TheEvergreenStateCollege bioinformatics issues

TheEvergreenStateCollege / bioinformatics

Plant genome sequencing

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issues

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Merge sysmem changes

#50 learner-long-life opened 3 weeks ago
0
Taylor's suffix tree property checks as unit tests

#49 learner-long-life closed 3 weeks ago
0
Suffix Tree Visualizer

#48 pointmeathesky closed 1 month ago
0
Git LFS and .gitignore

#47 learner-long-life closed 1 month ago
1
Ricard and Dom's work on low system memory in rusty-plants

#46 learner-long-life closed 1 month ago
2
Comment and strip out unneeded parts of suffix_tree.rs

#45 AbyssalRemark opened 1 month ago
0
WIP: start sqlx access in Rust

#44 learner-long-life opened 1 month ago
0
Crowded suffix tree rendering

#43 learner-long-life opened 1 month ago
4
Create a test database in NodeJS + Prisma to read back

#42 learner-long-life opened 1 month ago
2
Placeholder cpp-plants project

#41 learner-long-life opened 1 month ago
0
pnpm build warnings in web

#40 learner-long-life opened 2 months ago
0
Add starter NextJS web project

#39 learner-long-life closed 2 months ago
0
How to partially render a suffix tree from db

#38 learner-long-life opened 2 months ago
1
Visualize suffix links from duplicate edges

#37 learner-long-life opened 2 months ago
1
Brainstorming web UI ideas

#36 learner-long-life opened 2 months ago
1
Record a screenshare video stepping through and narrating Ukkonen's algorithm

#35 learner-long-life opened 2 months ago
0
Continue explaining Ukkonen's algorithm

#34 learner-long-life closed 1 month ago
1
Select optimal portion of suffix tree to offload to database

#33 learner-long-life opened 2 months ago
1
Write part of suffix tree to database

#32 learner-long-life opened 2 months ago
0
DB queries to extend suffix trees

#31 learner-long-life closed 2 months ago
0
Add Dominic's google slides link

#30 learner-long-life closed 1 month ago
0
Fail gracefully when system free memory is too low

#29 learner-long-life opened 2 months ago
0
Consider ways to model edge string fragments in database schema

#28 learner-long-life opened 2 months ago
1
Gavin's work on read alignment

#27 learner-long-life closed 2 months ago
2
Test functions should not contain the word "test"

#26 AbyssalRemark opened 3 months ago
0
Reorganize directories for rust, c++, web

#25 learner-long-life closed 3 months ago
1
Cleanup

#24 poperigby closed 3 months ago
0
Suffix tree rewrite

#23 Gavin-Bowers closed 3 months ago
0
Fix issues caused from rename to smarty_plants

#22 poperigby closed 3 months ago
1
Update Cargo.toml

#21 poperigby closed 3 months ago
0
(Temporary) Reorganize howtocpp suffix tree printout and Rust suffix tree tests.

#20 learner-long-life closed 3 months ago
0
Possibly make repo private

#19 learner-long-life opened 4 months ago
1
Create Rust CI

#18 poperigby closed 4 months ago
0
Remove cruft

#17 poperigby closed 4 months ago
1
Edit distance

#16 poperigby closed 3 months ago
4
Edit distance dynamic programming approach

#15 learner-long-life closed 4 months ago
0
Pull request for rewrite branch as requested at meeting today

#14 TW-Starbuyer closed 3 months ago
1
Remove old CLI

#13 poperigby closed 4 months ago
0
Array2D

#12 poperigby closed 4 months ago
1
Add unit-test-in-progress for suffix tree.

#11 learner-long-life closed 4 months ago
1
Modify SuffixTree:find_substring to return all occurrences

#10 learner-long-life opened 4 months ago
0
Add a test for SuffixTree::find_substring method

#9 learner-long-life closed 1 month ago
1
Write unit tests for standard suffix tree cases

#8 learner-long-life opened 4 months ago
1
Some syntax and path fixes

#7 learner-long-life closed 4 months ago
1
Web user interface

#6 learner-long-life closed 1 month ago
2
Write instructions to download fragments / genome

#5 learner-long-life closed 5 months ago
2
DNA mRNA RNA and others, what are we working with?

#4 AbyssalRemark opened 5 months ago
1
suffix trees for finding largest common substring

#3 AbyssalRemark opened 5 months ago
5
checking backwards and inverse.

#2 AbyssalRemark opened 5 months ago
1
Is the reconstructed sequence a line or a loop?

#1 learner-long-life closed 5 months ago
1