The YAML headers are necessary to process the Markdown (or HTML) files in the page collections. The Progenetix Jekyll template uses standard Jekyll headers, but also adds some additional parameters.
@mbaudis 2019-03-14: more ...
The Progenetix Jekyll template modifies the standard Jekyll file structure.
@mbaudis 2019-03-14: more ...
In an ideal scenario, your Github served website could be build locally, with the same output structure and layout.
@mbaudis 2019-03-14: more ...
The coordinate system that should be used throughout GA4GH standards is 0-based half open.
@mbaudis 2019-03-14: more ...
Beacons present an easy-to-implement strategy for determining whether an institution has genomic data in its data set that would be useful to share.
@mbaudis 2018-10-18: more ...
In current medical practice, doctors commonly share basic, de-identified information about patients’ conditions and genetic variations in the hopes of matching a second case that could be therapeutically transformative. This practice is a long-standing tradition in the medical community but it is neither standardized nor optimized. The Beacon Project turns that informal transaction into a more efficient and effective search that can be a key initial step for learning from valuable genomic information.
Since much of that information is currently collected and held in silos, researchers lack the broad-scale ability to know whether similar data exist that could provide important learning when combined with their own data.
The Beacon Project was created both to test the willingness of organizations to share at the most basic, yes/no level, and also to allow researchers to understand if a specific allele exists in other data sets. Now that a Beacon Network has been created, researchers have the ability to discover valuable information within organizations that have lit Beacons. This is often a needed first step to aggregate and learn from large scale genomic data.
@mbaudis 2018-10-18: more ...
When an institution “lights” a Beacon, it demonstrates its willingness and ability to share data.
@mbaudis 2018-10-18: more ...
Precise variants are such with annotated sequences of 0….n length, and bases of [ATCGN] for the referenceBases and alternateBases attributes (N for “not specified”).
@mbaudis 2018-10-17: more ...
A Beacon is an online web service that allows users to query an institution’s databases, to determine whether they contain a genetic variant of interest. The query is structured as a yes/no question of the form: “Do you have any genomes with an ‘X’ at position Y on chromosome Z?”
@mbaudis 2018-10-17: more ...
Any publica data resource containing “human derived” data has a potential for re-identification attacks, that is the identification of individuals contributing data to the resource.
Since its inception, the Beacon Project has been actively working with experts in GA4GH’s membership to address potential privacy concerns.
@mbaudis 2018-10-17: more ...
The adoption of
variantTypestartMin, startMaxendMin, endMaxinto the Beacon v0.4 release enabled the execution of
@mbaudis 2018-10-17: more ...