A graduate of the fourth cohort of the Open Life Science (OLS) program talks about his experience!

As a PhD student at Delft University of Technology, I participated in the fourth cohort (named Kenaz) of the Open Life Science (OLS) program. OLS is a 16-week program where participants receive personal mentoring and training through cohort-calls. The main objectives are to:

• Gain knowledge about open science practices from experts
• Share expertise and learn to create, lead and sustain an Open Science project
• Connect with OLS community members from different backgrounds, identities and work together on projects
• Become a contributing member of OLS and ambassador of open science

My motivation for starting an open science project

I started as a science rookie in november 2020, embarking on a PhD journey where I was going investigate how to image biological samples in 3D with a new type of electron microscope. I wanted to kickstart my science career with a firm background in open science and publish and share my work in an open way. Being able to tie my OLS training to my own PhD motivated me to initiate an open science project, Open Multibeam Scanning Electron Microscopy (OpenMB-SEM). The ideas behind this project are:

• No restrictions on access: If people want to validate the work, they should have all resources and instructions to do so.
• Solving challenges together: We have a way more powerful and faster electron microscope than previously possible, which stresses existing hurdles and creates additional challenges.
• Benefit to the EM community: As we are one of the first research groups to have such a microscope, we want other EM researchers to benefit as well!
• Early input on the design process: We are pioneering this technique. We could use help from experts in the field to help us write software, annotate data, think about sample preparation, etc.

My goals and expectations

I set out some goals at the beginning of the OLS-programme. I did not know how the project was going to look like at that moment. Luckily, my assigned mentor contacted an expert in my field to help co-mentor me. Together we consolidated the goals:

• Sharing research results in a way that others can effectively re-use them
• Start using GitHub for sharing software (Python).
• Improve documentation for my code
• Publish open access
• Extend our electron microscopy data viewer to include more info on the samples, types of experiments, etc.
• Build a website with methods, code, data and literature for multibeam electron microscopy (MB-SEM)

And suggested by my mentor:

• Consider re-activating Twitter (though honestly, I fail miserably at maintaining my socials…)

What I achieved, learned and accomplished during OLS-4

When I look back now at the OLS-journey, I am very proud of what we (my mentors and I) achieved in 16 weeks. The initial calls and exercises already helped me a great deal in defining the goal of my project. We were asked to create a vision statement and project canvas to clarify the goal of the project, who to attract as users and contributors, the necessary resources etc. I set up a project development plan and milestones and organized these into a list of todo’s. We were also instructed on how to create a GitHub repository for our project and add all the necessary components to make it open for anyone to contribute to the project’s materials (or reuse them).

My mentors helped me refine the vision statement and project canvas and gave me valuable input on how to manage the project in the early stages. This helped me to further clarify the project’s goals and who to attract as users and contributors. Together with my mentors we discussed ways to make it as attractive as possible to contribute to the project. With help of a Personas and Pathways exercise I clarified what kind of contributors I was looking for and how they would contribute to the project.

Through one of my mentors, an expert in my field, I came in contact with the UK community of my field and was introduced to a research software engineer working on the same topic. We had a very fruitful discussion and a I learned a lot about how it is like to work as a research software engineer.

And after a few weeks, Boom! I had a clear project plan and a functional project repository on GitHub! It included all essential elements for an open science community, including a code of conduct, license, informative readme, contributor guide and documentation. I could directly host all the information on a clear and tidy looking webpage.

The first OpenMB-SEM contribution

The showpiece of my project was an interactive JuPyter Notebook environment which I created to present my first research data. The Notebook contains info about the experiments and interactive elements which make it easy to look at the data. It is fully functional and comes with clear installation instructions which should make it easier to reproduce the results at home. Thanks to my mentors, who advised me on the format and helped me with testing, it is now almost ready to deploy it alongside a publication.

Looking back on my goals

I roughly achieved what I wanted to learn. While I did not achieve publishing open access yet, I did learn a thing or two about preprints. But in the end, I realized that I had learned much more about open science than I could hope for!

“This is a big unsolved problem: don’t get dishearthened if it seems like a lot. It is a lot and the whole community is wrestling with this! Your contribution is going to be crucial to solve this issue!”

What next?

I will soon be launching the GitHub page. This will be spread via Twitter and a Slack channel used within my field. I will be talking about it on a conference in the next few months, to promote the project further and come in contact with like-minded people. To make sure the project will get sustained attention, I would like to expand the contributor guide, make the home page more attractive, keep updating the website with the latest developments, write a blog and introduce a wiki to better separate the different topics and contributions.

Want to know more?

Visit the Project repository or the website! Also, if you’re interested, check out the OLS program!