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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 Tim Lugtenburg #78

Closed TimTheChemist123 closed 8 months ago

TimTheChemist123 commented 12 months ago

Introduction

Hi everyone, my name is Tim Lugtenburg and I am a PhD candidate in the field of Biocatalysis (TNW faculty).

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

In my research my aim is to engineer novel biocatalysts (enzymes) that are able to perform oxyfunctionalization reactions more efficiently. Improving these types of synthesis reactions is important in chemistry for the more sustainable and/or profitable production of e.g. pharmaceuticals, flavour compounds or fragrances.

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 No
Work with large data (images, simulation models) No
Other: N/A

Reflections on the importance of RDM videos

I very much agreed with the importance of having a well structured organization of research data, not only for your personal use, but even more importantly that it can be communicated to others. A horror story for me would be to reach a certain early stage conclusion and basing the rest of the research on that, but later on not being able to defend your decisions as the data is not findable anymore. This could be due to either improper labelling, but part of the difficulty is knowing which aspects of the experiment are relevant to write down, as this is not always clear at the start.

What would you like to learn during this course?

Ideally I would like to learn more about useful workflows for the organization of the data specific to my field of research. As I will not be working with a lot of code like other fields, nor with large datasets. However, the data I will produce consists of raw data from experiments in all kinds of formats, which are turned into graphs. Better organization of this data where I know where to store what, in a logical way, that does not require too much administration would be very helpful to me. Another thing I would like to discuss is the use of productivity tools like Notion for planning of my research, and whether the use of a 3rd party app like that does not violate privacy regulations of the TU.

Checklist assignments

EstherPlomp commented 11 months ago

Hi @TimTheChemist123! I'll respond here to your question on the use of third party apps:

Another thing I would like to discuss is the use of productivity tools like Notion for planning of my research, and whether the use of a 3rd party app like that does not violate privacy regulations of the TU.

This depends a bit on your research project and situation - privacy regulations are not physics unfortunately... Since you're not dealing with personal data and/or company data, you have less restrictions on what solutions you could use compared to other colleagues. In principle you can use these tools as long as you don't use them to process any sensitive information. You can argue that your name/email address is not that sensitive, as I can also access this personal data from the public TU Delft website. If you start adding people's birthdates in Notion it is a different story - but I doubt you'll need that information to be able to plan your research :). If you have any doubts about other tools, please let me know!

In short: you can use these tools, just be conscious about what type of data you're storing in them!

TimTheChemist123 commented 11 months ago

Hi!

Here is my assignment 2: https://surfdrive.surf.nl/files/index.php/s/HYOsMlQoIhd9LRr

-Tim

cfprimavera commented 11 months ago

Hi @TimTheChemist123,

Very nice data flow map! I really like the fact that you mention the 3-2-1 principle of data storage and that you're using the automated way of storing your data in this way.

I would like to comment on what you mention about the files irrelevant to others, such as administration. While I understand that others will not need this for anything it can be quite painful if you lose these data. A solution for backing this up could be to use the personal online drive that the TU provides for making backups of this every once in a while.

Best, Christian

RiccardoDalMas commented 11 months ago

Hi @TimTheChemist123,

Very nice and thorough data flow map!

I was wondering about how you plan to handle the transfer of the raw data generated by the instruments. You mention that the GC data are stored on the instrument itself, is it the case also for the other instruments you'll use (NMR, UV VIS, etc.)? If so, will you make a copy on the project drive of the raw data, and can you do this directly from the local terminal connected to the instrument?

Thank you, Cheers, Riccardo

Lloyd537 commented 11 months ago

I like your data flow map, very extensive! Especially the distinction between data that is relevant for the project and others, and data (notes, etc) that is only relevant to you. I do the same to some degree, I have some note documents that I use for my own project planning. While I agree that these are not relevant to others, it might still be a good idea to back these up as well, since you do need them to continue your project.

Cheers, Lloyd

EstherPlomp commented 11 months ago

Thanks for sharing assignment 2 @TimTheChemist123! It looks very clear and comprehensive - well done!

TimTheChemist123 commented 11 months ago

Here is my assignment 3: https://surfdrive.surf.nl/files/index.php/s/PtWSHcGf3h14QGj

-Tim

EstherPlomp commented 11 months ago

Thanks for sharing assignment 3 @TimTheChemist123! It again looks fantastic - well done! I therefore have very little feedback and just some thoughts:

Data Organisation

File Formats

HuaChenTUDelft commented 11 months ago

Hi Tim,

Really nice data flow map and thanks for sharing with us. I really agree with you that numbering batches of experiments does help to find the corresponding data if you have to change the folder structure in the future. And also name the data with corresponding charateristics also helps to organise it.

Best, Hua

FanJ-TUD commented 10 months ago

Hello Tim,

Very detailed data flow map. I really appreciate how you precisely describe the properties with flags in your map, which quite customize the function for understanding and reminding the exp process.