Main Page: Difference between revisions

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: @@
-<strong>MediaWiki has been installed.</strong>
+{{DISPLAYTITLE:<span style="position: absolute; clip: rect(1px 1px 1px 1px); clip: rect(1px, 1px, 1px, 1px);">{{FULLPAGENAME}}</span>}}
+__NOTOC__
+<!-- BANNER ACROSS TOP OF PAGE -->
+<div id="ggw-topbanner" style="clear:both; position:relative; box-sizing:border-box; width:100%; margin:1.2em 0 6px; min-width:47em; border:1px solid #ddd; background-color:#f9f9f9; color:#000;">
+    <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>
-Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User's Guide] for information on using the wiki software.
+<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;">
-== Getting started ==
-* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:Configuration_settings Configuration settings list]
+<div id="ggw_row2" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;">
-* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:FAQ MediaWiki FAQ]
+    <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://lists.wikimedia.org/postorius/lists/mediawiki-announce.lists.wikimedia.org/ MediaWiki release mailing list]
+        <h3>[[User guide|BioCompute Object (BCO) User Guide]]</h3>
-* [https://www.mediawiki.org/wiki/Special:MyLanguage/Localisation#Translation_resources Localise MediaWiki for your language]
+        <div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
-* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:Combating_spam Learn how to combat spam on your wiki]
+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].
+Read more: [[Introduction|Introduction to BioCompute Objects]]
+        </div>
+    </div>
+    <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.
+Read more: [[Faq|Frequently Asked Questions]]
+        </div>
+    </div>
+<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
+This section is intended to provide guidance on BCO™ creation, versioning, certification and authentication.
+Read more: [[Sop|BCO Curation SOP]]
+        </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>