Bulletin · UTC
Merged timeline: 188 items (blog publish time and listing createdAt in UTC). Page 2 of 4. For registry-only weekly slices, use /new.
### Scientific Brainstorming - name: "scientific-brainstorming" - description: "Creative research ideation and exploration. Use for open-ended brainstorming sessions, exploring interdisciplinary connections, challenging…
- Skillqiskit
### Qiskit - name: "qiskit" - description: "IBM quantum computing framework. Use when targeting IBM Quantum hardware, working with Qiskit Runtime for production workloads, or needing IBM optimization tools. Best for IBM…
- Skillrowan
### Rowan - name: "rowan" - description: "Rowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API. Use for pKa and macropKa prediction, conformer and tautomer ensembles, do…
- Skillpyzotero
### Pyzotero - name: "pyzotero" - description: "Interact with Zotero reference management libraries using the pyzotero Python client. Retrieve, create, update, and delete items, collections, tags, and attachments via th…
- Skillresearch-grants
### Research Grants - name: "research-grants" - description: "Write competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Agency-specific formatting, review criteria, budget preparation, broader impa…
- Skillresearch-lookup
### Research Lookup - name: "research-lookup" - description: "Look up current research information using parallel-cli search (primary, fast web search), the Parallel Chat API (deep research), or Perplexity sonar-pro-sea…
- Skillrdkit
### Rdkit - name: "rdkit" - description: "Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, re…
- Skillpytorch-lightning
### Pytorch Lightning - name: "pytorch-lightning" - description: "Deep learning framework (PyTorch Lightning / lightning package). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, imple…
- Skillpyhealth
### Pyhealth - name: "pyhealth" - description: "Build clinical/healthcare deep-learning pipelines with PyHealth — loading EHR/signal/imaging datasets (MIMIC-III/IV, eICU, OMOP, SleepEDF, ChestXray14, EHRShot), defining…
- Skillpysam
### Pysam - name: "pysam" - description: "Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines."
- Skillpydicom
### Pydicom - name: "pydicom" - description: "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 DICO…
- Skillnextflow
### Nextflow - name: "nextflow" - description: "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, process…
- Skillpytdc
### Pytdc - name: "pytdc" - description: "Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological predict…
- Skillpyopenms
### Pyopenms - name: "pyopenms" - description: "Complete mass spectrometry analysis platform. Use for proteomics workflows feature detection, peptide identification, protein quantification, and complex LC-MS/MS pipeline…
- Skillnetworkx
### Networkx - name: "networkx" - description: "Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python. Use when working with network/graph data structures, analyzing relati…
- Skillpeer-review
### Peer Review - name: "peer-review" - description: "Structured manuscript/grant review with checklist-based evaluation. Use when writing formal peer reviews with specific criteria methodology assessment, statistical v…
- Skillpptx-posters
### Pptx Posters - name: "pptx-posters" - description: "Create research posters using HTML/CSS that can be exported to PDF or PPTX. Use this skill ONLY when the user explicitly requests PowerPoint/PPTX poster format. Fo…
- Skillpylabrobot
### Pylabrobot - name: "pylabrobot" - description: "Vendor-agnostic lab automation framework. Use when controlling multiple equipment types (Hamilton, Tecan, Opentrons, plate readers, pumps) or needing unified programmi…
- Skillmolfeat
### Molfeat - name: "molfeat" - description: "Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML." - allowed…
- Skillopen-notebook
### Open Notebook - name: "open-notebook" - description: "Self-hosted, open-source alternative to Google NotebookLM for AI-powered research and document analysis. Use when organizing research materials into notebooks, i…
- Skillneurokit2
### Neurokit2 - name: "neurokit2" - description: "Comprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use this skill when processing cardi…
- Skillmedchem
### Medchem - name: "medchem" - description: "Medicinal chemistry filters for compound triage. Apply drug-likeness rules (Lipinski, Veber, CNS), structural alert catalogs (PAINS, NIBR, ChEMBL), complexity metrics, and t…
- Skillpufferlib
### Pufferlib - name: "pufferlib" - description: "High-performance reinforcement learning framework optimized for speed and scale. Use when you need fast parallel training, vectorized environments, multi-agent systems,…
- Skillpptx
### Pptx - name: "pptx" - description: "Use this skill any time a .pptx file is involved in any way — as input, output, or both. This includes: creating slide decks, pitch decks, or presentations; reading, parsing, or e…
- Skillpymoo
### Pymoo - name: "pymoo" - description: "Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems."…
- Skillmodal
### Modal - name: "modal" - description: "Modal is a serverless cloud platform for running Python on demand, including on-demand GPUs. Use when deploying or serving AI/ML models, running GPU-accelerated workloads (train…
- Skillparallel-web
### Parallel Web - name: "parallel-web" - description: "All-in-one web toolkit powered by parallel-cli, with a strong emphasis on academic and scientific sources. Use this skill whenever the user needs to search the web…
- Skillmolecular-dynamics
### Molecular Dynamics - name: "molecular-dynamics" - description: "Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minim…
- Skillpennylane
### Pennylane - name: "pennylane" - description: "Hardware-agnostic quantum ML framework with automatic differentiation. Use when training quantum circuits via gradients, building hybrid quantum-classical models, or nee…
