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keyboard bashing ⌨️ 🔨

Stefan Negru blankdots

:octocat:
keyboard bashing ⌨️ 🔨
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View keybase.md

Keybase proof

I hereby claim:

  • I am blankdots on github.
  • I am blankdots (https://keybase.io/blankdots) on keybase.
  • I have a public key ASC-cRq6uk6xRuuB5wtc9odLEQOZMU5F-VOy_s2VY6o62go

To claim this, I am signing this object:

View orch-api.yml
openapi: 3.0.0
info:
description: SDA orchestrator API for standalone Sensitive Data Archive
version: "1.0"
title: SDA Orchestrator API
license:
name: Apache 2.0
url: http://www.apache.org/licenses/LICENSE-2.0
tags:
- name: trigger
@blankdots
blankdots / Dockerfile
Last active Apr 24, 2020 — forked from viklund/Dockerfile
Crypt4gh docker experiments
View Dockerfile
FROM debian:10-slim
## Otherwise Java won't install
RUN mkdir -p /usr/share/man/man1
RUN apt-get update \
&& apt-get install -y gnupg2
## This is to get openjdk-11-jre to install on -slim
RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys EA8CACC073C3DB2A
View makefile
# this script works in both MacOS and Linux
.PHONY: upload submit user
SHELL := /bin/bash
DOCKER_PATH=$(shell pwd)
#GPG_EXEC=/usr/local/gnupg-2.2/bin/gpg2
GPG_EXEC=/usr/bin/gpg2
SSH_KEY_PUB=~/.ssh/dummy.key.pub
SSH_KEY_PRIV=~/.ssh/dummy.key
View makefile
.PHONY: upload submit user
DOCKER_PATH=/home/stenegru/Software/test/LocalEGA/deployments/docker
GPG_EXEC=/usr/bin/gpg2
# GPG_EXEC=gpg
SSH_KEY_PUB=~/.ssh/dummy.key.pub
SSH_KEY_PRIV=~/.ssh/dummy.key
INSTANCE_PORT=$(shell awk -F= '/DOCKER_PORT_inbox/ {print $$2}' $(DOCKER_PATH)/bootstrap/settings/swe1)
GPG_HOME=$(DOCKER_PATH)/private/swe1/gpg
View visualisation.txt
We can take inspiration in the visualisation from such a platform: https://github.com/refinery-platform/refinery-platform
short poster: Interactive Visualization of Provenance Graphs for Reproducible Biomedical Research http://gehlenborg.com/wp-content/uploads/refinery_poster_biovis-2015.pdf
or: SATORI: A System for Ontology-Guided Visual Exploration of Biomedical Data Repositories http://www.biorxiv.org/content/biorxiv/early/2016/04/05/046755.full.pdf
or more visualisation examples:
https://flekschas.github.io/d3-list-graph/
https://github.com/Data2Semantics/provoviz
http://www.caleydo.org/publications/2016_eurovis_avocado/ with: http://demo.caleydo.org/pathfinder/
@blankdots
blankdots / sparqlwrapper.py
Last active Jan 30, 2017
template for construct and select to rdflib
View sparqlwrapper.py
from rdflib import ConjunctiveGraph, URIRef, Literal
from SPARQLWrapper import SPARQLWrapper, JSON
# import json
#http://rdfextras.readthedocs.io/en/latest/working_with.html
graph = ConjunctiveGraph()
sparql = SPARQLWrapper("http://localhost:3030/ds/query")
# add a default graph, though that can also be in the query string
@blankdots
blankdots / pylama config
Last active Oct 29, 2019
pylama config
View pylama config
[pylama]
linters = mccabe,pep257,pep8,pyflakes
ignore = D203,D212,D213,D404,D406,D407,D408,D409,D100,D104
max_line_length = 160
[pylama:pycodestyle]
max_line_length = 300
[pylama:pylint]
max_line_length = 300
@blankdots
blankdots / genetic data.ipynb
Last active Oct 18, 2015
Software for Scientists - October 2015
View genetic data.ipynb
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View sparql queries
http://sparqles.okfn.org/availability
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX uni: <http://www.Department0.University0.edu/>
PREFIX ub: <http://www.lehigh.edu/~zhp2/2004/0401/univ-bench.owl#>
SELECT *
WHERE { ?subject ?predicate ?object }