Assignment 1 Pablo Velazquez

[PabloVelazquezGarcia]

Introduction

Hi there! I am Pablo Velazquez and I am a PhD candidate in the biotechnology department and in the biocatalysis group. I Love sports and cooking :D

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

My research focuses on the design and testing of new enzymes with potential applications in chemical and pharmaceutical processes. Using protein engineering tools, we aim for a new and greener and more sustainable chemistry.

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	Yes/
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)	Yes/

Reflections on the importance of RDM videos

What would you like to learn during this course?

I would like to learn how to manage different kinds of data, in different formats in a easy and intuitive way.

Checklist assignments

Checklist assignments

• [x] Assignment 1: creating a GitHub issue (before Class 1)
• [x] Respond to the GitHub issue on 'data challenge'
• [x] Assignment 2: Data Flow Map 1 (share a link in this issue before 17 May 13:00). Link:
• [x] Provide feedback to at least one Assignment 2 from another participant
• [x] Respond to the GitHub discussion on 'licenses'
• [x] Respond to the GitHub discussion on 'folder structure'
• [x] Respond to this GitHub issue with your readme file
• [x] Provide feedback to at least one readme file from another participant
• [x] Assignment 3: Data Flow Map 2 (share a link in this issue before 31 May 13:00). Link:
• [x] Provide feedback to at least one Assignment 3 from another participant
• [x] Assignment 4: Data Management Plan (before Class 2)
• [x] Respond to the GitHub discussion on 'Data Management Plans' if you have any questions (optional)
• [x] Assignment 5: Data Flow Map 3: submit your slide (before Class 2)

[PabloVelazquezGarcia]

Assignement 2

https://surfdrive.surf.nl/files/index.php/f/13024904754

[PabloVelazquezGarcia]

Assignement 3 Step 2

1. What folder structure will you use for your project? (and how does the data fit in there) The folder structure that I am following is a hierarchy structure with NameProject as the main folder, followed by 5 subfolders (Bibliography, Experiments, RawData, Protocols, Miscelaneous). In "Experiments" and "RawData" there are more subfolders arranged by experiment.
2. What naming convention are you going to use? (show us an example based on your expected dataset) YYYY-MM-DD_Experiment_Particularity_Version
3. Additional remarks I tend to change the conventions every now and then. Please dont Step 3
4. What type of documentation do you need to generate/write? (metadata, data collection process, data dictionary, code versioning, etc.) In my experiments I will need to generate data related with genetic sequencies, 3d models of enzymes, kinetics, graphs and spectroscopy data. I will be creating a data dictionary for my reactions (each reaction has a reaction code, which makes it easier to come back for the data later on.
5. Will you use a metadata standard to document your data? For now, I dont think I will be needing this. I feel the simplest and clearest way of keeping and organizing my data is the best for me 3.What tools are helpful to generate/write the documentation needed? I use both a notebook and a electronic lab journal. I also write down specific codes for different experiments so that I can easily know what is the experiment about and I can find it later on (also new people can).

Step 4

1. Are your files in an open file format? Or, is the code in an open programming language? My files are totally open format
2. Can you convert the proprietary file formats to an open file format? If yes, to which open file format? Is there anything more open than excel, word, pdf...?
3. If the data/code is in a proprietary format, what information/software would others need to re-use the data/code?

Step 5

1. Who will have access to this dataset during the project? Everyone in my research group

2. If others than you will have access to the dataset during the project, how will you share the data? In the shared drives of the TU Delft (M)

3. At the end of the project this dataset can be: Open - no confidential information in it , it can be published In which repository will you publish it? 4TU.RESEARCHDATA

[PabloVelazquezGarcia]

Assignement 3 https://surfdrive.surf.nl/files/remote.php/webdav/RDM101_Assignment1_Week1_DataFlowMap_PabloVelazquez.pptx https://surfdrive.surf.nl/files/remote.php/webdav/PABLOVELAZQUEZ_DATASET_Readme.txt

[EstherPlomp]

Thanks for sharing part of your assignment 3 @PabloVelazquezGarcia! I can't access the files you shared via SURFdrive - can you check again whether you have set up a public link to share the files? (See here for the steps you'll need to take). The same comment still applies to your assignment 2 as well. Please let me know if we need to set up a quick call with some screensharing to get this sorted!

Regarding your comment on open files: word/excel files are not an open format because you'll need a microsoft license to fully interact with these file types. Alternatives would be .txt or .md files for word, or .csv for Excel!

And good to see you're already documenting everything via (electronic) lab notes!

[PabloVelazquezGarcia]

Assignment 3 (password: datamanagement)

https://surfdrive.surf.nl/files/index.php/s/JrFP3v7TVOAjmyn https://surfdrive.surf.nl/files/index.php/s/Z0ClxI87ncsQsyF

[EstherPlomp]

Thank you @PabloVelazquezGarcia! These links now work! It looks like these are your assignment 2 and readme file. Please also provide a link to assignment 3, and then I can provide feedback later today (hopefully - otherwise tomorrow :)).

[EstherPlomp]

And the feedback! Hope it is helpful:

Assignment 2:

• Please be careful with storing data on USBs; they are easily lost and corrupted and should only be used to transfer files, not as a storage solution.
• What do you mean with TU Delft.net? Is this one of the network drives?
• Do you also have analysis protocols? Figures/images you'll have to work with?

README:

• For the title of the dataset it is good to be a bit more descriptive. This can be difficult now if you don't have a particular dataset to share yet, but for example: dataset underlying the article "title article" or another title that describes the dataset itself a bit more.
• Please do add the last names of contributors to the datasets that you plan to share externally: otherwise it will be difficult to find/contact individuals. With the ORCID you can identify researchers more easily. You can set up your own ORCID here: https://orcid.org/register
• For the licenses/restrictions you can indicate the license for the data that you have to share in the license thread.
• For the recommended citation I would list out the full contributor list, and then also the title of the dataset. This is similar to a regular publication reference and should here be written out fully.
• When technicians and students are involved in the research project, you can ask them if they want to be listed as a contributor on the dataset with their contact details
• Please be sparing with the use of caps in your README. All caps text is not accessible for screen readers and it can be more difficult to read generally
• For the quality procedures/calibration curves: it would be helpful to describe this in a bit more detail. You can compare the methodological information in the readme file to the methods section in an article. It can be worthwhile to copy past some of the text in your future article to the readme file of your future dataset :)
• And lastly; If any of the questions are unhelpful or not relevant to a particular dataset, you can also delete them. This also helps with the readability of your READme.