- Permalink: https://gist.github.com/stain/4cd4cb1763a4ac57f1de270aa6f1a996 (this review)
- Authors: Gabriele Scalia, Matteo Pelucchi, Alessandro Stagni, Alberto Cuoci, Tiziano Faravelli, Barbara Pernici
- Title: Scholarly data analysis to aid scientific model development
- Submitted to: Data Science (Research Paper)
- Special issue: Selection of extended papers from SAVE-SD 2017 and Save-SD 2018
- Submitted on: 2018-12-16
Stian Soiland-Reyes stain
stain
/ .notmuch-config
Last active
November 13, 2023 08:17
NotMuch hooks for selectively sorting to inbox, moving archived messages to other folder. offlineimap syncs to /home/USER/mail/company and /home/USER/mail/org1
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| [database] | |
| path=/home/USER/mail | |
| [user] | |
| name=MyName MySurname | |
| primary_email=me@example.com | |
| other_email=me@example.org | |
stain
/ manifest.jsonld
Last active
March 20, 2019 16:53
A Research Object expressed with RO and schema.org contexts combined -- https://researchobject.github.io/ro-lite/ and https://github.com/craig-willis/bdbag-water-tale/blob/master/metadata/manifest.json
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| { | |
| "@context": [ | |
| "https://schema.org/", | |
| "https://w3id.org/bundle/context", | |
| { | |
| "name": "http://schema.org/name" | |
| } | |
| ], | |
| "@id": "https://data.wholetale.org/api/v1/tale/5c875b6feff2c60001d2810f", | |
| "@type": ["DataCatalog", "ro:ResearchObject"], |
stain
/ manifest.jsonld
Created
March 20, 2019 16:40
A Research Object expressed with schema: prefix -- https://researchobject.github.io/ro-lite/ and https://github.com/craig-willis/bdbag-water-tale/blob/master/metadata/manifest.json
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| { | |
| "@context": [ | |
| "https://w3id.org/bundle/context", | |
| { | |
| "schema": "http://schema.org/", | |
| "name": "schema:name", | |
| "schema:image": { | |
| "@type": "@id" | |
| }, | |
| "schema:isPartOf": { |
stain
/ manifest.jsonld
Last active
March 20, 2019 16:52
A Research Object expressed solely with schema.org -- https://researchobject.github.io/ro-lite/ and https://github.com/craig-willis/bdbag-water-tale/blob/master/metadata/manifest.json
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| { | |
| "@context": "https://schema.org/", | |
| "@id": "https://data.wholetale.org/api/v1/tale/5c875b6feff2c60001d2810f", | |
| "@type": ["DataCatalog", "http://purl.org/wf4ever/ro#ResearchObject"], | |
| "dataset": [ | |
| { | |
| "@id": "doi:10.5065/D6862DM8", | |
| "identifier": "doi:10.5065/D6862DM8", | |
| "name": "Humans and Hydrology at High Latitudes: Water Use Information", | |
| "publisher": { |
stain
/ linkset.jsonld
Last active
March 13, 2019 19:56
Linkset JSON as JSON-LD https://github.com/dret/I-D/issues/119
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| { | |
| "@context": [ | |
| { | |
| "@vocab": "https://www.iana.org/assignments/link-relations/", | |
| "anchor": "@id", | |
| "href": "@id", | |
| "dct": "http://purl.org/dc/terms/", | |
| "link": "https://www.iana.org/assignments/link-relations#", | |
| "title": { | |
| "@id": "http://purl.org/dc/terms/title" |
stain
/ Dockerfile
Last active
February 6, 2019 16:14
Dockerfile for GROMACS. Compile with nvidia-docker
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| ############################################################################### | |
| # Ubuntu 16.04, CUDA 9.0, OpenMPI, and GROMACS. | |
| # | |
| # Requirements: | |
| # * gromacs directory in build directory with source for GROMACS. | |
| # | |
| # Build with: | |
| # sudo nvidia-docker build -t gromacs . \ | |
| # --build-arg GROMACS_VERSION=gromacs_version \ | |
| # --build-arg JOBS=16 |
stain
/ 00-review-datasciencehub-549-1529.md
Last active
May 24, 2019 13:52
Review of DataScienceHub submission #549-1529
stain
/ 00-review-GIGA-D-18-00427.md
Last active
May 24, 2019 13:54
Review of GigaScience manuscript GIGA-D-18-00428
- Permalink: https://gist.github.com/stain/30e49363238d5a35e26f9fb1a31ebf8e
- Date: 2018-12-18
- Title: Accumulating computational resource usage of genomic data analysis workflow to optimize cloud computing instance selection
- Authors: Tazro Ohta, Tomoya Tanjo, Osamu Ogasawara
- Call: GigaScience Technical Note
- Submitted preprint:
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| 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 |
stain
/ blah.log
Last active
September 12, 2018 09:25
https://github.com/common-workflow-language/cwlprov-py
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| (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 |