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: [email protected] To: "Mark D'Souza" <[email protected]> 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

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No problem, I made the changes.

Regards, Mark

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From: [email protected] To: "Mark D'Souza" <[email protected]> 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.

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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

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From: [email protected] To: "Mark D'Souza" <[email protected]> Cc: [email protected] 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

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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

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From: [email protected] To: "Mark D'Souza" <[email protected]> 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

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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

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From: [email protected] To: "Mark D'Souza" <[email protected]> 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

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Hi,

I will take a look into this and get back to you.

-- Regards, Mark D'Souza -- for the MG-RAST team

[email protected] http://metagenomics.anl.gov/

If you need to respond to this email please address it to the mailing-list [email protected]

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From: [email protected] To: "Jared Wilkening" <[email protected]> Cc: [email protected] 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

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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, <[email protected]> wrote:

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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