Short Paper Postprints

Workshop name/title (and acronym is applicable)

1. Workshop name/title (and acronym is applicable)

Reproducible Research Publications at AGILE (RR@AGILE)

2. Description of the workshop by listing topic(s), objective(s) and planned outcome(s)

2.1 Topic(s)

reproducible research, open science, reproducibility, software carpentry, data carpentry, reproducible paper

2.2 Objective(s)

The workshop aims to continue the efforts started at AGILE 2017 in establishing the topic of reproducible research at AGILE conferences. In fact, the workshop is co-organized by last years organizers and participants.

Skills about reproducing other researcher’s work and creating own publications in a reproducible way are crucial for future scientists as more and more research is based on data and computer algorithms. In this workshop, the participants learn about concrete tools and best practices for working reproducibly, thus being able to increase the reproducibility and subsequently the quality of future AGILE contributions.

2.3 Planned outcome(s)

3. Abstract (max 1000 characters)

Reproducibility and replicability of research gains more attention each year across many domains, but at AGILE conferences the topic is underrepresented. This half-day workshop introduces interested scientists to reproducible research and gives hands-on guidance on how to increase reproducibility of their work.

Agenda:

  1. Introduction to reproducible research [15 min.]
  2. Reproducibility at AGILE today [15 min.]
  3. Hands-on: Reproducing a publication [180 min. including break]
    • Reproduce a prepared computational analysis from a real paper (eiher R or Python code)
    • Transform typical publication into a reproducible document (literate programming with R Markdown, Jupyter Notebook, scripted GIS)
    • Publish the analysis in a research data repository
  4. Reproducibility at AGILE tomorrow & Feedback [30 min.]

Registration is open until April 22 2018 via a new issue on the workshop repository.

Details on the workshop website: https://reproducible-agile.github.io

4. Short description of the intended length (half or full day) and the format of the workshop

Half day workshop with a mixture of lecture, hands-on practical work, and discussion.

5. Brief statement of the relevance of the workshop for AGILE

This workshop is a follow-up to last year’s successful introduction of reproducible research at AGILE. The relevance of Open Science and reproducible research has not changed! On the contrary, the overarching challenge to develop guidelines and feature examples for the AGILE community still prevails.

While the workshop format had to be adjusted last year as the submissions were too low for the then planned format, the topic was taken up during the conference in many conversations and by presenters during their talks. This year, the organizing committee is strengthened further and wants to keep the steady pace to establish reproducible research practices at the AGILE conference.

The workshop’s hands-on approach is a complementary feature to the list of AGILE workshops and relevant to all of AGILE’s attendees, but especially valuable for early career scientists, who are just beginning to establish their way of practicing science.

6. What is the approximate number of expected participants?

10-20

7. Names and e-mail addresses of the organizing member(s)

Leading AGILE member (or sponsor) and contact person:

Institute for Geoinformatics, University of Münster, Daniel Nüst, daniel.nuest@uni-muenster.de

Contributing AGILE members (including the persons involved):

Organizing Committee: see involved persons at contributing AGILE members

8. Additional information about previous workshops, if held.

https://reproducible-agile.github.io/2017/

9. Expected resources needed

10. Other information

The workshop potentially targets the same audience, i.e. people interested in open science and data science, as another workshop proposal on research data management. For people interested in both topics, it would be very welcome to schedule the workshops after each other: research data in the morning, and writing the reproducible publication in the afternoon.

X. Workshop description - unshortened for workshop website

Reproducibility and replicability of research gains more attention each year across many domains, some of which even struggle with a “reproducibility crisis”. However, at AGILE conferences, the topic is underrepresented. Recent research (submitted to AGILE 2017) found that none of the last years nominees for best papers (both short & full papers) provided sufficient information (i.e. instructions, data, and code) to be reproduced independently by a third party. This workshop introduces interested scientists and developers to reproducible research and gives hands-on guidance on how to increase the degree of reproducibility for their own work. Participants explore the practical principles of reproducible papers by reproducing a provided real-world publication. Together with the instructors they create a reproducible document from text, code, and data of a scholarly publication and publish it in a data repository.

The planned agenda for the half-day workshop (4 hours in total) is as follows:

  1. Introduction to reproducible research: relevant literature, challenges, and solutions (lecture) [15 min.]
  2. Reproducibility at AGILE today (presentation) [15 min.]
  3. Hands-on reproducible research [180 mins. including breaks, two break-out sessions]
    • Goal: Reproducing a paper with either R or Python code
      • Participants make first-hand experiences in trying to reproduce a prepared computational analysis from a real paper
      • Transform a “typical” publication into a reproducible document
      • Publish the analysis in a research data repository
    • Skills: Tools for creating reproducible documents (literate programming wit R Markdown or Jupyter Notebook), scripted geospatial workflows for GIS
  4. Reproducibility at AGILE tomorrow (discussion, presentation) & Feedback [30 min.]

Participants are required to register until April 22 2018 (parallel to end of early registration for conference) via creating a new issue on the workshop repository on GitHub [both links to be created after acceptance].

The registration must include (i) preferred hands-on session (R or Python), (ii) a short description of experience in R and/or Python, (iii) a summary of computational work, if available with references to published papers, data or code, ans (iv) plans for future computer-based research. Basic skills, ideally with practical experiences as part of a research project, in the selected programming language are required to participate in the workshop - please get in touch if you are unsure!

In case of a high number of publications, participants may be selected based on the submitted material. Participants must bring their own computers and be prepared to install software before the workshop.

The number and topics of hands-on sessions depend on room availability and participants’ interests. They will be announced on May 15 2018.

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