January 2013 - Microbe - mailman3.cels.anl.gov

Re: [Microbe] [Kbase-devel] Blast Services for KBase
by Shreyas Cholia 04 Jan '13

04 Jan '13

I believe this is pretty much the model we had in mind On Fri, Jan 4, 2013 at 12:55 PM, Christopher Henry <chrisshenry(a)gmail.com> wrote: > User => Blast Service => Cluster blast/Cloud blast As for documentation, the REST API to cluster services is documented here: http://140.221.92.67/services/cluster_service/docs/ (It is also in the cluster services repo) It might be useful for us to present something on how you (as a KBase service developer) can make use of cluster services at an upcoming dev telecon. -Shreyas

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Re: [Microbe] [Kbase-devel] Blast Services for KBase
by Christopher Henry 04 Jan '13

04 Jan '13

So my question is, if I want to blast a particular sequence against a particular set of genomes (which I have… and which may or may not be in the NR or CDM), can I do this using the cluster blast service? In other words, can I provide my own NR and query sequences to your service? Can I run TBlastN specifically? Is the BLAST service for the cluster documented somewhere? Can you point me at the documentation? Based on what I've seen from responses to this query, it seems like we need to create a "BLAST" service that presents a simple user-friendly ability to blast user submitted sequences against sequence data available in KBase (either in workspace or CDM). Something like this: User => Blast Service => Cluster blast/Cloud blast It wouldn't be hard to make… but I do think we need it. And I'd prefer it be designed to work with "Genome typed objects" rather than only the CDM, because I want people to be able to run the analysis on new genome sequences submitted to KBAse (via our assembly and annotation pipelines), rather than being restricted to only sequences already loaded to the CDM. On Jan 4, 2013, at 2:33 PM, Shreyas Cholia <scholia(a)lbl.gov> wrote: > Yes - hopefully I should have those mods done in the next week or so. > That would allow us to kick off small jobs in real time on a magellan > cloud node. > > -Shreyas > > On Fri, Jan 4, 2013 at 11:49 AM, Shane Canon <scanon(a)lbl.gov> wrote: >> >> Also Shreyas is making mods that would allow us to use cluster services to distribute jobs to cloud resources for scalable real time computation. >> >> Shane >> >> Sent from my iPhone >> >> On Jan 4, 2013, at 1:27 PM, Shreyas Cholia <scholia(a)lbl.gov> wrote: >> >>> We do have a blast service in cluster services if you need to perform >>> a long running blast computation. >>> >>> -Shreyas >>> >>> On Fri, Jan 4, 2013 at 9:46 AM, Michael Sneddon <mwsneddon(a)lbl.gov> wrote: >>>> Hi Chris, >>>> >>>> The sim service provides access to a precomputed all-to-all blast search, so >>>> I don't think it will help for the query you need. I've been >>>> exploring/testing the idea of using blast for the Translation service, to be >>>> able to map sequences or gene calls to features of a specific genome. I can >>>> say that blast is installed on the kbase images (including tblastn), so it >>>> is easy to call from a kbase service, but it is not yet wrapped as a general >>>> kbase service as far as I know. That said, you could take a look at the >>>> blast_tester.pl in the Translation repo or the implementation of the >>>> map_to_fid method of the Translation service for an example of how I'm >>>> calling blastp and creating a blast database for a specific genome. >>>> >>>> let me know if you have questions on this. >>>> >>>> -michael >>>> >>>> >>>> >>>> >>>> >>>> On Fri, Jan 4, 2013 at 5:41 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: >>>>> >>>>> Have you checked out the sim service Bob stood up? >>>>> >>>>> >>>>> On Jan 3, 2013, at 10:10 PM, Christopher Henry <chrisshenry(a)gmail.com> >>>>> wrote: >>>>> >>>>>> So I'm wondering what kinds of blast services exist for KBase at the >>>>>> moment. >>>>>> >>>>>> Do we offer services that enable a user to blast a particular sequence >>>>>> against all genomes in our database? >>>>>> >>>>>> Specifically, I'm interested in a service that lets me "TBlastN" a >>>>>> series of candidate protein sequences against a specified set of KBase >>>>>> genomes. The idea is I think these proteins might be in these genomes, but >>>>>> they're not being spotted in part because of an error or omission in the >>>>>> gene calls. >>>>>> >>>>>> Do we have something that does this? If not, it seems like a good >>>>>> service to create. Seems like KBase should support all forms of blast if >>>>>> possible. If it's missing and we think we want to create it, is there an >>>>>> existing service in KBase that this would fit nicely into? Perhaps the >>>>>> genome annotation service? >>>>>> >>>>>> Chris >>>>>> _______________________________________________ >>>>>> Kbase-devel mailing list >>>>>> Kbase-devel(a)lists.kbase.us >>>>>> https://lists.kbase.us/mailman/listinfo/kbase-devel >>>>> >>>>> Thomas Brettin >>>>> 865-603-7760 (cell) >>>>> brettin(a)mcs.anl.gov >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe

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Re: [Microbe] [Kbase-devel] Blast Services for KBase
by Shreyas Cholia 04 Jan '13

04 Jan '13

Yes - hopefully I should have those mods done in the next week or so. That would allow us to kick off small jobs in real time on a magellan cloud node. -Shreyas On Fri, Jan 4, 2013 at 11:49 AM, Shane Canon <scanon(a)lbl.gov> wrote: > > Also Shreyas is making mods that would allow us to use cluster services to distribute jobs to cloud resources for scalable real time computation. > > Shane > > Sent from my iPhone > > On Jan 4, 2013, at 1:27 PM, Shreyas Cholia <scholia(a)lbl.gov> wrote: > >> We do have a blast service in cluster services if you need to perform >> a long running blast computation. >> >> -Shreyas >> >> On Fri, Jan 4, 2013 at 9:46 AM, Michael Sneddon <mwsneddon(a)lbl.gov> wrote: >>> Hi Chris, >>> >>> The sim service provides access to a precomputed all-to-all blast search, so >>> I don't think it will help for the query you need. I've been >>> exploring/testing the idea of using blast for the Translation service, to be >>> able to map sequences or gene calls to features of a specific genome. I can >>> say that blast is installed on the kbase images (including tblastn), so it >>> is easy to call from a kbase service, but it is not yet wrapped as a general >>> kbase service as far as I know. That said, you could take a look at the >>> blast_tester.pl in the Translation repo or the implementation of the >>> map_to_fid method of the Translation service for an example of how I'm >>> calling blastp and creating a blast database for a specific genome. >>> >>> let me know if you have questions on this. >>> >>> -michael >>> >>> >>> >>> >>> >>> On Fri, Jan 4, 2013 at 5:41 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: >>>> >>>> Have you checked out the sim service Bob stood up? >>>> >>>> >>>> On Jan 3, 2013, at 10:10 PM, Christopher Henry <chrisshenry(a)gmail.com> >>>> wrote: >>>> >>>>> So I'm wondering what kinds of blast services exist for KBase at the >>>>> moment. >>>>> >>>>> Do we offer services that enable a user to blast a particular sequence >>>>> against all genomes in our database? >>>>> >>>>> Specifically, I'm interested in a service that lets me "TBlastN" a >>>>> series of candidate protein sequences against a specified set of KBase >>>>> genomes. The idea is I think these proteins might be in these genomes, but >>>>> they're not being spotted in part because of an error or omission in the >>>>> gene calls. >>>>> >>>>> Do we have something that does this? If not, it seems like a good >>>>> service to create. Seems like KBase should support all forms of blast if >>>>> possible. If it's missing and we think we want to create it, is there an >>>>> existing service in KBase that this would fit nicely into? Perhaps the >>>>> genome annotation service? >>>>> >>>>> Chris >>>>> _______________________________________________ >>>>> Kbase-devel mailing list >>>>> Kbase-devel(a)lists.kbase.us >>>>> https://lists.kbase.us/mailman/listinfo/kbase-devel >>>> >>>> Thomas Brettin >>>> 865-603-7760 (cell) >>>> brettin(a)mcs.anl.gov >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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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Re: [Microbe] [Kbase-devel] Blast Services for KBase
by Shane Canon 04 Jan '13