- Skillpydeseq2
### Pydeseq2 - name: "pydeseq2" - description: "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."
- Skillomero-integration
### Omero Integration - name: "omero-integration" - description: "Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-con…
- Skillneuropixels-analysis
### Neuropixels Analysis - name: "neuropixels-analysis" - description: "Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen…
- Skilllamindb
### Lamindb - name: "lamindb" - description: "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 managin…
- Skilldeepchem
### Deepchem - name: "deepchem" - description: "Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurizati…
- Skillflowio
### Flowio - name: "flowio" - description: "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."
### Clinical Decision Support - name: "clinical-decision-support" - description: "Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient coho…
- Skillcobrapy
### Cobrapy - name: "cobrapy" - description: "Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis." - allowed-tools:…
### Get Available Resources - name: "get-available-resources" - description: "This skill should be used at the start of any computationally intensive scientific task to detect and report available system resources (CPU…
- Skillclinical-reports
### Clinical Reports - name: "clinical-reports" - description: "Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3…
- Skillmatchms
### Matchms - name: "matchms" - description: "Spectral similarity and compound identification for metabolomics. Use for comparing mass spectra, computing similarity scores (cosine, modified cosine), and identifying unkn…
### Exploratory Data Analysis - name: "exploratory-data-analysis" - description: "Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzi…
- Skillexa-search
### Exa Search - name: "exa-search" - description: "Web toolkit powered by Exa, tuned for scientific and technical content. Use this skill when the user needs to search the web or fetch/extract URL content. Covers: web…
- Skilldocx
### Docx - name: "docx" - description: "Use this skill whenever the user wants to create, read, edit, or manipulate Word documents (.docx files). Triggers include: any mention of 'Word doc', 'word document', '.docx', or…
- Skillgeopandas
### Geopandas - name: "geopandas" - description: "Python library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files. Use when working with geographic data for spatial analysis, g…
- Skilldatamol
### Datamol - name: "datamol" - description: "Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors,…
- Skillliteparse
### Liteparse - name: "liteparse" - description: "Local document and PDF parsing with spatial text and bounding boxes. Use for extracting text from PDFs, DOCX, Office files, and images; OCR on scans; layout-preserved JS…
- Skillmatplotlib
### Matplotlib - name: "matplotlib" - description: "Low-level plotting library for full customization. Use when you need fine-grained control over every plot element, creating novel plot types, or integrating with speci…
- Skillmatlab
### Matlab - name: "matlab" - description: "MATLAB and GNU Octave numerical computing for matrix operations, data analysis, visualization, and scientific computing. Use when writing MATLAB/Octave scripts for linear alge…
- Skilldnanexus-integration
### Dnanexus Integration - name: "dnanexus-integration" - description: "DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pi…
- Skillmarkitdown
### Markitdown - name: "markitdown" - description: "Convert files and office documents to Markdown. Supports PDF, DOCX, PPTX, XLSX, images (with OCR), audio (with transcription), HTML, CSV, JSON, XML, ZIP, YouTube URLs,…