playing with ideas about BioCompute Objects while at https://hive.biochemistry.gwu.edu/htscsrs/workshop_2017
Live at https://mathbiol.github.io/bco !
In this experiment we'll look for ways to assembled biocompute objects taken very broadly as a concept
- GDrive Notes.
- Workshop 2017.
- Vahan Simonyan, Jeremy Goecks and Raja Mazumder2,3 (2016) Bio-compute objects - a step towards evaluation and validation of bio-medical scientific computations PDA J Pharm Sci Technol doi:10.5731/pdajpst.2016.006734
- An API will be developed to traverse the data structure.
- Common Worflow Language is a foundational abstraction. See commonwl.org as reference.
- There are other worflow languages that need to be considered in equal footing with CWL, such Workflow Description Language (WDL).
- It may be worth exploring some non-declarative solution such as functional (prototypal) inheritance of code. Never a bad idea visiting one of Eliot's discussions on this topic.
- Thank you Michael :-), have a look at W3C's Cool URIs.
- Example of a BCO at hive.biochemistry.gwu.edu/htscsrs/examples.
- BCO is a meta standard (meta object), an example might be precison FDA which was awarded do NDAnexus.
- There is an humbrella organization for open standards, researchworkflows.org.
- Study https://github.com/common-workflow-language/hive-cwl-examples. and study this one too: https://view.commonwl.org/workflows/github.com/NCI-GDC/gdc-dnaseq-cwl/tree/vizu/workflows/dnaseq.
- --> Open Science workshop document. OSF is midleware for open science!
- BioCompute Object at HL7/FHIR
- FDA-HIVE code base open source at https://github.com/FDA/fda-hive.
- Keep an eye on GA4GH's server.
- Ben's slides and hackathons.
- Ring of FHIR with sync4genes.org (thank you Gil!).