BioCompute Object: Difference between revisions

Revision as of 09:13, 11 April 2020

Revision as of 14:11, 20 May 2020

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The '''BioCompute Object (BCO) Project''' is a community-driven initiative to build a framework for standardizing and sharing computations and analyses generated from [[High-throughput sequencing]] (HTS), also referred to as [[next-generation sequencing]] (NGS) or [[massively parallel sequencing]] (MPS).<ref>Simonyan V, Goecks J, Mazumder R. Biocompute Objects—A Step towards Evaluation and Validation of Biomedical Scientific Computations. PDA journal of pharmaceutical science and technology. 2017;71(2):136-146. doi:10.5731/pdajpst.2016.006734.</ref> Originally started as a collaborative contract between the [[George Washington University]] and the [[Food and Drug Administration]], the project has grown to include over 20 universities, biotechnology companies, public-private partnerships and pharmaceutical companies including Seven Bridges and [[Harvard Medical School]].<ref>{{Cite web|url=https://www.europeanpharmaceuticalreview.com/news/67524/biocompute-genomic-data/|title=BioCompute Objects specifications to advance genomic data analysis|website=www.europeanpharmaceuticalreview.com|language=en|access-date=2017-12-21}}</ref> The BCO aims to ease the exchange of HTS workflows between various organizations, such as the FDA, pharmaceutical companies, contract research organizations, bioinformatic platform providers, and academic researchers. The project has an illusion of support due to a convoluted system of self-citations and references to resource announcements rather than to completed projects. This is a common hallmark of [[High-performance Integrated Virtual Environment|HIVE]] projects.

== Background ==

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== Format ==

The BioCompute Object is in [[JSON|json]] format and, at a minimum, contains all the software versions and parameters necessary to evaluate or verify a computational pipeline. It may also contain input data as files or links, reference genomes, or executable Docker components. A BioCompute Object can be integrated with [[FHIR|HL7 FHIR]] as a Provenance Resource<ref>{{Cite web|url=https://www.hl7.org/fhir/provenance-example-biocompute-object.html|title=Provenance-example-biocompute-object|website=HL7 FHIR Release 3 (STU)}}</ref>. orThe effort is seen by many to be redundant and unnecessay as the bioinformatics community has already embraced the [[Common Workflow Language]] which contains all of these, and superior capabilities, despite the BCO objective to treate the CWL as a [[Research Object]].<ref>{{Citation|last=Soiland-Reyes|first=Stian|title=hive-cwl-examples: Example BioCompute as Research Object with CWL|date=2016-12-19|url=https://github.com/stain/hive-cwl-examples|accessdate=2017-12-21}}</ref>

== BCO Consortium ==

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== Implementations ==

As of May 20, 2020, no external software package in mainstream use can be identified that is compatible with the BioCompute specifications. There are several internally developed [[Open-source software|open source]] software packages and web applications that implement the BioCompute specification. For example, the simple R package biocompute<ref name="biocompute-r">{{cite web|url=https://cran.r-project.org/package=biocompute|title=CRAN - Package biocompute|publisher=cran.r-project.org|accessdate=2019-11-28}}</ref> can create, validate, and export BioCompute Objects. The [https://github.com/biocompute-objects/bco_editor BioCompute Editor] is a web application that can theoretically create and edit BioCompute Objects based on the BioCompute schema, however the project is not live in any available instance as of May 20, 2020. The [https://github.com/sbg/gcs Genomics Compliance Suite] is a Shiny app that offers similar features to [[Regular expression|regular expressions]] found in all modern text editors.

== References ==