July 2011 - Mg-rast - mailman3.cels.anl.gov

Re: [mg-rast] taxonomic classification in mg rast 3
by Folker Meyer 19 Jul '11

19 Jul '11

do we not have an algorithms page on the blog? if not lets write one. I have some diagrams and docs for the paper/.... On Jul 19, 2011, at 11:50 AM, Mark D'Souza wrote: > Hi, > > The taxonomic classification in MG-RAST is obtained from the sequence similarity results against the database selected under 'annotation sources'. > > Regards, > Mark D'Souza > -- for the MG-RAST team > > mg-rast(a)mcs.anl.gov > http://metagenomics.anl.gov/ > > If you need to respond to this email please address it to the mailing-list mg-rast(a)mcs.anl.gov > > > > > On Jul 19, 2011, at 9:02 AM, <shuang(a)mpi-bremen.de> <shuang(a)mpi-bremen.de> wrote: > >> Good afternoon, dear mg-rast maintainers. >> >> I have a question about the taxonomic classification in mg-rast. I see this >> feature in the result page of my metagenome but even after I searched the >> help, no information regarding the tool, method, algorithm and so on. So I >> would really want to know which tool or tools are mg rast is using and are >> there any metatools or so are employed. Thank you very much. >> >> >> Sixing Huang >

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Fwd: bug for tree generation
by Mark D'Souza 19 Jul '11

19 Jul '11

Hi Travis, any hope for this guy? Mark Begin forwarded message: > From: Mark D'Souza <dsouza(a)mcs.anl.gov> > Date: July 19, 2011 12:05:00 PM CDT > To: amarots(a)iqsc.usp.br > Cc: mg-rast(a)mcs.anl.gov > Subject: Re: [mg-rast] bug for tree generation > > Hi, > > The database query required to create the trees becomes more complex with number of metagenomes and increasing number of filtering steps causing lengthy times for retrieval of data and may cause the tree visualization to fail, we will check and see what can be done. > > Regards, > Mark D'Souza > -- for the MG-RAST team > > mg-rast(a)mcs.anl.gov > http://metagenomics.anl.gov/ > > If you need to respond to this email please address it to the mailing-list mg-rast(a)mcs.anl.gov > > > > > On Jul 19, 2011, at 9:03 AM, amarots(a)iqsc.usp.br wrote: > >> Hello MG-RAST team, >> I wonder if you could give me a help. I can't visualize a specific data >> set saved at workbench as a tree scheme. I picked metagenomes: 4461456.3, >> 4461455.3, 4461454.3, 4461453.3,4461452.3, 4461451.3, 4453374.3, >> 4461444.3, and pooled the Bacteria domain related proteins (total of 48557 >> unique proteins, using GenBank and cutoff of 1e-5 and Min Alig Length of >> 50bp). When I try to generate a tree using this set of ptns the "data >> generation progress" keep going forever. When I use all ptns info from >> this group of metagemones, a shorter workbench set of ptns or less >> metagenomes I could get the tree scheme tough. So, it seems to be a bug >> that happens specificaly with the set of ptns that I chose. >> Thanks, >> Amaro >> >> >> >> >

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Re: [mg-rast] bug for tree generation
by Mark D'Souza 19 Jul '11

19 Jul '11

Hi, The database query required to create the trees becomes more complex with number of metagenomes and increasing number of filtering steps causing lengthy times for retrieval of data and may cause the tree visualization to fail, we will check and see what can be done. Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.anl.gov/ If you need to respond to this email please address it to the mailing-list mg-rast(a)mcs.anl.gov On Jul 19, 2011, at 9:03 AM, amarots(a)iqsc.usp.br wrote: > Hello MG-RAST team, > I wonder if you could give me a help. I can't visualize a specific data > set saved at workbench as a tree scheme. I picked metagenomes: 4461456.3, > 4461455.3, 4461454.3, 4461453.3,4461452.3, 4461451.3, 4453374.3, > 4461444.3, and pooled the Bacteria domain related proteins (total of 48557 > unique proteins, using GenBank and cutoff of 1e-5 and Min Alig Length of > 50bp). When I try to generate a tree using this set of ptns the "data > generation progress" keep going forever. When I use all ptns info from > this group of metagemones, a shorter workbench set of ptns or less > metagenomes I could get the tree scheme tough. So, it seems to be a bug > that happens specificaly with the set of ptns that I chose. > Thanks, > Amaro > > > >

