Supporting Science in the Open

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If you wonder why we are using this HackMD thing and Markdown format, click here.

You might be wondering why people use Markdown instead of a WYSIWYG editor.
Some reasons from Why Use Markdown?:

  • Markdown can be used for everything. People use it to create websites, documents, notes, books, presentations, email messages, and technical documentation.
  • Markdown is portable. Files containing Markdown-formatted text can be opened using virtually any application. If you decide you don’t like the Markdown application you’re currently using, you can import your Markdown files into another Markdown application. That’s in stark contrast to word processing applications like Microsoft Word that lock your content into a proprietary file format.
  • Markdown is platform independent. You can create Markdown-formatted text on any device running any operating system.
  • Markdown is future proof.
  • Markdown is everywhere.

🗣️ Welcome to the interactive document for the workshop!

A few reminders:

  1. This workshop is meant to be interactive.
  2. If you are reading this, that means you did open the document! https://hackmd.io/@openscience/nsymp
  3. You will discuss with others during breakout sessions.

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Goal of the workshop

Understand and identify how you can make a difference in Science as a grad student by integrating more open science in your workflow.

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Getting into Open Science by Samuel

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Questions

  • Write down questions here or use the Q&A function in Remo

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Comments & Resources to share

  • Write down your thoughts or comments, and resources you would like to share

First interactive question
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What does Open Science mean to you?

  • Answers:
  • Being able to ask a scientist whether they know that they have to check if their data is normally distributed, and they know what I am asking … and why.
  • To me, it is fixing science - I love science - but I being on the inside, I see how unefficient it is - and we all know it. But I am glad that we will make it better. More useful.
  • Sharing scientific data and materials and making it accessible to everyone.
  • Actually science
  • science being available for everyone and having individuals not studying science being interested and learning about science as well. Making science accessible.
  • open access
  • Not hoarding your data at the expense of new discoveries / findings
  • streamline collaboration
  • free articles (open access)
  • Robust methods sections (detailed supplementary methods)
  • Not having to make taxpayers more than once to get access to scientific discoveries (i.e., once for the research, the other for reading the publication)
  • being able to discuss animal research with confidence and public support
    *making data accessible to encourage better science and more robust results

Breakout session: Sharing in science isn’t always straightforward.

INSTRUCTIONS: Every group has a set of questions.
Assign a note taker in your group
Pick one of the questions assigned to your group and discuss the issues.
Make sure to take notes under each question you discuss so others can read later on!

  • Floor 1: Open collaboration

    • If I share my work with other researchers, they might try to claim my work as their own.
      • Answers: Some larger labs have access to more funding, so they can accomplish things faster than smaller labs, and there are a lot of unscrupulous researchers out there
    • Contributing to collaborative projects has helped improve my productivity.
      • Answers:Can team up with other labs or groups who have different expertise –> can further the project.
    • If I choose to collaborate with other researchers on a project, I don’t understand who will be the first author of the publication.
      • Answers:Authorship (first and last) should be discussed and possibly decided in advance.

  • Floor 2: Open Access

    • My supervisor doesn’t want me to submit my work to preprint servers.

      • Answers: are they even a scientist? hehe

    • I would like to publish in an open access journal but can’t afford the fees.

      • Answers: put it on bioRxiv!

    • I want my research to be published in the most prestigious journals only, even if they don’t have open access policies.

      • Answers: well well well …

  • Floor 3: Open Data

    • I’m worried that other researchers will make use of my data and get better results.
      • Answer: We should stop giving importance to the credits, but to the value of the research contribution/discoveries. Other bigger laboratories might have greater resources to make bigger discoveries, but you can even become involved on them or you can follow up how your research is having impact, it is an all win.
    • My research is so specific. Nobody else would be interested in or be able to understand my data.
      • Answer:
    • I’m fine with my personal data being used for important or groundbreaking scientific research as long as it’s anonymized.
      • Answer:

  • Floor 4: Open Source

    • I’m nervous that others will find faults with my research results if my code is open.
      • Answer:This might actually be helpful if someone on the outside comes in and tells you something is incorrect. It can add a new view/ layer to our analysis that we hadn't thought of. Might be better to find the mistake rather than have incorrect information about it. It would be more detrimental to science as a whole if there is something that is incorrect and it should be retracted but it isn't, people will think it's true and this isn't good for the community and future directions of science.
    • My institution pays to purchase licenses so I don’t need to use open source projects.
      • Answer:
    • I use open source software but to be honest I don’t know how to contribute
      • Answer: Yeah, we have no idea!

  • Floor 5: Open Education

    • I spent hours working on my slides and my syllabus, so I don’t see why I should share them.
      • Answer:
    • I want to be credited for all the work I put into designing the curriculum, even if I share it with other educators.
      • Answer:
        We need to figure out how to get really good teachers, teaching at university level. Let the really good post-docs become super extra post docs, doing what they do well ("publishing") - and the people who are good at moving education and science forwards "professors". I don't think it's a question of "giving credit" per se -> we need to really rebuild the strucutre of the scientific project: science, and science education (are likely one thing)"
    • I’ve been told that commercial educational materials are more reliable but I’m not sure.
      • Answer:

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Getting into Open Science by Dylan

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Questions

  • Write down questions here or use the Q&A function in Remo

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Comments & Resources to share

  • Write down your thoughts or comments, and resources you would like to share.

  1. What is the role of academic science in society?

  2. What do you think the role of ethics is in science?

  3. Have you encountered issues in getting ethics approval for your research? If so what were the major issues?

  4. What do you think the role of intellectual property in scientific research is?

  5. Do you use open source software in your work? If so, what is an example?

  6. Do you use open source hardware in your work? If so, what is an example?

  7. Have you ever sent scientific materials (e.g. reagents, model organisms, cell lines) to researchers at other institutions?

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Discussion

Resources:

https://docs.google.com/document/d/1rLyZhDGebBRpqgw1bqHteNHKHNdHtXO4qY1HhhPLCoQ/edit?usp=sharing

Thanks to the Open Life Science program for the format of the breakout session :)
GitHub repository for the questions: https://github.com/baricks/opentodiscussion

Select a repo