• Protocol development

    Two years ago I developed a software app called SkySaw for use on my teaching shift at the COEGM. SkySaw allows clinicians to structure patient encounters as a linked network (technically a directed acyclic graph). What made this attractive was that these individual networks could be connected together into a great network. One could then use graphing tools to data-mine relationships, trends and outcomes.  As the first stage of Opus23 Pro moves to completion, I decided to port this app over to Opus.  What follows is the online doc file for PROTO, the Opus 23 app.

     

    PROTO allows you to develop a flow-chart (network) based approach to health protocol management. Creating a protocol network in PROTO is easy. Protocols can then be added to the client report, allowing for a more client-friendly way of relating your clinical decisions.

    Actions are classified by various roles you can assign any node:

    avatars

    Just choose and option from the menu at the top right-window:


    From left the right, the options are:

    • Reset the screen: Ticking this will reset the screen and zoom level. You can zoom in and out by using the scroll function of your mouse. You can move the network around by click-grabbing the network and moving your mouse.
    • Back to protocol dataset list: Ticking this will return you to the list of datasets for the various protocols you’ve created
    • Add a new node (plus sign): Ticking this will launch a popup window that allows you to add a new node to the network. You then give the node a name and a type (food, drug, molecular target, lab test, etc.) and if you wish provide a short bit of accompanying text.
    • Add a new edge (two connected nodes): Ticking this will launch a popup window that allows you to add a new edge to the network. Edges connect nodes. The input fields will autosuggest nodes to use based on the existing nodes in the network.
    • Info screen: Ticking this will launch this popup window.
    • Active dataset indicator: This icon shows if the protocol you are working on is the active dataset (i.e this is the protocol that will go on to be included in the client report, if you desire.)

    Editing nodes and edges: You can edit any node of edge in the map by clicking on it. This will launch the appropriate popup that will be populated with the existing data. You can make any changes and then save.

    Map direction: The map is designed to proceed in its development from left to right.

    Adding nodes on the fly: Certain node types (molecular targets, agents and foods) can be added from their own information popups. For example, clicking on any gene symbol in Opus 23 Pro launches the gene information popup for that gene. Clicking on the ‘add to protocol’ icon


    will add that gene to the current protocol as a ‘molecular target’ node.

     

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  • Pearl of an idea

    Like most of my coding projects Opus 23 Pro is written primarily in the Perl scripting language. Perl handles most of the basic server-side functions (like disk reading, etc) and sends its output out to the browser via HTML, Javascript, etc.

    Perl is widely used in bioinformatics, and has been nicknamed “the Swiss Army chainsaw of scripting languages” because of its flexibility and power, and has also referred to as the “duct tape that holds the Internet together.” The Perl language borrows features from other programming languages, most significantly C++. It has powerful and unsurpassed text processing facilities, one of the reasons it saw major use during the development of the Human Genome project.

    Why, despite the protestations of my daughter that I should move to Python, I continue to code in Perl:

    • It is universal.
    • It is robust. Perl has an amazing library of existing modules that perform a variety of functions. If you can think of a task, CPAN (the Comprehensive Perl Archive Network) probably contains a module that will spare you the job of having to re-invent the wheel
    • It has strong bioinformatics roots. Perl was than computer language credited with ‘saving’ the Human Genome Project. Perl also has an extraordinary library of existing bioinformatics modules (BioPerl). Perl has a robust library of Application Programming Interfaces (APIs) that interface with the National Center for Biotechnology Information (NCBI) server, including access to PubMed, MeSH, etc.
    • It has a great didactic heritage. Perl has an enormous library of books, ranging from ‘Perl for Dummies’ to advanced bioinformatics textbooks

    One of the great qualities of Perl is its ability to do any one thing in any number of ways. According to it’s creator Larry Wall, Perl has two slogans. The first is “There’s more than one way to do it”, commonly known as TMTOWTDI. The second slogan is “Easy things should be easy and hard things should be possible.”

    Thanks to Perl, Opus 23 Pro has been made possible.

