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stain / a.md
Created July 5, 2018 16:25

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"
    ]
@stain
stain / ro2018.md
Created June 26, 2018 12:55
Cf

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

@stain
stain / a.html
Last active June 19, 2018 22:07
http://forgethtml.sourceforge.net/ demo
<!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>
@stain
stain / names.html
Last active June 8, 2018 22:53
<!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">
@stain
stain / default.vcl
Created May 11, 2018 10:26
# 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";
@stain
stain / cwlpressrelease.html
Last active April 10, 2018 21:01
From https://pad.sfconservancy.org/p/CWL-announcement
<!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 April 4, 2018 02:24
Research Object OAI-ORE manifest (JSON-LD) after running cwlprov https://zenodo.org/record/1208478
{
"@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",
@stain
stain / manifest.json
Created March 29, 2018 13:32
Research Object BagIt manifest JSON-LD (and converted Turtle) from http://identifiers.org/ark/ark:/57799/b91w9r
{
"@context": [
"https://w3id.org/bundle/context"
],
"@id": "../",
"aggregates": [
{
"bundledAs": {
"filename": "ENCFF031MXQ.fastq.gz",
"folder": "../data/"
@stain
stain / pasc2018-cwl.md
Created March 9, 2018 09:02
PASC2018 abstract: Facing compute platform portability challenges with scientific workflows - experiences from Common Workflow Language

Facing compute platform portability challenges with scientific workflows - experiences from Common Workflow Language

Stian Soiland-Reyes, The University of Manchester; Apache Software Foundation

  • Talk abstract submitted to PASC 2018 minisymposium, Advances in Automation and Efficiency for the Exascale Era - Experiences from the Biomolecular Sciences.

Scientific Workflow systems are well established for computational analysis in all science domains, following the rapid development of workflow technology and community practices spanning the two recent decades, the eScience era. Workflow systems have gained traction in the era of Big Data Science due to their “ASAP" properties”: Automation over repetitive pipelines and simulation sweep campaigns; Scaling over computational infrastructure & handle large data; Abstraction to shield users and programs from complexity and incompatibilities and Provenance to auto-document execution logs and data

@stain
stain / paper.ttl
Last active February 14, 2018 14:57
Unable to upload to https://linkedresearch.org/inbox/linkedresearch.org/cloud/ -- see https://github.com/linkedresearch/linkedresearch.org/issues/21
@prefix as: <http://www.w3.org/ns/activitystreams#>.
@prefix prov: <http://www.w3.org/ns/prov#>.
@prefix dct: <http://purl.org/dc/terms/>.
@prefix schema: <http://schema.org/>.
@prefix foaf: <http://xmlns.com/foaf/0.1/>.
@prefix xsd: <http://www.w3.org/2001/XMLSchema#>.
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>.
<>
a as:Announce ;