Open Science Programme for PhD candidates of AS/TNW

Open Science
TU Delft
Author

Esther Plomp

Published

June 4, 2023

Course Description

This course provides PhD candidates from the Faculty of Applied Sciences with essential Open Science knowledge and skills. You will learn to manage your research project according to recommended Open Science practices. Learners are introduced to Open Science terms and principles and will apply those principles directly to their projects. During the program you will be supported by a mentor with a connection to your discipline/project. Your mentor will guide your progress by providing constructive feedback.

Mandatory activities in the course:

  • Complete course assignments

  • Set up a GitHub repository for the project (a GitHub tutorial is part of the program)

  • Engage in the bi-weekly online calls with the full Open Seeds group

  • Attend bi-weekly mentor calls to discuss your project's progress

  • Present a 5 minute demo of your project at the end of the program

Objectives 

At the end of the program you will be able to:

  • Describe and define the terms openness, Open Science, FAIR data/software, open leadership, community interactions, value exchanges, inclusivity, accessibility

  • Give original examples for the types of openness in science

  • Design

    • Illustrate the need for a project, its vision, and its goals

    • Embrace and communicate the benefits of Open Science and how to strategically apply different open practices to your project

    • Identify public resources to share data

    • Identify different type of Open Access and associated journals

  • Build

    • Start any project with openness in mind from day one

    • Setup a project repository on GitHub using recommended practices for enabling collaboration

    • Choose and apply open licenses appropriately

  • Empower

    • Create and enforce a safe working environment

    • Promote the values of Open Science to empower others to lead and collaborate

    • Include a broad range of contributors in your work

    • Communicate your work and vision in a 5 minute demo/elevator pitch

  • Lead an open project in science

Get inspired by the experiences of two PhD-colleagues with this program! 

OLS 4 project 'Multibeam electron microscopy for imaging large tissue volumes' by Arent Kievits (ImPhys)

From September 2021 till January 2022 I participated in the Open Life Science program, with the intention to get familiar with open science while simultaneously applying this to my PhD project. The program allows you to sign up as a team, but individual participation is also possible. I signed up individually. For me, a valuable thing from the Open Life Science program was the mentor program to guide the progress in the program and the project. I had two mentors, one expert in my field and one expert in open data. I got valuable feedback on my assignments / progress and made new connections in the UK community of my research field. The group calls (up to now) have taught me other valuable skills for my PhD project, such as setting up and managing a GitHub repository, basic (software) project development skills, designing and leading an open community and publishing open (preprints, software citation). The course covers a mix of basic and more advanced topics for people that are in different stages of their career. Therefore, not every aspect was valuable to me, but they may be for other people. Overall, I think this course is useful for both early and later stage PhD students, as it covers many aspects of doing science in a new (open) way. Because you can tailor the course to your own PhD project (e.g. work on a paper, computational method), it is a valuable contribution to your PhD.

OLS 5 project 'Increasing the usability of ChemSpaX, a Python tool for chemical space exploration' by Adarsh Kalikadien (ChemE)

I participated in the Open Life Science (OLS-5) Program from February 2022 until June 2022. During this program, I aimed at improving a Python package that I created such that it could be used by a larger community. When I signed up for the OLS program, I was surprised to learn about the many aspects of open science. The technical aspects (code/data management and version control) were very valuable, but so were the social aspects (community building and open publishing for example). Apart from the cohort and skill-up calls, where various topics were taught, I was assigned two mentors. Together with my mentors, Esther Plomp (data steward of AS) and Maurits Kok (research software engineer of digital competence center), we managed to divide my milestones into smaller and executable steps. Since I chose to work on something that is relevant to my PhD, the time spent on the program was a valuable contribution to my research. I am able to implement these new skills in my future projects. Overall, I think that this program is useful for early stage PhD students who have a desire to do science in an open way. After all, open science is not as easy and straightforward as it sounds.

Course setup

The 8th Open Seeds cohort (OLS-8) program will run from September 18 to January 15, 2024. See https://openlifesci.org/ols-8 for more details.

Week 1
Meet your mentor and discuss your personal motivation, expectations, working practices and project goals.

Week 2
First cohort call, where you meet other members of your cohort, share project vision and will be introduced to working openly (open canvas).

Week 3
Meet your mentor and discuss assignments from the cohort call and concrete implementations in your project.

Week 4
Learn more about tools that are available to make your project more open (GitHub as a community hub, Markdown as a tool to make websites, Licences, Goals and Roadmap, Contributors, Code of Conduct).

Week 5
Meet your mentor to discuss your progress and follow a GitHub tutorial if you have no previous experience.

Week 6
Learn more about developing Open Projects: Iterative and agile project management, Open- Source, Open Software, Open Hardware, and Open Data.

Week 7
Meet your mentor to discuss your progress

Week 8
Learn more about sharing your project's outputs: Preprints, DOI and citation, Open protocols, Open Education and Training.

Week 9
Meet your mentor to discuss your progress.

Week 10
Learn more about how you can apply the FAIR principles to your project.

Week 11
Meet your mentor to discuss your progress.

Week 12
Learn more about Open Leadership in academia, industry and beyond.

Week 13
Meet your mentor to discuss your progress.

Week 14
Learn about how to design your project for inclusivity (personas and pathways for contributors, implicit bias and community interactions).

Week 15
Meet your mentor to prepare your graduation call and join a preparation call to practise your 5 minute demo.

Week 16
Final presentations and graduation call, where you have to present a 5 minute demos of your project.
 

Graduate School Credits

By completing the 16 week program you will receive 5 GS credits (Discipline-related skills). Please see the Faculty Graduate School intranet page for more information about GS credits.

Course Enrolment and Preparation

To participate in this program you will need to submit an application before the 7 of July. You can apply as an individual or as a team. Applicants are welcome from all research disciplines.

Please notify Esther if you plan to submit an application or need any support with your application. If you need more information about the program or the application process, please join the information session on 3 July at 16:00 (outdated Zoomlink). A recording from a previous information webinar is available on the Open Life Science YouTube channel.