Release Notes

For people amusement, while reviewing new studies on PubMed, I got a pleasant surprise! My citizen science project (MicrobiomePrescription) is referenced in BMC Bioinformatics article published June 3 2021. Adding to my prior mentions in New Scientist and The Lancet. “Dysbiosis of the gut microbiome is a risk factor for osteoarthritis in older female adults: a case control study

  • Nov 21 Added Reported Symptoms to Predicted Symptoms pages. See this post for more details
  • Nov 20th, quality review found that recent EndProducts computations had errored
    • Fixed issue
    • Recomputed EndProducts for all uploads
    • Updated Percentiles for all users (for everything)
  • Nov 19, Logins were timing out for a few. Identified it to be specific to people with a lot of uploads. Refactored.
  • Nov 18 Finished monthly review of recent PubMed articles
  • Nov 17 Add GMRepo pages to site
  • Nov 14th, for bacteria and modifier lookup, add search link to Kyoto Enc. of Genes for more information
  • Nov 13 Refactored /library/detail page on bacteria to:
    • Show (for a login person) values for the bacteria being viewed
    • Show the Bacteria Associations for this bacteria
  • Nov 12: Build out Consensus Report Framework see Multiple Conditions Microbiome Analysis 11th
  • Nov 8: Refactor Citizen Science Symptom Association, see
  • Nov 6-: reworked /sample/Why to use the new bacteria 2 bacteria relationshipVisualization improved
    • Deprecated two older inferior tables used with older method
  • Nov 5th, dropped the in-the-database percentile computations and replaced it with /sample/update web page that was much faster
  • Nov 4th, added Gut Zoomer (vibrant-wellness)
  • Nov 3rd, Updated with the addition of the [Update Percentages] button on each sample. Bulk updates were burning more and more bandwidth and CPU as the number of samples grew
  • Nov 2nd, added GanzImmun Diagnostics AG Befundbericht
  • Nov 1st, started refactoring the generation of distributions by standardizing the code, aim is to deprecate the old code that has become filled with ad hoc code updates. Goal is to make it lean enough to run once a day,
  • Sep 26 recomputed the bacteria 2 bacteria relationship — there was a code error discovered while documenting the algorithm (it’s many hours of running a CPU full out to do all of the cross products to do a recompute)
  • Sep 26, Discovered we still had non-gut samples in the database. Data purged (23 samples, 6000 point — all from uBiome days)
  • Sep 25 Added rankings across 16s and other labs for Pub Med Medical Conditions
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New Column Added to https://microbiomeprescription.com/Library/PubMed
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Example of report (auto updated as new data comes in)
Not logged in appearance
When logged in
https://microbiomeprescription.com/labs/compare
  • Sept 19, Added Bacteria Association Page. This is linked to from the bacteria detail page
https://microbiomeprescription.com/library/details?taxon=1578
https://microbiomeprescription.com/library/Associations?taxon=1578
https://microbiomeprescription.com/library/provider16s
  • Sept 15th, Restored ability to save Other Labs Data and created samples page for it.
Two sample lists are available

  • Jul 26 – Added Special Topics
  • July 15 Added Long COVID Microbiome Profile
    • Blog using #1 and #2
  • July 12 – Fixed Bug, see this page
  • July 9th finished periodic review of new studies and updating database
  • July 8 – implemented KEGG Products and Substrate(Consumers) estimations for retail probiotics.
  • July 7th Implemented support for Consultant and Client to share a sample transferred from biomesight automatically with the transfer.
  • July 5, Add computed Substrate and Product totals for a sample from KEGG data
  • July 3, Added Increase or decreases to citations for suggestions
  • Extended uploads to include “Custom” via the partner transfer page
  • Change the emailing address to MicrobiomePrescription/at\gmail.com to address some issues
  • June 26th — Updated “Core Supplements Suggested” page to current pattern (added charts, Kaltoft-Moldrup Ranges, Suggested Dosages, etc)
    • Added more dosage citations
    • Added percentage option for statistics charts
  • June 25th — Added [Search PubMed Citations and Clinical Trials] feature
  • June 23rd –Modified percentile calculations to ignore duplicate uploads (on different accounts).
    • The odd “flat spot” seen is some curves (because of duplicate samples) should be removed
    • Approximately 10% of samples were flagged as duplicates and ignored.
  • June 19th — End Products — still obsolete but a reader had some issues with them.
    • Removed items that were ‘subphylum’,’order’,’phylum’,’superkingdom’ from the taxonomy
    • Fixed inconsistent calculation (a simple sum was not done, rather a logistic style aggregation
    • Removed use of the “DisplayCache” — it was originally done for performance and has since been made obsolete (and no longer updated) – hence inconsistent data between pages.
  • June 5th -Added Lab specific distributions for:
    • Taxonomy (Bacteria)
    • End Products
    • Conditions
    • KEGG Modules
    • KEGG Enzymes
    • KEGG Products
  • June 4 – Fixed bugs on Library/statistic Distribution Chart. Would error our on change of sample.
  • June 1, 2021 — Periodic review of new PubMed studies finished. Database updated.
  • May 29th — Frequency changes to by lab.source on Sample Pages.
    • Added a page giving frequency for the sample by lab.
  • May 28th – announced and released the levels of citations.
    • Update algorithm for rolling up data from providers that do not follow the NCBI hierarchy. Applied it to all samples. Required iterative loop to cascade consistent numbers up. Issue was that a higher taxonomy count was less then the sum of the children.
    • Issues with Krona Charts were resolved as a consequence
  • May 27th, Implemented COSMOS data imports from their PDF reports

