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

Re: [mg-rast] Organismal PCoA
by Mark DSouza 30 Aug '11

30 Aug '11

Hi, Sorry about that, unfortunately this is not something you can fix on your end. We will look into this and get it fixed, thanks for bringing it to our attention. -- 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: "Julia P Galkiewicz" <jgalkiewicz(a)usgs.gov> > To: mg-rast(a)mcs.anl.gov > Sent: Monday, August 29, 2011 12:03:36 PM > Subject: [mg-rast] Organismal PCoA > Hi- > > When I make a PCoA plot and try to group the various libraries, the > colors don't correspond with the library numbers. So I'm not sure if > the dots are mislabeled with the library numbers, or if the mechanism > to color in the dots is incorrect. This is a recent problem, because I > was able to correctly group PCoAs just a few weeks ago. Is there > anything I can do to fix the problem on my end? > > -Julie > > > Julie Galkiewicz > Marine Microbiology Lab > USGS St. Petersburg > jgalkiewicz(a)usgs.gov

1 0

Re: [mg-rast] A quick question
by Mark DSouza 30 Aug '11

30 Aug '11

Hi, Once you have selected your features to the workbench the workbench tab will have a link 'download metagenome dna FASTA annotated by' where you can select a dabase source and download the sequence data. The md5s do refer to protein sequences, these are clickable and will display all the annotations from the databases used to create the m5nr non-redundant protein database. Regards, Mark ----- Original Message ----- > From: "fancy-yf" <fancy-yf(a)163.com> > To: "Mark DSouza" <dsouza(a)mcs.anl.gov> > Sent: Tuesday, August 30, 2011 7:20:59 AM > Subject: Re: Re: [mg-rast] A quick question > Hello, Mark > > Do you mean the column of md5s?Is it refer to the protein sequences? > Actually, I can't find other specific column in the workbench on > downloading fasta-formatted sequences. > Would you mind tell me how to find that? > > Thanks! > > > 2011-08-30 > > fancy-yf > > 发件人： Mark DSouza > 发送时间： 2011-08-22 23:18:49 > 收件人： fancy-yf > 抄送： mg-rast > 主题： Re: [mg-rast] A quick question > > > Hi, > > The workbench enables download of individual sequences, select the > rows for the function under the 'to workbench column'. The workbench > is then accessed through the 'Workbench tab' where you can download > fasta formatted metagenomic sequence data for the selected sequences. > > -- > 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: "fancy-yf" <fancy-yf(a)163.com> > > To: "mg-rast" <mg-rast(a)mcs.anl.gov> > > Sent: Sunday, August 21, 2011 9:15:45 PM > > Subject: [mg-rast] A quick question > > Hello, > > > > Here I have a question and might need your help. For the MG-RAST > > annotation result of my metagenomic data downloaded from MG-RAST > > server (as attached). Here I want to find the exact sequence of > > specific object in function column (eg. Alanine racemase (EC > > 5.1.1.1) > > ). How could I get that sequence? > > > > Hope for your replies! > > > > fancy > > > > > > 2011-08-22 > > > > fancy-yf

1 0

Re: [mg-rast] 2 problems
by Mark DSouza 30 Aug '11

30 Aug '11

Hi, And thanks, glad to hear the system is useful to you. The recruitment plot should work for all datasets, including private ones. Please send us the MG-RAST ID for the dataset and a description of the failure mode, with screenshots if possible and we will look into it. You can also examine the data analysis through the organism hierarchical classification tools (table, barchart, heatmap, tree) to determine dominant species through the abundance counts. We will be adding a delete function in the next release, till then if you send me the MG-RAST IDs for the datasets to be deleted I can do this for you. -- 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: panoble(a)washington.edu > To: mg-rast(a)mcs.anl.gov > Sent: Tuesday, August 30, 2011 10:15:02 AM > Subject: [mg-rast] 2 problems > Hi, > > 1) I want to do a recruitment plot of a certain bacterial species and > my private data sets but mg-rast will only let me use public data > sets.... why? How can I test to see if I have a dominant known species > in my 454 samples, as my analyses show? > > 2) There appears to be function to delete files. I put a couple test > files on your site to see how your web site works. However, they are > now useless. How do I get rid of them.... I looked for delete > functions but could not find. > > Lastly, nice programs.... I am having fun playing with my data. > > Peter

1 0

Re: [mg-rast] deleting jobs
by Mark DSouza 30 Aug '11

30 Aug '11

Hi, If you let me know the MG-RAST IDs for the datasets to be deleted I can do this, we will add this functionality later on. -- 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: "Jim Wallace" <jwallace(a)u.washington.edu> > To: mg-rast(a)mcs.anl.gov > Sent: Tuesday, August 30, 2011 10:34:54 AM > Subject: [mg-rast] deleting jobs > Hello, > > How can I delete projects that are obsolete or redundant? > > Thanks, > > Jim Wallace

