Help Docs

  • Rhythmus – prescribing clarity

    Rhythmus is a new app that makes prescribing natural agents simpler than before when using the Opus23 database of natural agent effects on genes.

    Taking an overview of all SNPs for the client, the main Rhythmus screen shows a list of genes sorted by combined SNP effect power factor, with the color scheme of orange for overall downregulated and green for overall upregulated genes. With over 7,800 individual associations of genes and natural agents in the database, all based on and hyperlinked to PubMed published studies, Opus23 makes visualisation simple for the genes with the highest editor-defined power factor and with associated natural agents that affect the gene function.

    Rhythmus Prescribing App

    Taking the Agency app one step further, Rhythmus also includes the gene visualising ability of Powerspot to help the practitioner choose the best agents for the clientThe AI Pre fills the option of upregulating or downregulating the gene function and the effect required from the agents (although these can be changed manually if required). The numbers of agents associated with the gene function is also listed.

    Rhythmus can be used by checking some genes and other options, then click the Run Rhythmus button. The result is a network map of the genes in the query along with the natural agents that influence their function.

    Rhythmus network map

    The relative size of the agent indicates the confidence of the effect on the gene, and as with other network maps on Opus23, clicking on the gene or agent opens a popup for that element, from where it can be curated to the Client Report or the Protocol Report.

    The AI saves time in selecting the best options according to the available data, but this can alway be overridden by the practitioner, who may have other information about the client. Opus23 subscribes to the philosophy of ‘TMTOWTDI’ (There’s more than one way to do it, pronounced ‘Tim Toady’.) The program was designed with this idea in mind, in that it ‘doesn’t try to tell the practitioner how to parse the data.’ Rather, it presents many different frameworks and cross-sections of the available client data, using a myriad of infographic treatments. Therefore Rhythmus also offers the practitioner a user-defined alternative visualisation of up to five manually entered genes, again with an up- or downregulatory effect and the required effect size. The user-defined visualisation gives a Manhattan map of the combined effect of the possible agents, similar to one side of the Psychic app.

    Result of the user-defined selection in Rhythmus

    As before, clicking on the agent opens the agent popup, where it can be curated. Rhythmus takes Opus23 to another level of utility for data mining and analysing its huge database of PubMed-based gene-agent interactions.

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  • Utopia: Advice, Intelligent interface with Opus23

    Advice: Intelligent Interface with OPUS23

    ADVICE is an app in Utopia that gives algorithmic considerations of multiple bacterial strains in conjunction with the client’s own genome to provide true/false clinical outcomes. ADVICE automatically pulls the client’s Opus23 genetic data where relevant, and incorporates it into algorithmic calculations. (comparable to LUMEN in Opus23).

    Getting around ADVICE

    From the Utopia drop down menu, hover over ‘Algorithms’ until a second list appears, then select ‘Advice’. You are presented with a list of algorithms, those that are true are at the top and display the word ‘TRUE’ in a green box, followed by those that are false, which display the word ‘FALSE’ in an orange box. Each algorithm will display the repute (risk, benefit or neutral), and the magnitude. If an algorithm suggests prescriptive metabolites which enhance or reduce specific bacteria, they will be listed under Encourage or Discourage.

    The client’s relevant genes will be displayed beneath the listed ‘microbiota’ information in the same format found in the Opus23 LUMEN app. Clicking on the colored semicircle will open a pop-up window with a description of the gene and giving details of the client’s SNPs for the gene from their Opus23 data.

    Utopia Advice algorithm

    An ADVICE algorithm for gluten-induced immunopathology

    All metabolites and taxa are clickable. Clicking a metabolite opens a pop-up window with a list of bacteria affected by it. Clicking a bacterium opens a pop-up window as described in previous apps. To add an algorithm to the client report, click on the ‘Add/ Uncurated’ button.

    Individual genera may also be curated and added to the client report for the current dataset by selecting the taxon to open its pop-up information and then clicking the ‘Add/Uncurated’ button.

