Put AMR Classifier tutorial on the PATRIC site

[hyoo]

are you referring this ?

https://www.patricbrc.org/public/pdfs/Workshop-Antimicrobial-Resistance.pdf

Antimicrobial Resistance https://www.patricbrc.org/content/Tutorials

[rkenyon]

I believe he means here: https://www.patricbrc.org/content/UserGuide

I think it should probably go as part of Genome Annotations, or maybe under it. https://www.patricbrc.org/content/Genome_Annotations

[rkenyon]

Still not really sure what is meant by AMR Classifier tutorial. @mshukla1 ?

There is a tutorial now on Examining AMR Data in PATRIC: https://docs.patricbrc.org//tutorial/amr/amr.html

[mshukla1]

This was long time ago, so hard to remember. I believe it was the following tutorial, which is available from the seed tutorial site, but not PATRIC.

http://tutorial.theseed.org/AdaBoost_Installation_Tutorial.htm http://tutorial.theseed.org/AdaBoost_Installation_Tutorial.htm

On Jul 26, 2018, at 12:58 PM, rkenyon notifications@github.com wrote:

Still not really sure what is meant by AMR Classifier tutorial. @mshukla1 https://github.com/mshukla1 ?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/PATRIC3/patric3_website/issues/1392#issuecomment-408182388, or mute the thread https://github.com/notifications/unsubscribe-auth/ABLd7wF-a56HEx4DGBn5XSElH12l45TDks5uKgNGgaJpZM4LSHzS.

[mshukla1]

We also need detailed explanation for the AMR classifier predictions and features in PATRIC tutorials / FAQs. similar to the one below.

http://tutorial.theseed.org/RAST_Predictions.htm http://tutorial.theseed.org/RAST_Predictions.htm

On Jul 26, 2018, at 1:10 PM, Maulik Shukla mshukla@anl.gov wrote:

This was long time ago, so hard to remember. I believe it was the following tutorial, which is available from the seed tutorial site, but not PATRIC.

http://tutorial.theseed.org/AdaBoost_Installation_Tutorial.htm http://tutorial.theseed.org/AdaBoost_Installation_Tutorial.htm

On Jul 26, 2018, at 12:58 PM, rkenyon <notifications@github.com mailto:notifications@github.com> wrote:

Still not really sure what is meant by AMR Classifier tutorial. @mshukla1 https://github.com/mshukla1 ?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/PATRIC3/patric3_website/issues/1392#issuecomment-408182388, or mute the thread https://github.com/notifications/unsubscribe-auth/ABLd7wF-a56HEx4DGBn5XSElH12l45TDks5uKgNGgaJpZM4LSHzS.

[rkenyon]

Thanks, I'll work on it. That same info should have been sent for inclusion on PATRIC as well as RAST.

On Thu, Jul 26, 2018 at 2:12 PM Maulik Shukla notifications@github.com wrote:

We also need detailed explanation for the AMR classifier predictions and features in PATRIC tutorials / FAQs. similar to the one below.

http://tutorial.theseed.org/RAST_Predictions.htm < http://tutorial.theseed.org/RAST_Predictions.htm>

On Jul 26, 2018, at 1:10 PM, Maulik Shukla mshukla@anl.gov wrote:

This was long time ago, so hard to remember. I believe it was the following tutorial, which is available from the seed tutorial site, but not PATRIC.

http://tutorial.theseed.org/AdaBoost_Installation_Tutorial.htm < http://tutorial.theseed.org/AdaBoost_Installation_Tutorial.htm>

On Jul 26, 2018, at 12:58 PM, rkenyon <notifications@github.com mailto:notifications@github.com> wrote:

Still not really sure what is meant by AMR Classifier tutorial. @mshukla1 https://github.com/mshukla1 ?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/PATRIC3/patric3_website/issues/1392#issuecomment-408182388>, or mute the thread < https://github.com/notifications/unsubscribe-auth/ABLd7wF-a56HEx4DGBn5XSElH12l45TDks5uKgNGgaJpZM4LSHzS .

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/PATRIC3/patric3_website/issues/1392#issuecomment-408186631, or mute the thread https://github.com/notifications/unsubscribe-auth/ADCnWv6W38d3Ykk7Iw7s7ZRNWNnhWkafks5uKgaAgaJpZM4LSHzS .[image: Web Bug from https://github.com/notifications/beacon/ADCnWnnsgSSNSdwF1j6NG_zdCkG9Gpw9ks5uKgaAgaJpZM4LSHzS.gif]

-- Note: My email has changed to rkenyon@bi.vt.edu.

Ron Kenyon, Project Director Biocomplexity Institute of Virginia Tech PATRIC Project Manager www.patricbrc.org rkenyon@bi.vt.edu

[rkenyon]

Is there an up-to-date list of classifiers and scores somewhere? The information in the RAST prediction page is from Jan 2017.

http://tutorial.theseed.org/RAST_Predictions.htm

On Thu, Jul 26, 2018 at 2:15 PM Ron Kenyon rkenyon@bi.vt.edu wrote:

Thanks, I'll work on it. That same info should have been sent for inclusion on PATRIC as well as RAST.

