BCO Resources: Difference between revisions

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__NOTOC__
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         <h3>BCODB API</h3>
         <h3>[https://biocomputeobject.org/api/docs/ BCODB API]</h3>[[File:Swagger.png|frameless|211x211px]]<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
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Explore the BioCompute database RESTful APIs, generated by Swagger.
Explore the BioCompute database RESTful APIs, generated by Swagger.
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         <h3>[[Faq|Frequently Asked Questions]]</h3>
         <h3>[https://github.com/nextflow-io/nf-prov Nextflow]</h3>[[File:Nextflow.png|frameless|121x121px]]<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
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Automatically generate BCO from Nextflow pipelines with provenance information
The FAQ section contains a list of questions asked by users regarding using the portal, pipeline steps, and extensions as well as questions related to the prerequisite, knowledgebase recommendation, and saving and publishing BCOs.
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Read more: [[Faq|Frequently Asked Questions]]
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        <h3>[https://github.com/NovoNordisk-OpenSource/whirl Whirl]</h3>[[File:Octocat.png|frameless|121x121px]]<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
Documentation tool from Novo Nordisk with support for BCOs
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=== [https://hive.biochemistry.gwu.edu/dna.cgi?cmd=main HIVE Platform] ===
[[File:Hive.png|frameless|155x155px]]<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
The High-throughput Integrated Virtual Environment (HIVE) for genome analysis has platform specific tools for generating BioCompute Objects from workflows.
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        <h3>[https://github.com/biocompute-objects/bcotool/tree/1.1.0 BCO-TOOL]</h3>[[File:Octocat.png|frameless|96x96px]]<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
Command line tool for to create, validate, and export BioCompute Objects.
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         <h3>[https://cran.r-project.org/web/packages/biocompute/index.html CRAN BioCompute Tool]</h3>[[File:Cran.png|frameless|71x71px]]<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
Tools to create, validate, and export BioCompute Objects in R. Users can encode information in data frames, and compose BioCompute Objects from the domains defined by the standard.
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        <h3>[[Sop|BCO Curation SOP]]</h3>
=== [https://hub.docker.com/r/dnanexus/bconexus BCO Nexus] ===
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[[File:Dnanexus.png|frameless|60x60px]]<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
Intended audience: authors and developers
BCOnexus developed by DNAnexus, as a platform-free Docker tool for quick BCO evaluation.
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This section is intended to provide guidance on BCO™ creation, versioning, certification and authentication.
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=== Galaxy Platform ===
[[File:Galaxy.png|frameless|162x162px]]<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
The Galaxy BCO API Extension enables Galaxy users to the export of Galaxy “workflow invocations” (i.e. realizations of a computational pipeline) in BCO format.
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Read more: [[Sop|BCO Curation SOP]]
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=== [https://www.cancergenomicscloud.org/ Cancer Genomics Cloud Seven Bridges] ===
 
[[File:CGC v2.0.png|frameless|159x159px]]<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
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Tools to create, validate, and export BioCompute Objects in R.
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         <h3>[[BioCompute Conference and Workshop|Workshop]]</h3>
         <h3>[[File:Biocomputing.gif|frameless|42x42px]]BioCompute Citations</h3>
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We hosted an in-person workshop on May 10, 2024. Learn more [[BioCompute Conference and Workshop|here]].
# Keeney JG, Gulzar N, Baker JB, Klempir O, Hannigan GD, Bitton DA, Maritz JM, King CHS 4th, Patel JA, Duncan P, Mazumder R.. Communicating computational workflows in a regulatory environment. Drug Discov Today. 2024 Mar;103884(3) [https://pubmed.ncbi.nlm.nih.gov/38219969/ PMID:38219969.]
For all previous workshop materials, click [https://hive.biochemistry.gwu.edu/publications#Multimedia here].
# King CH, Keeney J, Guimera N, Das S, Weber M, Fochtman B, Walderhaug MO, Talwar S, Patel JA, Mazumder R, Donaldson EF. Communicating regulatory high-throughput sequencing data using BioCompute Objects. Drug Discov Today. 2022 Jan 22; [https://pubmed.ncbi.nlm.nih.gov/35077912/ PMID: 35077912].
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# Stian Soiland-Reyes, Peter Sefton, Mercè Crosas, Leyla Jael Castro, Frederik Coppens, José M. Fernández, Daniel Garijo, Björn Grüning, Marco La Rosa, Simone Leo, Eoghan Ó Carragáin, Marc Portier, Ana Trisovic, RO-Crate Community, Paul Groth, Carole Goble. [https://doi.org/10.3233/DS-210053 Packaging research artefacts with RO-Crate]. Data Science, 2022
# Patel JA, Dean DA, King CH, Xiao N, Koc S, Minina E, Golikov A, Brooks P, Kahsay R, Navelkar R, Ray M, Roberson D, Armstrong C, Mazumder R, Keeney J. Bioinformatics tools developed to support BioCompute Objects. Database (Oxford).2021 March 31; [https://pubmed.ncbi.nlm.nih.gov/33784373/ PMID:33784373].
# Alterovitz G, Dean D A, Goble C, Crusoe M R, Soiland-Reyes S, Bell A, Hayes A, King, C H S, Taylor D, Johanson E, Thompson E E, Donaldson E, Morizono H, Tsang H S, Goecks J, Yao J, Almeida J S, Krampis K, Guo L, Walderhaug M, Walsh P, Kahsay R, Gottipati S, Bloom T, Lai Y, Simonyan V, Mazumder R. [https://doi.org/10.1371/journal.pbio.3000099 Enabling Precision Medicine via standard communication of HTS provenance, analysis, and results.] PLOS Biology; 16(12): e3000099.2018.
# Simonyan V, Goecks J, Mazumder R. BioCompute objects - a step towards evaluation and validation of bio-medical scientific computations. PDA J Pharm Sci Technol. 2017;71(2):136-146 [https://pubmed.ncbi.nlm.nih.gov/27974626/ PMID:27974626].</div>
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Latest revision as of 21:10, 24 June 2025


