Major Refactor is ready for testing and comments

The analysis site for 16s microbiome results (ubiome, thryve, etc) http://microbiomeprescription.azurewebsites.net/ has been revised to improve usability and to give more options.

Sample Selection Page

This has been de-cluttered

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Ability To Edit some Meta Data

Clicking on Edit or Remove a sample.

  • Some Json files did not include a date, so you may manually correct it.
  • There are a few non-US medical professionals who uses this site, so support for adding a person name
  • I have had requests to remove samples — this makes it easy to do. You must enter the email as a validation step (to stop accidental removals)

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New Analysis Page

This page is rich in options, but to get there you must have selected a specific gut sample. If you uploaded ear samples, this page will not be available.

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Informational Reports

Microbiome Tree

This shows the hierarchy of bacteria you have with the ration to the reference range. High values are in Red.  This allows you to see exactly where shifts are happening.  For example we see Veillonellaceae are high — but this is because two specific genus are high in this family.

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Species

Your species are usually not shown on the ubiome report but is in the data. This lists the species. Each species is hyperlink to information on modifiers.

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Example of a report

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Contribute More Information

This allows you to add additional information — symptoms when you did your sample, the KEGG information from ubiome reports.

Experimental Analysis

This is experimental — it has resulted in some strong associations with the symptom explorers.

Suggestions

People can argue endlessly about what is significant or insignificant. To save the arguments, I give 4 different ways to evaluate deviations. I have done the 4 options on the same data below.

When you click thru you will see suggestions with the new filtering options:

Simple High Low

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Count Above or Below

So an item that is a little high or low is not given as much weight as an item that is very high or low.

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Log of Count

As above, but by taking the log, the severe impacts are scaled down.

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Simple Count with Rare Bacteria deemed to be Highs

For rare bacteria, we often do not know if it is bad or good. We assume that it may be bad.

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Suggestions Filter

The filter has been updated to give better control (less noise) of suggestions. The default values are expected to work for most people.

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Condition Profiles

This is informational and definitely not diagnostic. When you click on one, you will see how well your shift matches those reported in studies.

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Bottom Line

I suspect that there are bugs, so please email me at ken/at/lassesen/dot/com when you find them. I have taken the next three days off to respond to bugs quickly.