    Screen shot of Metabolomics pop-up window

    Pop-up window in ADVICE showing metabolomics information

    Using the Algorithm Aggregate Analysis

    At the bottom of the page is the Algorithm Aggregate Analysis. This is a summary of all advice for the client listed under either an ‘increase’ and ‘decrease’ section heading. Each section provides both the microbiota and beneficial/ harmful metabolites that are suggested to be increased or decreased by your client. The ‘result’ information can be a useful tool for streamlining complex treatment strategies. Each metabolite listed in the Algorithm Aggregate Analysis details whether or not the metabolite has mixed results (included as both encourage and discourage in ADVICE algorithms), and whether it is specific to an algorithm.

    Algorithm Aggregate Analysis screenshot

    Algorithm Aggregate Analysis for the ADVICE app

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  • Utopia: Pansophia, sequential outcome analysis

    PANSOPHIA – sequential outcome analysis

    The genomic DNA analysis software Opus 23 includes the Utopia suite of apps for analyzing sequential uBiome data, comparing sequencing-based clinical microbiome data with the client’s own genomic DNA.

    Utopia logo

    PANSOPHIA is an Utopia app that gives you the power to sort your client’s data based upon associations with health and disease as well as several other useful categories including keystone, probiotic, core species and butyrate production.  For those clients who have more than one data sample, PANSOPHIA allows you to visualize treatment progress in a graphical format that can be easily added to your client’s report.

    Navigating PANSOPHIA

    pansophia

    From the Utopia drop down menu, hover over ‘analytics’ until a second list appears, then select PANSOPHIA. You will then be presented with the default table which shows ‘everything’ and is sorted by ‘rank’ or ‘percent’.

    At the bottom of the window is a jump screen that allows you to move from one screen to the next. You can control how many rows to display be selecting an option from the ‘Show’ pull down menu. The default is 15.

    Pansophia initial screen

    Filtering and sorting results

    PANSOPHIA allows you to parse the taxon data based upon desired treatment goals. Taxa are sortable by benefit as well as pathogenic potential.  There are two ways to filter the data.

    Using category tabs:

    You can use the category tabs at the top of app’s main screen to select taxa grouped by their associations with health and disease. Once a category is selected, the information will be displayed in graph form.

    Pansophia screenshot

    The PANSOPHIA graph uses the following symbols:

    • An orange dot  denotes average %, the bar graphic represents the client data- specific %
    • For those with multiple data sets, a blue diamond denotes % change

    Click on any desired taxon to open up its information pop—up window for detailed information including taxonomy, an overview of known disease or health benefit associations, interactions and metabolomics. Click ‘add/ curate’ to include it in your clients report. Additionally, the graph itself can be printed or added to your client’s report.

    Using individual taxon selections:

    From the main screen, you can sort the taxa by ‘name’ or ‘client %’ then select desired taxa individually using the display box selections on the left hand side of the screen.  Once you have made your selections, click the orange ‘display selections’ button at the top of the screen. The individual taxon information will be displayed in graph form. Click ‘add/curate’ to include the graph in your client’s report.

       

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  • Utopia: Spectrum, visual community organization

    SPECTRUM: Visual community organization

    Utopia logo

    SPECTRUM provides a visual representation of the taxonomic data at both the genus and phylum levels. The app demonstrates the weight, influence and diversity of your client’s microbiome in two helpful display formats, each of which are clickable for a deeper look and easy report curation.

    Navigating  SPECTRUM

    Spectrum logo

    From the Utopia drop down menu, hover over ‘analytics’ until a second list appears, then select SPECTRUM.  Phyla and genus are displayed in pie chart format, which is accompanied by the spectrum profiler found below.

    The pie charts follow the color-coding conventions found in OPUS23 indicating beneficial, neutral as well as pathogenic organisms. Click on any desired section to open up its information pop—up window for detailed information including taxonomy, an overview of known disease or health benefit associations, descendants and metabolomics. Click ‘add/ curate’ to include it in your client’s report.

    Spectrum pie charts

    The spectrum profiler demonstrates the trends in your client’s biome diversity in a graphical format. Clicking on any of the category headings will open a pop-up window listing the organisms found in your client’s sample. Each genus listed is also clickable, opening a pop-up window for detailed information, including taxonomy, an overview of known disease or health benefit associations, descendants and metabolomics. Click ‘add/ curate’ to include it in your client’s report.

