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Science Comp.

Simulation and numerical analysis.

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scientific-computing

9

interpret-nmr-spectrum

Interpretiere 1H- und 13C-NMR-Spektren zur Strukturaufklaerung organischer Verbindungen durch systematische Analyse von chemischen Verschiebungen, Kopplungsmustern, Integralen und DEPT-Daten. Verwende diesen Skill beim Zuweisen von NMR-Signalen zu spezifischen Protonen oder Kohlenstoffen, beim Ableiten funktioneller Gruppen und Konnektivitaet aus Spektraldaten, beim Unterscheiden von Strukturisomeren und beim Kombinieren von NMR-Evidenz mit anderen Spektraldaten zur vollstaendigen Strukturbestimmung.

pjt222

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scientific-computing

9

model-markov-chain

Build and analyze discrete or continuous Markov chains including transition matrix construction, state classification, stationary distribution computation, and mean first passage times. Use when modeling a memoryless system with observed transition counts or rates, computing long-run steady-state probabilities, determining expected hitting times or absorption probabilities, classifying states as transient or recurrent, or building a foundation for hidden Markov models or reinforcement learning MDPs.

pjt222

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scientific-computing

9

scikit-bio

Library for bioinformatics and community ecology statistics. Provides data structures and algorithms for sequences, alignments, phylogenetics, and diversity analysis. Essential for microbiome research and ecological data science. Use for alpha/beta diversity metrics, ordination (PCoA), phylogenetic trees, sequence manipulation (DNA/RNA/Protein), distance matrices, PERMANOVA, and community ecology analysis.

tondevrel

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scientific-computing

9

simulate-stochastic-process

模拟随机过程（马尔可夫链、随机游走、随机微分方程、MCMC），包括收敛诊断、方差缩减和可视化。适用于生成用于估计、预测或可视化的样本路径；当解析解不可得时；运行需要收敛保证的蒙特卡洛估计；对比解析结果与经验模拟进行验证；或通过 MCMC 从复杂后验分布中采样时。

pjt222

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scientific-computing

9

rdkit

Open-source cheminformatics and machine learning toolkit for drug discovery, molecular manipulation, and chemical property calculation. RDKit handles SMILES, molecular fingerprints, substructure searching, 3D conformer generation, pharmacophore modeling, and QSAR. Use when working with chemical structures, drug-like properties, molecular similarity, virtual screening, or computational chemistry workflows.

tondevrel

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scientific-computing

9

interpret-raman-spectrum

Raman-Spektren systematisch interpretieren um Molekuelschwingungen zu identifizieren, polarisierbarkeitsgetriebene Auswahlregeln zu bewerten, mit komplementaeren IR-Daten zu vergleichen und Depolarisationsverhaeltnisse fuer die Symmetriezuordnung zu evaluieren. Umfasst Identifikation Raman-aktiver Moden, Minderung von Fluoreszenzinterferenzen und Abgleich mit Referenzspektren.

pjt222

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scientific-computing

9

analyze-diffusion-dynamics

確率微分方程式、フォッカー・プランク方程式、初通過時間分布、パラメータ感度分析を使用して拡散過程のダイナミクスを分析する。連続時間拡散過程の確率密度の時間発展を導出する時、有界拡散の平均初通過時間を計算する時、ドリフトと拡散パラメータがプロセスの挙動にどう影響するかを分析する時、閉形式解を確率シミュレーションに対して検証する時に使用する。

pjt222

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scientific-computing

9

qutip

Quantum Toolbox in Python. Framework for simulating the dynamics of open quantum systems. Provides data structures for quantum objects (kets, bras, operators) and solvers for master equations, Monte Carlo trajectories, and time-dependent Hamiltonians. Use for quantum dynamics simulation, open quantum systems, master equations, quantum optics, cavity QED, Jaynes-Cummings model, Rabi oscillations, Wigner functions, quantum correlations, entanglement analysis, and quantum control.

tondevrel

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scientific-computing

9

qiskit

Comprehensive guide for Qiskit - IBM's quantum computing framework. Use for quantum circuit design, quantum algorithms (VQE, QAOA, Grover, Shor), quantum simulation, noise modeling, quantum machine learning, and quantum chemistry calculations. Essential for quantum computing research and applications.

tondevrel

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scientific-computing

9

prody

Protein Dynamics, Evolution, and Structure analysis. Specialized in Normal Mode Analysis (NMA) using Anisotropic (ANM) and Gaussian Network Models (GNM). Features tools for structural ensemble analysis, PCA, and co-evolutionary analysis (Evol). Use for protein flexibility prediction, collective motions, structural ensemble comparison, hinge region identification, binding site analysis, MD trajectory filtering, and evolutionary analysis.

tondevrel

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scientific-computing

9

openbabel

A chemical toolbox designed to speak the many languages of chemical data. Supports over 110 formats and provides tools for conversion, 3D structure generation, molecular searching (SMARTS), and force field calculations. Use for chemical file format conversion (SDF, PDB, SMILES, CIF, Gaussian), 3D coordinate generation from 2D structures, substructure searching with SMARTS patterns, molecular docking preparation, force field minimizations (UFF, GAFF, MMFF94), molecular fingerprints and Tanimoto coefficients, and batch processing of chemical databases.

