Getting Started — ABG Compute Environment¶
Welcome to the ABG compute platform on ironGate. This notebook walks you through the pre-installed tools and how to install additional packages.
Observers: You are viewing a read-only preview. Compute users log in to JupyterHub and use the ABG Bioinfo (Python 3.12) kernel for full access.
What's pre-installed¶
The bioinfo environment ships with 300+ packages including core data science and bioinformatics tools. Run the cell below to see them all.
| Package | Version |
|---|---|
| numpy | 2.4.4 |
| pandas | 3.0.2 |
| scipy | 1.17.1 |
| matplotlib | 3.10.9 |
| seaborn | 0.13.2 |
| statsmodels | 0.14.6 |
| scikit-learn | not in this env |
| biopython | not in this env |
| pysam | not in this env |
Compute users see 300+ packages via !pip list in the bioinfo kernel.
Installing additional packages¶
Need a package that isn't pre-installed? Just use %pip install:
%pip install scanpy
This installs into your personal environment (~/.venv/bioinfo/) without
affecting other users. Packages come from a local cache, so installs are
fast and don't need internet access.
After installing, restart the kernel (Kernel menu → Restart Kernel) and
then import the package as usual.
Package not available?¶
If %pip install says it can't find a package, it hasn't been added to
the local cache yet. Ask an admin to add it:
# Admin runs this on irongate (has internet access):
bash deploy/wheelhouse_sync.sh add <package-name>
Once added, every compute user can install it immediately.
Available kernels¶
| Kernel | Language | Use for |
|---|---|---|
| ABG Bioinfo (Python 3.12) | Python | Data science, bioinformatics, ML |
| ABG R Bioinfo | R | Statistical analysis, DESeq2, Bioconductor |
Switch kernels from the top-right menu or Kernel → Change Kernel.
Your workspace¶
| Path | What | Writable? |
|---|---|---|
~/notebooks/ |
Your notebooks | Yes |
~/results/ |
Your output files | Yes |
~/notebooks/shared/ |
Shared ABG workspace | Read-only |
~/notebooks/shared/commons/ |
Community notebooks (like this one) | Read-only |
~/notebooks/shared/showcase/ |
Voila dashboards | Read-only |
| Tier | observer (public preview) |
| Home | /home/voila |
| Python | /usr/bin/python3 |