PyDNA: Simulating cloning for genetic documentation. One step more towards FAIR data

When we plan the creation of a plasmid, we need to simulate the process. This way we will have the final sequence ready, so when we finally get the sequencing result from the plasmids we fabricated in the lab, we can check and detect any mistakes in the sequence.
After looking at different programs, I found PyDNA (https://github.com/BjornFJohansson/pydna) for the cloning in-silico, and plasmapR (https://github.com/BradyAJohnston/pla...) for drawing the maps.
In this video I show you a mini simulation to determine how the code works and what we should keep in mind when simulating our cloning. (References at the bottom) Once we know our code in the Jupyter notebook works as it is supposed to, we just need to change the location of the files for vector and insert, and the enzymes used. Then run the cells in the jupyter notebook and you should have the sequences of the new plasmid as gb and the plasmid map as png.
(PS: sorry for the sound. Trying new microphones. This was the fourth take)

00:00 Purpose of cloning simulation in relation to Open Science
02:34 Objective of the code - Simulation with a mini plasmid to get to know the software
03:48 Intro to Jupyter Notebook and pyDNA
05:24 Visualization of mini plasmid (created by PlasMapper 3.0)
07:03 Visual description of a genebank file (*.gb)
10:00 Digesting vector and insert, inspecting fragments when circularized vector is used
15:25 Ligation from circularized vector digest and insert (spoiler: It does not work)
18:58 Redoing the digestion of vector as linearized DNA.
19:54 Re-ligating with the fragments of plasmid and the insert
21:22 Verifying the final vector sequence visually
21:54 Verifying the final vector sequence with the unique cutting sites function
22:36 Creating the map using the R script with plasmapR
23:44 Discussion using the plasMapper 3 visualization of the final plasmid

If you want the simulation folder containing the jupyter notebook and the Drawing_map.R script, write in the comments. I will be happy to share it with you. Maybe you can find the reason why it does not really simulate the lab cloning process :-)

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Credits:
Thanks to all the community posting questions and answers, and my students for showing me what is really necessary to explain in order to start with great data management practices!
Sounds were from the from freesound.org, all under CC0 and https://soundcloud.com/user-993631319...

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Publications

1. PlasMapper 3.0: Wishart, D. S., Ren, L., Leong-Sit, J., Saha, S., Grant, J. R., Stothard, P., Singh, U., Kropielnicki, A., Oler, E., Peters, H., Gautam, V. (2023), PlasMapper 3.0 - A Web Server for Generating, Editing, Annotating and Visualizing Publication Quality Plasmid Maps, Nucleic Acids Research, https://doi.org/10.1093/NAR/GKAD276

2. PlasMapper 2.0: Dong, X., Stothard, P., Forsythe, I. J., & Wishart, D. S. (2004). PlasMapper: a web server for drawing and auto-annotating plasmid maps. Nucleic Acids Research, 32(Web Server Issue), W660. https://doi.org/10.1093/NAR/GKH410

3. Johnston B (2023). plasmapR: Create Plasmid Maps in R. R package version 0.3.1, https://github.com/bradyajohnston/pla....

4. Pereira, F., Azevedo, F., Carvalho, Â., Ribeiro, G. F., Budde, M. W., & Johansson, B. (2015). Pydna: a simulation and documentation tool for DNA assembly strategies using python. BMC Bioinformatics, 16(142), 142.