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  • 21:44, 14 April 2026 ‎White Paper (hist | edit) ‎[107 bytes] ‎Lorikrammer (talk | contribs) (Created page with "center|1800x1800px center|1680x1680px")
  • 21:41, 14 April 2026 ‎Creating a BCO on Galaxy (hist | edit) ‎[910 bytes] ‎Lorikrammer (talk | contribs) (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...")
  • 21:38, 14 April 2026 ‎Galaxy Workflow Converter (hist | edit) ‎[1,655 bytes] ‎Lorikrammer (talk | contribs) (Created page with "Workflows can be directly downloaded from Galaxy but file conversion is needed in order to transfer into BCODB successfully. Please follow the following steps to convert the file and validation: == File conversion == # Download the converter [https://github.com/FDA-ARGOS/data.argosdb/blob/main/lib/galaxy%20converter.py script] from GitHub. # On the local terminal, run the following command <code>python [converter script's name.py] -b [path to the file that needs to be co...")
  • 21:38, 14 April 2026 ‎External References (hist | edit) ‎[2,422 bytes] ‎Lorikrammer (talk | contribs) (Created page with "'''Go back to BCO Domains.''' == 3.2 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...")
  • 21:36, 14 April 2026 ‎SCM Extension (hist | edit) ‎[1,817 bytes] ‎Lorikrammer (talk | contribs) (Created page with "'''Go 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":{...")
  • 21:35, 14 April 2026 ‎FHIR Extension (hist | edit) ‎[2,647 bytes] ‎Lorikrammer (talk | contribs) (Created page with "'''Go 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 no...")
  • 21:34, 14 April 2026 ‎Contact Us (hist | edit) ‎[794 bytes] ‎Lorikrammer (talk | contribs) (Created page with "Go back to Prefix Registration The best way to get help for any issues is go to '''Contact Us''' on the bottom of the BioCompute web page for a quick response and '''Report Bug or request feature''' for a less immediate problem.800px|thumb|center ''<u><big>'''Note a few suggested key points to include in a message:'''</big></u>'' *Issue location and ID if possible (e.g. provide a specific draft URL:https://www.biocomputeobject.org/builder/http...")
  • 21:33, 14 April 2026 ‎Common Errors (hist | edit) ‎[1,735 bytes] ‎Lorikrammer (talk | contribs) (Created page with "Return to the tutorial. Here is showing a list of common errors that a user might encounter while creating a BCO, please see possible solutions below: #Description Domain: autogenerated step numbers are incorrect or not in sequential order most times. #* Solution: Manually change the step numbers starting to 1, 2, 3…… #Description Domain: manually entered step numbers could be considered as strings during validation, which need to be integers. See...")
  • 21:31, 14 April 2026 ‎Prefix Registration (hist | edit) ‎[1,879 bytes] ‎Lorikrammer (talk | contribs) (Created page with "To create a Prefix, see the following steps: # Go to '''Prefix Registry''' on the Navigation Bar:center|thumb|800x800px #On the '''Prefix Registry''' page, users can achieve both prefix search and prefix registration functionalities. #*'''Prefix Search:''' users can search prefixes in three ways: '''My Prefixes''', '''Return all''', and '''Search Prefix Name.''' Select the desired searching option. If chose '''Search Prefix Name''', the...")
  • 21:30, 14 April 2026 ‎Account Registration (hist | edit) ‎[1,509 bytes] ‎Lorikrammer (talk | contribs) (Created page with "==Account Registration== Before building a BioCompute Object (BCO), please register an account first by following the listed steps: # Go to '''Log in''' on the header:center|thumb|804x804px #For first-time users, please click on “'''Don’t have an account? Sign up'''”, fill out the required information and click '''SUBMIT'''. thumb|centerGoogle authentication is also enabled on BioCompute. Users c...")
  • 21:28, 14 April 2026 ‎User Guide (hist | edit) ‎[5,611 bytes] ‎Lorikrammer (talk | contribs) (Created page with "'''Go Back to BioCompute Objects.''' == Quick Links == *BioCompute Cheat Sheet *Introduction to BioCompute Objects *BCO Domains *General User Tutorial *[https://standards.ieee.org/ieee/2791/7337/ IEEE-2791-2020: IEEE Standard for Bioinformatics Computations and Analyses Generated by High-Throughput Sequencing (HTS) to Facilitate Communication] *BCO Portal Local Deployment|API Tutorial: BCO Portal Local De...")
  • 21:26, 14 April 2026 ‎Top Level Fields (hist | edit) ‎[3,543 bytes] ‎Lorikrammer (talk | contribs) (Created page with "'''Go 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": {...")
  • 21:23, 14 April 2026 ‎Error Domain (hist | edit) ‎[3,335 bytes] ‎Lorikrammer (talk | contribs) (Created page with "'''Go back to BCO Domains.''' == Error Domain (''error_domain)'' == This section, also known as the ''acceptable range of variability'', is an optional domain comprised of two subdomains: empirical and algorithmic. The error domain IEEE schema and definition can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/blob/master/error_domain.json here]. The possible keys within each subdomain are workflow-specific, human-readable free text. For data i...")
