MG RAST v2.0 FAQ - Revision history

FolkerMeyer at 22:38, 20 June 2008

2008-06-20T22:38:59Z

FolkerMeyer at 21:07, 20 June 2008

2008-06-20T21:07:38Z

FolkerMeyer at 17:54, 20 June 2008

2008-06-20T17:54:15Z

FolkerMeyer at 17:53, 20 June 2008

2008-06-20T17:53:02Z

FolkerMeyer: /* What level of privacy does MG-RAST v2.0 provide? */

2008-06-20T17:51:39Z

What level of privacy does MG-RAST v2.0 provide?

FolkerMeyer: /* Where can people access the "public" metagenomes? */

2008-06-20T17:50:44Z

Where can people access the "public" metagenomes?

FolkerMeyer at 17:50, 20 June 2008

2008-06-20T17:50:23Z

FolkerMeyer at 17:46, 20 June 2008

2008-06-20T17:46:27Z

FolkerMeyer at 17:37, 20 June 2008

2008-06-20T17:37:28Z

New page

=== What are projects? ===
Projects are related sets of metagenomes. If you for example plan on studying a set of samples from a chronoseries, it might me useful to group them into a project.

=== What level of privacy does MG-RAST v2.0 provide? ===
We provide password control and the ability for the submitting entity to control access on a username/password basis to the submitted data sets.

=== Do you support BLASTing against my private database XYZ? ===
We currently do not explicitly support this, however the underlying software design end system architecture support this.

=== How frequently do you update the underlying NR for MG-RAST? ===
With version 2.0 we have added the support for multiple concurrent sets of sequence similarity results to be stored per metagenome. We can add results for newer NRs. However once you start comparing results for metagenomes (say you are interested in the phylogenetic reconstruction) different versions of the NR used for the underlying data will lead to incorrect comparison results as older versions of NR will miss certain organisms and or annotations.

@@ Line 29: / Line 29: @@
 === What about HIPAA relevant data? ===
 MG-RAST is provided under the assumption that all data is anonymized, no [http://en.wikipedia.org/wiki/HIPAA HIPAA] relevant data should be stored on MG-RAST.
 === How are the numbers computed? ===
 <font color="red">NEEDS TO BE FILLED</font>

← Older revision		Revision as of 21:07, 20 June 2008
Line 29:		Line 29:
	=== What about HIPAA relevant data? ===		=== What about HIPAA relevant data? ===
	MG-RAST is provided under the assumption that all data is anonymized, no [http://en.wikipedia.org/wiki/HIPAA HIPAA] relevant data should be stored on MG-RAST.		MG-RAST is provided under the assumption that all data is anonymized, no [http://en.wikipedia.org/wiki/HIPAA HIPAA] relevant data should be stored on MG-RAST.
		+
		+
		+	=== How are the numbers computed? ===
		+	<font color="red">NEEDS TO BE FILLED</font>

@@ Line 15: / Line 15: @@
 === How long does it take to analyze my Metagenome? ===
 The answer depends on two factors a) the size of your data set and b) the current server load. Under optimal conditions, it takes about 18 hours to run a 100 million basepair 454 metagenome through the pipeline.
 === What parameters should I use to analyze my data? ===

← Older revision		Revision as of 17:53, 20 June 2008
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	Future versions will continue to support this feature, also we will provide a metadata based selection tool, that will allow the user to focus on metagenome data sets from the environment or condition etc they are interested in.		Future versions will continue to support this feature, also we will provide a metadata based selection tool, that will allow the user to focus on metagenome data sets from the environment or condition etc they are interested in.
		+
		+	=== What about HIPAA relevant data? ===
		+	MG-RAST is provided under the assumption that all data is anonymized, no [http://en.wikipedia.org/wiki/HIPAA HIPAA] relevant data should be stored on MG-RAST.

