BCOeditor Wiki - User contributions [en]

Publications

2022-08-25T14:56:15Z

Soiland-Reyes: isbn

# Charles Hadley S King 4th, Jonathon Keeney, Nuria Guimera, Souvik Das, Michiel Weber, Brian Fochtman, Mark O Walderhaug, Sneh Talwar, Janisha A Patel, Raja Mazumder, Eric F Donaldson (2022): <br />'''Communicating regulatory high-throughput sequencing data using BioCompute Objects'''. <br />''Drug Discovery Today'' '''27'''(4). PMID: [https://pubmed.ncbi.nlm.nih.gov/35077912/ 35077912] https://doi.org/10.1016/j.drudis.2022.01.007
# 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 (2022): <br />'''Packaging research artefacts with RO-Crate'''. <br /> ''Data Science'' '''5'''(2) https://doi.org/10.3233/DS-210053.
# Janisha A Patel, Dennis A Dean, Charles Hadley King, Nan Xiao, Soner Koc, Ekaterina Minina, Anton Golikov, Phillip Brooks, Robel Kahsay, Rahi Navelkar, Manisha Ray, Dave Roberson, Chris Armstrong, Raja Mazumder, Jonathon Keeney (2021): <br /> '''Bioinformatics tools developed to support BioCompute Objects'''. <br /> ''Database'' 2021:baab008 PMID:[https://pubmed.ncbi.nlm.nih.gov/33784373/ 33784373] https://doi.org/10.1093/database/baab008
# Gil Alterovitz, Dennis Dean, Carole Goble, Michael R. Crusoe, Stian Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Anjan Purkayastha, Charles H. King, Dan Taylor, Elaine Johanson, Elaine E. Thompson, Eric Donaldson, Hiroki Morizono, Hsinyi Tsang, Jeet K. Vora, Jeremy Goecks, Jianchao Yao, Jonas S. Almeida, Jonathon Keeney, KanakaDurga Addepalli, Konstantinos Krampis, Krista M. Smith, Lydia Guo, Mark Walderhaug, Marco Schito, Matthew Ezewudo, Nuria Guimera, Paul Walsh, Robel Kahsay, Srikanth Gottipati, Timothy C. Rodwell, Toby Bloom, Yuching Lai, Vahan Simonyan, Raja Mazumder (2018): <br /> '''Enabling Precision Medicine via standard communication of HTS provenance, analysis, and results'''. <br /> ''PLOS Biology'' '''16'''(12):e3000099. https://doi.org/10.1371/journal.pbio.3000099
# Vahan Simonyan, Jeremy Goecks and Raja Mazumder (2017): <br /> '''BioCompute objects—a step towards evaluation and validation of bio-medical scientific computations'''. <br /> ''PDA Journal of Pharmaceutical Science and Technology'' '''71'''(2):136-146 PMID:[https://pubmed.ncbi.nlm.nih.gov/27974626/ 27974626] https://doi.org/10.5731/pdajpst.2016.006734
# Nan Xiao, Soner Koc, David Roberson, Phillip Brooks, Manisha Ray, Dennis Dean (2020): <br /> '''BCO App: tools for generating BioCompute Objects from next-generation sequencing workflows and computations''' [version 1; peer review: 2 approved]. <br /> ''F1000Research'' '''9''':1144 https://doi.org/10.12688/f1000research.25902.1
# Naila Gulzar, Jonathon Keeney, Jack B. Baker, Ondrej Klempir, Geoffrey Hannigan, Danny A. Bitton, Julia M Maritz, Charles Hadley S. King IV, Janisha A. Patel, Paul Duncan, Raja Mazumder (2021): <br /> '''BioCompute Objects to communicate a viral detection pipeline with potential for use in a regulatory environment'''. <br /> ''bioRxiv'' https://doi.org/10.1101/2021.10.19.465010
# Raja Mazumder, Vahan Simonyan (eds), IEEE P2791 BioCompute Working Group (BCOWG) (2020): <br /> '''IEEE Standard for Bioinformatics Analyses Generated by High-Throughput Sequencing (HTS) to Facilitate Communication'''. <br /> ''IEEE Std'' 2791-2020. IEEE SA Standards Board. <nowiki>ISBN 9781504464666</nowiki> https://doi.org/10.1109/IEEESTD.2020.9094416 [[https://www.research.manchester.ac.uk/portal/en/publications/ieee-standard-for-bioinformatics-analyses-generated-by-highthroughput-sequencing-hts-to-facilitate-communication(936de52b-ac53-4f0e-9927-77fd7073e88d).html preprint]]

