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

Re: [mg-rast] regarding the MG-RAST already uploaded genomes
by Mark D'Souza 26 Apr '11

26 Apr '11

Dear Dr. Sena, The two jobs you submitted to MG-RAST were completed on April 2nd and are available for viewing. If you log in to the MG-RAST version 3 site at http://metagenomics.anl.gov/metagenomics.cgi and click on the 'Browse' button in the top right hand corner and then you can view the list of your metagenomes by clicking on the number next to 'Available for analysis' as shown in the attached image. We encourage you to make your data public through MG-RAST after publication, our policy regarding data retention is available at http://blog.metagenomics.anl.gov/mg-rast-v3-0-faq/#question8 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 Apr 25, 2011, at 10:01 PM, suchitra sena wrote: > Sir, > I have uploaded two metagenomes in the month of January 3rd week i.e., job No.'s assigned as 13802 and 13803. Now I am unable to see the data and these jobs are not there in my login account and I would like to know how I can get these data or kindly provide me this as I am in the process of data analysing and preparing for publications. Kindly also let me know that till how many days the data can be visualised further after sending. Submitted for an earlier reply in this regard. > Thanking you, > Yours faithfully, > D. Suchitra Sena, > Senior Scientist,

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Re: [mg-rast] Help taxonomic classification
by Mark D'Souza 26 Apr '11

26 Apr '11

Hi, It sounds like your analysis is in a fairly advanced stage. I am afraid we can not help you with the results you have in the excel file and I don't know of any software package that will use your results. The taxonomy information should be available on the website of the database used to obtain the 5 most similar hits, for example, NCBI has their entire taxonomy database available for download. It sounds like the data processing you require is fairly straightforward and your university will certainly have some people who will be able to help you. If you wish to, you could also submit the fasta file to the MG-RAST server for analysis. 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 Apr 26, 2011, at 9:32 AM, Inês Alexandra Fernandes Martins wrote: > I'm doing a bioinformatic project and I have a large excel file, containing > a large amount of annotated sequences (with the five most similar hits for > each) that were obtained from root-soil samples. (I have also the file > contigs.fasta) > Since there are sequences of all taxonomic groups (Plant, Animal, Fungi, > bacterial, protist) i would like to find some software application that > could discriminate between sequences from each taxonomic group. > > How can i do this? Do you know? can you advise me some person knowing this > kind of things? > > Inês Martins > University of Minho > Portugal > > > > >

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Re: [mg-rast] graph generation
by Mark D'Souza 26 Apr '11

26 Apr '11

Folker, anticipating your response ... Tobi pretty much has this done already and will put it in. Mark ----- Original Message ----- > From: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > To: "Michael Morowitz" <michael.morowitz(a)chp.edu> > Cc: mg-rast(a)mcs.anl.gov > Sent: Tuesday, April 26, 2011 11:10:21 AM > Subject: Re: [mg-rast] graph generation > Hi, > > Some of the graphs are regular images and can be saved using the > normal right-click and save option in your browser. Others are not > regular images and cannot be downloaded or exported right now. I will > make this a feature request and we will add this capability to the > system in the future, it may take up to a couple of weeks to become > available. > > 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 Apr 26, 2011, at 8:22 AM, Morowitz, Michael wrote: > > > Hi, > > > > How can I save or export the graphs generated in the metagenome data > > analysis? > > > > Michael J. Morowitz, MD > > Assistant Professor of Surgery > > University of Pittsburgh School of Medicine > > Attending Pediatric Surgeon, Division of Pediatric General and > > Thoracic Surgery > > Children's Hospital of Pittsburgh of UPMC > > Faculty Pavilion 7th Floor > > 4401 Penn Avenue > > Pittsburgh, PA 15224 > > > > Office: 412 692 5976 > > Fax: 412 692 8299

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Re: [mg-rast] graph generation
by Mark D'Souza 26 Apr '11

26 Apr '11

Hi, Some of the graphs are regular images and can be saved using the normal right-click and save option in your browser. Others are not regular images and cannot be downloaded or exported right now. I will make this a feature request and we will add this capability to the system in the future, it may take up to a couple of weeks to become available. 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 Apr 26, 2011, at 8:22 AM, Morowitz, Michael wrote: > Hi, > > How can I save or export the graphs generated in the metagenome data analysis? > > Michael J. Morowitz, MD > Assistant Professor of Surgery > University of Pittsburgh School of Medicine > Attending Pediatric Surgeon, Division of Pediatric General and Thoracic Surgery > Children's Hospital of Pittsburgh of UPMC > Faculty Pavilion 7th Floor > 4401 Penn Avenue > Pittsburgh, PA 15224 > > Office: 412 692 5976 > Fax: 412 692 8299