    Screenshot of Spectrum Profiler

    Metabolomics is a powerful addition to the spectrum profiler that provides a comprehensive list of metabolites associated with GI biome species. A list of all metabolites active in your client is included. Click on an individual metabolite for detailed information, including genera that are enhanced, inhibited, and those which generate the metabolite as an end product. Click on the Metabolomics link to open a pop-up with all active and inactive genera.

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  • Utopia: Loam, a fertile soil

    Announcing the launch of Utopia, the suite of apps within Opus 23 that analyzes and reports on sequential data from uBiome tests. uBiome is the world’s first sequencing-based clinical microbiome screening test, giving the user insight into the bacterial population of multiple body areas. Utopia recognizes all bacteria found by uBiome, but is specifically interested in the gut bacteria and its interaction with the client’s own genomic DNA. Utopia is free for existing clients: Once you have uploaded 23andMe raw data for your client, you can add as many uBiome tests as you want for that client without additional charge. Utopia will then give you access to multiple apps to analyze the data and reference it to the client’s genomic data where appropriate.

    Utopia logo

    LOAM: Adaptable taxon data

    LOAM is a highly flexible search and sort tool that allows you to easily navigate through your client’s Ubiome results by taxon. LOAM allows you to filter taxonomic data based upon several useful parameters as well as sort the filtered results. It is similar to the ARGONAUT app in Opus 23.

    loam

    Navigating LOAM

    From the Utopia drop down menu, hover over ‘analytics’ until a second list appears, then select LOAM. You will then be presented with the default table which shows ‘everything’ and is sorted by ‘repute’ or ‘interpretation’.

    At the bottom of the window is a jump screen that allows you to move from one screen to the next. You can control how many rows to display be selecting an option from the ‘Show’ pull down menu. The default is 15.

    Loam Screenshot

    Filtering and sorting results

    LOAM allows you to parse the taxon data based upon desired treatment goals. Taxons are sortable by benefit as well as pathogenic potential.

    The LOAM table displays the following data by column:

    • Taxon name
    • Repute, displaying beneficial !, neutral ! and pathogenic ! 
    • Rank
    • Client-specific % population
    • Average % (if available)
    • Standard deviation (if available)
    • Interpretation (displayed up to +6 times the standard deviation, populations found in a greater abundance are indicated by )
    • Normal variance
    • Order magnitude

    Click on any desired taxon to open up its information pop—up window for detailed information including taxonomy, an overview of known disease or health benefit associations, interactions and metabolomics. Click ‘add/ curate’ to include it in your clients report. The Curated column will then show a green checkmark against all curated taxon after refreshing the page. 

    LOAM columns are sortable. Click on any column title to sort by that column. Click that column again to reverse the sort order.

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  • Don’t Fall into the Methyl Trap!

    Methyl trapping is a situation in which folate becomes trapped and unusable by the body. It is defined as a functional folate deficiency that alters homocysteine metabolism such that folatedependent resynthesis of methionine is compromised.

    Methyl trapping was originally described in Downs Syndrome (trisomy 21) where plasma levels of homocysteine, methionine, S-adenosylhomocysteine and S-adenosylmethionine were all significantly decreased, suggesting a depression in cellular methylation capacity.  Elevated transsulfation activity with depletion of glutathione was also observed in Downs Syndrome due to the presence of an additional CBS allele, and up-regulated chromosome 21 SOD SNPs causing oxidative stress.(1)

    DS HcyThe term methyl trapping is now applied to the cascade of symptoms of neuroexcitation following supplementation with folate,  or B12 or SAMe as a first line treatment for MTHFR SNPs. The unassuming consumer who takes supplements with methylating B vitamins may experience varying degrees of neurotoxic symptoms manifested as apparently unprovoked insomnia, rage, anxiety, brain fog and alcohol intolerance (induced sulfite and aldehyde toxicity), often after experiencing a brief period of improvement from low energy and cognitive impairment.