Publications

2022-08-25T14:55:35Z

Soiland-Reyes: Include IEEE 2791 specs

# Charles Hadley S King 4th, Jonathon Keeney, Nuria Guimera, Souvik Das, Michiel Weber, Brian Fochtman, Mark O Walderhaug, Sneh Talwar, Janisha A Patel, Raja Mazumder, Eric F Donaldson (2022): <br />'''Communicating regulatory high-throughput sequencing data using BioCompute Objects'''. <br />''Drug Discovery Today'' '''27'''(4). PMID: [https://pubmed.ncbi.nlm.nih.gov/35077912/ 35077912] https://doi.org/10.1016/j.drudis.2022.01.007
# 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 (2022): <br />'''Packaging research artefacts with RO-Crate'''. <br /> ''Data Science'' '''5'''(2) https://doi.org/10.3233/DS-210053.
# Janisha A Patel, Dennis A Dean, Charles Hadley King, Nan Xiao, Soner Koc, Ekaterina Minina, Anton Golikov, Phillip Brooks, Robel Kahsay, Rahi Navelkar, Manisha Ray, Dave Roberson, Chris Armstrong, Raja Mazumder, Jonathon Keeney (2021): <br /> '''Bioinformatics tools developed to support BioCompute Objects'''. <br /> ''Database'' 2021:baab008 PMID:[https://pubmed.ncbi.nlm.nih.gov/33784373/ 33784373] https://doi.org/10.1093/database/baab008
# Gil Alterovitz, Dennis Dean, Carole Goble, Michael R. Crusoe, Stian Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Anjan Purkayastha, Charles H. King, Dan Taylor, Elaine Johanson, Elaine E. Thompson, Eric Donaldson, Hiroki Morizono, Hsinyi Tsang, Jeet K. Vora, Jeremy Goecks, Jianchao Yao, Jonas S. Almeida, Jonathon Keeney, KanakaDurga Addepalli, Konstantinos Krampis, Krista M. Smith, Lydia Guo, Mark Walderhaug, Marco Schito, Matthew Ezewudo, Nuria Guimera, Paul Walsh, Robel Kahsay, Srikanth Gottipati, Timothy C. Rodwell, Toby Bloom, Yuching Lai, Vahan Simonyan, Raja Mazumder (2018): <br /> '''Enabling Precision Medicine via standard communication of HTS provenance, analysis, and results'''. <br /> ''PLOS Biology'' '''16'''(12):e3000099. https://doi.org/10.1371/journal.pbio.3000099
# Vahan Simonyan, Jeremy Goecks and Raja Mazumder (2017): <br /> '''BioCompute objects—a step towards evaluation and validation of bio-medical scientific computations'''. <br /> ''PDA Journal of Pharmaceutical Science and Technology'' '''71'''(2):136-146 PMID:[https://pubmed.ncbi.nlm.nih.gov/27974626/ 27974626] https://doi.org/10.5731/pdajpst.2016.006734
# Nan Xiao, Soner Koc, David Roberson, Phillip Brooks, Manisha Ray, Dennis Dean (2020): <br /> '''BCO App: tools for generating BioCompute Objects from next-generation sequencing workflows and computations''' [version 1; peer review: 2 approved]. <br /> ''F1000Research'' '''9''':1144 https://doi.org/10.12688/f1000research.25902.1
# Naila Gulzar, Jonathon Keeney, Jack B. Baker, Ondrej Klempir, Geoffrey Hannigan, Danny A. Bitton, Julia M Maritz, Charles Hadley S. King IV, Janisha A. Patel, Paul Duncan, Raja Mazumder (2021): <br /> '''BioCompute Objects to communicate a viral detection pipeline with potential for use in a regulatory environment'''. <br /> ''bioRxiv'' https://doi.org/10.1101/2021.10.19.465010
# Raja Mazumder, Vahan Simonyan (eds), IEEE P2791 BioCompute Working Group (BCOWG) (2020): <br /> '''IEEE Standard for Bioinformatics Analyses Generated by High-Throughput Sequencing (HTS) to Facilitate Communication'''. <br /> ''IEEE Std'' 2791-2020. IEEE SA Standards Board. https://doi.org/10.1109/IEEESTD.2020.9094416 [[https://www.research.manchester.ac.uk/portal/en/publications/ieee-standard-for-bioinformatics-analyses-generated-by-highthroughput-sequencing-hts-to-facilitate-communication(936de52b-ac53-4f0e-9927-77fd7073e88d).html preprint]]

