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<div style="font-size:160%; padding:.1em;">Welcome to BioCompute Objects Wiki,</div> | <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> | <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>You can also find the BioCompute White paper [[White paper|here]]. | ||
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<h3>[[User guide|BioCompute Object (BCO) User Guide]]</h3> | <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/ | 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_Specification 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]. | 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]. | ||
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<h3>[[ | <h3>[[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. | 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: [[ | Read more: [[Faq|Frequently Asked Questions]] | ||
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<h3>[[BioCompute Conference and Workshop|Workshop]]</h3> | |||
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We are hosting an in-person workshop on May 10, 2024. Learn more [[BioCompute Conference and Workshop|here]]. | |||
For all previous workshop materials, click [https://hive.biochemistry.gwu.edu/publications#Multimedia here]. | |||
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<h3>[[Publication]]</h3> | <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 | '''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 == | === Other links === | ||
# [[CDISC]] | # [[CDISC]] | ||
# [[Galaxy]] | # [[Galaxy]] | ||
# [[RO-Crate | # [[RO-Crate]] | ||
# [[CWL]] | # [[CWL|Common Workflow Language (CWL)]] | ||
# [https://fairsharing.org/4293 FAIRsharing] | |||
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Latest revision as of 20:52, 16 May 2024
BioCompute Object (BCO) User Guide
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 GitHub repository where contributions are welcome. This document was created by the BioCompute Object Consortium members (BCOC).
It is offered as support for IEEE-2791-2020: IEEE Standard for Bioinformatics Computations and Analyses Generated by High-Throughput Sequencing (HTS) to Facilitate Communication.
Read more: Introduction to BioCompute Objects
Frequently Asked Questions
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: Frequently Asked Questions
BCO Curation SOP
Intended audience: authors and developers
This section is intended to provide guidance on BCO™ creation, versioning, certification and authentication.
Read more: BCO Curation SOP
About
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:
Publication
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.