    Methylation ModulationLow energy and irritability occur because of a dysregulation within the methionine cycle due to one-carbon metabolism SNPcausing an accumulation of Homocysteine Pathwaymethyl compounds often complicating histamine degradation. A build up of homocysteine is the consequence, often worsened by a bottleneck at CBS (cystathionine beta synthase) due to down-regulating SNPs in the homocysteine clearing transsulfation pathway.

    Neuroexcitatory and depression symptoms ensue from the complication of BH2-BH4 pathway reversal, resulting in incomplete ammonia-clearing by the urea cycle and reduced neurotransmitter formation.BH4-Chart3

    SNPs in MAO and COMT reduce degradation and transporter protein SNPs contribute to dopamine-serotonin imbalance.(2) Patients can also experience poor wound healing, aggravated digestive symptoms of bloating, alternating constipation and diarrhoea, or worsened IBS as a result of reduced methylation capacity.

    Clinicians should screen for conditions that may overwhelm transsulfation and detoxification pathways including infection, autoimmunity, toxic body burden, problems with blood sugar and fat metabolism and other inflammatory indications. Non-methylating nutritional support should be provided for mutations in MTR/MTRR, BHMT, SHMT2, MAT1A, CBS, QDPR, OTC, CPS, ARG2, PCBD1, MAOA or B, COMT, HNMT, DHPR, NOS1, 2, 3, SOD1, SOD2, PEMT, PON1, ABCB1, cytochrome P 450 genes and Soluble Carrier Family transporter protein SNPs, ACAT1-02, in deciding when to support Methylation cycle SNPs.

    Methyl trapping at a glance:

    Practitioners can use cutting-edge cloud-based software curated by naturopathic physicians. Mobocaster is a cutting edge application in Opus23 Pro offering the practitioner scenario-specific genetic analysis including power factors and relevant descriptions.

    References:

    1. Pogribna M, Melnyk S, Pogribny I, Chango A, Yi P, James SJ. Homocysteine
      metabolism in children with Down syndrome: in vitro modulation. Am J Hum Genet.
      2001 Jul;69(1):88-95. PMID: 11391481.
    2. Finkelstein JD. Pathways and regulation of homocysteine metabolism in mammals.
      Semin Thromb Hemost. 2000;26(3):219-25. Review. PMID: 11011839.
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  • Getting started

     

    NOTE: Opus 23 Pro is in the later stages of field testing. We expect to go public with the program on January 15, 2016.

    Opus 23 Pro is available for use by licensed health professionals. To begin using Opus 23 you must first have the necessary tools and abilities.

    To receive email updates, make sure that you join our mailing list.

    Basic requirements:

    • Technical requirements: Opus 23 Pro is completely web-based and runs on all modern Internet browsers. Opus 23 utilizes many features that require that you have JavaScript enabled on your browser. This is usually the default setting, so you probably need not worry. However, if you’ve turned JavaScript off, you’ll need to turn it back on. Opus 23 Pro also uses cookies to maintain your connection to your data. Again, this is usually the default setting, but if you’ve turned cookies off, you’ll need to turn them back on. We recommend the Google Chrome browser but Opus will work well on Firefox and later versions of Internet Explorer
    • Mobile devices: Opus 23 Pro is designed to be “responsive,” i.e. it will conform visually to whatever device you are viewing it with. It works well with most tablet devices, such as the iPad. However we do not recommend using devices with very small viewports, such as smartphones

    Creating an Opus 23 Pro account

    To begin using Opus 23 Pro you must have an account. Creating an account is a simple two-step process and is free of charge. After you create your Opus 23 Account you will have the option of moving onto the next screen and purchasing 1-10 client licenses.

    Basic licencing

    Each Opus 23 Pro client license is $75 USD. This will allow you to upload raw data for one client. There is no time limit of working with uploaded clients. You are free to develop, redevelop and evolve your use of Opus 23 analytics and reporting on that client indefinitely.  You can organize curation elements into multiple datasets and generate any number of different client reports, depending the particular needs of the moment.

    INGM member

    If you are a current member of the Institute for Naturopathic Generative Medicine (INGM) or the International College of Generative Medicine (ICGM) you qualify for a discounted license fee of $65 USD per each single use license.

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