isaura 2.3.0

A lake of precalculated properties of biomedical entities based on the Ersilia Model Hub

Ersilia's Precalculation Store

Fast, reproducible access to precalculated model outputs from the Ersilia Model Hub — with a CLI and Python API built for batch workflows.

Installation · CLI · Configuration · Docs

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Why Isaura?

Isaura is Ersilia's precalculation store: it persistently stores model outputs so researchers can retrieve results instantly instead of repeatedly running time-consuming inference. This delivers a major research speed-up — especially in low-resource settings where compute, bandwidth, or infrastructure are limited — by turning repeated calculations into reusable shared artifacts. To support equitable access, Ersilia also provides free access to public precalculations, making high-value model outputs available even when local compute isn't.

Isaura provides a structured store for model results so you can:

• ⚡ Skip recomputation by reusing precalculated outputs
• 🧱 Keep artifacts versioned and organized (model → version → bucket/project)
• 📦 Store and retrieve results via S3-compatible object storage (MinIO)
• 🔎 Enable fast retrieval using its engine built on top of DuckDB

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Installation

Prerequisites

• Python 3.10+ — download here
• Git — download here
• Docker Desktop — download here — must be open before starting local services

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Step 1 — Clone and install

git clone https://github.com/ersilia-os/isaura.git
cd isaura
pip install -e .

Using uv? Run uv sync instead and activate the environment with source .venv/bin/activate.

A local configuration file is created automatically at ~/.isaura/.env with sensible defaults the first time you run any isaura command.

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Step 2 — Start local services

Make sure Docker Desktop is open, then run:

isaura engine --start

This starts a local MinIO instance and automatically creates the isaura-public and isaura-private buckets. You can explore the MinIO console at http://localhost:9001 (user: minioadmin123, password: minioadmin1234).

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Step 3 — (Optional) Set up remote credentials

If you have access to Ersilia's remote store, add your cloud credentials interactively:

isaura configure --remote

You will be prompted for the cloud endpoint and access keys. Credentials are saved locally to ~/.isaura/.env — nothing is sent anywhere.

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Step 4 — Verify your setup

isaura configure --test-credentials

This checks connectivity for local and cloud (if configured) and prints a result table. All rows you care about should show ✓ connected.

┏━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┓
┃ Target        ┃ Bucket         ┃ Result      ┃
┡━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━┩
│ Local         │ isaura-public  │ ✓ connected │
│ Cloud public  │ isaura-public  │ ✓ connected │
│ Cloud private │ isaura-private │ ✓ connected │
└───────────────┴────────────────┴─────────────┘

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CLI

Configuration

isaura configure                     # show current configuration
isaura configure --remote            # add or update remote/cloud credentials
isaura configure --update            # update a single credential interactively
isaura configure --show-secrets      # show all credential values unmasked
isaura configure --test-credentials  # test local and cloud connectivity

Local services

isaura engine           # show status of Docker and MinIO
isaura engine --start   # start local MinIO
isaura engine --stop    # stop local MinIO

Projects

A project is a named MinIO bucket used as a staging area before data reaches the canonical isaura-public or isaura-private buckets.

isaura info                  # list local projects with access type and creation date
isaura info --remote         # list remote projects

isaura create -pn myproject --access public   # create a new local project
isaura destroy -pn myproject                  # destroy an entire project
isaura destroy -pn myproject -m eos8a4x -v v1 # destroy a specific model version

isaura-public and isaura-private are reserved — they cannot be fully destroyed, but individual model versions inside them can be removed with --model-id and --version.

Writing outputs

Store model outputs in a project bucket:

isaura write -i data/ersilia_output.csv -m eos8a4x -v v1 -pn myproject

The model ID in --model-id is validated against the filename — if you accidentally pass a file from a different model, isaura will warn you before writing anything.

Reading outputs

Retrieve stored outputs for a set of inputs:

# explicit version
isaura read -i data/inputs.csv -m eos8a4x -v v1 -pn myproject -o data/outputs.csv

# omit --version to automatically use the latest stored version
isaura read -i data/inputs.csv -m eos8a4x -pn myproject -o data/outputs.csv

--project-name is required. --output is optional — without it results are printed but not saved.

Inspecting what is stored

Check which molecules from an input file are already cached:

isaura inspect --model_id eos8a4x -v v1 --access public -i data/inputs.csv -o reports/available.csv

Browse all models in a project:

isaura catalog -pn myproject           # local
isaura catalog -pn isaura-public -r    # remote

Publishing to the cloud

The cloud hosts two canonical buckets: isaura-public and isaura-private. Write to a local project first, persist it into the canonical bucket, then push to cloud.

Step 1 — write to your local project:

isaura write -i data/ersilia_output.csv -m eos8a4x -v v1 -pn myproject

Step 2 — persist into the canonical bucket:

isaura persist -m eos8a4x -v v1 -pn myproject

This routes molecules tagged public → isaura-public and private → isaura-private based on the project's access setting.

Step 3 — push to cloud:

isaura push -m eos8a4x -v v1 -pn isaura-public

Cloud credentials must be configured first with isaura configure --remote.

Pulling from the cloud

Download precalculations from the remote store into your local MinIO:

# explicit version
isaura pull -i data/inputs.csv -m eos8a4x -v v1 -pn isaura-public

# omit --version to automatically pull the latest stored version
isaura pull -i data/inputs.csv -m eos8a4x -pn isaura-public

Storage statistics

Generate a JSON inventory of all models in a bucket:

isaura stats -pn isaura-public -o ./reports
isaura stats -pn myproject --remote -o ./reports

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Configuration

Configuration is stored in ~/.isaura/.env and created automatically on first run. You can view or update it at any time with:

isaura configure                 # view current config
isaura configure --update        # update any value interactively
isaura configure --remote        # add cloud credentials

See the full list of available variables: CONFIGURATION →

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Docs

• 📘 How it works: here
• ⚙️ Configuration: here
• 🧰 CLI and API reference: here
• 🧪 Benchmark: here
• 🩹 Troubleshooting / recovery: here

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About the Ersilia Open Source Initiative

The Ersilia Open Source Initiative is a tech-nonprofit organization fueling sustainable research in the Global South. Ersilia's main asset is the Ersilia Model Hub, an open-source repository of AI/ML models for antimicrobial drug discovery.