Main Page

2022-08-25T14:53:18Z

Soiland-Reyes: Fix links to publications

{{DISPLAYTITLE:<span style="position: absolute; clip: rect(1px 1px 1px 1px); clip: rect(1px, 1px, 1px, 1px);">{{FULLPAGENAME}}</span>}}
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<div style="font-size:160%; padding:.1em;">Welcome to BioCompute Objects Wiki,</div>
<div style="font-size:100%;">The [https://www.mediawiki.org/wiki/MediaWiki MediaWiki] for the BioCompute Objects project. This wiki system provides complementary information to the [https://www.biocomputeobject.org/ BioCompute portal] and is divided into the following main sections: General information for the [https://www.biocomputeobject.org/ BioCompute portal], [[User_guide|Quick Start and User Guide]], [[Faq|FAQ]], [[Sop|Curation SOP]], and [[About|About]] for the [https://www.biocomputeobject.org/ BioCompute portal].</div>
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<h3>[[User guide|BioCompute Object (BCO) User Guide]]</h3>
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This document specifies the structure of BioCompute Objects. The specification is split into multiple parts linked to this top-level document and is maintained in a [https://github.com/biocompute-objects/BCO%20Specification GitHub repository] where contributions are welcome. This document was created by the [[Main_Page#BioCompute_Object_Consortium_members_(BCOC)|BioCompute Object Consortium members (BCOC)]].

It is offered as support for IEEE-2791-2020: [https://standards.ieee.org/ieee/2791/7337/ IEEE Standard for Bioinformatics Computations and Analyses Generated by High-Throughput Sequencing (HTS) to Facilitate Communication].

Read more: [[Introduction|Introduction to BioCompute Objects]]

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<h3>[[Bco faq|Frequently Asked Questions]]</h3>
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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.

Read more: [[Bco faq|Frequently Asked Questions]]

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<h3>[[Sop|BCO Curation SOP]]</h3>
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Intended audience: authors and developers

This section is intended to provide guidance on BCO™ creation, versioning, certification and authentication.

Read more: [[Sop|BCO Curation SOP]]

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<h3>[[About]]</h3>
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
A BioCompute Object (BCO) is an instance of the BioCompute standard and is a computational record of a bioinformatics pipeline. A BCO is not an analysis but is a record of which analyses were executed and in exactly which ways. In this way, a BCO acts as an interface for existing standards. A BCO contains all of the necessary information to repeat an entire pipeline from FASTQ to result and includes additional metadata to identify provenance and usage.

Read more:
*[[About|What is BioCompute?]]
*[[About|Wifi Analogy]]
*[[About|BioCompute Description]]
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<h3>[[Publications|Publication]]</h3>
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'''For Citation Purpose:''' Simonyan, V., Goecks, J., & Mazumder, R. (2017). Biocompute Objects — A Step towards Evaluation and Validation of Biomedical Scientific Computations. PDA Journal of Pharmaceutical Science and Technology, 71(2), 136–146. doi: 10.5731/pdajpst.2016.006734

See also full list of [[publications]] about BioCompute Object.

== Other links ==
# [[CDISC]]
# [[Galaxy]]
# [[RO-Crate]]
# [[CWL|Common Workflow Language (CWL)]]