1 0

Re: [mg-rast] MG-RAST version 3.0 beta test
by Mark D'Souza 30 Aug '11

30 Aug '11

Hi, Sorry about that, we did add user edit capabilities, the overview page has a 'Edit Metadata' button which will take you to the editor where you can make the changes, click on the green tabs or step through them with the 'next' button and go to the last step with the 'finish' button to save the changes. I would be happy to make the changes listed in your second email, let me know the MG-RAST ID(s) for the dataset for which the changes should be applied. Regards, Mark On Aug 30, 2011, at 9:21 AM, Hilary Morrison wrote: > Has this edit ability been implemented? Because I have multiple datasets that are apparently still credited to Laura Katz--hearing this from a data user. > > Yes, that must be right, the abstract for the paper you mention is down as the project description on the MG-RAST page. I am guessing that is not an accurate description either, if you would like to replace it send the text over to me. > > We will make it possible for the owner of a data set to edit the related metadata of course, it is not fully functional in the beta version. > > Regards, > Mark > > ----- Original Message ----- > > From: "Hilary Morrison" <morrison(a)mbl.edu> > > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > > Sent: Tuesday, December 21, 2010 3:13:15 PM > > Subject: Re: MG-RAST version 3.0 beta test > > Mark, > > > > There are ~20 different libraries under this project "NIH Protist cDNA > > Survey". So far, the only published paper was from the Katz lab, with > > 1st author currently at UMass. PMID: 20656852 . I am a coauthor on the > > paper. > > > > I communicated with Katya Dribinsky about it in June and sent her the > > reference but didn't expect the PI and institution to get changed. > > > > Thank you; this explains the mystery. > > > > Hilary > > > > > > > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > Hilary G. Morrison, Ph.D. > > Associate Research Scientist > > Josephine Bay Paul Center, MBL > > 7 MBL Street > > Woods Hole, MA 02543-1015 > > > > 508-289-7339 > > morrison(a)mbl.edu > > > > ----- Original Message ----- > > From: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > > To: "Hilary Morrison" <morrison(a)mbl.edu> > > Cc: mg-rast-beta(a)mcs.anl.gov > > Sent: Tuesday, December 21, 2010 3:43:27 PM > > Subject: Re: MG-RAST version 3.0 beta test > > > > Hi, > > > > Sorry about that, this has now been corrected to: > > Job Bodoxxx (4442415.3) > > Project NIH Protist cDNA Survey > > PI Hilary Morrison > > Organization Marine Biological Laboratory > > > > We entered the project metadata from the literature and email > > communication with authors as far as possible, I guess in this case > > something went wrong. Please let us know if you see anything else that > > needs correcting. > > > > -- > > 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: "Hilary Morrison" <morrison(a)mbl.edu> > > > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > > > Sent: Tuesday, December 21, 2010 7:36:34 AM > > > Subject: Re: MG-RAST version 3.0 beta test > > > Here's an immediate problem, raised by another beta tester. > > > > > > Job Bodoxxx (4442415.3) > > > Project NIH Protist cDNA Survey > > > PI Laura Katz > > > University of Massachusetts > > > > > > > > > Laura Katz was NOT the PI on the NIH Protist cDNA Survey projects, I > > > was. I submitted the datasets, made them publicly available, and > > > added > > > Laura to one or more as a user in the interim. Neither she nor I is > > > affiliated with UMass. She is at Smith; I am at MBL. > > > > > > Please correct this. Where did you come up with these project > > > metadata > > > anyway? > > > > > > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > Hilary G. Morrison, Ph.D. > > > Associate Research Scientist > > > Josephine Bay Paul Center, MBL > > > 7 MBL Street > > > Woods Hole, MA 02543-1015 > > > > > > 508-289-7339 > > > morrison(a)mbl.edu > >

1 0

deleting jobs
by Jim Wallace 30 Aug '11

30 Aug '11

Hello, How can I delete projects that are obsolete or redundant? Thanks, Jim Wallace

1 0

2 problems
by panoble＠washington.edu 30 Aug '11

30 Aug '11

Hi, 1) I want to do a recruitment plot of a certain bacterial species and my private data sets but mg-rast will only let me use public data sets.... why? How can I test to see if I have a dominant known species in my 454 samples, as my analyses show? 2) There appears to be function to delete files. I put a couple test files on your site to see how your web site works. However, they are now useless. How do I get rid of them.... I looked for delete functions but could not find. Lastly, nice programs.... I am having fun playing with my data. Peter

1 0

Organismal PCoA
by Galkiewicz, Julia P 29 Aug '11

29 Aug '11

Hi- When I make a PCoA plot and try to group the various libraries, the colors don't correspond with the library numbers. So I'm not sure if the dots are mislabeled with the library numbers, or if the mechanism to color in the dots is incorrect. This is a recent problem, because I was able to correctly group PCoAs just a few weeks ago. Is there anything I can do to fix the problem on my end? -Julie Julie Galkiewicz Marine Microbiology Lab USGS St. Petersburg jgalkiewicz(a)usgs.gov

