?
>>>>
>>>> Thanks,
>>>> - Dylan
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Thu, May 16, 2013 at 12:21 PM, Folker Meyer <folker(a)mcs.anl.gov> wrote:
>>>> We are super busy right now. Can we do this next week over the phone. I still need some input on the actual goals of this.
>>>>
>>>>
>>>> --
>>>> Sent from mobile device
>>>>
>>>> On May 16, 2013, at 14:14, Matthew Henderson <mhenderson(a)lbl.gov> wrote:
>>>>
>>>>> Paramvir, Mike and I are at Freund Lodge currently, and you guys (Andreas?) are welcome to come over and be part of the excitement of the KBase build and "stuff". Mike and I will also be here tomorrow morning, but will have to leave around lunchtime to get back to the airport for the trip back home.
>>>>>
>>>>> Paramvir is less concerned at the moment about thresholding and just wants to see some functionality.
>>>>>
>>>>> Alternatively, if you are not feeling Freundlich, an email pointing us in the proper direction would also be appreciated.
>>>>>
>>>>> Thanks,
>>>>> Matt
>>>>>
>>>>>
>>>>> On Thu, May 16, 2013 at 1:28 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote:
>>>>> Paramvir is a stakeholder here, so we should get his input, including on which identity thresholds he'd like to see.
>>>>>
>>>>> Thanks,
>>>>> - Dylan
>>>>>
>>>>>
>>>>> On Thu, May 16, 2013 at 11:10 AM, Dylan Chivian <dcchivian(a)lbl.gov> wrote:
>>>>> Hi guys,
>>>>>
>>>>> instead of the call today, probably the time would be best spent with Folker and Andreas working with Matt and Mike directly on the metagenomics species search functionality for the Taxon pages. I expect it is an expensive operation, so it is probably something that should be a one-time compute and stored somewhere associated with each taxon rather than on-the-fly when someone calls up the Taxon page. There should probably also be separate lists for 99% identity and 97% identity (not sure other thresholds make any sense).
>>>>>
>>>>> Thoughts? Are there other things to discuss and we should have the call anyway?
>>>>>
>>>>> Thanks,
>>>>> - Dylan
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>>
>>>> _______________________________________________
>>>> 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
>
> _______________________________________________
> Kbase-microcomm mailing list
> Kbase-microcomm(a)lists.kbase.us
> https://lists.kbase.us/mailman/listinfo/kbase-microcomm
in the WGS Metagenome contig example in most cases you don't have 16s .so you would need to do some kind of best guess from
the protein sequences and probably not just one protein but some kind of voting or perhaps a classifier specially designed for this.
It clearly could be and would be computed when the MG is processed .. but then you would need to work out how to decide what
to call something if the match is not great or you have hits with no clear consensus (which is what we see sometimes).
Also many of the 16s entries are not valid names but simply point to another environmental sample?
It would be nice to have though.
On May 16, 2013, at 3:14 PM, Rick stevens <stevens(a)anl.gov> wrote:
> For isolate genomes we can use metadata and 16s precomputed mapping.
>
> For WGS and WGS contigs we need to workout precisely what you mean by assign to a taxon grouping.
>
>
>
>
> Sent from my iPad
>
> On May 16, 2013, at 2:58 PM, Rick stevens <stevens(a)anl.gov> wrote:
>
>> Dylan
>>
>> I'm trying Ti understand what you want to build.
>>
>> I think you want some way to have some one select a taxon and bring up in a taxon page all genomes and metagenomes and metagenome derived contigs associated with that taxon..
>>
>> Is that correct ?
>>
>> Sent from my iPad
>>
>> On May 16, 2013, at 2:26 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote:
>>
>>> I'm confused. Isn't this week a joint hack-a-thon? My guys flew out there to work with your guys. Is that not happening?
