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EstherPlomp / TNW-RDM-101

Self paced materials of the RDM101 course
https://estherplomp.github.io/TNW-RDM-101/
Creative Commons Attribution 4.0 International
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Assignment 1 Minco Polinder #50

Closed MPolinder closed 1 year ago

MPolinder commented 1 year ago

Introduction

Hi, I'm Minco, PhD candidate in the Cees Dekker lab (Bionanoscience).

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

My research focusses on chromosome dynamics during prokaryotic cell division. By visualizing the dynamics of two mixed DNA constructs in a nanoconfinements, I want to learn about entropy-driven chromosome segregation.

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

The 'horror-stories' are of course exceptions and not daily reality. I do not have an experience like that myself, other than that I have wasted time on figuring out what the precise experimental conditions of certain datasets were since I did not properly link the data to my labjournal. Therefore, I realize that proper data management makes a project more structured and accessible, both for yourself and for others. The other advantages of proper data management that are discussed in the video/paper speak for themselves.

What would you like to learn during this course?

I would like to get inspiration for setting up my own data management strategy for my own project.

Checklist assignments

EstherPlomp commented 1 year ago

Hi @MPolinder! Thanks for handing in your assignment 2!

Well done on the assignment: your storage strategy looks good and comprehensive! TU Delft ICT tends to recommend the project drive for research data instead of the N/M drives, but if this is how your group is doing things you may disregard this comment :). I see you're working with large imaging files, and for that the project drive may also be a solution if you start to run out of storage space in your other locations (as it can scale up to multiple TBS).

Other than this I have little to add: well done!

jmvanede commented 1 year ago

Hi Minco, I think you have a very nice and clear data flow map! It gives a good impression on the data you will create/collect and the size of it. You also seem to have an extensive infrastructure on where you will store your data.

MPolinder commented 1 year ago

Thank you @EstherPlomp and @jmvanede .

@EstherPlomp As far as I know our group does not really use the U: drive but the other drives with copies on local HDD's/PC's, I will ask around though!

MPolinder commented 1 year ago

I think many things in the template do not really apply to imaging data of an exploratory study (which is what I am doing predominantly).

README.txt

EstherPlomp commented 1 year ago

No worries about some of the questions in the readme file template not being applicable to your research @MPolinder! If these questions are not helpful, you can also delete them since they are then just taking up space and cluttering your READme file. I think the way you set up your READme file is very clear: well done! I do see several 'available upon request' in your READme: if the scripts are developed as part of your PhD project, TU Delft expects you to follow the FAIR principles and share the code publicly using a Data Repository such as 4TU.ResearchData or Zenodo. You can also set up your own ORCID account, which will be more helpful later on when you have multiple research outputs that you can then gather in one space.

Your assignment 3 looks very clear and comprehensive as well: well done!

File formats:

Data publication:

Banalikwu commented 1 year ago

Hi Minco well done on the readme file. I have a only a few suggestions/questions: You write that you have 5D .tiff-stacks (Wow 5D...) and I could imagine that it is hard to keep track of the order and how the stacks are ordered by dimensions. Do you have a way to keep track of that? Perhaps that is already part of the metadata, but that would depend on the microscope. In your readme, you also write that you have custom-made microfluidic devices and I remember you telling us about different designs. Perhaps you can add to your data & file overview a way to keep track of designs and corresponding acquisitions.

Banalikwu commented 1 year ago

Hi Minco!

Some comments/suggestions on your data flow map: You wrote that you will store some very important details of the autoCAD designs in the metadata (purpose, dimensions, fabrication details), I really like that! One thing in our group that is often missing is exactly this kind of information. So storing this in the metadata should really help out when others look through your stuff and potential next students on your project. Perhaps a note on the data publication, specifically the code part: Do keep in mind that a lot of packages that you might be using have licenses of their own. This might impact your freedom in choosing licenses (something that I'm thinking of now and haven't considered for myself yet...) On the documentation of your code: If you want, we can have a talk about various options for code documentation. I already convinced you of switching to pycharm which helps you with docstrings (automatically generated lines of documentation for your functions/classes), but pycharm there is much more!