Overview issue [Ivy Liang]

[ivyliang98]

Introduction

Hi everyone, my name is Ivy Liang, I'm a PhD student in Gijsje Koenderink's lab in the department of Bionanoscience.

Describe your research in 2-3 sentences to someone that is not from your field (please avoid abbreviations)

I study the human wound healing process at the cellular level. I look at how the direct environment of cells determine the outcome of wound healing, so whether it heals correctly or you're left with significant amount of scar tissue.

My research entails the following aspects:

Research Aspect	Answer
Use/collect personal data (health data, interviews, surveys)	No
Use/collect experimental data (lab experiments, measurements with instruments)	Yes
Collaborate with industry	No
Write/develop software as the main output of the project	No
Use code (as in programming) for data analysis	Yes
Work with large data (images, simulation models)	Yes
Other:	N/A

Reflections on the importance of RDM videos

I understand the importance of good data management. For me, a horror story was that I was analyzing microscopy images on my laptop, but my laptop had some issues. So, the screen turned black after a while, and I was panicking that I had lost my results of the analysis. Luckily it still turned on and I made a back up immediately.

What would you like to learn during this course?

How to properly/professionally manage my data, so that it's easy to find and easy to find back what I've done.

Checklist assignments

• [x] Assignment 1: creating a GitHub issue (the overview issue) (before 15 February, 10:00)
• [x] Respond to the GitHub issue #101
• [x] Assignment 2: Data Flow Map 1 (share a link in this issue before 22 February 13:00). Link: https://tud365-my.sharepoint.com/:p:/g/personal/ivyliang_tudelft_nl/EX8k1eDUWFpHkwrz2V34VGQB4VJKjwyW5wdbvmkilH3iJQ?e=Unx0lJ
• [x] Provide feedback to at least one Assignment 2 from another participant
• [x] Respond to the GitHub discussion #103
• [x] Respond to the GitHub discussion #102
• [x] Assignment 3: Data Flow Map 2 (share a link in this issue before 5 March 13:00). Link: https://tud365-my.sharepoint.com/:p:/g/personal/ivyliang_tudelft_nl/EXW3uHZMpc1IpBmj5q_Ye7AB6VOlRiX3RZ3OWzlY6AHMTQ?e=biG8lO
• [x] Provide feedback to at least one Assignment 3 from another participant
• [x] Assignment 4: Data Management Plan (before 8 March, 13:00)
• [x] Respond to the GitHub discussion #104 if you have any questions (optional)
• [x] Assignment 5: Data Flow Map 3: submit your slide (before 11 March, 17:00)

[lettema1]

Hi Ivy, I had a look at your Data Flow Map, and I think it looks good! You've included a lot of different types of data. Using the M: drive and a proper back-up seems to be a safe way for storing all your data. Looking at all types of data, I can imagine that (as you mentioned in the Data Challenge discussion) it can be hard to find a good way of structuring your data and results.

[EstherPlomp]

Thanks for sharing assignment 2 @ivyliang98! And thanks for the feedback @lettema1!

It looks very clear and comprehensive: well done! I therefore have very little feedback:

• I like how you're also considering your presentations and literature files in the data workflow!
• Perhaps you already included lab notes in the protocol dataflow: this is indeed also information is also data that should be managed!
• For managing your R-scripts you may also want to consider using version control, or GitHub/GitLab: we'll go a bit into that in the documentation module.

[SIM1-S]

Hi Ivy, I've taken a look at your Assigment 3, and i'm very impressed! Your slides are quite detailed and you have clear answers to most questions. I do have some comments:

• I read that you plan to make folders for each year of your PhD. I could imagine for (sub)projects that span more than 1 year (or start and finish in different years) that this might be a bit confusing.

• Further, it also strikes me that your file names are a bit long. This might be difficult to read, especially for someone outside of your project.

• Lastly, you do not have any metadata mentioned with your Edited images from the Microscopy Data. I could be useful to also save metadata (or notes) with these images, as you could specify what edits have you made to the images and how could someone else achieve the same.

[EstherPlomp]

Thanks for sharing assignment 3 @ivyliang98! Like @SIM1-S is saying - it is very clear and comprehensive!

I agree with @SIM1-S feedback: particularly on the organisation. Sorting your data per year might be complicated if projects do not adhere to a yearly planning - that will be up to you to decide what will work easiest!

Some additional suggestions, and a concern regarding the restricted access status that you indicate for all of your data:

• Most importantly: it seems like you label all your data as restricted access whereas I do not see any red flags that would require this restricted access. It looks like you have no valid reason to not share the data/code underlying your publications. I think you may need to have another look at the data publication materials to consider a data repository to share your data/code!
• In slide 11, the format of the data is not entirely clear, so I can't really judge whether it is open or not! Regarding .xlsx and .docx files: These are now interoperable with other software, but they are not open as you'll need a microsoft license to fully interact with these file formats. Open alternatives would be .csv and .txt. Conversion might not always make sense - that is again up to you if that is needed!
• And a smaller note on Zotero: Using Zotero it is still possible to organise files via folders/maps and tags! You can, for example, organise literature per publication to have a better overview of what you are citing!