>>>
>>> Thanks,
>>> - Dylan
>>>
>>>
>>>
>>>
>>>
>>> On Thu, May 16, 2013 at 12:21 PM, Folker Meyer <folker(a)mcs.anl.gov> wrote:
>>> We are super busy right now. Can we do this next week over the phone. I still need some input on the actual goals of this.
>>>
>>>
>>> --
>>> Sent from mobile device
>>>
>>> On May 16, 2013, at 14:14, Matthew Henderson <mhenderson(a)lbl.gov> wrote:
>>>
>>>> Paramvir, Mike and I are at Freund Lodge currently, and you guys (Andreas?) are welcome to come over and be part of the excitement of the KBase build and "stuff". Mike and I will also be here tomorrow morning, but will have to leave around lunchtime to get back to the airport for the trip back home.
>>>>
>>>> Paramvir is less concerned at the moment about thresholding and just wants to see some functionality.
>>>>
>>>> Alternatively, if you are not feeling Freundlich, an email pointing us in the proper direction would also be appreciated.
>>>>
>>>> Thanks,
>>>> Matt
>>>>
>>>>
>>>> On Thu, May 16, 2013 at 1:28 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote:
>>>> Paramvir is a stakeholder here, so we should get his input, including on which identity thresholds he'd like to see.
>>>>
>>>> Thanks,
>>>> - Dylan
>>>>
>>>>
>>>> On Thu, May 16, 2013 at 11:10 AM, Dylan Chivian <dcchivian(a)lbl.gov> wrote:
>>>> Hi guys,
>>>>
>>>> instead of the call today, probably the time would be best spent with Folker and Andreas working with Matt and Mike directly on the metagenomics species search functionality for the Taxon pages. I expect it is an expensive operation, so it is probably something that should be a one-time compute and stored somewhere associated with each taxon rather than on-the-fly when someone calls up the Taxon page. There should probably also be separate lists for 99% identity and 97% identity (not sure other thresholds make any sense).
>>>>
>>>> Thoughts? Are there other things to discuss and we should have the call anyway?
>>>>
>>>> Thanks,
>>>> - Dylan
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> 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
>>>
>>> _______________________________________________
>>> 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
this is something that is supported by the API now. But not fast.
The query is one of the uses cases we are re-designing the search for MG-RAST for. We expect it to be done in a couple (read 2) of weeks.
once that is done, we will implement simple searches in MG-RAST like which taxon is present in which geographic region etc.
currently it is very slow. you are going 90 degrees to the way the system is optimized
Best,
Folker
On May 16, 2013, at 3:17 PM, Paramvir Dehal <psdehal(a)lbl.gov> wrote:
> Yeah, those methods would work, I just need to know the function call and how to execute it.
>
>
> On Thu, May 16, 2013 at 3:14 PM, Rick stevens <stevens(a)anl.gov> wrote:
> For isolate genomes we can use metadata and 16s precomputed mapping.
>
> For WGS and WGS contigs we need to workout precisely what you mean by assign to a taxon grouping.
>
>
>
>
> Sent from my iPad
>
> On May 16, 2013, at 2:58 PM, Rick stevens <stevens(a)anl.gov> wrote:
>
>> Dylan
>>
>> I'm trying Ti understand what you want to build.
>>
>> I think you want some way to have some one select a taxon and bring up in a taxon page all genomes and metagenomes and metagenome derived contigs associated with that taxon..
>>
>> Is that correct ?
>>
>> Sent from my iPad
>>
>> On May 16, 2013, at 2:26 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote:
>>
>>> I'm confused. Isn't this week a joint hack-a-thon? My guys flew out there to work with your guys. Is that not happening?
>>>
>>> Thanks,
>>> - Dylan
>>>
>>>
>>>
>>>
>>>
>>> On Thu, May 16, 2013 at 12:21 PM, Folker Meyer <folker(a)mcs.anl.gov> wrote:
>>> We are super busy right now. Can we do this next week over the phone. I still need some input on the actual goals of this.