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Fwd: KEGG Mapper
by Mark D'Souza 19 Jul '11

19 Jul '11

forward Begin forwarded message: > From: yanwei lim <ywlim.s(a)gmail.com> > Date: July 19, 2011 11:47:52 AM CDT > To: Mark DSouza <dsouza(a)mcs.anl.gov> > Subject: Re: [mg-rast] KEGG Mapper > > Hi, > > Thanks for the reply. I was using Google Chrome. I tried on Firefox and it works. > > Thank you! > > Best, > Yan Wei > > On Mon, Jul 18, 2011 at 11:16 PM, Mark DSouza <dsouza(a)mcs.anl.gov> wrote: > Hi, > > It sounds like you are using the KEGG mapper correctly, you need to select some metagenomes under the available list, move them to the selected list and then click on 'load data' to add them to the Data A or B sets. Which browser are you using? The MG-RAST site works best on the latest version of FireFox and all the features may not work on other browsers. The Mapper is working correctly for me, let us know which browser you are using. > > -- > Regards, > Mark D'Souza > -- for the MG-RAST team > > mg-rast(a)mcs.anl.gov > http://metagenomics.anl.gov/ > > If you need to respond to this email please address it to the mailing-list mg-rast(a)mcs.anl.gov > > > ----- Original Message ----- > > From: "yanwei lim" <ywlim.s(a)gmail.com> > > To: mg-rast(a)mcs.anl.gov > > Sent: Monday, July 18, 2011 6:27:01 PM > > Subject: [mg-rast] KEGG Mapper > > Hi, > > > > > > I would like to know whether the KEGG Mapper is functioning. When I > > tried to upload my metagenomes into the KEGG Mapper, nothing shows up > > on the Data A column, nor Data B. First, I select the metagenomes, > > click ok, and click "load data". I assumed there should be something > > in the Data A and Data B boxes on the right. > > > > > > Please explain how to use the KEGG Mapper and if it is working. > > > > > > Thank you very much. Your help is very appreciated. > > > > > > Thanks, > > Yan Wei Lim >

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Re: [mg-rast] taxonomic classification in mg rast 3
by Mark D'Souza 19 Jul '11

19 Jul '11

Hi, The taxonomic classification in MG-RAST is obtained from the sequence similarity results against the database selected under 'annotation sources'. Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.anl.gov/ If you need to respond to this email please address it to the mailing-list mg-rast(a)mcs.anl.gov On Jul 19, 2011, at 9:02 AM, <shuang(a)mpi-bremen.de> <shuang(a)mpi-bremen.de> wrote: > Good afternoon, dear mg-rast maintainers. > > I have a question about the taxonomic classification in mg-rast. I see this > feature in the result page of my metagenome but even after I searched the > help, no information regarding the tool, method, algorithm and so on. So I > would really want to know which tool or tools are mg rast is using and are > there any metatools or so are employed. Thank you very much. > > > Sixing Huang

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bug for tree generation
by amarots＠iqsc.usp.br 19 Jul '11

19 Jul '11

Hello MG-RAST team, I wonder if you could give me a help. I can't visualize a specific data set saved at workbench as a tree scheme. I picked metagenomes: 4461456.3, 4461455.3, 4461454.3, 4461453.3,4461452.3, 4461451.3, 4453374.3, 4461444.3, and pooled the Bacteria domain related proteins (total of 48557 unique proteins, using GenBank and cutoff of 1e-5 and Min Alig Length of 50bp). When I try to generate a tree using this set of ptns the "data generation progress" keep going forever. When I use all ptns info from this group of metagemones, a shorter workbench set of ptns or less metagenomes I could get the tree scheme tough. So, it seems to be a bug that happens specificaly with the set of ptns that I chose. Thanks, Amaro