04 Jan '13

Also Shreyas is making mods that would allow us to use cluster services to distribute jobs to cloud resources for scalable real time computation. Shane Sent from my iPhone On Jan 4, 2013, at 1:27 PM, Shreyas Cholia <scholia(a)lbl.gov> wrote: > We do have a blast service in cluster services if you need to perform > a long running blast computation. > > -Shreyas > > On Fri, Jan 4, 2013 at 9:46 AM, Michael Sneddon <mwsneddon(a)lbl.gov> wrote: >> Hi Chris, >> >> The sim service provides access to a precomputed all-to-all blast search, so >> I don't think it will help for the query you need. I've been >> exploring/testing the idea of using blast for the Translation service, to be >> able to map sequences or gene calls to features of a specific genome. I can >> say that blast is installed on the kbase images (including tblastn), so it >> is easy to call from a kbase service, but it is not yet wrapped as a general >> kbase service as far as I know. That said, you could take a look at the >> blast_tester.pl in the Translation repo or the implementation of the >> map_to_fid method of the Translation service for an example of how I'm >> calling blastp and creating a blast database for a specific genome. >> >> let me know if you have questions on this. >> >> -michael >> >> >> >> >> >> On Fri, Jan 4, 2013 at 5:41 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: >>> >>> Have you checked out the sim service Bob stood up? >>> >>> >>> On Jan 3, 2013, at 10:10 PM, Christopher Henry <chrisshenry(a)gmail.com> >>> wrote: >>> >>>> So I'm wondering what kinds of blast services exist for KBase at the >>>> moment. >>>> >>>> Do we offer services that enable a user to blast a particular sequence >>>> against all genomes in our database? >>>> >>>> Specifically, I'm interested in a service that lets me "TBlastN" a >>>> series of candidate protein sequences against a specified set of KBase >>>> genomes. The idea is I think these proteins might be in these genomes, but >>>> they're not being spotted in part because of an error or omission in the >>>> gene calls. >>>> >>>> Do we have something that does this? If not, it seems like a good >>>> service to create. Seems like KBase should support all forms of blast if >>>> possible. If it's missing and we think we want to create it, is there an >>>> existing service in KBase that this would fit nicely into? Perhaps the >>>> genome annotation service? >>>> >>>> Chris >>>> _______________________________________________ >>>> Kbase-devel mailing list >>>> Kbase-devel(a)lists.kbase.us >>>> https://lists.kbase.us/mailman/listinfo/kbase-devel >>> >>> Thomas Brettin >>> 865-603-7760 (cell) >>> brettin(a)mcs.anl.gov >>> >>> >>> >>> _______________________________________________ >>> 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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Re: [Microbe] [Kbase-devel] Blast Services for KBase
by Shreyas Cholia 04 Jan '13

04 Jan '13

We do have a blast service in cluster services if you need to perform a long running blast computation. -Shreyas On Fri, Jan 4, 2013 at 9:46 AM, Michael Sneddon <mwsneddon(a)lbl.gov> wrote: > Hi Chris, > > The sim service provides access to a precomputed all-to-all blast search, so > I don't think it will help for the query you need. I've been > exploring/testing the idea of using blast for the Translation service, to be > able to map sequences or gene calls to features of a specific genome. I can > say that blast is installed on the kbase images (including tblastn), so it > is easy to call from a kbase service, but it is not yet wrapped as a general > kbase service as far as I know. That said, you could take a look at the > blast_tester.pl in the Translation repo or the implementation of the > map_to_fid method of the Translation service for an example of how I'm > calling blastp and creating a blast database for a specific genome. > > let me know if you have questions on this. > > -michael > > > > > > On Fri, Jan 4, 2013 at 5:41 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: >> >> Have you checked out the sim service Bob stood up? >> >> >> On Jan 3, 2013, at 10:10 PM, Christopher Henry <chrisshenry(a)gmail.com> >> wrote: >> >> > So I'm wondering what kinds of blast services exist for KBase at the >> > moment. >> > >> > Do we offer services that enable a user to blast a particular sequence >> > against all genomes in our database? >> > >> > Specifically, I'm interested in a service that lets me "TBlastN" a >> > series of candidate protein sequences against a specified set of KBase >> > genomes. The idea is I think these proteins might be in these genomes, but >> > they're not being spotted in part because of an error or omission in the >> > gene calls. >> > >> > Do we have something that does this? If not, it seems like a good >> > service to create. Seems like KBase should support all forms of blast if >> > possible. If it's missing and we think we want to create it, is there an >> > existing service in KBase that this would fit nicely into? Perhaps the >> > genome annotation service? >> > >> > Chris >> > _______________________________________________ >> > Kbase-devel mailing list >> > Kbase-devel(a)lists.kbase.us >> > https://lists.kbase.us/mailman/listinfo/kbase-devel >> >> Thomas Brettin >> 865-603-7760 (cell) >> brettin(a)mcs.anl.gov >> >> >> >> _______________________________________________ >> 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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Re: [Microbe] [Kbase-devel] Blast Services for KBase
by Michael Sneddon 04 Jan '13