Publications

2022-08-25T14:51:29Z

Soiland-Reyes: Soiland-Reyes moved page Publication to Publications: Plural s

Publications

2022-08-25T14:51:08Z

Soiland-Reyes: linebreaks

Publications

2022-08-25T14:47:32Z

Soiland-Reyes: additional publication

# Charles Hadley S King 4th, Jonathon Keeney, Nuria Guimera, Souvik Das, Michiel Weber, Brian Fochtman, Mark O Walderhaug, Sneh Talwar, Janisha A Patel, Raja Mazumder, Eric F Donaldson (2022): '''Communicating regulatory high-throughput sequencing data using BioCompute Objects'''. ''Drug Discovery Today'' '''27'''(4). PMID: [https://pubmed.ncbi.nlm.nih.gov/35077912/ 35077912] https://doi.org/10.1016/j.drudis.2022.01.007
# 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 (2022): '''Packaging research artefacts with RO-Crate'''. ''Data Science'' '''5'''(2) https://doi.org/10.3233/DS-210053.
# Janisha A Patel, Dennis A Dean, Charles Hadley King, Nan Xiao, Soner Koc, Ekaterina Minina, Anton Golikov, Phillip Brooks, Robel Kahsay, Rahi Navelkar, Manisha Ray, Dave Roberson, Chris Armstrong, Raja Mazumder, Jonathon Keeney (2021): '''Bioinformatics tools developed to support BioCompute Objects'''. ''Database'' 2021:baab008 PMID:[https://pubmed.ncbi.nlm.nih.gov/33784373/ 33784373] https://doi.org/10.1093/database/baab008
# Gil Alterovitz, Dennis Dean, Carole Goble, Michael R. Crusoe, Stian Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Anjan Purkayastha, Charles H. King, Dan Taylor, Elaine Johanson, Elaine E. Thompson, Eric Donaldson, Hiroki Morizono, Hsinyi Tsang, Jeet K. Vora, Jeremy Goecks, Jianchao Yao, Jonas S. Almeida, Jonathon Keeney, KanakaDurga Addepalli, Konstantinos Krampis, Krista M. Smith, Lydia Guo, Mark Walderhaug, Marco Schito, Matthew Ezewudo, Nuria Guimera, Paul Walsh, Robel Kahsay, Srikanth Gottipati, Timothy C. Rodwell, Toby Bloom, Yuching Lai, Vahan Simonyan, Raja Mazumder (2018): '''Enabling Precision Medicine via standard communication of HTS provenance, analysis, and results'''. ''PLOS Biology'' '''16'''(12):e3000099. https://doi.org/10.1371/journal.pbio.3000099
# Vahan Simonyan, Jeremy Goecks and Raja Mazumder (2017): '''BioCompute objects—a step towards evaluation and validation of bio-medical scientific computations'''. ''PDA Journal of Pharmaceutical Science and Technology'' '''71'''(2):136-146 PMID:[https://pubmed.ncbi.nlm.nih.gov/27974626/ 27974626] https://doi.org/10.5731/pdajpst.2016.006734
# Nan Xiao, Soner Koc, David Roberson, Phillip Brooks, Manisha Ray, Dennis Dean (2020): '''BCO App: tools for generating BioCompute Objects from next-generation sequencing workflows and computations''' [version 1; peer review: 2 approved]'''.''' ''F1000Research'' '''9''':1144 https://doi.org/10.12688/f1000research.25902.1
# Gulzar N, Keeney J, Baker JB, Klempir O, Hannigan G, Bitton DA, Maritz JM, King CHS, Patel JA, Duncan P, Mazumder R (2021): '''BioCompute Objects to communicate a viral detection pipeline with potential for use in a regulatory environment'''. ''bioRxiv'' https://doi.org/10.1101/2021.10.19.465010

Publications

2022-08-25T14:17:18Z

Soiland-Reyes: consistent formatting and more journal info

# King CH, Keeney J, Guimera N, Das S, Weber M, Fochtman B, Walderhaug MO, Talwar S, Patel JA, Mazumder R, Donaldson EF (2022): '''Communicating regulatory high-throughput sequencing data using BioCompute Objects'''. ''Drug Discovery Today'' '''27'''(4). PMID: [https://pubmed.ncbi.nlm.nih.gov/35077912/ 35077912] https://doi.org/10.1016/j.drudis.2022.01.007
# 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 (2022): '''Packaging research artefacts with RO-Crate'''. ''Data Science'' '''5'''(2) https://doi.org/10.3233/DS-210053.
# 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. (2021): '''Bioinformatics tools developed to support BioCompute Objects'''. ''Database'' 2021:baab008 PMID:[https://pubmed.ncbi.nlm.nih.gov/33784373/ 33784373] https://doi.org/10.1093/database/baab008
# 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. (2018): '''Enabling Precision Medicine via standard communication of HTS provenance, analysis, and results'''. ''PLOS Biology'' '''16'''(12):e3000099. https://doi.org/10.1371/journal.pbio.3000099
# Simonyan V, Goecks J, Mazumder R. (2017): '''BioCompute objects - a step towards evaluation and validation of bio-medical scientific computations'''. ''PDA Journal of Pharmaceutical Science and Technology'' '''71'''(2):136-146 PMID:[https://pubmed.ncbi.nlm.nih.gov/27974626/ 27974626] https://doi.org/10.5731/pdajpst.2016.006734

Publications

2022-08-25T14:11:53Z

Soiland-Reyes: DOIs and formatting

# King CH, Keeney J, Guimera N, Das S, Weber M, Fochtman B, Walderhaug MO, Talwar S, Patel JA, Mazumder R, Donaldson EF (2022): Communicating regulatory high-throughput sequencing data using BioCompute Objects. ''Drug Discov Today'' PMID: [https://pubmed.ncbi.nlm.nih.gov/35077912/ 35077912] https://doi.org/10.1016/j.drudis.2022.01.007
# 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'' '''5'''(2), 2022; https://doi.org/10.3233/DS-210053.
# 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:[https://pubmed.ncbi.nlm.nih.gov/33784373/ 33784373] https://doi.org/10.1093/database/baab008
# 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. (2018): Enabling Precision Medicine via standard communication of HTS provenance, analysis, and results. ''PLOS Biology'' '''16'''(12):e3000099. https://doi.org/10.1371/journal.pbio.3000099
# Simonyan V, Goecks J, Mazumder R. (2017): BioCompute objects - a step towards evaluation and validation of bio-medical scientific computations. ''PDA J Pharm Sci Technol.'' '''71'''(2):136-146 PMID:[https://pubmed.ncbi.nlm.nih.gov/27974626/ 27974626] https://doi.org/10.5731/pdajpst.2016.006734