BCODB API

Swagger.png

Explore the BioCompute database RESTful APIs, generated by Swagger.

Nextflow

Nextflow.png

Automatically generate BCO from Nextflow pipelines with provenance information

Whirl

Octocat.png

Documentation tool from Novo Nordisk with support for BCOs

HIVE Platform

Hive.png

The High-throughput Integrated Virtual Environment (HIVE) for genome analysis has platform specific tools for generating BioCompute Objects from workflows.

BCO-TOOL

Octocat.png

Command line tool for to create, validate, and export BioCompute Objects.

CRAN BioCompute Tool

Cran.png

Tools to create, validate, and export BioCompute Objects in R. Users can encode information in data frames, and compose BioCompute Objects from the domains defined by the standard.

BCO Nexus

Dnanexus.png

BCOnexus developed by DNAnexus, as a platform-free Docker tool for quick BCO evaluation.

Galaxy Platform

Galaxy.png

The Galaxy BCO API Extension enables Galaxy users to the export of Galaxy “workflow invocations” (i.e. realizations of a computational pipeline) in BCO format.

Cancer Genomics Cloud Seven Bridges

CGC v2.0.png

Tools to create, validate, and export BioCompute Objects in R.

Biocomputing.gifBioCompute Citations

  1. Keeney JG, Gulzar N, Baker JB, Klempir O, Hannigan GD, Bitton DA, Maritz JM, King CHS 4th, Patel JA, Duncan P, Mazumder R.. Communicating computational workflows in a regulatory environment. Drug Discov Today. 2024 Mar;103884(3) PMID:38219969.
  2. King CH, Keeney J, Guimera N, Das S, Weber M, Fochtman B, Walderhaug MO, Talwar S, Patel JA, Mazumder R, Donaldson EF. Communicating regulatory high-throughput sequencing data using BioCompute Objects. Drug Discov Today. 2022 Jan 22; PMID: 35077912.
  3. Stian Soiland-Reyes, Peter Sefton, Mercè Crosas, Leyla Jael Castro, Frederik Coppens, José M. Fernández, Daniel Garijo, Björn Grüning, Marco La Rosa, Simone Leo, Eoghan Ó Carragáin, Marc Portier, Ana Trisovic, RO-Crate Community, Paul Groth, Carole Goble. Packaging research artefacts with RO-Crate. Data Science, 2022
  4. Patel JA, Dean DA, King CH, Xiao N, Koc S, Minina E, Golikov A, Brooks P, Kahsay R, Navelkar R, Ray M, Roberson D, Armstrong C, Mazumder R, Keeney J. Bioinformatics tools developed to support BioCompute Objects. Database (Oxford).2021 March 31; PMID:33784373.
  5. Alterovitz G, Dean D A, Goble C, Crusoe M R, Soiland-Reyes S, Bell A, Hayes A, King, C H S, Taylor D, Johanson E, Thompson E E, Donaldson E, Morizono H, Tsang H S, Goecks J, Yao J, Almeida J S, Krampis K, Guo L, Walderhaug M, Walsh P, Kahsay R, Gottipati S, Bloom T, Lai Y, Simonyan V, Mazumder R. Enabling Precision Medicine via standard communication of HTS provenance, analysis, and results. PLOS Biology; 16(12): e3000099.2018.
  6. Simonyan V, Goecks J, Mazumder R. BioCompute objects - a step towards evaluation and validation of bio-medical scientific computations. PDA J Pharm Sci Technol. 2017;71(2):136-146 PMID:27974626.
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