bioinformatics-projectlisted

# Bioinformatics Project Organization Set up a computational-biology project so a stranger can understand what was done and why, and so every analysis can be rerun end-to-end from a script. Apply this when creating, restructuring, or reproducibility-hardening any genomics, metagenomics, sequencing, or computational-biology project — and when running any single analysis command that should be reproducible. Two assumptions drive every rule below (Noble 2009): a stranger must be able to reconstruct the analysis from the files alone, and everything will be rerun — with new data, new parameters, or a fixed bug — so build each experiment to re-execute from a script, never from memory. ## Instructions ### New project startup workflow Before creating directories or running the first command, turn the project into a small written contract: 1. Name the project with a durable, specific directory name. 2. Write the objective, analysis tracks, expected deliverables, input data types, compute environment, and known reference databases in `README.md`. 3. Create `tasks/METHODS.md` immediately and record every setup command, software version, database path, option, seed, and SLURM job ID as work proceeds. 4. Create `SUMMARY.md` for current status and high-level counts. 5. Create `tasks/todo.md` for active work and `tasks/lessons.md` for corrections and prevention rules. When memd is available, initialize its project scope and let `memd memory-md` maintain the root `memory.md