@@ Line 17: / Line 17: @@
 The answer depends on your sample. In any case we recommend that you modify e-value, minimal alignment length and percent identity requirements for the BLAST results underlying the results. The effects of this are different for each sample. Depending on sample complexity, sample size, number of  species an diversity of species present your results will vary dramatically when modifying these parameters. For RNA based phylogenetic reconstruction, we recommend requiring a minimum alignment length of 50bp for exact matches.
-=== Where can people access the "public" metagenomes? ===
+=== Where can people access my "published" metagenomes? ===
-The MG-RAST v2.0 Homepage has a list of publicly accessible metagenomes. Future versions will continue to support this feature, also we will provide a metadata based selection tool, that will allow the user to focus on metagenome data sets from the environment or condition etc they are interested in.
+The MG-RAST v2.0 Homepage has a list of publicly accessible metagenomes.

@@ Line 4: / Line 4: @@
 === What level of privacy does MG-RAST v2.0 provide? ===
 We provide password control and the ability for the submitting entity to control access on a username/password basis to the submitted data sets.
 === Do you support BLASTing against my private database XYZ? ===

← Older revision		Revision as of 17:50, 20 June 2008
Line 16:		Line 16:
	=== What parameters should I use to analyze my data? ===		=== What parameters should I use to analyze my data? ===
	The answer depends on your sample. In any case we recommend that you modify e-value, minimal alignment length and percent identity requirements for the BLAST results underlying the results. The effects of this are different for each sample. Depending on sample complexity, sample size, number of species an diversity of species present your results will vary dramatically when modifying these parameters. For RNA based phylogenetic reconstruction, we recommend requiring a minimum alignment length of 50bp for exact matches.		The answer depends on your sample. In any case we recommend that you modify e-value, minimal alignment length and percent identity requirements for the BLAST results underlying the results. The effects of this are different for each sample. Depending on sample complexity, sample size, number of species an diversity of species present your results will vary dramatically when modifying these parameters. For RNA based phylogenetic reconstruction, we recommend requiring a minimum alignment length of 50bp for exact matches.
		+
		+	=== Where can people access the "public" metagenomes? ===
		+	The MG-RAST v2.0 Homepage has a list of publicly accessible metagenomes. Future versions will continue to support this feature, also we will provide a metadata based selection tool, that will allow the user to focus on metagenome data sets from the environment or condition etc they are interested in.

← Older revision		Revision as of 17:46, 20 June 2008
Line 10:		Line 10:
	=== How frequently do you update the underlying NR for MG-RAST? ===		=== How frequently do you update the underlying NR for MG-RAST? ===
	With version 2.0 we have added the support for multiple concurrent sets of sequence similarity results to be stored per metagenome. We can add results for newer NRs. However once you start comparing results for metagenomes (say you are interested in the phylogenetic reconstruction) different versions of the NR used for the underlying data will lead to incorrect comparison results as older versions of NR will miss certain organisms and or annotations.		With version 2.0 we have added the support for multiple concurrent sets of sequence similarity results to be stored per metagenome. We can add results for newer NRs. However once you start comparing results for metagenomes (say you are interested in the phylogenetic reconstruction) different versions of the NR used for the underlying data will lead to incorrect comparison results as older versions of NR will miss certain organisms and or annotations.
		+
		+	=== How long does it take to analyze my Metagenome? ===
		+	The answer depends on two factors a) the size of your data set and b) the current server load. Under optimal conditions, it takes about 18 hours to run a 100 million basepair 454 metagenome through the pipeline.
		+
		+	=== What parameters should I use to analyze my data? ===
		+	The answer depends on your sample. In any case we recommend that you modify e-value, minimal alignment length and percent identity requirements for the BLAST results underlying the results. The effects of this are different for each sample. Depending on sample complexity, sample size, number of species an diversity of species present your results will vary dramatically when modifying these parameters. For RNA based phylogenetic reconstruction, we recommend requiring a minimum alignment length of 50bp for exact matches.