Genomic Foundation — Foundation Learning Guide¶
For a reader with no background in this area. If you have watched the Foundations film series, this follows directly from it.
The one idea to hold¶
A variant is a difference from a reference sequence. Most differences mean nothing; a few change a protein's shape, and a very few cause disease.
What this subject does with that idea¶
Turns raw sequencing reads into a list of the specific letters where a person's genome differs from the reference.
Every downstream answer — which variant, which drug, which trial — depends on this list being right.
Decision support for a qualified clinician — never autonomous diagnosis or prescribing. Every output on this page is intended to inform a clinician's judgement, not replace it.
What it cannot do¶
Alignment and variant calling require NVIDIA Parabricks, which is not installed on this box. Results shown today are pre-computed.
Stating the limit is not a disclaimer bolted on the end — it is how you tell a tool that helps from a tool that misleads.
Vocabulary you will meet¶
| Term | Plain meaning |
|---|---|
| Capability | One named thing the platform can do, registered in capabilities.json |
live / planned |
Whether a capability actually answers today, or is intended |
| Decision support | Output that informs a clinician; it never decides |
| LIVE / REPRESENTATIVE / BURST | Whether a demo ran now, was pre-computed, or ran on remote GPUs |
Try it¶
The demo for this subject is E1:
.venv/bin/python scripts/run_demo.py E1
If it reports BLOCKED, the message names exactly what is missing. That is intentional — a demo
that cannot run says so rather than showing you something canned.