Results for “genbi”

Query NCBI Gene via the E-utilities and Datasets APIs, searching by gene symbol or Gene ID and retrieving gene information (RefSeqs, GO terms, genomic locations, associated phenotypes) including batch lookups. Use when resolving gene symbols to IDs, annotating gene lists, or pulling functional and positional gene metadata for downstream analysis. Part of the AlterLab Academic Skills suite.

Access Google's most advanced AI models using the Gemini API in Agent Platform (formerly Vertex AI) with SDK installation, authentication, and code examples.

Predicts enhancer activity in DNA sequences using the hosted Genomic Intelligence G0 DeepSTARR model, returning per-window activity scores.

Builds or debugs Google Gemini features using @google/generative-ai, covering generateContent, function calling, grounding, multimodal input, and streaming, with guidance for editing src/lib/ai/clients/google.ts.

Build applications with Gemini API hosted models, including multimodal content, function calling, and structured outputs, using the latest SDKs and model specifications.

Use when working with GenBank format files and need to create reference indexers for sequence data retrieval or processing within the Entrez Direct toolkit.

Access NCBI GEO (Gene Expression Omnibus) for gene expression and functional genomics data — search and download microarray and RNA-seq datasets by GSE, GSM, GPL, or GDS accession and retrieve SOFT, MINiML, and series matrix files. Use when locating public expression datasets, fetching processed expression matrices, downloading a study's supplementary files, or sourcing per-study transcriptomics data for differential-expression analysis. For raw FASTQ sequencing reads by SRA/ENA run accession use alterlab-ena; for reference tissue-expression baselines (median TPM across human tissues) use alterlab-gtex; for cancer cohort somatic mutations and copy-number use alterlab-cbioportal. Part of the AlterLab Academic Skills suite.

Guides usage of the Gemini API on Agent Platform with the Google Gen AI SDK, covering SDK usage (Python, JS/TS, Go, Java, C#), capabilities like multimodal inputs, tools, media generation, caching, batch prediction, and Live API.

Authenticate, initialize, and use the stateful Gemini Interactions API for multi-turn conversations, streaming, structured output, and function calling on the Gemini Enterprise Agent Platform.

Call the Gemini API for text generation, chat, multimodal understanding, image/video/audio generation, streaming, function calling, structured output, and managed agents using the Interactions API in Python and TypeScript.

Authenticates and connects to Google Cloud Agent Platform for inference with Gemini and third-party OpenMaaS models (Llama, DeepSeek, Qwen). Generates code for multiple SDKs, configures endpoints, and troubleshoots common errors.

Generate images using AI from OpenAI or Google Gemini, with support for textures, icons, sprites, and visual assets.

Generate and edit videos using the Gemini Omni Flash model: text-to-video, image-to-video, video editing, and turn-by-turn refinement via the official google-genai SDK.

Build applications with Gemini API hosted models, including Gemini and Gemma 4, using multimodal content, function calling, structured outputs, and current SDKs for Python, JavaScript, Go, and Java.

Fine-tune open models or Gemini models using Agent Platform infrastructure, from environment setup through data preparation, job configuration, monitoring, and deployment.

Predicts gene and transcript structure from a DNA sequence using the hosted Genomic Intelligence API, producing a report and JSON output.

Use this skill when building applications with Gemini models, Gemini API, working with multimodal content (text, images, audio, video), implementing function calling, using structured outputs, or needing current model specifications. Covers SDK usage (google-genai for Python, @google/genai for JavaScript/TypeScript, com.google.genai:google-genai for Java, google.golang.org/genai for Go), model selection, and API capabilities.

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.

Predicts tissue or cell-type gene expression (log TPM and TPM) from a TSS-centered DNA sequence using the hosted Genomic Intelligence G0 Expression model, conditioned on a free-text cell-type description.

Writes Python and TypeScript code that calls the Gemini Interactions API for text generation, chat, multimodal understanding, image generation, streaming, research, function calling, and structured output, including migration from the legacy generateContent API.

Use Geniml for audited local genomic-interval workflows: validate BED and universe contracts, plan Region2Vec or scEmbed runs, inspect model/tokenizer compatibility, and assess consensus universes.

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.

Quickly query genomic reference databases for Ensembl IDs, gene metadata, sequences, BLAST searches, and enrichment analysis using the gget CLI or Python package.

Configure Gemini and Codex CLI tools with Cloudflare AI Gateway endpoints and MCP servers.

Query Belgian railway (NMBS/SNCB) schedules via the irail CLI.

Automates genome-wide association studies from genotype files to publication-ready results, running PLINK2 QC and REGENIE regression with Manhattan and QQ plots.

Generate Image (gemini / openai backends)

Build applications with the Google Gemini API, covering chat completions, multimodal inputs, function calling, streaming, and grounding with Google Search.

Builds real-time, bidirectional streaming applications with the Gemini Live API, covering WebSocket audio/video/text streaming, VAD, function calling, session management, ephemeral tokens, and live translation across Python and JavaScript SDKs.

Predicts chromatin state across 919 tracks (histone marks, DNase, TF binding) for DNA sequences via the hosted Genomic Intelligence API, producing a report and JSON results.

Detect promoter regions in DNA sequences by calling the Genomic Intelligence G0 transformer (GENA-LM BERT Large) hosted API. Returns per-window promoter probabilities and called regions as a report and JSON, from a single FASTA input.

Downloads genomes, genes, virus sequences, and taxonomy data from NCBI using the datasets and dataformat CLI tools.

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.

Develop AI-powered applications using Genkit in Node.js/TypeScript. Use when the user asks about Genkit, AI agents, flows, or tools in JavaScript/TypeScript, or when encountering Genkit errors, validation issues, type errors, or API problems.

Unified multimedia generation API for images, videos, and text-to-speech, replacing separate providers for a single workflow.