{"id":489,"date":"2018-09-01T11:48:02","date_gmt":"2018-09-01T11:48:02","guid":{"rendered":"https:\/\/dadamo.com\/dangerous\/?p=489"},"modified":"2018-09-07T13:22:40","modified_gmt":"2018-09-07T13:22:40","slug":"pathfinding-gene-circuits","status":"publish","type":"post","link":"https:\/\/dadamo.com\/dangerous\/2018\/09\/01\/pathfinding-gene-circuits\/","title":{"rendered":"Pathfinding gene circuits"},"content":{"rendered":"

The UB\/COEGM Pathfinder Scholarship Program is a partnership between the University of Bridgeport School of Health Sciences and the Center of Excellence in Generative Medicine. Its mission is to groom developing physicians in the skills of twenty-first century precision medicine through the use of bioinformatics. It’s been my honor and privilege to act as a mentor for Pathfinder program for the past five years.<\/p>\n

We’ve finally built a website for the program,<\/a> which, in addition providing information on the program, also hosts biographical data on the Pathfinders, and will act as a code repository for their own explorations. Feel free to explore the site and get to known the students. Most have quite fascinating pre-Pathfinder lives and biographies.<\/p>\n

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Pathfinder scholars with old dude.<\/p><\/div>\n

The Pathfinder program has taken on what appears to be a very significant challenge to modern medicine: Today\u2019s physicians cannot easily process the increasingly available large amounts of data (such as produced by genome or microbiome reporting services) in any sort of real-time efficient manner. This is indeed a dilemma, as \u2018big data\u2019 approaches (in particular those employing machine learning algorithms) are increasingly pointing the way to a more precise, personalized type of treatment based on high-value conclusions. <\/p>\n

In fact it’s been said that ‘more data is better than better data.’ But that is another blog.<\/p>\n

On August 25 2018, the COEGM announced the release of \u2018Circuits\u2019 a gene-based open source platform combining genomic data in a variety of disparate dimensions. Circuits is web-based, has an imaginative and intuitive user interface, and is free to use.<\/a> Pathfinders will continue to build new applications into Circuits, including tools to analyze the microbiome (microorganisms) and metabolome (small molecules).<\/p>\n

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Circuits employs a variety of popups to provide additional contextual data. For example, clicking on any agent linked to the expression of the target gene will trigger a popup window that draws a unique radar plot that we call the \u2018genomic logo\u2019 of the agent. This logo depicts the strength, action and targets of the indicated agent using a complex algorithm based on study design, scope and subject type.<\/p>\n

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Radar plot of Alpha-Linolenic acid<\/p><\/div>\n

Most of the data used by Circuits was developed initially for use by the Opus23<\/a> application from publicly available repositories. Exceptions include the SNP and agent expression datasets, which were developed entirely by Datapunk human curators. A few of the larger sources are listed as references. [1-6] <\/p>\n

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Data connections featured in Circuits<\/p><\/div>\n

Readers are encouraged to \u2018surf\u2019 Circuits and explore the target genes that seem more interesting. Click away! However here are a few hard links to can help get you started.<\/p>\n