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Latest revision as of 20:52, 16 May 2024

Welcome to BioCompute Objects Wiki,

The MediaWiki for the BioCompute Objects project. This wiki system provides complementary information to the BioCompute portal and is divided into the following main sections: General information for the BioCompute portal, Quick Start and User Guide, FAQ, Curation SOP, and About for the BioCompute portal.

You can also find the BioCompute White paper here.

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.

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.

BCO Curation SOP

Intended audience: authors and developers

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

Workshop

We are hosting an in-person workshop on May 10, 2024. Learn more here. For all previous workshop materials, click here.

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.

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.

@@ Line 1: / Line 1: @@
-== The BioCompute Standard ==
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+__NOTOC__
+<!-- BANNER ACROSS TOP OF PAGE -->
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+    <div style="margin:0.4em; text-align:center;">
+        <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>You can also find the BioCompute White paper [[White paper|here]].
+</div>
+</div>
+<div style="clear: both;"></div>
-Because of the many different ways to organize data, a major goal of the BioCompute project is to build and maintain a formal standard through recognized, accredited standards setting organizations like the Institute for Electrical and Electronics Engineers (IEEE) and the International Standards Organization (ISO). A formal, consensus-based standard builds predictability and even more stability into the way in which bioinformatic methods are communicated.
+<div style="clear: both;"><br />
+        <div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><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;">
-The standard, officially known as 2791-2020, has two parts: the standards document and the schema, which is maintained in an open source repository:
-* The current version of the standard can be found [here](https://standards.ieee.org/standard/2791-2020.html)**.
+<div id="ggw_row2" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;">
-* The schema can be found [here](https://opensource.ieee.org/2791-object/ieee-2791-schema)**.
+    <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>[[User guide|BioCompute Object (BCO) User Guide]]</h3>
+        <div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
+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)]].
-Since the base BioCompute schema is maintained as an open source repository, it can be cloned and integrated into an organization in unique ways, which allows organizations to build off of this schema to create dependent standards for specific applications. This is similar to the different versions of WiFi based on usage, such as the 802.11a standard for fast speed, but high cost and shorter range, or the 802.11b for slower top speed, but lower cost, etc. --- all of which are built on the 802.11 base standard. It can also be used to further extend the schema, such as for handling proprietary, internal content, while still being compatible with the base standard. The open source schema also enables individuals or organizations to suggest changes to be incorporated into future versions the standard.
+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].
-=== Citation ===
+Read more: [[Introduction|Introduction to BioCompute Objects]]
-This standard was originaly prepared by [The BioCompute Object working group](/BCO_Spec_V1.2.md#biocompute-object-consortium-members-bcoc) during preparation for the [2017 HTS Computational Standards for Regulatory Sciences Workshop](https://hive.biochemistry.gwu.edu/htscsrs/workshop_2017).
-To reference the BCO standards, please use the following
+        </div>
-citation inclusive of the DOI:
+    </div>
-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](http://doi.org/10.5731/pdajpst.2016.006734)
+    <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>[[Faq|Frequently Asked Questions]]</h3>
+        <div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
+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.
-=== Support, Community and Contributing ===
+Read more: [[Faq|Frequently Asked Questions]]
-To suggest changes to [this repository](https://github.com/biocompute-objects/BCO_Specification) we welcome contributions as a [pull request](https://github.com/biocompute-objects/BCO_Specification/pulls) or [issue](https://github.com/biocompute-objects/BCO_Specification/issues) submission.
-BCO_Specification is licensed under the [BSD 3-Clause "New" or "Revised" License](https://github.com/biocompute-objects/BCO_Specification/blob/main/LICENSE.md)
+        </div>
+    </div>
-A permissive license similar to the BSD 2-Clause License, but with a 3rd clause that prohibits others from using the name of the project or its contributors to promote derived products without written consent.
+<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>[[Sop|BCO Curation SOP]]</h3>
+        <div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
+Intended audience: authors and developers
-=== Mailing List ===
+This section is intended to provide guidance on BCO™ creation, versioning, certification and authentication.
-As a subscriber to the BCO mailing list, you can post to it by sending a message tobiocomputels@hermes.gwu.edu (using the email address that is subscribed). This list is semi-automated and will send your message for review.
+Read more: [[Sop|BCO Curation SOP]]
-To subscribe or unsubscribe, please visit https://hermes.gwu.edu/cgi-bin/wa?A0=BIOCOMPUTELS and click `Subscribe` or `Unsubscribe` on the lower right. You can also unsubscribe from the list at any time by sending an email to listserv@hermes.gwu.edu, in which the body says: `unsubscribe biocomputes`
-This repository is in support of [2791-2020](https://standards.ieee.org/standard/2791-2020.html) - IEEE Approved Draft Standard for Bioinformatics Computations and Analyses Generated by High-Throughput Sequencing (HTS) to Facilitate Communication. Please also see our [OSF page](https://osf.io/h59uh/) or our [main page](https://biocomputeobject.org/)
+        </div>
+    </div>
+</div>
+    </div>
-== BioCompute Object (BCO) User Guide ==
+<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;">
+        <h3>[[BioCompute Conference and Workshop|Workshop]]</h3>
+        <div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
+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].
+</div>
+    </div>
-This document was created by the BioCompute Object Consortium members (BCOC).
+<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;">
+        <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.
-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.[https://standards.ieee.org/ieee/2791/7337/]
+Read more:
+*[[About|What is BioCompute?]]
+*[[About|Wifi Analogy]]
+*[[About|BioCompute Description]]
+</div>
+    </div>
-=== Introduction ===
+<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;">
+        <h3>[[Publications|Publication]]</h3>
+        <div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
+'''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
-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.
+See also full list of [[publications]] about BioCompute Object.
-Read more: '''[https://docs.biocomputeobject.org/introduction/ Introduction to BioCompute Objects]
+=== Other links ===
-'''
+# [[CDISC]]
-=== BioCompute Domains ===
+# [[Galaxy]]
+# [[RO-Crate]]
-BCOs are represented in JSON (JavaScript Object Notation) formatted text, adhering to [https://json-schema.org/specification.html JSON schema draft-07]. The JSON format was chosen because it is both human and machine-readable/writable. For a detailed description of JSON see [http://www.json.org www.json.org].
+# [[CWL|Common Workflow Language (CWL)]]
+# [https://fairsharing.org/4293 FAIRsharing]
-BioCompute data types are defined as aggregates of the critical fields organized into the following domains: the provenance domain, the usability domain, the extension domain, the description domain, the execution domain, the parametric domain, the input and output domains, and the error domain. At the time of creation with actual values compliant to the schema the BCO should be assigned a unique identifier, '''a [[https://docs.biocomputeobject.org/top-level/#202-biocompute-object-identifier-object_id|object_id]]'''. The object could then be assigned a unique digital etag.
+</div>
+    </div>