Results for “implant-generation”

Simulates meiotic recombination to produce offspring genomes from parent pairs, modeling Mendelian segregation, de novo mutation, sex determination, trait inference, and clinical evaluation against a disease registry.

Casting personas: rapid generation from diverse inputs, registry-based persistence and lifecycle, data-driven evolution, inter-agent sync. Not for UI walkthroughs (Echo) or user research (Field).

Machine learning on genomic interval data (BED files) with the geniml Python package — region embeddings (Region2Vec), joint region+metadata embeddings (BEDspace/StarSpace), single-cell ATAC-seq embeddings (scEmbed), consensus peak sets / universes (build-universe), tokenization, BEDshift randomization, and BBClient/BEDbase caching. Use when training or using region/cell embeddings, clustering scATAC-seq, building a tokenization universe from BED collections, or any ML/feature-learning task over genomic regions. NOT for plain interval arithmetic (overlap/intersect/merge counts) — that is gtars, not geniml. Part of the AlterLab Academic Skills suite.

Generates synthetic brain MRI volumes using NVIDIA's NV-Generate-CTMR workflow, with configurable modality and random seed.

Designs and automates identity governance lifecycle processes including joiner-mover-leaver workflows, role mining, access requests, periodic recertification, and orphaned account remediation using IGA platforms.

Spiral inductors, interdigital capacitors, baluns, resonators, phase shifters for impedance matching, DC blocking, and bias tees. TRIGGER: user asks to design or create a spiral inductor, interdigital capacitor, balun, resonator, phase shifter, or other passive RF component. Invoke BEFORE writing code — class names and property patterns are non-obvious. SKIP: filter design (use matlab-design-pcb-filter), coupler/splitter design (use matlab-design-pcb-coupler), transmission line design (use matlab-design-pcb-transmission-line), EM analysis (use matlab-analyze-em), material setup only (use matlab-manage-pcb-material).

Builds or modifies a RAG pipeline with intent-based routing, vector store search, citation rendering, and book fidelity enforcement.

Expert en biotechnologies avancées (bioinformatics, genomics, CRISPR, drug discovery, DZ research)

Infer gene regulatory networks (GRNs) from expression matrices using arboreto's scalable GRNBoost2 and GENIE3 tree-ensemble algorithms with Dask-distributed computation. Use when analyzing bulk or single-cell RNA-seq transcriptomics to map transcription-factor-to-target-gene regulatory interactions, build adjacency networks, or run the GRN-inference step of a SCENIC pipeline on large datasets. Part of the AlterLab Academic Skills suite.

Generate natural AI voices, text-to-speech, and voice synthesis using the inference.sh CLI with models like Inworld TTS, ElevenLabs, and Kokoro TTS for voiceovers, audiobooks, podcasts, and more.

Apply the scGPT single-cell foundation model (Cui 2024) to annotate and embed cells — zero-shot and fine-tuned cell-type annotation, gene/cell embeddings, batch integration, and gene-regulatory / perturbation inference from AnnData. Use when annotating cell types with a pretrained foundation model, generating scGPT embeddings, integrating batches with a transformer, or running zero-shot single-cell inference on an h5ad. For probabilistic latent models (scVI/scANVI) prefer alterlab-scvi-tools; for the standard QC→cluster→UMAP→DE pipeline prefer alterlab-scanpy; for the AnnData data structure itself prefer alterlab-anndata; for protein language models prefer alterlab-esm. Part of the AlterLab Academic Skills suite.

Generates structured VGL JSON for Bria FIBO models, giving deterministic control over objects, lighting, camera, composition, and style instead of natural language prompts.

Generate a structured specification document before writing implementation code, validating scope, drafting specs, and registering them in the project.

Seed minimal agent harness v0 — manifest, eval checks stub, governance. AUTO-INVOKED after project-setup or retroactive-project-setup when docs/harness/manifest.json is missing. Also triggers on: generate harness, scaffold agents, agent bootstrap, first time agents in this repo, new project agent setup, set up agent harness, agent onboarding files, missing agent configuration, agent instructions setup, make agents read project rules, agent reliability setup, agents not configured. Pairs with project-setup. Evolution is harness-evolution.

NIH grant research skill for clinical researchers. Grill-me intake (research idea + career stage + preliminary data + environment + submission posture + known institute targets) locks down the funding strategy before any search runs. Runs a 5-facet Consensus positioning analysis (with draft Significance/Innovation language), maps the research to the right NIH institutes and study sections via RePORTER, finds NOSIs and funded overlap, and produces an editable Word document (.docx) with budget/scope-aware mechanism recommendations, submission timelines, and a mandatory program officer recommendation. Use when the user asks about research funding or makes any grant-related request (e.g., 'grants for [topic]', 'find grants for my research idea', 'what grants match my research', 'help me find NIH funding', 'grant opportunities for my research'). NIH-only scope — non-NIH funders (PCORI, DOD CDMRP, VA, foundations) are out of scope and flagged at intake.

