I’ve noticed there can be a barrier to entry for starting using Biopython. The official tutorial is excellent documentation, but too exhaustive for new users. Peter’s Biopython workshop is a great resource (and could feature more prominently on the Biopython github), but I also wanted something more biological and in a Jupter notebook.
Given the times, with people working remotely, I was motivated to finally create a draft notebook tutorial, using a genome sequence from SARS-CoV-2 as a topical theme. The idea is to use several parts of Biopython to demonstrate the broad functionality, while keeping it lightweight, and biologically informative. In this case, there is an “unknown sequence”, which the tutorial reveals derives from SARS-CoV-2 and shows how to extract some simple metadata and perform rather basic analyses. I'm sure it could be expanded quite a bit if people like the idea.
I hope that no-one feels this is an insensitive choice on my part, given the pandemic is ongoing.
Currently, I’m storing this as a gist:
EDIT: the gist links have now been deleted, see instead, the github repo
I would very much like any feedback on the concept and tutorial content and any suggestions to improve it?
Also, is there an interest to integrate this into Biopython or not? If not, no worries, I will put it in a separate repo. At some point, I planned to give a Biopython workshop at my university, so it might be useful for this
I’ve noticed there can be a barrier to entry for starting using Biopython. The official tutorial is excellent documentation, but too exhaustive for new users. Peter’s Biopython workshop is a great resource (and could feature more prominently on the Biopython github), but I also wanted something more biological and in a Jupter notebook.
Given the times, with people working remotely, I was motivated to finally create a draft notebook tutorial, using a genome sequence from SARS-CoV-2 as a topical theme. The idea is to use several parts of Biopython to demonstrate the broad functionality, while keeping it lightweight, and biologically informative. In this case, there is an “unknown sequence”, which the tutorial reveals derives from SARS-CoV-2 and shows how to extract some simple metadata and perform rather basic analyses. I'm sure it could be expanded quite a bit if people like the idea.
I hope that no-one feels this is an insensitive choice on my part, given the pandemic is ongoing.
Currently, I’m storing this as a gist:
EDIT: the gist links have now been deleted, see instead, the github repo
I would very much like any feedback on the concept and tutorial content and any suggestions to improve it?
Also, is there an interest to integrate this into Biopython or not? If not, no worries, I will put it in a separate repo. At some point, I planned to give a Biopython workshop at my university, so it might be useful for this