BCO Resources: Difference between revisions
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<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;"> | <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;"> | ||
Automatically generate BCO from Nextflow pipelines with provenance information | Automatically generate BCO from Nextflow pipelines with provenance information | ||
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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] | === [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;"> | [[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. | The High-throughput Integrated Virtual Environment (HIVE) for genome analysis has platform specific tools for generating BioCompute Objects from workflows. | ||
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=== [https://hub.docker.com/r/dnanexus/bconexus BCO Nexus] === | === [https://hub.docker.com/r/dnanexus/bconexus BCO Nexus] === | ||
[[File:Dnanexus.png|frameless|60x60px | [[File:Dnanexus.png|frameless|60x60px]]<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"> | ||
BCOnexus developed by DNAnexus | BCOnexus developed by DNAnexus, as a platform-free Docker tool for quick BCO evaluation. | ||
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=== Galaxy Platform === | |||
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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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=== [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;"> | |||
Tools to create, validate, and export BioCompute Objects in R. | |||
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<h3>[[ | <h3>[[File:Biocomputing.gif|frameless|42x42px]]BioCompute Citations</h3> | ||
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# 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.] | |||
# 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]. | |||
</div> | # 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
HIVE Platform
The High-throughput Integrated Virtual Environment (HIVE) for genome analysis has platform specific tools for generating BioCompute Objects from workflows.
CRAN BioCompute Tool
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.
Galaxy Platform
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.
BioCompute Citations
- 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.
- 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.
- 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
- 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.
- 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.
- 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.