On Thu, Jul 26, 2018 at 2:12 PM Maulik Shukla notifications@github.com wrote:

We also need detailed explanation for the AMR classifier predictions and features in PATRIC tutorials / FAQs. similar to the one below.

http://tutorial.theseed.org/RAST_Predictions.htm < http://tutorial.theseed.org/RAST_Predictions.htm>

On Jul 26, 2018, at 1:10 PM, Maulik Shukla mshukla@anl.gov wrote:

This was long time ago, so hard to remember. I believe it was the following tutorial, which is available from the seed tutorial site, but not PATRIC.

http://tutorial.theseed.org/AdaBoost_Installation_Tutorial.htm < http://tutorial.theseed.org/AdaBoost_Installation_Tutorial.htm>

On Jul 26, 2018, at 12:58 PM, rkenyon <notifications@github.com mailto:notifications@github.com> wrote:

Still not really sure what is meant by AMR Classifier tutorial. @mshukla1 https://github.com/mshukla1 ?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/PATRIC3/patric3_website/issues/1392#issuecomment-408182388>, or mute the thread < https://github.com/notifications/unsubscribe-auth/ABLd7wF-a56HEx4DGBn5XSElH12l45TDks5uKgNGgaJpZM4LSHzS .

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/PATRIC3/patric3_website/issues/1392#issuecomment-408186631, or mute the thread https://github.com/notifications/unsubscribe-auth/ADCnWv6W38d3Ykk7Iw7s7ZRNWNnhWkafks5uKgaAgaJpZM4LSHzS .[image: Web Bug from https://github.com/notifications/beacon/ADCnWnnsgSSNSdwF1j6NG_zdCkG9Gpw9ks5uKgaAgaJpZM4LSHzS.gif]

-- Note: My email has changed to rkenyon@bi.vt.edu.

Ron Kenyon, Project Director Biocomplexity Institute of Virginia Tech PATRIC Project Manager www.patricbrc.org rkenyon@bi.vt.edu

-- Note: My email has changed to rkenyon@bi.vt.edu.

Ron Kenyon, Project Director Biocomplexity Institute of Virginia Tech PATRIC Project Manager www.patricbrc.org rkenyon@bi.vt.edu

[mshukla1]

Jim,

Can you provide updated list of AMT classifiers? Even better would be if you can draft AMR classifier tutorial/faq pages for PATRIC doc site.

-Maulik

On Jul 26, 2018, at 1:17 PM, rkenyon notifications@github.com wrote:

Is there an up-to-date list of classifiers and scores somewhere? The information in the RAST prediction page is from Jan 2017.

http://tutorial.theseed.org/RAST_Predictions.htm

On Thu, Jul 26, 2018 at 2:15 PM Ron Kenyon rkenyon@bi.vt.edu wrote:

Thanks, I'll work on it. That same info should have been sent for inclusion on PATRIC as well as RAST.

On Thu, Jul 26, 2018 at 2:12 PM Maulik Shukla notifications@github.com wrote:

We also need detailed explanation for the AMR classifier predictions and features in PATRIC tutorials / FAQs. similar to the one below.

http://tutorial.theseed.org/RAST_Predictions.htm < http://tutorial.theseed.org/RAST_Predictions.htm>

On Jul 26, 2018, at 1:10 PM, Maulik Shukla mshukla@anl.gov wrote:

This was long time ago, so hard to remember. I believe it was the following tutorial, which is available from the seed tutorial site, but not PATRIC.

http://tutorial.theseed.org/AdaBoost_Installation_Tutorial.htm < http://tutorial.theseed.org/AdaBoost_Installation_Tutorial.htm>

On Jul 26, 2018, at 12:58 PM, rkenyon <notifications@github.com mailto:notifications@github.com> wrote:

Still not really sure what is meant by AMR Classifier tutorial. @mshukla1 https://github.com/mshukla1 ?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/PATRIC3/patric3_website/issues/1392#issuecomment-408182388>, or mute the thread < https://github.com/notifications/unsubscribe-auth/ABLd7wF-a56HEx4DGBn5XSElH12l45TDks5uKgNGgaJpZM4LSHzS .

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/PATRIC3/patric3_website/issues/1392#issuecomment-408186631, or mute the thread https://github.com/notifications/unsubscribe-auth/ADCnWv6W38d3Ykk7Iw7s7ZRNWNnhWkafks5uKgaAgaJpZM4LSHzS .[image: Web Bug from https://github.com/notifications/beacon/ADCnWnnsgSSNSdwF1j6NG_zdCkG9Gpw9ks5uKgaAgaJpZM4LSHzS.gif]

-- Note: My email has changed to rkenyon@bi.vt.edu.

Ron Kenyon, Project Director Biocomplexity Institute of Virginia Tech PATRIC Project Manager www.patricbrc.org rkenyon@bi.vt.edu

-- Note: My email has changed to rkenyon@bi.vt.edu.

Ron Kenyon, Project Director Biocomplexity Institute of Virginia Tech PATRIC Project Manager www.patricbrc.org rkenyon@bi.vt.edu — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/PATRIC3/patric3_website/issues/1392#issuecomment-408188319, or mute the thread https://github.com/notifications/unsubscribe-auth/ABLd77T1WZrp_KjH8eTxu_gZC0-crJ4Vks5uKgfOgaJpZM4LSHzS.

[rkenyon]

This is effectively covered now by the updated AMR Phenotypes Tab user guide (https://docs.patricbrc.org/user_guides/organisms_taxon/amr_phenotypes.html) that includes references to AMR Prediction paper and the Classifier Software instructions at theseed.org; plus the AMR Resistance tutorial (https://docs.patricbrc.org/tutorial/amr/amr.html).

Closing the ticket.