Review preprint sources and see what needs to be updated

ohnosequences / mg7

Configurable and scalable 16S metagenomics data analysis

https://goo.gl/y3rZFD

GNU Affero General Public License v3.0

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Review preprint sources and see what needs to be updated #82

Closed eparejatobes closed 8 years ago

eparejatobes commented 8 years ago

@marina-manrique @rtobes @laughedelic I have converted the preprint sources to the PeerJ format, and I want to start updating everything. Could you please take a look at the pdf file, and add here what do you think needs to be updated? The pdf is here:

https://github.com/ohnosequences/mg7/blob/2b457b3d0dc06438bcf524dbb8aa00d900ae14c7/docs/mg7-paper/out/paper.pdf

rtobes commented 8 years ago

I have added the pdf with comments with the sections to be updated highlighted in yellow here: https://github.com/ohnosequences/mg7/blob/master/docs/mg7-paper/MG7_paper_PeerJ_RT.pdf

marina-manrique commented 8 years ago

@eparejatobes I'm adding some comments on this PDF docs/mg7-paper/MG7_paper_PeerJ_RT_MM.pdf can you please let me know if you can see them in Linux?

marina-manrique commented 8 years ago

@eparejatobes @rtobes I have added more notes, really good job here :)

I miss just two things (besides the sections discussing the results with the mock communities (illumina and Pacbio)

Saying something about MG7 is platform independent (works with Illumina, PacBio...)
A Figure with the architecture and AWS resources used (using this kind of icons https://aws.amazon.com/architecture/icons/)

rtobes commented 8 years ago

I agree. The first idea could be commented at the beginning of the tests with PacBio and illumina. The second would be good because people likes that kind of figures.

eparejatobes commented 8 years ago

@marina-manrique about the 18S db it is more or less OK, but we don't have any (public) test data for it, right?

eparejatobes commented 8 years ago

@rtobes @marina-manrique I have included all your minor edits/comments.

About the figures, we'd then have

a generic process description (what is now Figure 1)
another for the LCA (what is now Figure 2)
a description of the AWS resources/architecture

is that OK?

I have added issues for the rest of your comments: #89 #88 #87 #90

marina-manrique commented 8 years ago

And I 'd just add another figure explaining the results of the mock communities. Like bar charts or smth

marina-manrique commented 8 years ago

but we don't have any (public) test data for it, right?

Nope, we don't. I could take a look whether there is a public dataset we could use

eparejatobes commented 8 years ago

I added #91 and #92 for figures. LGTM.

eparejatobes commented 8 years ago

@rtobes @marina-manrique I think that for all of your comments either there's already an issue for that, or is already included in the paper. If so, let's remove your commented pdfs from the repo.