All public logs
Jump to navigation
Jump to search
Combined display of all available logs of BCOeditor Wiki. You can narrow down the view by selecting a log type, the username (case-sensitive), or the affected page (also case-sensitive).
(newest | oldest) View (newer 50 | older 50) (20 | 50 | 100 | 250 | 500)- 19:22, 24 August 2022 Twang9 talk contribs created page File:Objects3.png
- 19:22, 24 August 2022 Twang9 talk contribs uploaded File:Objects3.png
- 19:21, 24 August 2022 Twang9 talk contribs created page File:Object.png
- 19:21, 24 August 2022 Twang9 talk contribs uploaded File:Object.png
- 19:20, 24 August 2022 Twang9 talk contribs created page File:Objects1.png
- 19:20, 24 August 2022 Twang9 talk contribs uploaded File:Objects1.png
- 19:18, 24 August 2022 Twang9 talk contribs created page File:Account.png
- 19:18, 24 August 2022 Twang9 talk contribs uploaded File:Account.png
- 19:12, 24 August 2022 Twang9 talk contribs created page Tutorials (Created page with "== Register for a portal account == Before building a BioCompute Object (BCO), please register an account first by following the listed steps: # Go to Log in on the header: 800px|thumb|center")
- 19:11, 24 August 2022 Twang9 talk contribs created page File:Login.png
- 19:11, 24 August 2022 Twang9 talk contribs uploaded File:Login.png
- 20:51, 19 August 2022 Twang9 talk contribs created page CDISC (Created page with "== Background == CDISC stands for Clinical Data Interchange Standards Consortium, a standards developing organization (SDO) that has developed data standards for clinical and translational research for over 20 years. Its primary goal is to “enable information system interoperability to improve medical research and related areas of healthcare.” If applied early in the research phase, this standard has been authorized to cut overall resource requirements by 60%. CDISC...")
- 16:25, 19 August 2022 Twang9 talk contribs created page Galaxy (Created page with "== Background == Galaxy (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987906/) is a web-based computational workbench that provides thousands of researchers with scientific workflow, data integration, and data analysis for performing accessible, reproducible, and transparent massive biomedical datasets such as genomics, proteomics, and imaging sciences. The platform is currently used as a general bioinformatics workflow management system. Complex analysis tools and work...")
- 16:20, 19 August 2022 Twang9 talk contribs created page RO-Crate (Created page with "== Background == RO-Crate refers to Research Object Crate, which aggregates and describes research data with associated metadata, such as files, URI-addressable resources, or use other addressing schemes to locate digital or physical data. Use of metadata aid in the discovery, re-use, and long-term management of data. RO-Crate uses a series of linked JSON-LD objects to express metadata, describing data resources. The [https://www.researchobject.org/ro-crate/1.1/introduc...")
- 15:06, 19 August 2022 Twang9 talk contribs created page CWL (Created page with "== Background == [https://www.commonwl.org/ Common workflow Language] (CWL) is an open and free standard developed by multi-vendor working groups of organizations and individuals/contributors with open and transparent governance, which describes how to run command line tools and connect them to create workflows. It enables scientists to reuse and reproduce data analysis workflows and is easy to upscale for parallelization to other high-performance computing environments....")
- 21:06, 15 August 2022 Twang9 talk contribs created page Publication (Created page with "# King CH, Keeney J, Guimera N, Das S, Weber M, Fochtman B, Walderhaug MO, Talwar S, Patel JA, Mazumder R, Donaldson EF. Communicating regulatory high-throughput sequencing data using BioCompute Objects. Drug Discov Today. 2022 Jan 22; PMID: 35077912. # 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 Trisovi...")
- 15:23, 15 August 2022 Twang9 talk contribs created page Cheatsheet (Created page with "800px|thumb|center 800px|thumb|center")
- 15:23, 15 August 2022 Twang9 talk contribs created page File:Screen Shot 2022-08-15 at 11.21.50.png
- 15:23, 15 August 2022 Twang9 talk contribs uploaded File:Screen Shot 2022-08-15 at 11.21.50.png
- 15:22, 15 August 2022 Twang9 talk contribs created page File:Screen Shot 2022-08-15 at 11.21.31.png
- 15:22, 15 August 2022 Twang9 talk contribs uploaded File:Screen Shot 2022-08-15 at 11.21.31.png
- 17:56, 10 August 2022 Twang9 talk contribs created page File:CheatSheet V07 jgk1 hk1.pdf
- 17:56, 10 August 2022 Twang9 talk contribs uploaded File:CheatSheet V07 jgk1 hk1.pdf
- 16:04, 10 August 2022 Hadleyking talk contribs created page File:GCC2022.poster.pdf
- 16:04, 10 August 2022 Hadleyking talk contribs uploaded File:GCC2022.poster.pdf
- 15:46, 10 August 2022 Hadleyking talk contribs deleted page File:Order Success.pdf
- 15:46, 10 August 2022 Hadleyking talk contribs created page File:Order Success.pdf
- 15:46, 10 August 2022 Hadleyking talk contribs uploaded File:Order Success.pdf
- 22:19, 9 August 2022 Twang9 talk contribs moved page Bco faq to Faq (match https://docs.biocomputeobject.org/faq/)
- 16:08, 8 August 2022 Twang9 talk contribs created page User guide (Created page with "== Table of contents == *Galaxy BioCompute Objects *Introduction to BioCompute Objects *BCO domains **Top-level fields **Provenance domain **Usability domain **Extension Domain ***FHIR extension ***SCM extension **Description domain **Execution domain **Parametr...")
