synthetic-sciences/openscience - الصفحة ٢

status

Show live session, plan, artifact, model, and workspace state. Use when the user invokes /status or asks for a concise progress and workspace summary.

لغة النص الأصلي: الإنجليزية

stop

Stop active work in the current session. Use when the user invokes /stop or asks to cancel the current turn, active compute jobs, session kernels, or all running session work.

لغة النص الأصلي: الإنجليزية

compare

Compare runs, artifacts, methods, models, or claims on a fair and explicit decision basis.

لغة النص الأصلي: الإنجليزية

export

Package results with provenance, reproduction instructions, declared gaps, and the requested output format.

لغة النص الأصلي: الإنجليزية

reproduce

Reproduce a claim, paper result, artifact, or run with exact inputs, environment, criteria, and evidence.

لغة النص الأصلي: الإنجليزية

review

Independently review code, results, claims, or an artifact and return prioritized, evidence-backed findings.

لغة النص الأصلي: الإنجليزية

sources

Audit sources, citations, and unsupported claims using a claim-level source ledger and primary evidence.

لغة النص الأصلي: الإنجليزية

verify

Run real checks for a claim, implementation, result, or artifact and report pass, fail, or not tested.

لغة النص الأصلي: الإنجليزية

scientific-problem-selection

This skill should be used when scientists need help with research problem selection, project ideation, troubleshooting stuck projects, or strategic scientific decisions. Use this skill when users ask to pitch a new research idea, work through a project…

لغة النص الأصلي: الإنجليزية

scholar-evaluation

Evaluate scholarly work with structured criteria for rigor, methodology, evidence, writing, and publication readiness.

لغة النص الأصلي: الإنجليزية

scanpy

Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and visualization. Best for exploratory scRNA-seq analysis with established workflows. For deep learning…

لغة النص الأصلي: الإنجليزية

ray-data

Scalable data processing for ML workloads. Streaming execution across CPU/GPU, supports Parquet/CSV/JSON/images. Integrates with Ray Train, PyTorch, TensorFlow. Scales from single machine to 100s of nodes. Use for batch inference, data preprocessing,…

لغة النص الأصلي: الإنجليزية

ray-train

Distributed training orchestration across clusters. Scales PyTorch/TensorFlow/HuggingFace from laptop to 1000s of nodes. Built-in hyperparameter tuning with Ray Tune, fault tolerance, elastic scaling. Use when training massive models across multiple machines…

لغة النص الأصلي: الإنجليزية

model-economics

Cost modeling and ROI analysis for specialized LLM development. Use when deciding whether to train a custom model, estimating total cost, or calculating break-even vs frontier APIs. Covers training costs, inference costs, and time-to-ROI projections.

لغة النص الأصلي: الإنجليزية

anndata

Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for…

لغة النص الأصلي: الإنجليزية

benchling-integration

Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.

لغة النص الأصلي: الإنجليزية

bioimage-analysis

Microscopy image analysis for cell biology. Cell segmentation (Cellpose, watershed), object tracking (trackpy), morphology quantification, colony counting, colocalization analysis, and cytoskeleton characterization. For pathology WSI use pathml; for flow…

لغة النص الأصلي: الإنجليزية

biopython

Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick…

لغة النص الأصلي: الإنجليزية

bioservices

Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database…

لغة النص الأصلي: الإنجليزية

cancer-genomics-analysis

Computational cancer genomics workflows. Somatic mutation detection and annotation, structural variation characterization, copy number analysis, tumor purity/ploidy estimation, NMF metagene extraction, and DNA damage response network analysis. For cancer…

لغة النص الأصلي: الإنجليزية

clinical-decision-support

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…

لغة النص الأصلي: الإنجليزية

clinical-imaging

Clinical and physiological imaging analysis. Diffusion MRI ADC maps, micro-CT bone morphometry, hemodynamic parameter analysis, circadian rhythm cosinor analysis, ciliary beat frequency (FFT), and tissue deformation optical flow. For DICOM file handling use…

لغة النص الأصلي: الإنجليزية

clinical-reports

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,…

لغة النص الأصلي: الإنجليزية

cobrapy

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

لغة النص الأصلي: الإنجليزية

curated-bio-datasets

Guide to accessing curated biological datasets for computational biology. COSMIC cancer data, GTEx expression, GWAS catalog, GeneBass exome variants, BioGRID interactions, MSigDB gene sets, DisGeNET disease-gene associations, and GO ontology. For specific…

لغة النص الأصلي: الإنجليزية

deeptools

NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.

لغة النص الأصلي: الإنجليزية

dnanexus-integration

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.

لغة النص الأصلي: الإنجليزية

esm

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,…

لغة النص الأصلي: الإنجليزية

etetoolkit

Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.

لغة النص الأصلي: الإنجليزية

flow-cytometry-analysis

Complete flow cytometry analysis pipeline. FCS file handling, compensation, manual/automated gating, immunophenotyping, CFSE proliferation analysis, cell cycle analysis (Dean-Jett-Fox), and apoptosis assays. Extends flowio with analytical workflows. For raw…

لغة النص الأصلي: الإنجليزية

flowio

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.

لغة النص الأصلي: الإنجليزية

gget

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…

لغة النص الأصلي: الإنجليزية

glycobiology

Glycosylation site prediction and glycobiology analysis. N-glycosylation motif finding, O-glycosylation hotspot prediction, glycan structure resources. Lightweight, pure Python. For protein function queries use uniprot-database; for structure analysis use…

لغة النص الأصلي: الإنجليزية

histolab

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…

لغة النص الأصلي: الإنجليزية

immunology-assays

Computational analysis of immunology experimental data. ATAC-seq differential accessibility, immune cell tracking from microscopy, ELISA data processing with 4-parameter logistic fitting, immunohistochemistry quantification, antibody titer analysis, and cell…

لغة النص الأصلي: الإنجليزية

lamindb

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…

لغة النص الأصلي: الإنجليزية

latchbio-integration

Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.

لغة النص الأصلي: الإنجليزية

microbial-dynamics

Microbial population dynamics modeling and analysis. Bacterial growth curve fitting (logistic, Gompertz, Baranyi), Lotka-Volterra community dynamics, Gillespie stochastic simulation, biofilm quantification, CFU enumeration, and genome annotation. For…

لغة النص الأصلي: الإنجليزية

molecular-cloning

Molecular cloning simulation and design. PCR amplicon prediction, restriction enzyme digestion, Golden Gate and Gibson assembly simulation, primer design, CRISPR sgRNA design, and plasmid annotation. For protein-level sequence analysis use biopython or esm;…

لغة النص الأصلي: الإنجليزية

neurokit2

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…

لغة النص الأصلي: الإنجليزية