May 26 Revised the Kegg Probiotic algorithm. a reader identified a bug that was traced to misinterpretation of KEGG data (Kegg Organism Code can be strain specific, hence for some species I was triple counting in the algorithm)
May 17 onwards: Revisions of Citations pages are ongoing

May 16 – Added new Researched Probiotics pages.
May 15 – Refactor the My Biome View page (ditching the slow javascript) and updating it to use Kaltoft-Moldrup ranges for concerning highs and lows.

May 14, 2021 – UI Improvements

Ability to share data with a registered consultant OR send to your MD or ND etc.
Ability to subset your samples for easier analysis
Ability to save login link as a favorite. On log in, you are presented an opportunity via a new page. You can choose to bypass this page on subsequent logins.
Improved Editing of sample information, including adding short notes.
Customized downloads of one or more samples — with ability to select fields to include
Example of Download ordered by Hierarchy in Excel

Older Notes

  • May 8/9th: Implemented on demand computation of Percentile for KEGG analysis (instead of periodic batch processing). Typical computation time is 60-90 seconds of server time.
  • May 3: Cleanup data to insure full NCBI hierarchy.
    • Missing layers are computed by totally known children of a layer. This is known to under estimate these synthetic counts.
    • Bug appear on UrlLogin page (timeouts) – feedback to user was missing
      • Cause was side-effect of above data update
  • May 1: Fix error on /library/bacteria when sample is changed
  • Added or Improved Suggestions on
    • Nat.Lib. of Medicine Patterns
    • Citizen Science Patterns
    • Create video below showing the features in the context of selecting probiotics
  • Apr 26-27: Added SIBO. Hydrogen+ Methane to End Products using Kegg data
  • Apr 25,2021: Add MicrobiomePrescription :(mainly Amino Acids – more will be added)
  • Apr 23-25, 2021: Update of data from PubMed
  • April 21, 2021 – Update Pathogenic and Health impacting bacteria.
  • April 21, 2021 – Added Gram-Positive data to bacteria taxonomy
  • April 20, 2021 – Added Sample Kegg Products Percentile Computations
  • Apr 15-22, 2021: Kegg Computed Probiotics
    • Kegg Enzyme computations for Probiotics
    • Kegg Products computations for Probiotics
    • Kegg Module computations for Probiotics
    • Aggregation of all of the above
https://microbiomeprescription.com/sample/KeggProbiotic?sampleId=39861033
  • April 16, 2021 — Added Testing for statistical significance for Kegg Products to Symptoms
  • April 12, 2021 — Impmented Kegg Product calculations on samples
  • April 10, 2021 — Added Nat.Lib.Of Medicine Progression calculation and page
https://microbiomeprescription.com/sample/Health?sampleId=33365380
  • 2018
    • Sept 2nd – Major refactor of suggestions, consolidating suggestions into one code base
    • Sept 3rd
      • Bug Fix – Low Bacteria were being incorrectly handled in suggestions
      • Added more symptoms, i.e. Osteoporosis and some dementias
      • Fixed Filter bacteria to those associated with: “All AutoImmune Templates” <= Produces zero results ( not sure if thats a bug or not)
      • Fixed: Link appearing as text on same page above footerSee  Making sense of Avoid and Take onRecommendations  “
      • Fixed bug that excluded items with (Probiotics) in the title 
    • Sept 5th
      • Fixed the email for registrations
      • If a user have forgotten their email, the flow is simpler (and works)
      • Clean up login so there is only one login page
      • Fixed centre align issues in <TD>’s
      • Updated Autoimmune chart to read directly from database
        http://microbiomeprescription.com/Library/AutoImmuneChart
      • Changed home page to a “What do you want to do today” motif
      • Trimmed menu items.
    • September 8th
      • When do deviations entered for /labs/ definitions, no longer goes to error page, instead returns to page with message.
      • Fixed redirect to Login when sample Species were requested. ( /biome/species?sampleid=)
      • Fixed Values of 1000000 for stdDev on /condition/endproducts?sampleid= , this was caused by mishandling of NULL value.
        • Fixed data entry issue on Norepinephrine