Main Page: Difference between revisions

From BCOeditor Wiki
Jump to navigation Jump to search
No edit summary
No edit summary
 
(25 intermediate revisions by 3 users not shown)
Line 5: Line 5:
     <div style="margin:0.4em; text-align:center;">
     <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: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], Quick Start and User Guide, FAQ, Curation SOP, News and Events, and 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]].
    </div>
</div>
</div>
</div>
<div style="clear: both;"></div>
<div style="clear: both;"></div>


<!-- News section -->
<div id="ggw_row1" 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: #f5fffa;">
        <h3>News</h3>
        <div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
'''2022-09-13'''
*BioCompute Workshop: [[New Tools for Building BioCompute Objects on DNAnexus, Seven Bridges, and Galaxy for deposit to the FDA's BioComputeDB]]
'''2022-01-12'''
*[[BioCompute Database and Transfer Mechanism Development Workshop]].
**Recording [https://www.youtube.com/watch?v=EEgV8R8G4dI here]
More [[Events|News and Events]] can be found here
        </div>
    </div>
</div>
<div style="clear: both;"><br />
<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="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;">
     <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>General Information</h3>
        <div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
== The BioCompute Standard ==
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.
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)**.
* The schema can be found [here](https://opensource.ieee.org/2791-object/ieee-2791-schema)**.
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.
=== Citation ===
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
citation inclusive of the DOI:
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)
=== Support, Community and Contributing ===
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)
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.
=== Mailing List ===
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.
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></div>


<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;">
Line 77: Line 19:
         <h3>[[User guide|BioCompute Object (BCO) User Guide]]</h3>
         <h3>[[User guide|BioCompute Object (BCO) User Guide]]</h3>
         <div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
         <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%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)]].
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].
Line 87: Line 29:


     <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>[[Bco faq|Frequently Asked Questions]]</h3>
         <h3>[[Faq|Frequently Asked Questions]]</h3>
         <div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
         <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.
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]]
Read more: [[Faq|Frequently Asked Questions]]




Line 109: Line 51:
         </div>
         </div>
     </div>
     </div>
</div>
    </div>
<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>
<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.
Read more:
*[[About|What is BioCompute?]]
*[[About|Wifi Analogy]]
*[[About|BioCompute Description]]
</div>
    </div>
<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
See also full list of [[publications]] about BioCompute Object.
=== Other links ===
# [[CDISC]]
# [[Galaxy]]
# [[RO-Crate]]
# [[CWL|Common Workflow Language (CWL)]]
# [https://fairsharing.org/4293 FAIRsharing]
</div>
</div>
     </div>
     </div>

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.

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


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.

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.

Other links

  1. CDISC
  2. Galaxy
  3. RO-Crate
  4. Common Workflow Language (CWL)
  5. FAIRsharing
Retrieved from "https://wiki.biocomputeobject.org/index.php?title=Main_Page&oldid=797"