Cassidy Development Diary - TheEvergreenStateCollege/bioinformatics GitHub Wiki
- Hours I'd like to spend: 9
- What I'd like to do: Research DNA and CUDA with RUST, and start the initial graphing implementation
- How many hours I spent last week: 6
- How my learning went: I tried reading the paper linked in the README, got confused, and tried watching so videos. Still confused.
I watched a few videos on Eulerian paths, and started implementing an adjacency matrix based graph. I also talked with Gavin quite a bit about the best way forward, and whether we should be doing read alignment instead of sequencing.
- I organized Gavin's code
- I helped Gavin setup the code for reading FASTA files, and making a naive read alignment function.
- I watched this video: https://www.youtube.com/watch?v=axVN-SoPdOY
- I added a
serialize
method toFragment
. - I watched this video: https://www.youtube.com/watch?v=Oj1wKc3CRL0
- I made a very simple tree data structure that uses
Option<Rc<Leaf<T>>>
to allow multiple ownership of leaves.
I managed to create an edit distance function: https://github.com/TheEvergreenStateCollege/smarty-plants/pull/16
- After hours of tearing my hair out I finally got
edit_distance
to pass all the tests.