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SkillsMP ha recopilado 373 skills de synthetic-sciences/openscience. Abre una skill para revisar su origen y sus detalles.
synthetic-sciences/openscienceMostrando 40 de 373 skills recopiladas.
Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommendation reports (evidence-based guidelines with…
Idioma del texto original: inglés
Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries). Full support with templates,…
Idioma del texto original: inglés
Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
Idioma del texto original: inglés
Generate transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M. Use when you need spatial gene expression in log1p-CPM for 224x224 tiles at about 20x, want to query protein-coding genes by symbol instead of a fixed panel, or…
Idioma del texto original: inglés
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
Idioma del texto original: inglés
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
Idioma del texto original: inglés
Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences,…
Idioma del texto original: inglés
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
Idioma del texto original: inglés
Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.
Idioma del texto original: inglés
Retrieve ClinGen gene-disease validity assertions for a public gene or disease, and review source-linked public evidence and literature for one supported GRCh38 germline nuclear SNV or simple indel through Folklore Clinical Variant Interpretation MCP. Use…
Idioma del texto original: inglés
Predict regulatory features, gene structure, and expression directly from DNA sequence using Genomic Intelligence's hosted transformer DNA language models — no local GPU or model weights. Six tasks over a REST API and a hosted MCP server (keyless public…
Idioma del texto original: inglés
Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for interactive exploration, simple queries. For batch processing or advanced BLAST use biopython; for…
Idioma del texto original: inglés
Submit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab execution on Reconfigurable Automation Carts (RACs). Use when the user wants to run protein expression and purification (cell-free, E. coli,…
Idioma del texto original: inglés
Analyze and engineer protein glycosylation. Scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and access curated glycoengineering tools (NetOGlyc, GlycoShield, GlycoWorkbench). For glycoprotein engineering, therapeutic…
Idioma del texto original: inglés
Lightweight WSI tile extraction and preprocessing. Use for basic slide processing tissue detection, tile extraction, stain normalization for H&E images. Best for simple pipelines, dataset preparation, quick tile-based analysis. For advanced spatial…
Idioma del texto original: inglés
This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spatial, flow cytometry, etc.), tracking…
Idioma del texto original: inglés
Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.
Idioma del texto original: inglés
Comprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use this skill when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle…
Idioma del texto original: inglés
Build, run, and debug Nextflow data pipelines and nf-core workflows end to end. Use whenever the user mentions Nextflow, nf-core, .nf files, nextflow.config, DSL2, processes/channels/operators, samplesheets, or wants to run a community pipeline (e.g.…
Idioma del texto original: inglés
Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.
Idioma del texto original: inglés
Official Opentrons Protocol API for OT-2 and Flex robots. Use when writing protocols specifically for Opentrons hardware with full access to Protocol API v2 features. Best for production Opentrons protocols, official API compatibility. For multi-vendor…
Idioma del texto original: inglés
Operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs. Use this skill when the user needs to validate run inputs, generate pacsomatic-compliant samplesheets, prepare reproducible Nextflow launch artifacts, run locally or…
Idioma del texto original: inglés
Full-featured computational pathology toolkit. Use for advanced WSI analysis including multiplexed immunofluorescence (CODEX, Vectra), nucleus segmentation, tissue graph construction, and ML model training on pathology data. Supports 160+ slide formats. For…
Idioma del texto original: inglés
Query live pathogen genomic surveillance data through the GenSpectrum LAPIS API to find which viral lineages are circulating now, how fast they are growing, and what mutations they carry. Use whenever a question depends on the current state of a pathogen…
Idioma del texto original: inglés
Run pathway and gene-set enrichment analysis on gene lists or ranked gene data, then interpret the results. Use whenever the user has a set of genes (differentially expressed genes from PyDESeq2/Scanpy, CRISPR-screen hits, cluster marker genes, proteomics…
Idioma del texto original: inglés
Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and…
Idioma del texto original: inglés
High-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Overlap, nearest, merge, coverage, complement, subtract for BED/VCF/BAM/GFF intervals. Streaming, cloud-native, faster bioframe alternative.
Idioma del texto original: inglés
Integration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and materials; handle discussions and comments; organize…
Idioma del texto original: inglés
Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.
Idioma del texto original: inglés
Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying medical imaging data in DICOM format, extracting pixel data from medical images (CT, MRI, X-ray, ultrasound),…
Idioma del texto original: inglés
Comprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data. This skill should be used when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, drug…
Idioma del texto original: inglés
Vendor-agnostic lab automation framework. Use when controlling multiple equipment types (Hamilton, Tecan, Opentrons, plate readers, pumps) or needing unified programming across different vendors. Best for complex workflows, multi-vendor setups, simulation.…
Idioma del texto original: inglés
Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
Idioma del texto original: inglés
Multivariate severity assessment and humane endpoint prediction for laboratory animal studies using the RELSA (RELative Severity Assessment) score and ARIMA-based foRcast forecasting. Use when combining welfare readouts — body weight or weight loss, body…
Idioma del texto original: inglés
Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
Idioma del texto original: inglés
Comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival. Use this skill when working with censored survival data, performing time-to-event analysis, fitting Cox models, Random Survival Forests, Gradient Boosting…
Idioma del texto original: inglés
RNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajectory directions, compute latent time, and identify driver genes in single-cell RNA-seq data. Complements Scanpy/scVI-tools for trajectory…
Idioma del texto original: inglés
Deep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with uncertainty, or multi-modal integration (TOTALVI, MultiVI). Best for advanced modeling, batch effects,…
Idioma del texto original: inglés
Access a collection of open-source molecular design and structural biology tools on the Tamarind Bio platform, via its REST API or MCP server — no local GPUs required. Tamarind bundles popular open-source models for structure prediction (AlphaFold, Boltz,…
Idioma del texto original: inglés
Efficient storage and retrieval of genomic variant data using TileDB. Scalable VCF/BCF ingestion, incremental sample addition, compressed storage, parallel queries, and export capabilities for population genomics.
Idioma del texto original: inglés