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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).

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• 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
• 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
• 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...")
• 17:18, 4 August 2022 Twang9 talk contribs created page File:Workflow.png
• 17:18, 4 August 2022 Twang9 talk contribs uploaded File:Workflow.png
• 17:03, 4 August 2022 Twang9 talk contribs created page Introduction (Created page with "== Introduction to BioCompute Objects == BioCompute is a paradigm and a BioCompute Object (BCO) is an instance of that paradigm. High-throughput sequencing (HTS), also referred to as next-generation sequencing (NGS) or massively parallel sequencing (MPS), has increased the pace at which we generate, compute and share genomic data in biomedical sciences. As a result, scientists, clinicians and regulators are now faced with a new data paradigm that is less portable, more...")
• 21:06, 3 August 2022 Twang9 talk contribs created page External-references (Created page with "Back to BCO domains == Appendix-II: External reference database list == This list contains the databases that are currently being used in our BCOs. We use the CURIEs that map to URIs maintained by http://identifiers.org/ Identifiers.org is an established resolving system that enables the referencing of data for the scientific community, with a current focus on the Life Sciences domain. Identifiers.org provides direct access to the identified data us...")
• 20:12, 3 August 2022 Twang9 talk contribs created page Error-domain (Created page with "Back to BCO domains == Error Domain, acceptable range of variability “error_domain” == The error domain can be used to determine what range of input returns and outputs are within the tolerance level defined in this subdomain and therefore can be used to optimize the algorithm. It consists of two subdomains: empirical and algorithmic. The empirical error subdomain contains empirically determined values such as limits of detectability, false positiv...")
• 20:07, 3 August 2022 Twang9 talk contribs created page Parametric-domain (Created page with "Back to BCO domains == Parametric Domain “parametric_domain” == This optional domain represents the list of parameters customizing the computational flow which can affect the output of the calculations. These fields can be custom to each kind of analysis and are tied to a particular pipeline implementation. It is recommended that these fields be generated automatically, but that may not always be possible. Please refer to the documentation of indivi...")
• 19:59, 3 August 2022 Twang9 talk contribs created page Execution-domain (Created page with "Back to BCO domains == Execution Domain “execution_domain” == This section defines the execution_domain part of the BCO. The fields required for the execution of the BCO have been encapsulated together in order to clearly separate information needed for deployment, software configuration, and running applications in a dependent environment. One byproduct of an accurate BCO definition is the facilitation of reproducibility as defined...")
• 19:45, 3 August 2022 Twang9 talk contribs created page Extension-domain (Created page with "Back to BCO domains == Extension Domain “extension_domain” == The Extension Domain allows a user to define additional fields and is optional. The Extension Domain is for the inclusion of any additional structured information. A valid JSON schema for each extension used in this domain is expected to be specified. The schema should be namespaced, and it is recommended that resolving the namespaced URI will provide the extension’s JSON Schema. The UR...")
• 18:14, 3 August 2022 Twang9 talk contribs created page Best practices (Created page with "== General == *The required domains are defined by the IEEE. However, a BioCompute Object is considered complete when an Error Domain exists. *Versioning is allowed, but only if the changes do not affect the workflow or output. BCO versioning follows a minor.patch schema, no major versions are allowed (substantial changes result in a new BCO). Minor changes are things like a change of contact information for a contributor, patch changes are things like spelling and gram...")
• 16:58, 3 August 2022 Twang9 talk contribs created page Top-level (Created page with "Back to BCO domains ==Top Level Fields== These header fields uniquely define this BCO. These fields are required for every BCO and are represented at the top level object. Condensed example: { "object_id": "https://example.com/BCO_948701/1.0", "spec_version" : "https://w3id.org/ieee/ieee-2791-schema/2791object.json", "etag": "d41d8cd98f00b204e9800998ecf8427e", "provenance_domain": {...") Tag: Visual edit: Switched
• 16:56, 3 August 2022 Twang9 talk contribs created page Provenance-domain (Created page with "Back to BCO domains == Provenance Domain “provenance_domain” == This section defines the fields of the provenance_domain part of the BCO structure. Condensed example: "provenance_domain": { "name": "HCV1a ledipasvir resistance SNP detection", "version": "2.9", "review": [ ], "obsolete_after" : "2118-09-26T14:43:43-0400", "embargo" : { },...")
• 15:30, 3 August 2022 Twang9 talk contribs created page Bco faq (Created page with "== General == 1. '''Where would information regarding data sources and standard operating procedures be? Which specific domain?''' Data sources should be recorded as described by the input_subdomain in the “io_domain” and the input_list in the “description_domain”. Standard operating procedures and any other information about data transformations SHOULD be elaborated upon in the “usability_domain”....")
• 15:23, 3 August 2022 Twang9 talk contribs created page Usability-domain (Created page with "Back to BCO domains == Usability Domain “usability_domain” == This section defines the usability_domain part of the BCO structure. The Usability Domain of an Object is a plain language description of what was done in the workflow. This should align with the actual steps described elsewhere in the Object. The Usability Domain conveys the purpose of the Object. It is an array of free text values that should be consistent with the term...")
• 15:11, 3 August 2022 Twang9 talk contribs created page Description-domain (Created page with "Back to BCO domains == Description Domain “description_domain” == This section defines the fields of the description_domain part of the BCO structure. Structured field for description of external references, the pipeline steps, and the relationship of I/O objects. Information in this domain is not used for computation. This domain is meant to capture information that is currently being provided in FDA submission in a standardized fo...")
• 13:37, 3 August 2022 Twang9 talk contribs created page Iodomain (Created page with "== Input and Output Domain "io_domain" == This section defines the io_domain part of the BCO. This represents the list of global input and output files created by the computational workflow, excluding the intermediate files. These fields are pointers to objects that can reside in the system performing the computation or any other accessible system. Just like the fields of the parametric domain, these fields are expected to vary depending on the specific...")
• 20:26, 2 August 2022 Twang9 talk contribs moved page Bhco-domains to Bco-domains
• 20:26, 2 August 2022 Twang9 talk contribs created page Bhco-domains (Created page with "== BCO domains == A BCO JSON object is split into different parts, or domains, detailed below. Condensed example: "spec_version" : "https://w3id.org/biocompute/1.3.0/", "object_id": "https://example.com/bco/9487ae7e-c1aa-4a3c-b18f-3d3695b33ace", "type": "antiviral_resistance_detection", "etag": "584C7FE128717E1712426AB19CAAEA8BC1E27365B54285BBEA1221284C7D3A48", "provenance_domain": { }, "usability_domain": [ ], "extension_domain":{...")
• 14:38, 1 August 2022 User account Twang9 talk contribs was created

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