Nolan Nichols nicholsn

Welcome to the New Era of Scientific Publishing

— by Tobias Kuhn, 4 April 2022; reporting on work with Cristina Bucur, Davide Ceolin, and Jacco van Ossenbruggen [1,2] —

I believe we have made the first steps venturing into a new era of scientific publishing. Let me explain. [Update: At what point exactly a new era begins and what counts as first steps are of course subject to debate. I therefore added a section on related initiatives and further reading below.]

Science is nowadays communicated in a digital manner through the internet. We essentially have a kind of "scientific knowledge cloud", where researchers with the help of publishers upload their latest findings in the form of scientific articles, and where everybody who is interested can access and retrieve these findings. (This is in fact only true for articles that are published as Open Access, but that is not the point here.)

Methods of Signing Git Commits on MacOS

Last updated March 13, 2024

This Gist explains how to sign commits using gpg in a step-by-step fashion. Previously, krypt.co was heavily mentioned, but I've only recently learned they were acquired by Akamai and no longer update their previous free products. Those mentions have been removed.

Additionally, 1Password now supports signing Git commits with SSH keys and makes it pretty easy-plus you can easily configure Git Tower to use it for both signing and ssh.

For using a GUI-based GIT tool such as Tower or Github Desktop, follow the steps here for signing your commits with GPG.

This gist describes a flexible dicom converter for organizing brain imaging data into structured directory layouts.

it allows customizable directory layouts and naming schemes through heuristic file
it only converts the necessary dicoms, not everything in a directory
you can keep links to dicom files in the participant layout
it's faster than parsesdicomdir or mri_convert if you use dcm2nii option
it tracks the provenance of the conversion from dicom to nifti in w3c prov format
the example shows a conversion to openfmri layout structure

outputs:

Locate the section for your github remote in the .git/config file. It looks like this:

[remote "origin"]
	fetch = +refs/heads/*:refs/remotes/origin/*
	url = git@github.com:joyent/node.git

Now add the line fetch = +refs/pull/*/head:refs/remotes/origin/pr/* to this section. Obviously, change the github url to match your project's URL. It ends up looking like this:

	from SPARQLWrapper import SPARQLWrapper, JSON, DIGEST

	sparql = SPARQLWrapper("http://example.org/sparql")

	sparql.setHTTPAuth(DIGEST)
	sparql.setCredentials('login', 'password')

	sparql.setQuery("...")
	sparql.setReturnFormat(JSON)

	@prefix daniel: <http://mayor2.dia.fi.upm.es/oeg-upm/files/dgarijo/motifAnalysis/> .
	@prefix dc: <http://purl.org/dc/terms/> .
	@prefix ore: <http://www.openarchives.org/ore/terms/> .
	@prefix prov: <http://www.w3.org/ns/prov#> .
	@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
	@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
	@prefix ro: <http://purl.org/wf4ever/ro#> .
	@prefix schema: <http://schema.org/> .
	@prefix xhv: <http://www.w3.org/1999/xhtml/vocab#> .
	@prefix xml: <http://www.w3.org/XML/1998/namespace> .

	The regex patterns in this gist are intended only to match web URLs -- http,
	https, and naked domains like "example.com". For a pattern that attempts to
	match all URLs, regardless of protocol, see: https://gist.github.com/gruber/249502

	License: https://opensource.org/license/bsd-3-clause

	# Single-line version:

	(?i)\b((?:https?:(?:/{1,3}\|[a-z0-9%])\|[a-z0-9.\-]+[.](?:com\|net\|org\|edu\|gov\|mil\|aero\|asia\|biz\|cat\|coop\|info\|int\|jobs\|mobi\|museum\|name\|post\|pro\|tel\|travel\|xxx\|ac\|ad\|ae\|af\|ag\|ai\|al\|am\|an\|ao\|aq\|ar\|as\|at\|au\|aw\|ax\|az\|ba\|bb\|bd\|be\|bf\|bg\|bh\|bi\|bj\|bm\|bn\|bo\|br\|bs\|bt\|bv\|bw\|by\|bz\|ca\|cc\|cd\|cf\|cg\|ch\|ci\|ck\|cl\|cm\|cn\|co\|cr\|cs\|cu\|cv\|cx\|cy\|cz\|dd\|de\|dj\|dk\|dm\|do\|dz\|ec\|ee\|eg\|eh\|er\|es\|et\|eu\|fi\|fj\|fk\|fm\|fo\|fr\|ga\|gb\|gd\|ge\|gf\|gg\|gh\|gi\|gl\|gm\|gn\|gp\|gq\|gr\|gs\|gt\|gu\|gw\|gy\|hk\|hm\|hn\|hr\|ht\|hu\|id\|ie\|il\|im\|in\|io\|iq\|ir\|is\|it\|je\|jm\|jo\|jp\|ke\|kg\|kh\|ki\|km\|kn\|kp\|kr\|kw\|ky\|kz\|la\|lb\|lc\|li\|lk\|lr\|ls\|lt\|lu\|lv\|ly\|ma\|mc\|md\|me\|mg\|mh\|mk\|ml\|mm\|mn\|mo\|mp\|mq\|mr\|ms\|mt\|mu\|mv\|mw\|mx\|my\|mz\|na\|nc\|ne\|nf\|ng\|ni\|nl\|no\|np\|nr\|nu\|nz\|om\|pa\|pe\|pf\|pg\|ph\|pk\|pl\|pm\|pn\|pr\|ps

	MIT License

	Copyright (c) 2014 Piotr Kuczynski

	Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

	The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWAR

	import StringIO
	from flask import Flask, Response


	@app.route('/some_dataframe.csv')
	def output_dataframe_csv():

	output = StringIO.StringIO()
	some_dataframe.to_csv(output)