Cancer Systems Immunology Lab
Official@carmonalab · Switzerland
Single-cell omics data science at the Department of Pathology of Immunology of the University of Geneva
Agent Skills by Cancer Systems Immunology Lab
Showing 11 vetted skills indexed across 1 GitHub repositories.
carmonalabdomain-modeling
Build and maintain project glossaries and architecture decision records during design discussions.
carmonalabpubmed-database
Search PubMed and fetch abstracts, full text, and cross-database links via NCBI E-utilities APIs.
carmonalabembl-ebi-ols
Query the EMBL-EBI Ontology Lookup Service API for biomedical ontology terms and hierarchies.
carmonalabliterature-search-arxiv
Search arXiv for papers and download PDFs, HTML, or LaTeX sources.
carmonalabliterature-search-europepmc
Search Europe PMC and download open-access full texts, PDFs, citations, and references.
carmonalabliterature-search-openalex
Query the OpenAlex scholarly database for papers, authors, institutions, and bibliometric data.
carmonalabworkflow-skill-creator
Distills completed user workflows into reusable agent skills with SKILL.md files.
carmonalabliterature-search-biorxiv
Search and fetch bioRxiv and medRxiv preprint metadata by DOI or date range.
carmonalabgrill-with-docs
Interrogates plans and designs while generating ADRs and glossary documentation.
carmonalabdurable-hpc-gate-ecoda
Orchestrates durable Slurm gate lifecycles for ECODA pipelines on the Yggdrasil HPC cluster.
carmonalabgrilling
Interviews users in structured rounds to stress-test plans and design decisions.
Frequently Asked Questions About Cancer Systems Immunology Lab
FAQPage SchemaWhat tasks can I accomplish with Carmona Lab's skills?▼
You can search PubMed, arXiv, Europe PMC, OpenAlex, bioRxiv, and medRxiv for papers, download full-text PDFs and XML, resolve DOIs, aggregate citation metrics like h-index, query 250+ biomedical ontologies via EMBL-EBI OLS, and link publications to gene, protein, and PubChem compound records.
Who are these skills designed for?▼
They target biomedical researchers, computational biologists, and single-cell omics data scientists, particularly those in cancer immunology. The domain-modeling, grilling, and HPC-gate skills also serve research engineers maintaining documented codebases and running workloads on the Yggdrasil cluster.
What external services and dependencies do the literature skills require?▼
The literature skills interface NCBI E-utilities, PMC BioC, the arXiv, Europe PMC, OpenAlex, and bioRxiv/medRxiv endpoints, so network access to those public scholarly services is required. The OLS skill queries the EMBL-EBI Ontology Lookup Service for terms, hierarchies, and autocomplete.
How do the planning and documentation skills work?▼
The grilling and grill-with-docs skills stress-test a plan or design through relentless questioning while producing ADRs and a glossary. The domain-modeling skill sharpens codebase terminology in a CONTEXT.md, and workflow-skill-creator distills a completed multi-step interaction into a reusable packaged skill.
Are there constraints when searching bioRxiv and medRxiv preprints?▼
Yes. Keyword filtering is performed locally, so date ranges must be narrow, one to four weeks, and combined with a category filter to prevent timeouts. Paper metadata can also be fetched directly by DOI, and browsing supports date-range, category, and keyword filters.