Formulate testable hypotheses from observations, design experiments, and generate predictions using a structured scientific method framework.

Turn a pipeline target into a demand-generation plan that actually maps to the number. The ICP worth spending on, the offers by funnel stage, the channel mix that reaches them, the content that earns attention, and the pipeline math worked backward from the goal so you know if the plan can even hit it. Built for B2B marketing teams, customizable to your funnel and your channels. Trigger on "build a demand gen plan", "how do we hit our pipeline number", "what's our channel mix", "plan our content", "work the funnel math backward", or any demand-generation planning question.

Runs high-performance genomic interval analysis with gtars (databio), a Rust toolkit with Python bindings — the performance-critical backend for the geniml ML library. Use when computing overlaps/jaccard/coverage between BED region sets, indexing intervals with IGD, generating uniwig accumulation/coverage tracks, tokenizing genomic regions for ML, splitting single-cell fragments into pseudobulks, or computing GA4GH refget sequence digests. NOT for training region embeddings (use alterlab-geniml) or non-genomic spatial joins (use alterlab-geopandas). Part of the AlterLab Academic Skills suite.

Query cBioPortal via its keyless REST API for cancer genomics across TCGA, GENIE, MSK-IMPACT and hundreds of studies — somatic mutations, copy-number alterations (GISTIC), mRNA/protein expression, structural variants, and patient-level clinical/survival data. Use when asked how often a gene is mutated/amplified/deleted in a tumor type, to profile oncogenes or tumor suppressors across cancers (pan-cancer alteration frequency), to pull patient-level mutations joined to OS/clinical outcomes, or to validate a cancer target from cohort genomics. For germline variant pathogenicity use alterlab-clinvar; for mutational-signature (SBS) decomposition use alterlab-cosmic; for CRISPR/RNAi gene-dependency use alterlab-depmap; for aggregated target-disease evidence use alterlab-opentargets. Part of the AlterLab Academic Skills suite.

Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.

Generates synthetic body MRI volumes using NVIDIA's NV-Generate-CTMR rflow-mr model. Wraps the upstream diffusion inference pipeline with config staging, output validation, and NIfTI volume summarization.

Generate structured, machine-readable implementation plans for features, refactoring, upgrades, or infrastructure changes.

Generates synthetic CT volumes and masks using NVIDIA's rectified-flow pipeline for medical imaging research.

Finetunes the NV-Generate-CTMR MR-brain diffusion UNet from user-supplied NIfTI training volumes using a wrapper that stages configs and delegates to upstream scripts.

Finetune the NV-Generate-CTMR MAISI VAE/autoencoder on user-supplied CT or MRI NIfTI volumes using a staged config and datalist workflow.

Use this skill when the user requests to generate, create, or imagine videos. Supports structured prompts and reference image for guided generation.

This skill identifies adult childhood cancer survivors with isolated growth hormone deficiency and prior hypothalamic‑pituitary axis radiation exposure who require retesting to confirm persistence of GHD. Triggers include clinician questions such as “Should I retest for GHD in this adult survivor with childhood GHD and radiation history?” or “Is repeat GHD evaluation indicated in this patient?”

Infer gene regulatory networks from gene expression data using scalable algorithms (GRNBoost2, GENIE3) with support for distributed computation.

State-of-the-art text-to-image generation with Stable Diffusion models via HuggingFace Diffusers. Use when generating images from text prompts, performing image-to-image translation, inpainting, or building custom diffusion pipelines.

Gated PRD generation — interrogates problem, user, and metric before drafting; refuses to draft on unknowns. Usage: /prd <feature-or-problem>

Diagnose monogenic and syndromic obesity in children and adolescents using a structured step-by-step algorithm. Use this skill whenever a clinician suspects a genetic cause of obesity, asks about leptin deficiency, MC4R mutation, POMC deficiency, PCSK1 deficiency, leptin receptor deficiency, Bardet-Biedl syndrome, Prader-Willi syndrome, Alström syndrome, or any case of early-onset severe obesity with hyperphagia. Also trigger for questions about targeted pharmacotherapy including setmelanotide or metreleptin, or when to order a genomic obesity panel. Cross-references the NHS Genomic Test Finder skill to surface the relevant R-code once a diagnosis is reached.

Guarantee valid JSON/XML/code structure during generation, use Pydantic models for type-safe outputs, support local models (Transformers, vLLM), and maximize inference speed with Outlines - dottxt.ai's structured generation library

Generate and edit images using OpenAI's GPT-Image-2 model via the inference.sh CLI, supporting text-to-image, image editing, inpainting, and batch generation.

Team-Wiki Ingest

Configure Hilt dependency injection with proper scoping, modules, and constructor injection in Android. Use when changing the production Hilt graph; defer test overrides, Room wiring, navigation-specific scopes, and generic DI explanations to their specific skills.