Sebastian Lobentanzer

**Describe the bug** This page is not populated: https://biolink.github.io/biolink-model/docs/named_things.html

Hi @sierra-moxon, thanks for the great input yesterday! As you suggested, I will file a feature request for the data model supporting validation directly. I am not sure how exactly...

Hackathon: add `generic_ir_from_biocypher()` function to ingest TCR data

2

We will prepare a PR that generalises `datasets.vdjdb()` to ingest any immune receptor data that was preprocessed by BioCypher, to yield a generic AnnData object that can be flexibly updated...

For instance, looking for BRCA1, appending something like `&search=BRCA1` to the base URL should take the user to the same view that is achieved by searching `BRCA1` in the Genome-Spy...

Model link for Llama-3-instruct 70B is wrong

1

### Describe the bug Trying to use the builtin Llama-3-instruct 70B (gguf) from the Python client (`.launch_model()`) fails with this Traceback (excerpt): ``` Traceback (most recent call last): File "/Users/slobentanzer/miniforge3/envs/xinference/lib/python3.10/site-packages/huggingface_hub/utils/_errors.py",...

Meta-programming input modules for adapters (OntoWeaver)

1

Development by @jdreo in https://github.com/oncodash/oncodashkb

Add Pandas/Colab tutorial of real-world data (collectri)

1

Based on https://github.com/biocypher/collectri and the build script therein

Write some documentation about BioCypher's handling of identifiers

1

generic `id` field (uniqueness) and namespaces, etc.

CI: Python 3.9 not on MacOS latest any more, but 3.12 also fails

1

CI fails for the current 3.9-3.11 matrix, due to (https://github.com/biocypher/biocypher/actions/runs/8815890423) ``` The version '3.9' with architecture 'arm64' was not found for macOS 14.4.1. The list of all available versions can...

Quotes are a constant source of trouble in admin import, because most of the commonly used quotes are frequently found in free text annotations in the imported datasets. To avoid...