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@stain
stain / 00-review-GIGA-D-18-00427.md
Last active May 24, 2019
Review of GigaScience manuscript GIGA-D-18-00428
View 00-review-GIGA-D-18-00427.md
View cwlprov
stain@biggie:~/dropbox/work/cwlprov/newest-swift/rnaseqwf_0.5.0_mac$ cwlprov run
2018-09-24 20:30:12.438801 Flow 6458a48e-fabc-448f-9f17-0a1c6ff9a674 [ Run of workflow/packed.cwl#main
2018-09-24 20:30:26.239962 Step 201a6074-031a-4793-8719-863834d78cd9 Run of workflow/packed.cwl#main/run_star (0:02:31.016639)
2018-09-24 20:32:57.294541 Step ff48e829-82b5-48fb-a0fb-c7a8cd038bf8 Run of workflow/packed.cwl#main/sort_bam (0:00:02.014422)
2018-09-24 20:32:59.318559 Step 0128708d-e2a7-41f6-afe5-1833e4da59bc Run of workflow/packed.cwl#main/index_bam (0:00:01.680102)
2018-09-24 20:33:02.074684 Step 44f03c62-2d1b-478b-8f61-bfa1a3824d69 Run of workflow/packed.cwl#main/run_rsem (0:00:14.659971)
2018-09-24 20:33:16.748069 Step b5ff0180-5466-4cf5-b9c3-b71bc0542eaa Run of workflow/packed.cwl#main/run_markduplicates (0:00:03.764102)
2018-09-24 20:33:20.519469 Step e9a3b636-20d2-43f5-96b1-0cea68b43044 Run of workflow/packed.cwl#main/run_index_markduplicates_bam (0:00:01.502664)
2018-09-24 20:33:22.068415 S
View blah.log
(venv) stain@biggie:~/src/cwlprov-py$ cwlprov -d test/revsort-cwlprov-0.4.0/
Detected CWLProv research Object: test/revsort-cwlprov-0.4.0/
(venv) stain@biggie:~/src/cwlprov-py$ cwlprov -d test/revsort-cwlprov-0.4.0 validate
Valid: test/revsort-cwlprov-0.4.0
(venv) stain@biggie:~/src/cwlprov-py$ cwlprov -d test/revsort-cwlprov-0.4.0 info
Research Object of CWL workflow run
ID: arcp://uuid,d47d3d43-4830-44f0-aa32-4cda74849c63/
Profile: https://w3id.org/cwl/prov/0.4.0
View a.md

Some of the keys of the CWLProv manifest are explained below:

    "@context": [
        {
            "@base": "arcp://uuid,67f38794-d24a-435f-bd4a-0242a56a581b/metadata/"
        },
        "https://w3id.org/bundle/context"
    ]
View ro2018.md

In this workshop we will explore recent advancements in Research Objects and publishing of research data.

Scholarly Communication has evolved significantly in recent years, with an increasing focus on Open Research, FAIR data sharing and community-developed open source methods. The concepts of authorship and citation are changing, as researchers are increasingly reusing and evolving common software tools and datasets. Yet with a growing amount of cloud compute power and open platforms available, reproducibility of computational analyses becomes more challenging, and not yet commonly included in peer review. While recent advances in scientific workflows and provenance capture systems have improved on this situation, a question remains on how to publish, archive, explore and understand digital research outputs, as academic authors and publishers remain focused on PDFs and the occasional CSV file, with the Web and Open Research often left to “best effor

View a.html
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html>
<head>
<title>
Hello
</title>
<link href="http://example.com/" rel="canonical" />
</head>
<body>
View names.html
<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>The HTML5 Herald</title>
</head>
<body>
<div vocab="http://schema.org/" typeof="Person" resource="https://orcid.org/0000-0001-9842-9718">
View default.vcl
# This is a basic VCL configuration file for varnish. See the vcl(7)
# man page for details on VCL syntax and semantics.
#
# Default backend definition. Set this to point to your content
# server.
#
backend default {
.host = "127.0.0.1";
.port = "8080";
View cwlpressrelease.html
<!DOCTYPE html>
<html>
<head><title>Conservancy Welcomes the Common Workflow Language as a Member Project</title></head>
<body>
<h1>Conservancy Welcomes the Common Workflow Language as a Member Project</h1>
<em>2018-04-10. For immediate release.</em>
<p>Software Freedom Conservancy welcomes the <a href="http://www.commonwl.org/">Common Workflow Language (CWL) project</a> as Conservancy's newest member project. The project develops and maintains a specification for describing data analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, as well as a supporting reference implementation.</p>
<p>The Common Workflow Language project follows the <a href="https://open-stand.org/about-us/principles/">OpenStand principles for collaborative open standards development</a> to openly evolve the
@stain
stain / manifest.json
Created Apr 4, 2018
Research Object OAI-ORE manifest (JSON-LD) after running cwlprov https://zenodo.org/record/1208478
View manifest.json
{
"@context": [
{
"@base": "arcp://uuid,6805a5f5-e0bd-41a7-8775-fc578e3efc3a/metadata/"
},
"https://w3id.org/bundle/context"
],
"id": "/",
"manifest": "manifest.json",
"createdOn": "2018-04-04T03:21:28.093217",
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