>>>
>>>
>>> --
>>> Sent from mobile device
>>>
>>> On May 16, 2013, at 14:14, Matthew Henderson <mhenderson(a)lbl.gov> wrote:
>>>
>>>> Paramvir, Mike and I are at Freund Lodge currently, and you guys (Andreas?) are welcome to come over and be part of the excitement of the KBase build and "stuff". Mike and I will also be here tomorrow morning, but will have to leave around lunchtime to get back to the airport for the trip back home.
>>>>
>>>> Paramvir is less concerned at the moment about thresholding and just wants to see some functionality.
>>>>
>>>> Alternatively, if you are not feeling Freundlich, an email pointing us in the proper direction would also be appreciated.
>>>>
>>>> Thanks,
>>>> Matt
>>>>
>>>>
>>>> On Thu, May 16, 2013 at 1:28 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote:
>>>> Paramvir is a stakeholder here, so we should get his input, including on which identity thresholds he'd like to see.
>>>>
>>>> Thanks,
>>>> - Dylan
>>>>
>>>>
>>>> On Thu, May 16, 2013 at 11:10 AM, Dylan Chivian <dcchivian(a)lbl.gov> wrote:
>>>> Hi guys,
>>>>
>>>> instead of the call today, probably the time would be best spent with Folker and Andreas working with Matt and Mike directly on the metagenomics species search functionality for the Taxon pages. I expect it is an expensive operation, so it is probably something that should be a one-time compute and stored somewhere associated with each taxon rather than on-the-fly when someone calls up the Taxon page. There should probably also be separate lists for 99% identity and 97% identity (not sure other thresholds make any sense).
>>>>
>>>> Thoughts? Are there other things to discuss and we should have the call anyway?
>>>>
>>>> Thanks,
>>>> - Dylan
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> 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
>>>
>>> _______________________________________________
>>> 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
>
> _______________________________________________
> 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
Yeah, those methods would work, I just need to know the function call and
how to execute it.
On Thu, May 16, 2013 at 3:14 PM, Rick stevens <stevens(a)anl.gov> wrote:
> For isolate genomes we can use metadata and 16s precomputed mapping.
>
> For WGS and WGS contigs we need to workout precisely what you mean by
> assign to a taxon grouping.
>
>
>
>
> Sent from my iPad
>
> On May 16, 2013, at 2:58 PM, Rick stevens <stevens(a)anl.gov> wrote:
>
> Dylan
>
> I'm trying Ti understand what you want to build.
>
> I think you want some way to have some one select a taxon and bring up in
> a taxon page all genomes and metagenomes and metagenome derived contigs
> associated with that taxon..
>
> Is that correct ?
>
> Sent from my iPad
>
> On May 16, 2013, at 2:26 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote:
>
> I'm confused. Isn't this week a joint hack-a-thon? My guys flew out
> there to work with your guys. Is that not happening?
>
> Thanks,
> - Dylan
>
>
>
>
>
> On Thu, May 16, 2013 at 12:21 PM, Folker Meyer <folker(a)mcs.anl.gov> wrote:
>
>> We are super busy right now. Can we do this next week over the phone. I
>> still need some input on the actual goals of this.
>>
>>
>> --
>> Sent from mobile device
>>
>> On May 16, 2013, at 14:14, Matthew Henderson <mhenderson(a)lbl.gov> wrote:
>>
>> Paramvir, Mike and I are at Freund Lodge currently, and you guys
>> (Andreas?) are welcome to come over and be part of the excitement of the
>> KBase build and "stuff". Mike and I will also be here tomorrow morning,
>> but will have to leave around lunchtime to get back to the airport for the
>> trip back home.
>>
>> Paramvir is less concerned at the moment about thresholding and just
>> wants to see some functionality.
>>
>> Alternatively, if you are not feeling Freundlich, an email pointing us in
>> the proper direction would also be appreciated.