  • 21:22, 14 April 2026 ‎Parametric Domain (hist | edit) ‎[1,424 bytes] ‎Lorikrammer (talk | contribs) (Created page with "'''Go 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. The provenance domain IEEE schema and definition can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/blob/master/parametric_domai...")
  • 21:19, 14 April 2026 ‎Execution Domain (hist | edit) ‎[7,419 bytes] ‎Lorikrammer (talk | contribs) (Created page with "'''Go back to BCO Domains.''' == Execution Domain (''execution_domain'') == This section defines the ''execution_domain'' part of the BCO. The execution domain IEEE schema, and definition can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/blob/master/execution_domain.json here]. The fields required for the execution of the BCO have been encapsulated together in order to clearly separate information needed for deployment, softwa...")
  • 21:17, 14 April 2026 ‎Description Domain (hist | edit) ‎[9,628 bytes] ‎Lorikrammer (talk | contribs) (Created page with "'''Go back to BCO Domains.''' == Description Domain (''description_domain'') == This section defines the fields of the ''description_domain'' part of the BCO structure. The description domain IEEE schema and definition can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/blob/master/description_domain.json here]. Structured field for description of external references, the pipeline steps, and the relationship of I/O objects. Info...")
  • 21:16, 14 April 2026 ‎Extension Domain (hist | edit) ‎[2,892 bytes] ‎Lorikrammer (talk | contribs) (Created page with "'''Go back to BCO Domains.''' == Extension Domain ''(extension_domain)'' == The ''extension_domain'' is a space for a user to add additional structured information that is not defined in the BioCompute schema. It is '''optional'''. While the extension domain is not defined by IEEE-2791-2020, each extension in this domain must provide a reference to the schema that defines it in order to validate. The extension domain allows a user to define additional fields and is...")
  • 21:13, 14 April 2026 ‎Usability Domain (hist | edit) ‎[4,768 bytes] ‎Lorikrammer (talk | contribs) (Created page with "'''Go back to BCO Domains.''' == Usability Domain ''(usability_domain)'' == This section defines the ''usability_domain'' part of the BCO structure. The associated IEEE schema that contains the definition can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/blob/master/usability_domain.json here]. The usability domain provides a specific scientific use case and a description of the function of the BCO. Condensed example: <pre>...")
  • 21:05, 14 April 2026 ‎Build a BCO (hist | edit) ‎[2,202 bytes] ‎Lorikrammer (talk | contribs) (Created page with " #Click on '''BCO Builder''' icon on the Navigation Bar:center|thumb|1056x1056px #To begin filling out the BCO, click on '''Provenance Domain''' to expand the section. Fill out the information as needed. Red boxes are required fields, and plain boxes are optional fields. Click '''next''' to advancing to the next section.center|thumb|1054x1054px #For information to fill out each domain, please refer to these links: Provenance-domain|Pro...")
  • 20:45, 14 April 2026 ‎BCO Domains (hist | edit) ‎[2,949 bytes] ‎Lorikrammer (talk | contribs) (Created page with "a") Tag: Visual edit
  • 21:30, 10 February 2026 ‎Provenance Domain (hist | edit) ‎[8,098 bytes] ‎Lorikrammer (talk | contribs) (Created page with "'''Go back to BCO domains.''' == Provenance Domain (''provenance_domain'') == This section defines the fields of the provenance_domain part of the BCO structure. The provenance domain IEEE schema and definition can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/blob/master/provenance_domain.json here]. Condensed example: <pre> "provenance_domain": { "name": "HCV1a ledipasvir resistance SNP detection"...")
  • 20:31, 10 February 2026 ‎Input and Output Domain (hist | edit) ‎[7,230 bytes] ‎Lorikrammer (talk | contribs) (Created page with "'''Go back to BCO Domains.''' == Input and Output Domain | "io_domain" == This section defines the io_domain part of the BCO. The IEEE io domain schema can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/blob/master/io_domain.json here]. 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 resid...")
  • 21:08, 5 February 2026 ‎HCV1a ledipasvir resistance SNP detection (hist | edit) ‎[14,834 bytes] ‎Lorikrammer (talk | contribs) (Created page with "<pre> { "object_id": "https://raw.githubusercontent.com/biocompute-objects/BCO_Specification/1.4.2/examples/HCV1a.json", "etag": "11ee4c3b8a04ad16dcca19a6f478c0870d3fe668ed6454096ab7165deb1ab8ea", "spec_version": "https://w3id.org/ieee/ieee-2791-schema/", "provenance_domain": { "name": "HCV1a ledipasvir resistance SNP detection", "version": "2.9", "review": [ { "status": "approved", "revi...")
  • 20:56, 5 February 2026 ‎WGS Simulation of DUF1220 Regions (hist | edit) ‎[25,383 bytes] ‎Lorikrammer (talk | contribs) (Created page with "<code> { "object_id": "https://biocomputeobject.org/BCO_000545/1.0", "spec_version": "https://w3id.org/ieee/ieee-2791-schema/2791object.json", "provenance_domain": { "name": "WGS Simulation of DUF1220 Regions", "version": "4.0", "license": "https://opensource.org/licenses/MIT", "created": "2020-08-30T11:30:52.000Z", "modified": "2024-11-17T14:18:09.680Z", "derived_from": "https://biocomputeobject.org/viewer?https://biocompu...")
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