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  • Client-friendly reporting

    I designed Opus 23 Pro to serve two user audiences: the physician who works in the development environment to generate and curate information; and the client, who represents the end-user of that information. Both have widely differing needs and points of reference. One aspect of Opus 23 Pro that I am especially proud of is the great lengths the program goes to to make its final product (the Client Report) simple, concise and easy to understand. One area that has an especially interesting and dynamic quality is the way that Opus 23 explains the actions and consequences of genes to the client.

    Opus 23 Pro aggregates much of its data from public, peer-reviewed sources. This includes the descriptive text that accompanies information about genes. Typically Opus 23 grabs this information from genome.gov. However these short abstracts are often highly technical and cryptic -very unlikely to be very helpful to a patient who does not have a background in genetics. So we created an alternate database of gene descriptions specifically written for the layperson, which is used when Opus 23 Pro generates the client report.

    However, even simplified gene descriptions can be somewhat technical and often rely on the reader having some form of base knowledge.

    Here is a nice touch you don’t see very often. When Opus prints out the gene description in the client report it checks its internal glossary for any advanced medical concepts and if they are in the description the ‘smart owl’ will activate and give the client a simple description of the term.

    csf

    To avoid repeating itself endlessly, Opus only adds the glossary description to the first description that requires it. In this screen shot it is explaining what the terms ‘gene,’  ‘interleukin,’ cytokine and ‘protein’ mean.

     

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  • Multi-SNP algorithms

    Algorithms are perhaps the most significant and flexible aspect of Opus 23 data. They are usually the easiest result for the non-medical person to understand, because their conclusions are usually simplified statements in everyday language. Algorithms are processed by the LUMEN app in Opus 23 Pro.

    LUMEN is one of the most powerful apps in the Opus 23 Pro toolbox. This app allows you to examine the effects of multi-SNP, multi-gene consequences. Very few single SNPs exert their effects independently; they more typically interact through epistatic relationships (where the phenotypic expression of one gene influences the genotypic expression of another) or as a haplotype: a set of several SNPs, on a single chromatid of a chromosome pair that are associated statistically.

    LUMEN does this by using algorithms, small step by step programs that run inside of LUMEN and that look at the logical result of multi-SNP combinations. This type of logic is essentially ‘Boolean’ in that its queries yield a yes or no answer. The combination of both allows LUMEN to provide you with insight into complex SNP arrangements and relationships that might otherwise escape detection.

    It’s helpful to think of an Opus 23 algorithm as a tiny flowchart, that depending on which way the result branches, generates a ‘true or false’ result.

    For example, a simple algorithm to determine if you should get out of bed might be:

    • If you hear the alarm clock, open your eyes.
    • If it’s dark outside, go back to bed.
    • If it’s light outside, check the time.
    • If it’s earlier than 7AM, go back to bed.
    • If it’s later than 7AM, get up, check calendar
    • If it’s Saturday, go back to bed.

    As can be seen, there are a lot of ways you can go back to bed with this algorithm! And this is also true as well for the Opus 23 Pro algorithms: In order for an algorithm to be true, it must fufill all of several conditions. If even one condition fails, the whole algorithm will be false.

    Each algorithm is displayed in its own box, and contain information about the genes and SNPs used in its creation. The title of the algorithm is generally its conclusion. Typically, the client report contains only true algorithms, although you may choose to include false algorithms as well, especially if it would be helpful to make the client aware of something they’re likely to not be prone to. Thus:

    • An algorithm that returns a true will have a ‘check’ icon in the bottom left-hand box. The conclusions of these algorithms pertain to to the client based on their  genomic data results.
    • An algorithm that returns a false will have a ‘cross’ icon in the bottom left-hand box. The conclusions of these algorithms do not pertain to the client based on their genomic data, other than perhaps the added knowledge that this is one less thing in life to worry about.
    Opus 23 algorithm triangulates four genes/ 6 snps to estimate genomic variation in serum magnesium levels.
    Opus 23 algorithm triangulates four genes/ 6 snps to estimate genomic variation in serum magnesium levels.
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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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  • Webinar: An introduction to Opus 23 Pro

    This webinar highlights the features of the Opus 23 Pro genomic analysis software system. It was presented on 8/23/2015 by Peter D’Adamo, the programmer and designer of Opus 23 Pro. Although Opus 23 Pro has had its functionality grow by leaps and bounds since then, this video still manages to do a good job of demonstrating Opus 23 awesomeness.

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