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SkillsMP hat 207 Skills aus jaechang-hits/SciAgent-Skills gesammelt. Öffne einen Skill, um Quelle und Details zu prüfen.
jaechang-hits/SciAgent-SkillsEs werden 40 von 207 gesammelten Skills angezeigt.
Symbolic math in Python: exact algebra, calculus (derivatives, integrals, limits), equation solving, symbolic matrices, ODEs, code gen (lambdify, C/Fortran). Use for exact symbolic results. For numerical use numpy/scipy; for stats use statsmodels.
Quellsprache: Englisch
PyTorch Geometric (PyG) for graph neural networks: node/graph classification, link prediction with GCN, GAT, GraphSAGE, GIN. Message passing, mini-batches, heterogeneous graphs, neighbor sampling, explainability. Supports molecules (QM9, MoleculeNet),…
Quellsprache: Englisch
HuggingFace Transformers with biomedical LMs (BioBERT, PubMedBERT, BioGPT, BioMedLM) for scientific NLP: NER (genes, diseases, chemicals), relation extraction, QA, text classification, abstract summarization. Covers loading, biomedical tokenization, inference…
Quellsprache: Englisch
UMAP dimensionality reduction for visualization, clustering prep, and feature engineering. Fast nonlinear manifold learning preserving local and global structure. Standard UMAP (fit/transform, sklearn-compatible), supervised/semi-supervised, Parametric UMAP…
Quellsprache: Englisch
Access USPTO patent data via PatentsView REST API and Google Patents Public Data (BigQuery). Search by inventor, assignee, CPC, or keywords; download metadata and claims; analyze portfolios; track tech trends. For IP landscape analysis, competitor monitoring,…
Quellsprache: Englisch
Out-of-core DataFrame for billion-row data via lazy evaluation and memory-mapped files. Use when data exceeds RAM (10 GB–TB) for fast aggregation, filtering, virtual columns, and visualization without loading. Supports HDF5, Arrow, Parquet, CSV with cloud…
Quellsprache: Englisch
Cancer Research (AACR) figures: resolution (300-1200 DPI), formats (EPS/TIFF/AI), hierarchical panel labels (Ai, Aii, Bi), figure/table limits, legend requirements with replicate counts.
Quellsprache: Englisch
Cell (Cell Press) figure preparation: resolution (300-1000 DPI), formats (TIFF/PDF), RGB color, Avenir/Arial fonts, uppercase panel labels, strict image manipulation policies.
Quellsprache: Englisch
Selecting a reference manager and applying citation styles. Compares Zotero, Mendeley, EndNote, Paperpile; covers APA/Vancouver/ACS/Nature styles, DOI management, citation tracking, and Word/Google Docs/LaTeX integration. Use when setting up a reference…
Quellsprache: Englisch
eLife figure preparation: file formats (TIFF/EPS/PDF), striking image requirements (1800x900 px), figure supplement naming, and image screening policy treating selective enhancement as misconduct.
Quellsprache: Englisch
Universal QA checklist for generated scientific plots: overlapping labels, clipped text, missing axes/legends, overcrowded data, and cross-journal resolution/format guidance.
Quellsprache: Englisch
The Lancet figure preparation: resolution (300+ DPI at 120%), preferred editable formats (PowerPoint/Word/SVG), column widths (75/154 mm), Times New Roman, in-house redraw policy.
Quellsprache: Englisch
Conducting systematic, scoping, and narrative literature reviews. Covers PRISMA/PRISMA-ScR protocols, search strategy (Boolean, MeSH), database selection (PubMed, Scopus, Web of Science, Embase), screening, data extraction, evidence synthesis (narrative,…
Quellsprache: Englisch
Nature figure preparation: resolution (300+ DPI), formats (AI/EPS/TIFF), RGB color, Helvetica/Arial fonts, lowercase panel labels, image integrity requirements.
Quellsprache: Englisch
NEJM figure preparation: resolution (300-1200 DPI), editable vector formats (AI/EPS/SVG), in-house medical illustration policy, and strict image integrity requirements.
Quellsprache: Englisch
Structured peer review of manuscripts and grants. 7-stage evaluation: initial assessment, section review, statistical rigor, reproducibility, figure integrity, ethics, writing. Covers CONSORT/STROBE/PRISMA and report structure. For evidence quality see…
Quellsprache: Englisch
PNAS figure preparation: resolution (300-1000 PPI), formats (TIFF/EPS/PDF), strict RGB-only color, Arial/Helvetica fonts, italicized uppercase panel labels, automated image screening.
Quellsprache: Englisch
Science (AAAS) figure preparation: resolution (150-300+ DPI), formats (PDF/EPS/TIFF), RGB color, Myriad/Helvetica fonts, strict image manipulation policies including gamma adjustment disclosure.
Quellsprache: Englisch
Structured ideation methods: SCAMPER, Six Thinking Hats, Morphological Analysis, TRIZ, Biomimicry, plus more. Decision framework for picking methods by challenge type (stuck, improving, systematic exploration, contradiction). Use when generating research…
Quellsprache: Englisch
Evaluating scientific evidence and claims. Covers study design hierarchy (RCT to expert opinion), effect sizes (OR, RR, NNT, Cohen's d), confounding, p-value vs clinical significance, GRADE quality assessment, reproducibility, and bias types (selection,…
Quellsprache: Englisch
Designing scientific schematics, diagrams, and graphical abstracts. Covers tool selection (BioRender, Inkscape, Affinity, PowerPoint), design principles for pathway diagrams, mechanism schematics, experimental workflows, and journal graphical abstracts.…
Quellsprache: Englisch
Access AlphaFold DB's 200M+ predicted structures by UniProt ID. Download PDB/mmCIF, analyze pLDDT/PAE, bulk-fetch proteomes via Google Cloud. For experimental structures use PDB; for prediction use ColabFold or ESMFold.
