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May 01, 2023 280 likes •940 views

The Scholars Backpack: Using virtual environments to support modern research practice. Bret Davidson | Eka Grguric NCSU Libraries bretdavidson.github.io/las-2017 Agenda Open science as problem space Open science as modern research

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The Scholar’s Backpack: Using virtual environments to support modern research practice.

Bret Davidson | Eka Grguric NCSU Libraries bretdavidson.github.io/las-2017

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Agenda

Open science as problem space Open science as modern research practice Open science at NC State Scholar's Backpack

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Open Science: what is it?

Open Access Open Data Open Notebooks Open Source

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Open Science is a return to rst principles of scientic practice.

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Nullius in Verba

"Take nobody's word for it."

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Open Science can increase reproducibility.

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Five Schools of Thought

by Sönke Bartling & Sascha Friesike Editors, http://book.openingscience.org/ Infrastructure Public Measurement Democratic Pragmatic

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Why Libraries?

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Aligns with core library values

research support information access

  • pen peer review

community-based knowledge creation the preservation and dissemination of research libraries are champions of open (open source; open data)

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Libraries

are about

supporting their users

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Academic Libraries

are about

supporting research practice

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Ongoing disruption by digital technologies in modern research practice

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Hypothetical Open Science Workow

101 Innovations in Scholarly Communication, https://innoscholcomm.silk.co/

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Policy Shifts in support of open

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Ecosystem of Support for Research Practice at NCSU Libraries

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The NCSU Libraries' Open Science Initiative

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Goals

explore open science practice at NCSU better understand researcher needs in context

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Take a non-prescriptive user-centered approach.

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Create opportunities for communication.

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Open Science Unconference

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Follow-up Informal Interviews

Perceived Skills Gap Insufcient Incentives

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Goals

Hands on skill building Provide networking opportunities Increase visibility of library spaces & services

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Skills

Scholarly identity creation Scientic computing Building a website Data harvesting Code collaboration

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Summer of Open Science

Workshops Intro to the Command Line Interface Web Scraping with Python Understand and Build Your Scholarly Identity Scientic Computing with Python & Raspberry Pi Build Your Scholarly Website the Easy Way Events Meetups End-of-Summer Showcase

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Scientic Computing with Python & Raspberry Pi 40 person waiting list

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Interdisciplinary Need

  • ver 40 departments across ~16 colleges
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Takeaways

Libraries are well positioned to ll gaps in the curriculum "Open Science" attracted a range of disciplines High demand for introductory skill training, particularly coding skills (Python) Interest in interdisciplinary research sharing Summer presents interesting opportunities and challenges

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Virtual Environments for Reproducible Computing

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Technical workshops are ripe for disaster.

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What could go wrong?

Images reset overnight Improper permissions Network connectivity issues Language Versions Missing packages

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Instructor Challenges

Consistency across user environments Consistency of course materials Time to provision computing environments Ease of collaboration

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Student Challenges

Basic data types and structures Module system Retrieve a web page with Requests Parse content with Beautiful Soup Generate a word cloud with matplotlib Control Structures Exception Handling Working with le system

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Computing Tasks vs. Computing Environments

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Many Options

Custom Operating System Images Custom Distributions, e.g. Anaconda Interactive Environments, e.g. Jupyter

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Our Approach

Vagrant for managing operating system Ansible for provisioning and conguration Course or lab specic packages and resources

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Easy!

  • 1. Install Vagrant
  • 2. Install VirtualBox
  • 3. Clone project

repo

  • 4. `vagrant up`
  • 5. `vagrant ssh`
  • 6. Execute code!
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This is reproducible computing!

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Benets

Consistent environment user to user Single target for course materials Faster provisioning for new workshops Repeatable course to course

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Rise of Scholarly Code

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Researcher Challenges

Consistency across lab environments Ability to see results of code Consistency across time Ease of collaboration

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github.com/NCSU-Libraries/scholars-backpack

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Features

Python R and R Studio Jupyter Notebook Server Example Notebooks

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Vagrant

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Create and congure lightweight, reproducible, and portable development environments.

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Usage

Easy installation through binary package Flexible conguration via text-based conguration le Single command: `vagrant up`

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Ansible

"Automation engine" for provisioning and conguration management.

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Provisioning

"To make something available." Installation!

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Conguration Management

"Establish and maintain consistency of an environment."

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Provisioning

Text editor Python & R Git Web Browser etc.

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Conguration

Start Jupyter notebook server Set environment variables Set default login directory

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Benets

Improved consistency Ability to see results of code Ease of collaboration

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Future Work

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Richer Environment

Broader scientic computing Improved adherance to best practices Docker containers for portability

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Embedded Use

Curricular use Laboratory use

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Thanks!

bret_davidson@ncsu.edu eka_grguric@ncsu.edu | @egrguric github.com/NCSU-Libraries/scholars-backpack bretdavidson.github.io/las-2017