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Help taxonomic classification
by Inês Alexandra Fernandes Martins 26 Apr '11

26 Apr '11

I'm doing a bioinformatic project and I have a large excel file, containing a large amount of annotated sequences (with the five most similar hits for each) that were obtained from root-soil samples. (I have also the file contigs.fasta) Since there are sequences of all taxonomic groups (Plant, Animal, Fungi, bacterial, protist) i would like to find some software application that could discriminate between sequences from each taxonomic group. How can i do this? Do you know? can you advise me some person knowing this kind of things? Inês Martins University of Minho Portugal

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graph generation
by Morowitz, Michael 26 Apr '11

26 Apr '11

Hi, How can I save or export the graphs generated in the metagenome data analysis? Michael J. Morowitz, MD Assistant Professor of Surgery University of Pittsburgh School of Medicine Attending Pediatric Surgeon, Division of Pediatric General and Thoracic Surgery Children's Hospital of Pittsburgh of UPMC Faculty Pavilion 7th Floor 4401 Penn Avenue Pittsburgh, PA 15224 Office: 412 692 5976 Fax: 412 692 8299

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regarding the MG-RAST already uploaded genomes
by suchitra sena 25 Apr '11

25 Apr '11

Sir, I have uploaded two metagenomes in the month of January 3rd week i.e., job No.'s assigned as 13802 and 13803. Now I am unable to see the data and these jobs are not there in my login account and I would like to know how I can get these data or kindly provide me this as I am in the process of data analysing and preparing for publications. Kindly also let me know that till how many days the data can be visualised further after sending. Submitted for an earlier reply in this regard. Thanking you, Yours faithfully, D. Suchitra Sena, Senior Scientist,

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Re: [mg-rast] [rast] Regarding earlier annoted jobs
by Gordon D. Pusch 25 Apr '11

25 Apr '11

Dear D. Suchitra Sena --- You appear to be an MG-RAST user. Please note that you have reached the contact address for Whole-Genome RAST. Inquiries regarding MG-RAST should be directed to <mg-rast(a)mcs.anl.gov>. Sincerely, -- Dr. Gordon D. Pusch RAST development Team On 2011-Apr-25, at 6:58 PM, Suchitra sena Dande wrote: > Sir, > I have already submitted two jobs i.e., Rumen A and Rumen B and have successfully completed under private genomes. But now I am unable to view my data. Kindly help me in this regard. I have uploaded in the month of January. > > Thanking you > D Suchitra Sena > E-mail id: dssena26(a)gmail.com

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Re: [mg-rast] Early access of NIH HMP oral metagenome data
by Felicia Qi 25 Apr '11

25 Apr '11

Dear Mark, I am playing with the Keggmapper. It worked for Gary, but I could not load the data to the data box. Here is the screen shot. Could you help me solve the problem? Thanks. Felicia On Apr 21, 2011, at 1:31 PM, Mark D'Souza wrote: > Hi Gary, > > This job was run under both version 2 of MG-RAST (at http:// > metagenomics.anl.gov/v2/metagenomics.cgi) as well as version 3 > (http://metagenomics.anl.gov/metagenomics.cgi) the job is shared > with Felicia under both versions, but yes, she will have to log in > through the front page before accessing it. I tried this using both > your accounts, in both versions and had no problem, though Felicia > will have to agree to the terms of service in version 3 before > viewing the analysis. If you'll continue to have any problems > accessing this or other jobs let us know. > > Regards, > Mark > > > > On Apr 21, 2011, at 1:09 PM, Gary Xie wrote: > >> I believe you have to login first. If you have the same issue, you >> might want to contact the MG-rast team at mg-rast(a)mcs.anl.gov >> This site is maintained by them. >> Gary >> >> On Apr 21, 2011, at 11:59 AM, Felicia Qi wrote: >> >>> Gary, >>> >>> I cannot open any of these pages. here is the message I got: >>> >>> An error has occured: >>> >>> Unable to retrieve the job for metagenome '4453939.3'. >>> >>> To continue please go back to the start page. >>> >>> On Apr 21, 2011, at 12:07 PM, Gary Xie wrote: >>> >>>> Hi, Felicia, >>>> I just grant you to have an early access of our NIH oral HMP >>>> contigs >>>> (>300bp) and 454 reads. >>>> Please be aware that we should not publish anything using these >>>> data >>>> until the main NIH/HMP science/nature paper came out. >>>> Let me know if you have any question. Thanks, >>>> Gary >>> >> >

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Re: [mg-rast] functional data analysis
by Mark D'Souza 25 Apr '11