>>
>> Thanks,
>> Matt
>>
>>
>> On Thu, May 16, 2013 at 1:28 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote:
>>
>>> Paramvir is a stakeholder here, so we should get his input, including on
>>> which identity thresholds he'd like to see.
>>>
>>> Thanks,
>>> - Dylan
>>>
>>>
>>> On Thu, May 16, 2013 at 11:10 AM, Dylan Chivian <dcchivian(a)lbl.gov>wrote:
>>>
>>>> Hi guys,
>>>>
>>>> instead of the call today, probably the time would be best spent with
>>>> Folker and Andreas working with Matt and Mike directly on the metagenomics
>>>> species search functionality for the Taxon pages. I expect it is an
>>>> expensive operation, so it is probably something that should be a one-time
>>>> compute and stored somewhere associated with each taxon rather than
>>>> on-the-fly when someone calls up the Taxon page. There should probably
>>>> also be separate lists for 99% identity and 97% identity (not sure other
>>>> thresholds make any sense).
>>>>
>>>> Thoughts? Are there other things to discuss and we should have the
>>>> call anyway?
>>>>
>>>> Thanks,
>>>> - Dylan
>>>>
>>>>
>>>
>>> _______________________________________________
>>> 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
>>
>>
>> _______________________________________________
>> 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
>
>
> _______________________________________________
> Kbase-microcomm mailing list
> Kbase-microcomm(a)lists.kbase.us
> https://lists.kbase.us/mailman/listinfo/kbase-microcomm
>
>
For isolate genomes we can use metadata and 16s precomputed mapping.
For WGS and WGS contigs we need to workout precisely what you mean by assign to a taxon grouping.
Sent from my iPad
On May 16, 2013, at 2:58 PM, Rick stevens <stevens(a)anl.gov> wrote:
> Dylan
>
> I'm trying Ti understand what you want to build.
>
> I think you want some way to have some one select a taxon and bring up in a taxon page all genomes and metagenomes and metagenome derived contigs associated with that taxon..
>
> Is that correct ?
>
> Sent from my iPad
>
> On May 16, 2013, at 2:26 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote:
>
>> I'm confused. Isn't this week a joint hack-a-thon? My guys flew out there to work with your guys. Is that not happening?
>>
>> Thanks,
>> - Dylan
>>
>>
>>
>>
>>
>> On Thu, May 16, 2013 at 12:21 PM, Folker Meyer <folker(a)mcs.anl.gov> wrote:
>>> We are super busy right now. Can we do this next week over the phone. I still need some input on the actual goals of this.
>>>
>>>
>>> --
>>> Sent from mobile device
>>>
>>> On May 16, 2013, at 14:14, Matthew Henderson <mhenderson(a)lbl.gov> wrote:
>>>
>>>> Paramvir, Mike and I are at Freund Lodge currently, and you guys (Andreas?) are welcome to come over and be part of the excitement of the KBase build and "stuff". Mike and I will also be here tomorrow morning, but will have to leave around lunchtime to get back to the airport for the trip back home.
>>>>
>>>> Paramvir is less concerned at the moment about thresholding and just wants to see some functionality.
>>>>
>>>> Alternatively, if you are not feeling Freundlich, an email pointing us in the proper direction would also be appreciated.
>>>>
>>>> Thanks,
>>>> Matt
>>>>
>>>>
>>>> On Thu, May 16, 2013 at 1:28 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote:
>>>>> Paramvir is a stakeholder here, so we should get his input, including on which identity thresholds he'd like to see.
>>>>>
>>>>> Thanks,
>>>>> - Dylan
>>>>>
>>>>>
>>>>> On Thu, May 16, 2013 at 11:10 AM, Dylan Chivian <dcchivian(a)lbl.gov> wrote:
>>>>>> Hi guys,
>>>>>>
>>>>>> instead of the call today, probably the time would be best spent with Folker and Andreas working with Matt and Mike directly on the metagenomics species search functionality for the Taxon pages. I expect it is an expensive operation, so it is probably something that should be a one-time compute and stored somewhere associated with each taxon rather than on-the-fly when someone calls up the Taxon page. There should probably also be separate lists for 99% identity and 97% identity (not sure other thresholds make any sense).