Quellsprache: Englisch
Molecular docking with AutoDock Vina (Python API). Receptor/ligand prep (Meeko + RDKit), grid box, docking, pose and binding energy analysis, and batch virtual screening.
Quellsprache: Englisch
Query ClinicalTrials.gov API v2 for trial data. Search by condition, drug/intervention, location, sponsor, or phase; fetch details by NCT ID; filter by status; paginate; export CSV. For clinical research, patient matching, and trial portfolio analysis.
Quellsprache: Englisch
Query FDA drug labels (DailyMed) via REST API. Search structured product labels (SPLs) by name, NDC, set ID, or RxCUI; get indications, dosage, warnings, adverse reactions, packaging. No auth. For adverse events use fda-database; for DDIs use ddinter-database.
Quellsprache: Englisch
Pythonic RDKit wrapper with sensible defaults for drug discovery. SMILES parsing, standardization, descriptors, fingerprints, similarity, clustering, diversity selection, scaffold analysis, BRICS/RECAP fragmentation, 3D conformers, and visualization. Returns…
Quellsprache: Englisch
Query DDInter drug-drug interactions via REST API (1.7M+ interactions, 2,400+ drugs). Search by drug name/ID for severity (major/moderate/minor), mechanisms, and clinical recommendations. No auth. For FDA labeling use dailymed-database; for pharmacogenomics…
Quellsprache: Englisch
Deep learning for drug discovery. 60+ models (GCN, GAT, AttentiveFP, MPNN, ChemBERTa, GROVER), 50+ featurizers, MoleculeNet benchmarks, HPO, transfer learning. Unified load-featurize-split-train-evaluate API. For fingerprints use rdkit-cheminformatics; for…
Quellsprache: Englisch
Diffusion-based docking that predicts protein-ligand poses without a predefined site. Use for blind docking, when traditional docking fails, or exploring multiple binding modes. Pipeline: prep protein (PDB) and ligand (SMILES/SDF), run inference, analyze…
Quellsprache: Englisch
Parse local DrugBank XML for drug info, interactions, targets, and properties. Search by ID/name/CAS, extract DDIs with severity, map targets/enzymes/transporters, compute SMILES similarity. Primary via local XML; REST API rate-limited (3k/month dev). For…
Quellsprache: Englisch
Query openFDA REST API for adverse events (FAERS), labeling, product info, recalls, enforcement. Search by drug name, ingredient, MedDRA, or NDC. 1k req/day no key; 120k with free key. For trials use clinicaltrials-database-search; for structures use…
Quellsprache: Englisch
Analyze MD trajectories from GROMACS, AMBER, NAMD, CHARMM, LAMMPS. Reads topology/trajectory into Universe objects; supports RMSD, RMSF, radius of gyration, contact maps, H-bonds, PCA, and custom distance/angle calculations. Use for post-simulation structural…
Quellsprache: Englisch
Medicinal chemistry filters for compound triage. Drug-likeness rules (Lipinski Ro5, Veber, Oprea, CNS, leadlike, REOS, Golden Triangle, Ro3), structural alerts (PAINS, NIBR, Lilly Demerits), chemical group detectors, complexity metrics, and filter composition…
Quellsprache: Englisch
Therapeutics Data Commons (TDC) AI-ready drug discovery datasets. Curated ADME, toxicity, DTI, DDI with scaffold/cold splits, standardized metrics, molecular oracles, and ADMET benchmarks for therapeutic ML and property prediction. For chemical database…
Quellsprache: Englisch
Cheminformatics toolkit for molecular analysis and virtual screening: SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints (Morgan/ECFP, MACCS), Tanimoto similarity, SMARTS substructure filtering, Lipinski drug-likeness, reaction enumeration, 2D/3D…
Quellsprache: Englisch
Cloud quantum chemistry platform with Python SDK. Run geometry optimization, conformer generation, torsional scans, and energy minimization (DFT/semiempirical), and retrieve properties (dipole, partial charges, frontier orbitals) — no local QC software or HPC…
Quellsprache: Englisch
PyTorch-based ML platform for drug discovery: graph molecular representation learning, property prediction (ADMET, activity), retrosynthesis, drug-target interaction (DTI), and pretraining on large molecular datasets. Provides GNN layers (GraphConv, GAT,…
Quellsprache: Englisch
Query ZINC15/ZINC22 virtual compound libraries (1.4B compounds, 750M purchasable). Search lead/fragment/drug-like compounds by MW, logP, reactivity, or SMILES similarity; download 3D sets for docking. For bioactivity use chembl-database-bioactivity; for…
Quellsprache: Englisch
BRENDA Enzyme DB SOAP/REST queries: kinetic parameters (Km, Vmax, kcat, Ki), EC classes, substrate specificity, inhibitors, cofactors, organism data. 80K+ enzymes, 7M+ values. Free academic registration. For metabolic modeling use cobrapy-metabolic-modeling;…
Quellsprache: Englisch
Infer and visualize intercellular communication from scRNA-seq with CellChat (R). Build CellChat from Seurat/counts → subset CellChatDB ligand-receptor pairs → over-expressed genes per group → communication probabilities → pathway signaling → network…
Quellsprache: Englisch