25 Apr '11

Hi Amaro, I tried this and did not have any trouble, I was able to create the attached heatmap image using all your datasets. The tree allows comparison of only two datasets at a time as the visualization becomes too complex otherwise. Regards, Mark ----- Original Message ----- > From: amarots(a)iqsc.usp.br > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Sent: Monday, April 25, 2011 3:29:05 PM > Subject: functional data analysis > Hello Mark, > I've been analyzing my MGs data all together for "organism > classification", and that works very fine for all "data visualization" > tools available at MG-RAST 3 version (tree, table, heatmap, etc). > Although, I can't get an "all together" analysis when setting for > "functional classification". Instead, when I click on "generate", I > get > back a pairwise analysis, with the program considering only the two > MGs > firstly selected. > What should I do differently for being able to analyze all MGs > together at > "functional classification"? > Best regards, > Amaro > > > > > > > > No problem, I made the changes. > > > > Regards, > > Mark > > > > ----- Original Message ----- > >> From: amarots(a)iqsc.usp.br > >> To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > >> Sent: Wednesday, April 13, 2011 11:10:08 AM > >> Subject: Re: renaming MG data at MG-RAST > >> Thanks a lot Mark! > >> The changes would be: > >> 1) metagenome 4461449.3 - AmaroAb2, should be called "AmaroAbc2" > >> 2) metagenome 4461443.3 - Amaroc1c2, should be called "Amarostc1c2" > >> > >> That is it. > >> Best regards, > >> Amaro. > >> > >> > >> > >> > Hi, > >> > > >> > There is no way to do this from the web interface, let me know > >> > what > >> > the > >> > change is and I can do this for you. > >> > > >> > Regards, > >> > Mark > >> > > >> > ----- Original Message ----- > >> >> From: amarots(a)iqsc.usp.br > >> >> To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > >> >> Cc: mg-rast(a)mcs.anl.gov > >> >> Sent: Tuesday, April 12, 2011 5:57:59 PM > >> >> Subject: renaming MG data at MG-RAST > >> >> Dear MG-Rast developing team, > >> >> What should I do to rename a misnamed metagenome after upload it > >> >> on > >> >> MG-RAST? > >> >> Att, > >> >> Amaro > >> >> > >> >> > >> >> > Hi, > >> >> > > >> >> > When I login using your account the upload page diplays fine. > >> >> > When > >> >> > the > >> >> > page is opened you may need to grant permission for the applet > >> >> > to > >> >> > run, is > >> >> > it possible that your institution does not permit java applets > >> >> > to > >> >> > run on > >> >> > its computers? > >> >> > > >> >> > On my Mac, if I open the Java preferences, under Network I can > >> >> > view > >> >> > cache > >> >> > files. Try deleting the jumploader .jar file and restarting > >> >> > the > >> >> > browser > >> >> > and let us know if this has any effect. > >> >> > > >> >> > Regards, > >> >> > Mark > >> >> > > >> >> > > >> >> > ----- Original Message ----- > >> >> >> From: amarots(a)iqsc.usp.br > >> >> >> To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > >> >> >> Sent: Tuesday, April 12, 2011 2:04:07 PM > >> >> >> Subject: Re: [mg-rast] Unable to upload data > >> >> >> Hello Mark, > >> >> >> Well, here goes the print screen of the "upload" page at > >> >> >> MG-RAST. I > >> >> >> can > >> >> >> tell that it does not seems to be a problem regarding java > >> >> >> version. > >> >> >> I've > >> >> >> tryed to upload my data from different pcs, which I'm sure > >> >> >> are > >> >> >> running > >> >> >> an > >> >> >> updated version of Java. > >> >> >> Best, > >> >> >> Amaro > >> >> >> > >> >> >> > >> >> >> > >> >> >> > Hi, > >> >> >> > > >> >> >> > I am sorry you are still having a problem with the upload > >> >> >> > of > >> >> >> > your > >> >> >> > data, I > >> >> >> > did not get a response to my earlier email asking about the > >> >> >> > java > >> >> >> > applet > >> >> >> > box and had hoped this issue had been resolved. > >> >> >> > > >> >> >> > This appears to be a local problem as we are seeing uploads > >> >> >> > from > >> >> >> > other > >> >> >> > users proceeding normally. You should see a java applet > >> >> >> > window > >> >> >> > labelled > >> >> >> > 'Jumploader' with an add button which can be used to select > >> >> >> > the > >> >> >> > file > >> >> >> > to be > >> >> >> > uploaded. If you are not seeing the applet box, try > >> >> >> > restarting > >> >> >> > your > >> >> >> > browser after clearing the cache. If this does not work > >> >> >> > please > >> >> >> > let > >> >> >> > us know > >> >> >> > and include a description or screen-shot of the upload web > >> >> >> > page > >> >> >> > that > >> >> >> > you > >> >> >> > see. > >> >> >> > > >> >> >> > Regards, > >> >> >> > Mark > >> >> >> > > >> >> >> > > >> >> >> > ----- Original Message ----- > >> >> >> >> From: amarots(a)iqsc.usp.br > >> >> >> >> To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > >> >> >> >> Sent: Tuesday, April 12, 2011 11:56:27 AM > >> >> >> >> Subject: Re: [mg-rast] Unable to upload data > >> >> >> >> Hi MG-RAST team, > >> >> >> >> is this problem global or just local? I still unable to > >> >> >> >> load > >> >> >> >> my > >> >> >> >> metagenomic data. > >> >> >> >> best, > >> >> >> >> Amaro > >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> >> > Hi, > >> >> >> >> > > >> >> >> >> > I will take a look into this and get back to 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: amarots(a)iqsc.usp.br > >> >> >> >> >> To: "Jared Wilkening" <jared.wilkening(a)gmail.com> > >> >> >> >> >> Cc: mg-rast(a)mcs.anl.gov > >> >> >> >> >> Sent: Wednesday, April 6, 2011 2:47:39 PM > >> >> >> >> >> Subject: [mg-rast] Unable to upload data > >> >> >> >> >> Dear MG-Rast developing team, > >> >> >> >> >> I've been trying to upload data for hours and can't get > >> >> >> >> >> it > >> >> >> >> >> done. > >> >> >> >> >> The > >> >> >> >> >> "upload" link isn't performing as presented at the > >> >> >> >> >> tutorial. > >> >> >> >> >> In > >> >> >> >> >> fact I > >> >> >> >> >> can't even post the files to be loaded. Instead the > >> >> >> >> >> following > >> >> >> >> >> message > >> >> >> >> >> is > >> >> >> >> >> showing up: [please wait for your upload to complete > >> >> >> >> >> before > >> >> >> >> >> viewing > >> >> >> >> >> other > >> >> >> >> >> tabs]. Although, I have no upload in progress. > >> >> >> >> >> What should I do to upload the data? > >> >> >> >> >> Thanks, > >> >> >> >> >> Amaro > >> >> >> >> >> > >> >> >> >> >> > >> >> >> >> >> > >> >> >> >> >> > >> >> >> >> >> > >> >> >> >> >> > >> >> >> >> >> > >> >> >> >> >> > >> >> >> >> >> > Amaro, > >> >> >> >> >> > > >> >> >> >> >> > We are about ready to finalized the last round of > >> >> >> >> >> > recomputes > >> >> >> >> >> > so I > >> >> >> >> >> > would > >> >> >> >> >> > expect they would be done by the end week or at > >> >> >> >> >> > latest > >> >> >> >> >> > early > >> >> >> >> >> > next > >> >> >> >> >> > week. > >> >> >> >> >> > New > >> >> >> >> >> > jobs are generally taking about a week at the moment > >> >> >> >> >> > due > >> >> >> >> >> > to > >> >> >> >> >> > our > >> >> >> >> >> > heavy load > >> >> >> >> >> > and the recomputing. > >> >> >> >> >> > > >> >> >> >> >> > Cheers, > >> >> >> >> >> > Jared Wilkening > >> >> >> >> >> > - for the MG-RAST development team > >> >> >> >> >> > > >> >> >> >> >> > On Tue, Mar 29, 2011 at 4:53 PM, > >> >> >> >> >> > <amarots(a)iqsc.usp.br> > >> >> >> >> >> > wrote: > >> >> >> >> >> > > >> >> >> >> >> >> Dear MG-Rast developing team, > >> >> >> >> >> >> > >> >> >> >> >> >> I wonder if you have an estimated time for releasing > >> >> >> >> >> >> the > >> >> >> >> >> >> metagenomes > >> >> >> >> >> >> which > >> >> >> >> >> >> are still recomputing at the new MG-RAST version 3? > >> >> >> >> >> >> I'm > >> >> >> >> >> >> particularly > >> >> >> >> >> >> interested in the two metagenomes I'm signed as a > >> >> >> >> >> >> user: > >> >> >> >> >> >> 4453373.3 - > >> >> >> >> >> >> Amaro_RL1 and 4453374.3 - Amaro_RL2. > >> >> >> >> >> >> Also, I would like to know how long will it take to > >> >> >> >> >> >> process > >> >> >> >> >> >> new > >> >> >> >> >> >> data, > >> >> >> >> >> >> which is about to be loaded into the MG-RAST? > >> >> >> >> >> >> > >> >> >> >> >> >> I thank you in advance for the attention, > >> >> >> >> >> >> Best regards, > >> >> >> >> >> >> Amaro Trindade-Silva > >> >> >> >> >> >> > >> >> >> >> >> >> > >> >> >> >> >> >> > >> >> >> >> >> >> > >> >> >> >> >> > > >> >> >> >> > > >> >> >> > > >> >> > > >> > > >

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