tondevrel

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scientific-computing

9

analyze-diffusion-dynamics

使用随机微分方程、Fokker-Planck 方程、首达时间分布和参数灵敏度分析来分析扩散过程的动力学。适用于推导连续时间扩散过程的概率密度演化、计算有界扩散的平均首达时间、分析漂移和扩散参数如何影响过程行为，或将解析解与随机模拟进行对比验证。

pjt222

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scientific-computing

9

simpy

A process-based discrete-event simulation framework. Use for modeling queuing systems, supply chains, manufacturing processes, network simulation, project management, and any system where events occur at specific points in time. Load when working with discrete event simulation, process modeling, resource allocation, virtual time, simpy.Environment, simpy.Resource, or event-driven simulation.

tondevrel

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scientific-computing

9

mne

Open-source Python package for exploring, visualizing, and analyzing human neurophysiological data including EEG, MEG, sEEG, and ECoG.

tondevrel

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scientific-computing

9

interpret-mass-spectrum

Interpretar espectros de masas de ionización electrónica (IE), ionización química (IC) y espectrometría de masas de alta resolución (EMAR) para determinar masas moleculares, fórmulas moleculares y vías de fragmentación. Usar cuando se determine la masa molecular de un compuesto desconocido, se identifique la fórmula molecular exacta a partir de datos de alta resolución, se interpreten patrones de fragmentación para obtener información estructural, o se confirme la identidad de un producto de síntesis mediante búsqueda en biblioteca.

pjt222

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scientific-computing

9

interpret-nmr-spectrum

Interpretar espectros de resonancia magnética nuclear (RMN) de 1H, 13C, DEPT y 2D para determinar la estructura de moléculas orgánicas. Usar cuando se asigne la estructura de un compuesto desconocido, se verifique la pureza o identidad de un producto de síntesis, se interpreten experimentos de correlación 2D (COSY, HSQC, HMBC), o se identifiquen errores en datos espectrales informados.

pjt222

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scientific-computing

9

papi-compare

Compare papers for a decision. Use when user asks "which paper should I use", "compare approaches", or needs to choose between methods/algorithms.

hummat

research

scientific-computing

9

model-markov-chain

Construir y analizar cadenas de Markov discretas o continuas incluyendo construcción de matriz de transición, clasificación de estados, cálculo de distribución estacionaria y tiempos medios de primer paso. Usar al modelar un sistema sin memoria con conteos o tasas de transición observados, al calcular probabilidades de estado estacionario a largo plazo, al determinar tiempos de golpe esperados o probabilidades de absorción, al clasificar estados como transitorios o recurrentes, o al construir una base para modelos ocultos de Markov o MDPs de aprendizaje por refuerzo.

pjt222

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scientific-computing

9

ase

Atomic Simulation Environment - a set of tools for setting up, manipulating, running, visualizing, and analyzing atomistic simulations. Acts as a universal interface between Python and numerous quantum chemical and molecular dynamics codes. Use for building atomic structures, geometry optimization, molecular dynamics simulations, transition state searches (NEB), file format conversion (CIF, XYZ, POSCAR, PDB), electronic property calculations (DOS, band structures), and automating simulation workflows with DFT/MD codes like VASP, GPAW, Quantum ESPRESSO, LAMMPS.

tondevrel

research

scientific-computing

9

biopython

Comprehensive guide for Biopython - the premier Python library for computational biology and bioinformatics. Use for DNA/RNA/protein sequence analysis, file I/O (FASTA, FASTQ, GenBank, PDB), sequence alignment, BLAST searches, phylogenetic analysis, structure analysis, and NCBI database access.

tondevrel

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scientific-computing

9

cobrapy

Constraints-Based Reconstruction and Analysis for Python. Used for modeling large-scale metabolic networks in microorganisms.

tondevrel

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scientific-computing

9

derive-theoretical-result

第一原理または確立された定理からステップバイステップで理論的結果を導出する。すべてのステップを明示的に正当化し、特殊ケースをチェックする。第一原理からの公式や定理の導出時、論理的演繹による数学的命題の証明時、検証や適応のための教科書的結果の再導出時、既知の結果のより一般的な設定への拡張時、論文や学位論文のための自己完結的な導出の作成時に使用する。

pjt222

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scientific-computing

9

simulate-stochastic-process

Stochastische Prozesse (Markov-Ketten, Random Walks, SDEs, MCMC) mit Konvergenzdiagnostik, Varianzreduktion und Visualisierung simulieren. Verwenden beim Erzeugen von Stichprobenpfaden fuer Schaetzung, Vorhersage oder Visualisierung; wenn analytische Loesungen nicht handhabbar sind; bei Monte-Carlo-Schaetzung mit Konvergenzgarantien; bei Validierung analytischer Ergebnisse gegen empirische Simulation; oder beim Ziehen von Stichproben aus komplexen Posteriors via MCMC.

pjt222

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scientific-computing

9

solve-electromagnetic-induction

Probleme mit sich aenderndem magnetischen Fluss mittels Faradayschem Gesetz, Lenzscher Regel, Bewegungs-EMK, Gegen- und Selbstinduktivitaet sowie RL-Schaltungstransienten loesen. Verwenden bei der Berechnung induzierter EMK aus zeitveraenderlichen B-Feldern oder bewegten Leitern, bei der Bestimmung der Stromrichtung ueber die Lenzsche Regel, bei der Analyse von Induktivitaet und Energiespeicherung in Magnetfeldern oder beim Loesen von RL-Schaltungs-Differentialgleichungen fuer Schalttransienten.

pjt222

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