04 Jan '13

Hi Chris, The sim service provides access to a precomputed all-to-all blast search, so I don't think it will help for the query you need. I've been exploring/testing the idea of using blast for the Translation service, to be able to map sequences or gene calls to features of a specific genome. I can say that blast is installed on the kbase images (including tblastn), so it is easy to call from a kbase service, but it is not yet wrapped as a general kbase service as far as I know. That said, you could take a look at the blast_tester.pl in the Translation repo or the implementation of the map_to_fid method of the Translation service for an example of how I'm calling blastp and creating a blast database for a specific genome. let me know if you have questions on this. -michael On Fri, Jan 4, 2013 at 5:41 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > Have you checked out the sim service Bob stood up? > > > On Jan 3, 2013, at 10:10 PM, Christopher Henry <chrisshenry(a)gmail.com> > wrote: > > > So I'm wondering what kinds of blast services exist for KBase at the > moment. > > > > Do we offer services that enable a user to blast a particular sequence > against all genomes in our database? > > > > Specifically, I'm interested in a service that lets me "TBlastN" a > series of candidate protein sequences against a specified set of KBase > genomes. The idea is I think these proteins might be in these genomes, but > they're not being spotted in part because of an error or omission in the > gene calls. > > > > Do we have something that does this? If not, it seems like a good > service to create. Seems like KBase should support all forms of blast if > possible. If it's missing and we think we want to create it, is there an > existing service in KBase that this would fit nicely into? Perhaps the > genome annotation service? > > > > Chris > > _______________________________________________ > > Kbase-devel mailing list > > Kbase-devel(a)lists.kbase.us > > https://lists.kbase.us/mailman/listinfo/kbase-devel > > Thomas Brettin > 865-603-7760 (cell) > brettin(a)mcs.anl.gov > > > > _______________________________________________ > Kbase-devel mailing list > Kbase-devel(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/kbase-devel >

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Re: [Microbe] [Kbase-devel] Blast Services for KBase
by Thomas Brettin 04 Jan '13

04 Jan '13

Have you checked out the sim service Bob stood up? On Jan 3, 2013, at 10:10 PM, Christopher Henry <chrisshenry(a)gmail.com> wrote: > So I'm wondering what kinds of blast services exist for KBase at the moment. > > Do we offer services that enable a user to blast a particular sequence against all genomes in our database? > > Specifically, I'm interested in a service that lets me "TBlastN" a series of candidate protein sequences against a specified set of KBase genomes. The idea is I think these proteins might be in these genomes, but they're not being spotted in part because of an error or omission in the gene calls. > > Do we have something that does this? If not, it seems like a good service to create. Seems like KBase should support all forms of blast if possible. If it's missing and we think we want to create it, is there an existing service in KBase that this would fit nicely into? Perhaps the genome annotation service? > > Chris > _______________________________________________ > Kbase-devel mailing list > Kbase-devel(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/kbase-devel Thomas Brettin 865-603-7760 (cell) brettin(a)mcs.anl.gov

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Re: [Microbe] Blast Services for KBase
by Adam Arkin 03 Jan '13

03 Jan '13

Definitely-- this is a good example of services that are needed to round out expected capabilities for the system. We should enumerate as many of these as possible asap. Adam On Thu, Jan 3, 2013 at 8:10 PM, Christopher Henry <chrisshenry(a)gmail.com>wrote: > So I'm wondering what kinds of blast services exist for KBase at the > moment. > > Do we offer services that enable a user to blast a particular sequence > against all genomes in our database? > > Specifically, I'm interested in a service that lets me "TBlastN" a series > of candidate protein sequences against a specified set of KBase genomes. > The idea is I think these proteins might be in these genomes, but they're > not being spotted in part because of an error or omission in the gene calls. > > Do we have something that does this? If not, it seems like a good service > to create. Seems like KBase should support all forms of blast if possible. > If it's missing and we think we want to create it, is there an existing > service in KBase that this would fit nicely into? Perhaps the genome > annotation service? > > Chris > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe > -- Adam Paul Arkin Dean A. Richard Newton Memorial Chair ------------------------------------- Director, Physical Biosciences Division E.O. Lawrence Berkeley National Laboratory Professor, Department of Bioengineering University of California Berkeley, CA, 94720 CEO/CSO, DOE Systems Biology Knowledgebase, http://kbase.us Director, Berkeley Synthetic Biology Institute, http://synbio.berkeley.edu PI and Co-Director, Virtual Institute of Microbial Stress and Survival, http://vimss.lbl.gov Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org Office: 512C Energy Biosciences Building (Berkeley Campus) Mailing address: E.O. Lawrence Berkeley National Laboratory 1 Cyclotron Road, MS 955-512L Berkeley, CA 94720 Contact: W: http://genomics.lbl.gov V: 510-495-2366 C: 510-206-1389 F: 510-486-6219 Assistant: Gwyneth A. Terry V: 510-495-2116 E: GATerry(a)lbl.gov -------------------------------------

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Blast Services for KBase
by Christopher Henry 03 Jan '13

03 Jan '13

So I'm wondering what kinds of blast services exist for KBase at the moment. Do we offer services that enable a user to blast a particular sequence against all genomes in our database? Specifically, I'm interested in a service that lets me "TBlastN" a series of candidate protein sequences against a specified set of KBase genomes. The idea is I think these proteins might be in these genomes, but they're not being spotted in part because of an error or omission in the gene calls. Do we have something that does this? If not, it seems like a good service to create. Seems like KBase should support all forms of blast if possible. If it's missing and we think we want to create it, is there an existing service in KBase that this would fit nicely into? Perhaps the genome annotation service? Chris

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