Menü
Strategic scientific problem selection, project ideation, and troubleshooting based on the Fischbach & Walsh framework.
Creating algorithmic art using p5.js with seeded randomness and interactive parameter exploration. Use this when users request creating art using code, generative art, algorithmic art, flow fields, or particle systems. Create original algorithmic art rather than copying existing artists' work to avoid copyright violations.
Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS systems, data lakes, or downstream analysis. Supports auto-detection of instrument types. Outputs include full ASM JSON, flattened CSV for easy import, and exportable Python code for data engineers. Common triggers include converting instrument files, standardizing lab data, preparing data for upload to LIMS/ELN systems, or generating parser code for production pipelines.
Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core, Nextflow, FASTQ analysis, variant calling, gene expression, differential expression, GEO reanalysis, GSE/GSM/SRR accessions, or samplesheet creation.
Deep learning for single-cell analysis using scvi-tools and scverse ecosystem. This skill should be used when users need (1) data integration and batch correction with scVI/scANVI, (2) ATAC-seq analysis with PeakVI, (3) CITE-seq multi-modal analysis with totalVI, (4) multiome RNA+ATAC analysis with MultiVI, (5) spatial transcriptomics deconvolution with DestVI, (6) label transfer and reference mapping, (7) RNA velocity with veloVI, or (8) QC analysis of single-cell RNA-seq data. Triggers include scVI, scANVI, totalVI, QC, quality control, batch correction, integration, multi-modal.
A conversational framework for systematic scientific problem selection, project ideation, troubleshooting, and strategic decision making.
You MUST use this before any creative work (features, products, content, strategy, systems, or behavior changes). Start by classifying what we’re brainstorming, then run thorough one-question-at-a-time discovery, propose 2–3 approaches, and converge on a validated plan/spec.
| name | bio-research-strategy |
| description | Strategic scientific problem selection, project ideation, and troubleshooting based on the Fischbach & Walsh framework. |
A conversational framework for systematic scientific problem selection based on Fischbach & Walsh's "Problem choice and decision trees in science and engineering" (Cell, 2024).
Present users with three entry points:
1) Pitch an idea for a new project — to work it up together
2) Share a problem in a current project — to troubleshoot together
3) Ask a strategic question — to navigate the decision tree together
This conversational entry meets scientists where they are and establishes a collaborative tone.
Ask: "Tell me the short version of your idea (1-2 sentences)."
After the user shares their idea, return a quick summary (no more than one paragraph) demonstrating understanding. Note the general area of research and rephrase the idea in a way that highlights its kernel—showing alignment and readiness to dive into details.
Then ask for more detail: "Now give me a bit more detail. You might include, however briefly or even say where you are unsure:
From there, guide the user through the early stages of problem selection and evaluation:
I can access detailed guidance in the references/ folder of this skill.
Ask: "Tell me a short version of your problem (1-2 sentences or whatever is easy)."
After the user shares their problem, return a quick summary (no more than one paragraph) demonstrating understanding. Note the context of the project where the problem occurred and rephrase the problem—highlighting its core essence—so the user knows the situation is understood. Also raise additional questions that seem important to discuss.
Then ask: "Now give me a bit more detail. You might include, however briefly:
From there, guide the user through troubleshooting and decision tree navigation:
Always include workarounds that might be useful whether or not the problem can be fixed easily.
I can access detailed guidance in the references/ folder of this skill.
Ask: "Tell me the short version of your question (1-2 sentences)."
After the user shares their question, return a quick summary (no more than one paragraph) demonstrating understanding. Note the broader context and rephrase the question—highlighting its crux—to confirm alignment with their thinking.
Then ask: "Now give me a bit more detail. You might include, however briefly:
From there, draw on the specific modules from the problem choice framework most appropriate to the question:
See the complete reference materials in the references/ folder.
