2024‐04‐09 Meeting Notes - TheEvergreenStateCollege/bioinformatics GitHub Wiki

2024-04-09 | 10:00 AM - 12:00 PM

ATTENDING

  • Dee Dee (Minutes)
  • Dom
  • Cassidy
  • Ellie (running late)
  • Gavin (running late)
  • Rain (Facilitator)
  • Taylor

AGENDA

Last Meeting Follow-Up

  • Where are people out with last weeks action items
  • Graph discussion
  • File operations
  • String operations
  • Suffix Trees

New Business

  • CUDA

NOTES

  • We started with a check-in about where everyone is at (high-level).
    • Dom: thinks that thinking about what a suffix tree will look like will happen after the graph work is off the ground
    • Taylor: is researching different graph possibilities, how we'd implement it, error corrections, and determining k-mer length (dynamic k-mers).
    • Cassidy: has been watching videos on circuits and paths and making an adjacency implementation.
    • Rain: is learning Rust and has found resources for C++ programmers.
    • Dee Dee: Has been researching file and String operations in rust.
    • Gavin:
    • Ellie:
  • Graphs:
    • Is the graph weighted?
    • string people need to make sure the segments stay 3->5 prime
  • Control Flow:
    • File I/O
    • String Operations
      • Algorithms
    • Graph
      • Algorithms
  • We would like to walk through the paper together with Taylor presenting
  • Conversation about De Bruijn graphs
    • starting point: make the simplest most generic graph
    • Gavin suggested: read alignment as a stepping stone
  • Control flow of program:
    • high-level program visualization to be added later
  • CUDA
    • Parallel computing platform and programming model
    • People should look at wgpu
  • Suffix Trees
    • suffix tree O(n)
      • go through strings once
      • cost memory
  • DNA: We have been told we are working with DNA (Nancy) the files indicate RNA and the nucleotide are AUGC (not ATGC which is DNA). We will start thinking about building a program that can handle both. There was also the suggestion of working with E. coli DNA because of the number of resources.

ACTION ITEMS

  1. Everyone look at the paper by Friday An Eulerian path approach to DNA fragment assembly
  2. Complete Dev-diaries for the week:
    • planned work for this week
  3. Graphs:
    • Cassidy
    • Taylor
  4. Suffix Trees:
    • Dom
    • Dee Dee
    • Ellie
    • Rain
  5. Read Alignment:
    • Gavin
  6. Rain will create a Resources page on the repo wiki for links so they don't get lost in the discord channel.
  7. Dee Dee will Post the notes to the repo

NEXT MEETING’S AGENDA

  • Rust
  • Paul questions
    • Is the graph weighted?
  • Walk through paper with Taylor & Paul (2nd half of Friday meeting)
  • E.coli for DNA data?