May 2010 - Mg-rast - mailman3.cels.anl.gov

Re: [mg-rast] what is Clustering based subsystems?
by Folker Meyer 31 May '10

31 May '10

Dear Takashi Okubo, in the context of the SEED project (www.theseed.org) annotators have identified groups of genes ("clusters) that re-appear in multiple diverse genomes but still are unknown in function. These groups are summed up as cluster based subsystems. As annotation progresses, some of these cluster based subsystems will find their way into other functional groups or open up new groups. Hope this helps, FOlker On May 28, 2010, at 9:26 PM, okubo wrote: > Dear > > My name is Takashi Okubo and I am a researcher at Tohoku University in Japan. > Please tell me what Clustering based subsystems is. > > Sincerely, > Takashi Okubo >

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recruitment plots?
by Sheri Simmons 31 May '10

31 May '10

Hello, Apologies if this information is presented somewhere on the site, but I couldn't find it. What is the BLAST algorithm used to create the MG-RAST recruitment plots? I assume it is probably BLASTN, but what are the parameters used (match/mismatch penalties and gap scores)? Thanks Sheri ----------------------------------------------------------------------------------- Sheri Simmons Assistant Scientist | Bay Paul Center, Marine Biological Laboratory 7 MBL St, Woods Hole MA 02543 (508) 289-7177 http://jbpc.mbl.edu/cv-simmons.html

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forgot login and password
by Rodrigo De la Iglesia 31 May '10

31 May '10

Dear MG-RAST team: I'm a user of the MG-RAST service, but I change my computer and I forgot both my login and password. It is possible for you obtain that information just with my name?? I have a lot of data there I don't want to loose. All the Best -- Rodrigo De la Iglesia, PhD Profesor Asistente Laboratorio de Microbiología Marina Facultad de Ciencias Biológicas P. Universidad Católica de Chile Alameda 340, Casilla 114-D 56-2-6862845 (rdelaigl(a)bio.puc.cl) -- Rodrigo De la Iglesia, PhD Profesor Asistente Laboratorio de Microbiología Marina Facultad de Ciencias Biológicas P. Universidad Católica de Chile Alameda 340, Casilla 114-D 56-2-6862845 (rdelaigl(a)bio.puc.cl)

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username/password dont work
by Raul Bettencourt 31 May '10

31 May '10

Hello, My username/password doesn't work. Could you help? This the 2nd time I trying to login with new passwords given. Thank you Raul Raul Bettencourt, PhD Research Associate Scientist IMAR-Azores University of the Azores 9901-862 Horta Portugal Tel +351292200417 Fax +351292200411 email: raul(a)uac.pt <mailto:[email protected]>

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Query: Up-to-date MG-RAST Dump?
by Pier Luigi Buttigieg 31 May '10

31 May '10

Dear MG-RAST Team, I would like to download the MG-RAST annotations of all 479 public metagenomes in your database. I checked the FTP server and it seems to be a little out of date (i.e. only 387 metagenomes are available in ftp://ftp.theseed.org/metagenomes/public/, last update June 22 2009). Is there an up-to-date dump of the data available? In particular, I would like to download the .gbk.gz and functions.txt.gz files of each metagenome. Best regards and thank you for your time, Pier

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Re: [mg-rast] mg-rast down
by Folker Meyer 30 May '10

30 May '10

Hi Sheri, we are aware of the problem. It was DNS related. Should be fixed now. Like many things DNS (domain name service) it might take a while to propagate to all systems on the internet. Let us know if it not fixed by tomorrow. It is working for us now. Best, Folker On May 30, 2010, at 4:20 PM, Sheri Simmons wrote: > I was not able to access mg-rast today (5/30); the page at metagenomics.anl.gov was missing several elements and I could not see any of my pending jobs on the status page. Screenshot of the main page is attached. It looks like the problem is the inability to access any data from www.nmpdr.org. > > Sheri > > ----------------------------------------------------------------------------------- > Sheri Simmons > Assistant Scientist | Bay Paul Center, Marine Biological Laboratory > 7 MBL St, Woods Hole MA 02543 > (508) 289-7177 > http://jbpc.mbl.edu/cv-simmons.html > > <mg-rast-screenshot.gif>

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mg-rast down
by Sheri Simmons 30 May '10

30 May '10

I was not able to access mg-rast today (5/30); the page at metagenomics.anl.gov was missing several elements and I could not see any of my pending jobs on the status page. Screenshot of the main page is attached. It looks like the problem is the inability to access any data from www.nmpdr.org. Sheri ----------------------------------------------------------------------------------- Sheri Simmons Assistant Scientist | Bay Paul Center, Marine Biological Laboratory 7 MBL St, Woods Hole MA 02543 (508) 289-7177 http://jbpc.mbl.edu/cv-simmons.html

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Downloading annotation
by ssharmai＠uga.edu 29 May '10

29 May '10

Hi, Is it possible to download the annotation files from MG rast. Like in the download page its says bacteria, Archea etc, its it possible to download all bacterial annotation (like phylogenetic information about all bacterias). Thanks Shalabh Sharma ---- Shalabh Sharma Scientific Computing Professional Associate (Bioinformatics Specialist) Department of Marine Sciences University of Georgia Athens, GA 30602-3636 email: ssharmai(a)uga.edu

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what is Clustering based subsystems?
by okubo 28 May '10

28 May '10

Dear My name is Takashi Okubo and I am a researcher at Tohoku University in Japan. Please tell me what Clustering based subsystems is. Sincerely, Takashi Okubo

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(Job 5042 , ID 4445129.3) . is now publicly available.
by mg-rast＠mcs.anl.gov 28 May '10

28 May '10

Thibault Varin (WebServerBackend::User=HASH(0x1b4949c0)) has made the genome public. Link provided: http://mg-rast.mcs.anl.gov/mg-rast/FIG/linkin.cgi?metagenome=4445129.3.

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