BCO Resources - Revision history

Keeneyjg at 21:10, 24 June 2025

2025-06-24T21:10:15Z

← Older revision		Revision as of 21:10, 24 June 2025
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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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Twang9 at 13:54, 8 May 2025

2025-05-08T13:54:46Z

← Older revision		Revision as of 13:54, 8 May 2025
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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]]<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">		[[File:Dnanexus.png\|frameless\|60x60px]]<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
	BCOnexus developed by DNAnexus~~, now known as Velsera~~, as a platform-free Docker tool for quick BCO evaluation.		BCOnexus developed by DNAnexus, as a platform-free Docker tool for quick BCO evaluation.
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Twang9 at 14:45, 21 April 2025

2025-04-21T14:45:48Z

← Older revision		Revision as of 14:45, 21 April 2025
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	<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">		<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">
	=== [https://www.cancergenomicscloud.org/ Cancer Genomics Cloud Seven Bridges] ===		=== [https://www.cancergenomicscloud.org/ Cancer Genomics Cloud Seven Bridges] ===
	[[File:CGC v2.0.png\|frameless\|~~121x121px~~]]<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">		[[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.		Tools to create, validate, and export BioCompute Objects in R.
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Twang9 at 14:45, 21 April 2025

2025-04-21T14:45:15Z

← Older revision		Revision as of 14:45, 21 April 2025
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	<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">		<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">
	=== [https://www.cancergenomicscloud.org/ Cancer Genomics Cloud Seven Bridges] ===		=== [https://www.cancergenomicscloud.org/ Cancer Genomics Cloud Seven Bridges] ===
	[[File:CGC v2.0.png\|~~left~~\|121x121px]]<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">		[[File:CGC v2.0.png\|frameless\|121x121px]]<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
	Tools to create, validate, and export BioCompute Objects in R.		Tools to create, validate, and export BioCompute Objects in R.
	</div>		</div>

Twang9 at 14:44, 21 April 2025

2025-04-21T14:44:33Z

← Older revision		Revision as of 14:44, 21 April 2025
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	<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">		<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">
	=== [https://www.cancergenomicscloud.org/ Cancer Genomics Cloud Seven Bridges] ===		=== [https://www.cancergenomicscloud.org/ Cancer Genomics Cloud Seven Bridges] ===
	[[File:~~Cgc2~~.png\|~~frameless\|114x114px]][[File:Velsera.jpg\|frameless~~\|~~127x127px~~]]<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">		[[File:CGC v2.0.png\|left\|121x121px]]<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
	Tools to create, validate, and export BioCompute Objects in R.		Tools to create, validate, and export BioCompute Objects in R.
	</div>		</div>

Twang9 at 17:52, 11 March 2025

2025-03-11T17:52:00Z

← Older revision		Revision as of 17:52, 11 March 2025
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			__NOTOC__

	<div id="ggw_row2" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;">		<div id="ggw_row2" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;">
	<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">		<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">

Twang9: Added Citations

2025-03-11T17:46:43Z

Added Citations

← Older revision		Revision as of 17:46, 11 March 2025
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	<div id="ggw_row3" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;">		<div id="ggw_row3" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;">
	<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">		<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">
	<h3>[[~~BioCompute Conference and Workshop~~\|~~Workshop~~]]</h3>		<h3>[[File:Biocomputing.gif\|frameless\|42x42px]]BioCompute Citations</h3>
	<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">		<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
	~~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].
	</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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Twang9 at 15:54, 11 March 2025

2025-03-11T15:54:38Z

← Older revision		Revision as of 15:54, 11 March 2025
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	<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">		<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">
	=== [https://hub.docker.com/r/dnanexus/bconexus BCO Nexus] ===		=== [https://hub.docker.com/r/dnanexus/bconexus BCO Nexus] ===
	[[File:Dnanexus.png\|frameless\|60x60px~~]][[File:Velsera.jpg\|frameless\|127x127px~~]]<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">		[[File:Dnanexus.png\|frameless\|60x60px]]<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
	BCOnexus developed by DNAnexus, now known as Velsera, as a platform-free Docker tool for quick BCO evaluation.		BCOnexus developed by DNAnexus, now known as Velsera, as a platform-free Docker tool for quick BCO evaluation.
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	<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">		<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">
	=== ~~[https://hub.docker.com/r/dnanexus/bconexus BCO Nexus]~~ ===		=== Galaxy Platform ===
	[[File:~~Dnanexus~~.png\|frameless\|~~60x60px]][[File:Velsera.jpg\|frameless\|127x127px~~]]<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">		[[File:Galaxy.png\|frameless\|162x162px]]<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
	~~BCOnexus developed by DNAnexus, now known as Velsera, as~~ a ~~platform-free Docker tool for quick~~ BCO ~~evaluation~~.		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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	<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">		<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">
	=== [https://~~hub~~.~~docker~~.~~com~~/~~r/dnanexus/bconexus BCO Nexus~~] ===		=== [https://www.cancergenomicscloud.org/ Cancer Genomics Cloud Seven Bridges] ===
	[[File:~~Dnanexus~~.png\|frameless\|~~60x60px~~]][[File:Velsera.jpg\|frameless\|127x127px]]<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">		[[File:Cgc2.png\|frameless\|114x114px]][[File:Velsera.jpg\|frameless\|127x127px]]<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
	~~BCOnexus developed by DNAnexus~~, ~~now known as Velsera~~, ~~as a platform-free Docker tool for quick BCO evaluation~~.		Tools to create, validate, and export BioCompute Objects in R.
	</div>		</div>
	</div>		</div>

Twang9 at 15:41, 11 March 2025

2025-03-11T15:41:05Z

← Older revision		Revision as of 15:41, 11 March 2025
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Twang9 at 15:39, 11 March 2025

2025-03-11T15:39:54Z

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