1 0

Re: [mg-rast] HeatMap analysis?
by raw937＠gmail.com 29 Aug '11

29 Aug '11

Hello again, Would it be possible to make the rarefraction graph extractable into an image file? This is a really good new option but you can't extract it. Thanks Rick Sent from my “contract free” BlackBerry® smartphone on the WIND network. -----Original Message----- From: Mark DSouza <dsouza(a)mcs.anl.gov> Date: Mon, 29 Aug 2011 10:07:40 To: Rick White<raw937(a)gmail.com> Cc: <mg-rast(a)mcs.anl.gov> Subject: Re: HeatMap analysis? Hi, Thanks for the suggestions, I will add them as feature requests and we will consider making these changes. -- 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: "Rick White" <raw937(a)gmail.com> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov>, mg-rast(a)mcs.anl.gov > Sent: Saturday, August 27, 2011 2:50:22 AM > Subject: Re: HeatMap analysis? > Hello again, > I also noticed that you can't export the rarefaction plot in a figure > format. > > It would be great to have this. > > Thank you > Rick > > > On Fri, Aug 26, 2011 at 3:41 PM, Rick White < raw937(a)gmail.com > > wrote: > > > > Hello Mark, > I have noticed that the scale bar isn't included with the image. > Also, the order of the samples doesn't in the order that you select. > > For example > I pick samples > A , B , C > > The analysis moves them all around in a different order. Would it be > possible to make the output in the order you select like the barchart? > > Thanks > Rick > > -- > > Richard Allen White III M.S. > PhD Student - Suttle Lab > Department of Microbiology & Immunology > The University of British Columbia > Vancouver, BC, Canada > V6T 1Z4 > ph. (604) 827-5715 > cell. ***My new number is 604-440-5150 *** > http://www.ocgy.ubc.ca/~suttle/ > > For Shipping: > Richard Allen White III & Amy Chan > Suttle Lab > UBC-Botany/zoology/micro > 1316-6270 University Blvd. > Vancouver, BC > V6T 1Z4 > 1.604.827.5715 > > > > > -- > > Richard Allen White III M.S. > PhD Student - Suttle Lab > Department of Microbiology & Immunology > The University of British Columbia > Vancouver, BC, Canada > V6T 1Z4 > ph.(604) 827-5715 > cell. ***My new number is 604-440-5150 *** > http://www.ocgy.ubc.ca/~suttle/ > > For Shipping: > Richard Allen White III & Amy Chan > Suttle Lab > UBC-Botany/zoology/micro > 1316-6270 University Blvd. > Vancouver, BC > V6T 1Z4 > 1.604.827.5715

1 0

Fwd: HeatMap analysis?
by Mark DSouza 29 Aug '11

29 Aug '11

Couple of suggestions from a user. Mark ----- Forwarded Message ----- > From: "Rick White" <raw937(a)gmail.com> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov>, mg-rast(a)mcs.anl.gov > Sent: Saturday, August 27, 2011 2:50:22 AM > Subject: Re: HeatMap analysis? > Hello again, > I also noticed that you can't export the rarefaction plot in a figure > format. > > It would be great to have this. > > Thank you > Rick > > > On Fri, Aug 26, 2011 at 3:41 PM, Rick White < raw937(a)gmail.com > > wrote: > > > > Hello Mark, > I have noticed that the scale bar isn't included with the image. > Also, the order of the samples doesn't in the order that you select. > > For example > I pick samples > A , B , C > > The analysis moves them all around in a different order. Would it be > possible to make the output in the order you select like the barchart? > > Thanks > Rick > > -- > > Richard Allen White III M.S. > PhD Student - Suttle Lab > Department of Microbiology & Immunology > The University of British Columbia > Vancouver, BC, Canada > V6T 1Z4 > ph. (604) 827-5715 > cell. ***My new number is 604-440-5150 *** > http://www.ocgy.ubc.ca/~suttle/ > > For Shipping: > Richard Allen White III & Amy Chan > Suttle Lab > UBC-Botany/zoology/micro > 1316-6270 University Blvd. > Vancouver, BC > V6T 1Z4 > 1.604.827.5715 > > > > > -- > > Richard Allen White III M.S. > PhD Student - Suttle Lab > Department of Microbiology & Immunology > The University of British Columbia > Vancouver, BC, Canada > V6T 1Z4 > ph.(604) 827-5715 > cell. ***My new number is 604-440-5150 *** > http://www.ocgy.ubc.ca/~suttle/ > > For Shipping: > Richard Allen White III & Amy Chan > Suttle Lab > UBC-Botany/zoology/micro > 1316-6270 University Blvd. > Vancouver, BC > V6T 1Z4 > 1.604.827.5715

1 0