3:05 PM Maggie Hellstrom:
Peter's slides: https://www.rd-alliance.org/sites/default/files/web-workshop-intro.pptx
Stian Soiland-Reyes stain
stain
/ roum.owl
Last active
October 9, 2019 10:02
roum - research object upper model draft 2009-09-15 by Matthew Gamble, University of Manchester - see also http://150.146.207.114/lode/extract?url=https%3A%2F%2Fgist.githubusercontent.com%2Fstain%2Fe0cdd7ccf575082c6260f578d9d53204%2Fraw%2F4368341394b712f1a6c2b169659610466f69810f%2Froum.owl&owlapi=true&lang=en
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| <rdf:RDF xmlns="http://elab.org.uk/ontologies/roum#" xml:base="http://elab.org.uk/ontologies/roum" xmlns:owl2xml="http://www.w3.org/2006/12/owl2-xml#" xmlns:terms="http://purl.org/dc/terms/" xmlns:wordnet="http://xmlns.com/wordnet/1.6/" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:terms2="http://www.openarchives.org/ore/terms/" xmlns:roum="http://elab.org.uk/ontologies/roum#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:owl="http://www.w3.org/2002/07/owl#"> | |
| <owl:Ontology rdf:about=""> | |
| <owl:imports rdf:resource="http://dublincore.org/2008/01/14/dcterms.rdf"/> | |
| <owl:imports rdf:resource="http://www.openarchives.org/ore/1.0/terms"/> | |
| <owl:imports rdf:resource="http://xmlns.com/foaf/0.1/"/> | |
| </owl:Ontology> | |
| <!-- |
stain
/ LockQueue.java
Last active
October 9, 2019 00:04
A self-locking queue of locks - DO NOT USE https://twitter.com/soilandreyes/status/1181587178121502720
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| /* | |
| * Copyright 2019 Stian Soiland-Reyes | |
| * | |
| * Licensed under the Apache License, Version 2.0 (the "License"); | |
| * you may not use this file except in compliance with the License. | |
| * You may obtain a copy of the License at | |
| * | |
| * http://www.apache.org/licenses/LICENSE-2.0 | |
| * | |
| * Unless required by applicable law or agreed to in writing, software |
stain
/ mediainfo.sh
Created
August 12, 2019 11:50
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| (base) stain@biggie:~/Pictures/whatsapp$ mediainfo VID-20171005-WA0000.mp4 | |
| General | |
| Complete name : VID-20171005-WA0000.mp4 | |
| Format : MPEG-4 | |
| Format profile : Base Media / Version 2 | |
| Codec ID : mp42 (mp41/mp42/isom) | |
| File size : 3.27 MiB | |
| Duration : 3 min 22 s | |
| Overall bit rate : 135 kb/s | |
| Encoded date : UTC 2017-08-13 16:03:30 |
stain
/ inflation.tsv
Last active
July 30, 2019 10:34
Swiss inflation CHF compared to British inflation GDP since 1969 -- see https://twitter.com/soilandreyes/status/1156148657294663680 - sources https://www.inflation.eu/inflation-rates/great-britain/historic-inflation/cpi-inflation-great-britain.aspx https://www.inflation.eu/inflation-rates/switzerland/historic-inflation/cpi-inflation-switzerland.…
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| year | inflation from prev Y | inflated price | value chf | uk cpi | inflated price | value gbp | ||
|---|---|---|---|---|---|---|---|---|
| 1969 | CHF 0.50 | CHF 1.52 | 4.67 | £0.05 | £5.43 | |||
| 1970 | 5.44 | CHF 0.53 | CHF 1.44 | 7.89 | £0.05 | £5.19 | ||
| 1971 | 6.62 | CHF 0.56 | CHF 1.35 | 9.03 | £0.06 | £4.81 | ||
| 1972 | 6.86 | CHF 0.60 | CHF 1.26 | 7.65 | £0.06 | £4.41 | ||
| 1973 | 11.92 | CHF 0.67 | CHF 1.13 | 10.58 | £0.07 | £4.10 | ||
| 1974 | 7.55 | CHF 0.72 | CHF 1.05 | 19.14 | £0.08 | £3.71 | ||
| 1975 | 3.45 | CHF 0.75 | CHF 1.01 | 24.89 | £0.10 | £3.11 | ||
| 1976 | 1.27 | CHF 0.76 | CHF 1.00 | 15.07 | £0.12 | £2.49 | ||
| 1977 | 1.2 | CHF 0.77 | CHF 0.99 | 12.14 | £0.13 | £2.16 |
stain
/ properties-with-type-id.csv
Last active
July 30, 2019 09:08
curl -s -L -H "Accept: application/ld+json" https://schema.org/ | grep @type | grep @id | cut -d '"' -f 2,4 | sed 's/"/,/'
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| property | type | |
|---|---|---|
| actionableFeedbackPolicy | @id | |
| additionalType | @id | |
| afterMedia | @id | |
| arrivalTime | @id | |
| availabilityEnds | @id | |
| availabilityStarts | @id | |
| availableFrom | @id | |
| availableThrough | @id | |
| beforeMedia | @id |
stain
/ gist:87fc34a13eed60179447729cdf7f9ac7
Last active
July 2, 2019 10:55
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| ### Editing this command? Also update https://ci.commonwl.org/job/cwl-spec-pr/configure | |
| venv() { | |
| if ! test -d $1 ; then | |
| virtualenv $1 | |
| fi | |
| . $1/bin/activate | |
| } | |
| venv venv | |
| (. venv/bin/activate && pip install -U setuptools wheel pip) | |
| (. venv/bin/activate && pip install --ignore-installed --verbose -U cwltest cwltool) |
stain
/ domain-mapping.csv
Created
May 23, 2019 12:42
Mapping CWL outputs to concepts in EDAM etc. from https://github.com/EBI-Metagenomics/CWL-assembly/blob/5a63f965d5809dab3a8f79b5e08361c30ede7900/cwl/megahit_pipeline.cwl
We can make this file beautiful and searchable if this error is corrected: Unclosed quoted field in line 6.