>>>>>>
>>>>>> Thoughts? Are there other things to discuss and we should have the call anyway?
>>>>>>
>>>>>> Thanks,
>>>>>> - Dylan
>>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>
>>> _______________________________________________
>>> 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
Hi Rick,
Yeah, that's correct. Given a genome typed object, return the list of
metagenomes that potentially contain that genome. The method of determining
matches could be as simple as a 16S match above some %id and length. We
would also need the metagenome as a typed object from which we can link to
samples, sites and environments.
Paramvir
On Thu, May 16, 2013 at 2:58 PM, Rick stevens <stevens(a)anl.gov> wrote:
> Dylan
>
> I'm trying Ti understand what you want to build.
>
> I think you want some way to have some one select a taxon and bring up in
> a taxon page all genomes and metagenomes and metagenome derived contigs
> associated with that taxon..
>
> Is that correct ?
>
> Sent from my iPad
>
> On May 16, 2013, at 2:26 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote:
>
> I'm confused. Isn't this week a joint hack-a-thon? My guys flew out
> there to work with your guys. Is that not happening?
>
> Thanks,
> - Dylan
>
>
>
>
>
> On Thu, May 16, 2013 at 12:21 PM, Folker Meyer <folker(a)mcs.anl.gov> wrote:
>
>> We are super busy right now. Can we do this next week over the phone. I
>> still need some input on the actual goals of this.
>>
>>
>> --
>> Sent from mobile device
>>
>> On May 16, 2013, at 14:14, Matthew Henderson <mhenderson(a)lbl.gov> wrote:
>>
>> Paramvir, Mike and I are at Freund Lodge currently, and you guys
>> (Andreas?) are welcome to come over and be part of the excitement of the
>> KBase build and "stuff". Mike and I will also be here tomorrow morning,
>> but will have to leave around lunchtime to get back to the airport for the
>> trip back home.
>>
>> Paramvir is less concerned at the moment about thresholding and just
>> wants to see some functionality.
>>
>> Alternatively, if you are not feeling Freundlich, an email pointing us in
>> the proper direction would also be appreciated.
>>
>> Thanks,
>> Matt
>>
>>
>> On Thu, May 16, 2013 at 1:28 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote:
>>
>>> Paramvir is a stakeholder here, so we should get his input, including on
>>> which identity thresholds he'd like to see.
>>>
>>> Thanks,
>>> - Dylan
>>>
>>>
>>> On Thu, May 16, 2013 at 11:10 AM, Dylan Chivian <dcchivian(a)lbl.gov>wrote:
>>>
>>>> Hi guys,
>>>>
>>>> instead of the call today, probably the time would be best spent with
>>>> Folker and Andreas working with Matt and Mike directly on the metagenomics
>>>> species search functionality for the Taxon pages. I expect it is an
>>>> expensive operation, so it is probably something that should be a one-time
>>>> compute and stored somewhere associated with each taxon rather than
>>>> on-the-fly when someone calls up the Taxon page. There should probably
>>>> also be separate lists for 99% identity and 97% identity (not sure other
>>>> thresholds make any sense).
>>>>
>>>> Thoughts? Are there other things to discuss and we should have the
>>>> call anyway?
>>>>
>>>> Thanks,
>>>> - Dylan
>>>>
>>>>
>>>
>>> _______________________________________________
>>> 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
>>
>>
>> _______________________________________________
>> 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
>
>
> _______________________________________________
> Kbase-microcomm mailing list
> Kbase-microcomm(a)lists.kbase.us
> https://lists.kbase.us/mailman/listinfo/kbase-microcomm
>
>