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taxonomic classification in mg rast 3
by shuang＠mpi-bremen.de 19 Jul '11

19 Jul '11

Good afternoon, dear mg-rast maintainers. I have a question about the taxonomic classification in mg-rast. I see this feature in the result page of my metagenome but even after I searched the help, no information regarding the tool, method, algorithm and so on. So I would really want to know which tool or tools are mg rast is using and are there any metatools or so are employed. Thank you very much. Sixing Huang

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Re: [mg-rast] For interest....
by Jack Gilbert 19 Jul '11

19 Jul '11

thanks - this is good to know. When I am discussing these things at conferences it is useful to have these info. Cheers J On Tue, Jul 19, 2011 at 7:26 AM, Folker Meyer <folker(a)anl.gov> wrote: > For you education: the trick in clouds is that you need new paradigms for > data access. These guys have no clue in that department > > this framework just assumes that using ssh copy (scp) is a good way of > accessing data. This is just funny. not only is is slow, it also encrypts > and decrypts all the data before and after transport. Lets be nice and say > this is less than optimal. > > Good system though if your laptop cannot run clustal for a small job and > you want to run it somewhere. > > OMG > > Folker > > > > On Jul 19, 2011, at 4:29 AM, Jack Gilbert wrote: > > Thought you all might be keen to see this: > > http://code.google.com/p/yabi/wiki/WikiHome > > -- > Dr. Jack A. Gilbert B.Sc. Ph.D. > Argonne National Laboratory > Bldg. 202, Biosciences > Room B373 > 9700 South Cass Avenue > Argonne, IL, 60430 > Tel: +1 630 252-7489 > Cell: +1 630 915 2383 > Email: gilbertjack(a)anl.gov <gilbertjack(a)gmail.com> > > > -- Dr. Jack A. Gilbert B.Sc. Ph.D. Argonne National Laboratory Bldg. 202, Biosciences Room B373 9700 South Cass Avenue Argonne, IL, 60430 Tel: +1 630 252-7489 Cell: +1 630 915 2383 Email: gilbertjack(a)anl.gov <gilbertjack(a)gmail.com>

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Re: [mg-rast] For interest....
by Folker Meyer 19 Jul '11

19 Jul '11

For you education: the trick in clouds is that you need new paradigms for data access. These guys have no clue in that department this framework just assumes that using ssh copy (scp) is a good way of accessing data. This is just funny. not only is is slow, it also encrypts and decrypts all the data before and after transport. Lets be nice and say this is less than optimal. Good system though if your laptop cannot run clustal for a small job and you want to run it somewhere. OMG Folker On Jul 19, 2011, at 4:29 AM, Jack Gilbert wrote: > Thought you all might be keen to see this: > > http://code.google.com/p/yabi/wiki/WikiHome > > -- > Dr. Jack A. Gilbert B.Sc. Ph.D. > Argonne National Laboratory > Bldg. 202, Biosciences > Room B373 > 9700 South Cass Avenue > Argonne, IL, 60430 > Tel: +1 630 252-7489 > Cell: +1 630 915 2383 > Email: gilbertjack(a)anl.gov

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For interest....
by Jack Gilbert 19 Jul '11

19 Jul '11

Thought you all might be keen to see this: http://code.google.com/p/yabi/wiki/WikiHome -- Dr. Jack A. Gilbert B.Sc. Ph.D. Argonne National Laboratory Bldg. 202, Biosciences Room B373 9700 South Cass Avenue Argonne, IL, 60430 Tel: +1 630 252-7489 Cell: +1 630 915 2383 Email: gilbertjack(a)anl.gov <gilbertjack(a)gmail.com>

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