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| output name,Data Format,Data Concept,relationship | |
| assembly,edam:format_1929 (FASTA),"http://edamontology.org/data_0925 | |
| ""Sequence assembly""","derived from $(inputs.{forward,reverse,interleaved,single}_reads)" | |
| assembly_log,iana:text/plain,"http://edamontology.org/data_3181 | |
| ""Sequence assembly report""",describes $(outputs.assembly) | |
| samtools_index,edam:format_2572 (BAM) + index,"alignment of reads to assembled contigs | |
| http://edamontology.org/data_1383 is multiple sequence alignment, need a data concept for the result of http://edamontology.org/operation_0523 ""Mapping assembly""","derives from both $(inputs.{forward,reverse,interleaved,single}_reads) & $(outputs.assembly)" | |
| coverage_tab,iana:text/tab-separated-values,"""contig by bam depth matrix"", and evidence report and quality metric",derives from $(outputs.samtools_index) | |
| trimmed_sequences,gz-compressed edam:format_1929 (FASTA) ,"Contigs over a certain minimal length | |
| Need an EDAM concept for the result of http://edamontology.org/operation_3192 ""Sequence t |
stain
/ a.md
Last active
May 22, 2019 16:21
Chat log during GEDE Digital Object (DO) webinar 2019-05-22 https://rd-alliance.org/rda-gede-webinar-adaptation-repositories-digital-object-interface-protocol
stain
/ license-in-svg.xml
Created
April 29, 2019 14:27
RDF in https://taverna.incubator.apache.org/img/apache-taverna-logo.svg
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| <svg | |
| xmlns:dc="http://purl.org/dc/elements/1.1/" | |
| xmlns:cc="http://creativecommons.org/ns#" | |
| xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" | |
| xmlns:svg="http://www.w3.org/2000/svg" | |
| xmlns="http://www.w3.org/2000/svg" | |
| xmlns:xlink="http://www.w3.org/1999/xlink" | |
| xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd" | |
| xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape" |
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| 2019-04-18T12:36:44.978016564Z 2019-04-18 12:36:44 cwltool INFO: /usr/bin/arvados-cwl-runner 1.3.1, arvados-python-client 1.3.1, cwltool 1.0.20181116032456 | |
| 2019-04-18T12:36:44.978518764Z 2019-04-18 12:36:44 cwltool INFO: Resolved '/var/lib/cwl/run/workflows/rp2-to-rp2path.cwl' to 'file:///var/lib/cwl/run/workflows/rp2-to-rp2path.cwl' | |
| 2019-04-18T12:36:46.332686764Z 2019-04-18 12:36:46 cwltool INFO: ../../lib/cwl/run/workflows/rp2-to-rp2path.cwl:40:3: Unknown hint http://commonwl.org/cwldep#Dependencies | |
| 2019-04-18T12:36:46.810698664Z 2019-04-18 12:36:46 cwltool ERROR: Workflow error, try again with --debug for more information: | |
| 2019-04-18T12:36:46.810698664Z ../../lib/cwl/run/tools/RetroPath2/RetroPath2.cwl:9:5: While trying to get Docker image | |
| 2019-04-18T12:36:46.810698664Z 'ibisba/retropath2:latest', failed to | |
| 2019-04-18T12:36:46.810698664Z execute 'docker': [Errno 2] No such file or | |
| 2019-04-18T12:36: |