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UtrechtUniversity / programming-cafe

Repository for the Programming Cafe community event at @UtrechtUniversity
https://utrechtuniversity.github.io/programming-cafe/
MIT License
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ideas for the programming cafe! #3

Open nehamoopen opened 2 years ago

nehamoopen commented 2 years ago

Ideas from Jacques Flores (@Mish-JPFD): Text Mining in R & Python

jelletreep commented 2 years ago

Feel free to submit topics that you would like to hear more about below! If you would like to present something, even better! Also feel free to like topics proposed by others so we can keep that in mind when preparing.

nehamoopen commented 2 years ago

Data Visualization in R & Python (we can use https://www.data-to-viz.com/ as a guiding resource)

nehamoopen commented 2 years ago

Dependency Management in R & Python

jelletreep commented 1 year ago

Geospatial analysis

jelletreep commented 1 year ago

Communicating with APIs in R & Python

NiklasHohmann commented 1 year ago

Combining multiple languages into a consistent workflow. We're currently using multiple languages (Matlab, Fortran, Python, R, etc.) for simulation studies and analysis of the outputs, with some of the model outputs being run on surf infrastructure. As as result, there is a lot of manual copying of files, which is very error prone (and not amazing for reproducibility). Any hints at how to improve the design of the pipeline or potentially automate it would be great (also with a focus on data storage and archiving).

EmiliaJarochowska commented 1 year ago

Registering a protocol for a simulation pipeline. Most studies register lab or other data collection protocols: we want to pick people's brains on whether whether it is a good idea to make a registration of a simulation pipeline and have it reviewed before we run the simulations. The background is: they are computationally intensive and we are not 100% confident in our code. So it would be great to have it scrutinized before we run them. This is a very Open Science themed questions, but maybe too niche?

Peter-UU-2021 commented 1 year ago

something about Quarto and how to use it?

jelletreep commented 1 year ago

Thanks for the great suggestions!

Combining multiple languages into a consistent workflow. We're currently using multiple languages (Matlab, Fortran, Python, R, etc.) for simulation studies and analysis of the outputs, with some of the model outputs being run on surf infrastructure. As as result, there is a lot of manual copying of files, which is very error prone (and not amazing for reproducibility). Any hints at how to improve the design of the pipeline or potentially automate it would be great (also with a focus on data storage and archiving).

:arrow_up: This will be the topic for next week!

something about Quarto and how to use it?

@Peter-UU-2021, Great suggestion, we can definitely plan this in a future session (we are still learning more features). If someone reading this would like to give a demo, let us know!

Registering a protocol for a simulation pipeline. Most studies register lab or other data collection protocols: we want to pick people's brains on whether whether it is a good idea to make a registration of a simulation pipeline and have it reviewed before we run the simulations. The background is: they are computationally intensive and we are not 100% confident in our code. So it would be great to have it scrutinized before we run them. This is a very Open Science themed questions, but maybe too niche?

@EmiliaJarochowska, Sounds very interesting, we currently don't have the expertise ourselves to my knowledge, but if someone has expertise we would warmly welcome a demo!

Keep the suggestions and likes for topics coming so we can fill the next editions! We also warmly welcome contributions in the form of presentations/demos!

nehamoopen commented 1 year ago

Automate the Boring Stuff with Python: https://automatetheboringstuff.com/ Advent of Code? Hacktoberfest? Bring Your Own Code Why Your Code Doesn't Reproduce?: https://metahag.github.io/MP_reproducibility_workshop/#/readme-and-codebook-files

EmiliaJarochowska commented 1 year ago

My votes are for the following: Automate the Boring Stuff with Python: https://automatetheboringstuff.com/ Why Your Code Doesn't Reproduce?: https://metahag.github.io/MP_reproducibility_workshop/#/readme-and-codebook-files - this doesn't display properly for me but still interesting ;-)

jelletreep commented 9 months ago

Based on questionaire 11 januari programming cafe