MODOS DEMO
Multi-Omics Digital Object
Almut Lütge,
Cyril Matthey-Doret,
Irene Keller
Zürich, Dec 8th
Modos: Application
- Data Management:
- synced metadata and files
- distributed access
- remote storage
-
HTTP endpoint
- serve metadata, objects
-
Multiomics Services:
- Streaming
- Encryption
- ?
Modos: Tool Stack
- Data object: metadata + files
modos --anon --endpoint https://modos.dscompute.ch show -z s3://modos-demo/AAD
INFO | Using remote endpoint https://modos.dscompute.ch for s3://modos-demo/AAD
/
├── assay
│ ├── expr_assay_AAD
│ ├── genomic_assay_AAD
│ └── prot_assay_AAD
├── data
│ ├── expr_AAD
│ ├── prot_AAD
│ └── variants_AAD
├── reference
│ └── reference
├── sample
│ └── sample_AAD
└── sequenceModos: Tool Stack
- Data object: metadata + files
-
CLI + API
- Management:
create, update, delete, ... - Remote:
streaming, upload, download, login - Genomics:
encrypt, decrypt
- Management:
modos --help
Usage: modos [OPTIONS] COMMAND [ARGS]...
Multi-Omics Digital Objects command line interface.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --endpoint TEXT URL of modos server. [env var: MODOS_ENDPOINT] │
│ --anon Use anonymous access for S3 connections. │
│ [env var: AWS_SKIP_SIGNATURE] │
│ --version Print version of modos client. │
│ --debug Enable debug logging. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Read ───────────────────────────────────────────────────────────────────────╮
│ show Show the contents of a modo. │
│ publish Export a modo as linked data. Turns all paths into URIs. │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Write ──────────────────────────────────────────────────────────────────────╮
│ create Create a modo interactively or from a file. │
│ remove Removes an element and its files from the modo. │
│ add Add elements to a modo. │
│ enrich Enrich metadata of a digital object using file contents. │
│ update Update a modo based on a yaml file. │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Command groups ─────────────────────────────────────────────────────────────╮
│ c4gh Local encryption via crypt4gh. │
│ remote Remote object management. │
│ codes Terminology codes utilities. │
╰──────────────────────────────────────────────────────────────────────────────╯Modos: Tool Stack
- Data object: metadata + files
-
CLI + API
- Management:
create, update, delete, ... - Remote:
streaming, upload, download, login - Genomics:
encrypt, decrypt
- Management:
-
Services:
- Modos server
- S3 store
- Htsget server
- Refget server
Multiomics in YEast
- Quantitative comparison of proteome and transcriptome across different natural yeast strains --> weak correlation
- Comparison of eQTL and pQTL --> only 3% overlap
- Different ways of regulation, e.g. proteomic turnover rate
Discussion
- What would be needed - additional to the current functionality of modos to be useful for you?
- What do you use for data management? What python packages do you use in general
- What multiomics tools, services, standards do you use?
DEMO
- Demo cli
- commands
- login
- download
- swagger/metadata
- Demo python wflow
Minimal
By Almut Luetge