- 15:19, 8 August 2022 Twang9 talk contribs created page New Tools for Building BioCompute Objects on DNAnexus, Seven Bridges, and Galaxy for deposit to the FDA's BioComputeDB (Created page with "800px|thumb|center")
- 15:19, 8 August 2022 Twang9 talk contribs created page File:Screen Shot 2022-08-08 at 11.18.48.png
- 15:19, 8 August 2022 Twang9 talk contribs uploaded File:Screen Shot 2022-08-08 at 11.18.48.png
- 14:11, 8 August 2022 Hadleyking talk contribs deleted page File:2791-2020 Review.pdf
- 14:11, 8 August 2022 Hadleyking talk contribs created page File:2791-2020 Review.pdf
- 14:11, 8 August 2022 Hadleyking talk contribs uploaded File:2791-2020 Review.pdf
- 15:12, 5 August 2022 Twang9 talk contribs created page Events (Created page with "Welcome! This is the BioCompute Events page. Workshops are listed on the schedule below. For any questions, comments, or for a BioCompute Informational Session (15 minute WebEx) click here == Table of contents == *BioCompute Database and Transfer Mechanism Development Workshop *BioCompute Objects on High-performance Integrated Virtual Environment (HIVE) *Workflow Preservation and Reproducibility with BCO-RO *Towards Interoperability: Generating BioCompute Objects on Clo...")
- 21:49, 4 August 2022 Twang9 talk contribs created page About (Created page with "== What is BioCompute? == Tremendous insights can be found in genome data, and many of these insights are being used to drive personalized medicine. But the hundreds of millions of reads that come from a gene sequencer represent small, nearly random fragments of the genome that’s being sequenced, and there are countless ways in which that data can be transformed to yield insights into cancer, ancestry, microbiome dynamics, metagenomics, and many other areas of interes...")
- 21:26, 4 August 2022 Twang9 talk contribs created page File:Milestone for BCO.png
- 21:26, 4 August 2022 Twang9 talk contribs uploaded File:Milestone for BCO.png
- 21:20, 4 August 2022 Twang9 talk contribs created page File:Wifi analogy.png
- 21:20, 4 August 2022 Twang9 talk contribs uploaded File:Wifi analogy.png
- 21:19, 4 August 2022 Twang9 talk contribs created page File:About.3.png
- 21:19, 4 August 2022 Twang9 talk contribs uploaded File:About.3.png
- 21:08, 4 August 2022 Twang9 talk contribs created page Sop (Created page with "= BCO Curation SOP = Intended audience: authors and developers The following recommendations are intended to provide guidance on BCO™ creation, versioning, certification, and authentication. == BCO IDs and Versioning == Intended Audience: BCO authors *BioCompute IDs are used as persistent URLs. A novel usability domain must result in the creation of a new BCO with a new BCO ID. BCO IDs are immutable upon creation and are never deleted or retired. If the usability...")
- 21:04, 4 August 2022 Twang9 talk contribs created page File:Certification requirements.png
- 21:04, 4 August 2022 Twang9 talk contribs uploaded File:Certification requirements.png
- 17:37, 4 August 2022 Twang9 talk contribs created page Extension-scm (Created page with "Back to BCO domains == Extension to External References: Software Configuration Management (SCM) == The external references '''example''' extension to a SCM repository demonstrates how a BioCompute Object software source code can be stored/deposited/downloaded. The BCO would contain links to the SCM repository where the information is stored and easily retrieved. The links to the SCM can be added to the usability domain as well. "extension_domain":{...")
- 17:32, 4 August 2022 Twang9 talk contribs created page Extension-fhir (Created page with "Back to BCO domains == Extension to External References: SMART on FHIR Genomics == The external references example extension to FHIR resource demonstrates how specific data elements can be extracted from EHR systems or other secure FHIR endpoints via technologies such as SMART on FHIR Genomics (https://www.ncbi.nlm.nih.gov/pubmed/26198304) without compromising patient and providers’ information. This is because the portions being transferred contain n...")
- 17:19, 4 August 2022 Twang9 talk contribs created page Quick start (Created page with "== '''Creating a BCO on Galaxy''' == Galaxy has an extensive workflow system. They define a [https://galaxyproject.org/learn/advanced-workflow/ workflow] as “.. a series of tools and dataset actions that run in sequence as a batch operation”. An instance of a Galaxy workflow is known as an “invocation”. Since a BCO is a record of a specific instance of computation, the Galaxy invocations are used to generate the Galaxy BCOs. The first step in creating a well-doc...")
