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Biochemists and Biophysicists Skills | Skills Pool

OccupationsBiochemists and Biophysicists

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Biochemists and Biophysicists

2,070 skills

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2,070 skills

Philosophy & Ethics

think-scientific — Scientific and Structural Reasoning Methods

Scientific and structural reasoning methods — Scientific Method (hypothesis formation, experiment design, falsifiability), Systems Thinking (feedback loops, 8 systems archetypes, leverage points), and Formal Logic (propositional/predicate logic, formal proofs, soundness). Use when the user invokes `/think scientificmethod`, `/think systemsthinking`, or `/think formallogic`, or asks about experiment design, systemic behavior, or formal logical proofs.

Research Hypothesis Generator

Propose falsifiable hypotheses when evidence coverage is sufficient.

Data Engineering

Research Progressive Reader

Token-efficient staged literature reading plan with progressive disclosure.

Research Gap Finder

Detect literature blind spots and under-covered questions.

Literature & Writing

Create Proposal

Create research proposal notes with proper linking and structure

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Scientific Computing

Query Understanding Workflow

Parses natural language perturbation biology questions into structured query objects. Use when a user asks about gene knockouts, drug effects, CRISPR screens, perturbation experiments, or says "analyze this perturbation question" or "search for perturb-seq data". This is the pipeline entry point.

Scientific Computing

Paper Search Workflow

Searches for perturbation biology papers and datasets in the curated LanceDB database. Use when a user asks to "find papers", "search for datasets", "look up perturb-seq studies", or needs to retrieve publications about CRISPR screens, drug perturbations, or single-cell perturbation experiments.

Literature Search

Use this skill for paper discovery, title normalization, citation lookup, and concise evidence-backed research summaries.

Sales & Marketing

Result Interpretation

Interpreting and presenting query results to users

Scientific Computing

Packmol

This skill should be used when the user asks to "create a packmol input", "pack molecules with packmol", "solvate a protein", "build an initial configuration", "setup molecular dynamics", or discusses molecular packing, solvation, or building simulation starting structures.

Computational Chemistry

Ensemble Docking

Multi-engine ensemble docking pipeline for virtual screening. Use when docking ligand libraries against protein targets with tiered accuracy. Integrates Uni-Dock (GPU fast scan), DiffDock (deep learning), and GNINA (CNN scoring) for consensus-based hit ranking.

Reviewer Response

Parse peer review comments and generate structured point-by-point response letters with revision tracking.

Devils Advocate

Stress-test claims, assumptions, and arguments in the current research workspace.

Duivytools

DuIvyTools 是一个用于可视化 GROMACS 的 xvg 和 xpm 文件的命令行工具，包含 30+ 个命令。使用此技能来处理 GROMACS 模拟结果文件的可视化和数据处理。当用户需要可视化 xvg/xpm 文件、生成 mdp 模板、处理索引文件或执行其他 MD 分析任务时调用此技能。

Sc Cell Communication

Cell-cell communication inference from scRNA-seq using CellChat or LIANA. Input: --input <annotated.h5ad> --output <dir>. Output: communication_results.csv, interaction_chord_plot.png, bubble_plot.png.

garrisonfaridi0

Spatial Velocity

RNA velocity analysis for spatial transcriptomics data using scVelo with spatial embedding. Input: --input <.h5ad with spliced/unspliced> --output <dir>. Output: velocity.h5ad, velocity_embedding_plot.png, velocity_confidence.csv.

garrisonfaridi0

Lit Review Iterate

Iterates on an existing literature review collection through citation analysis and cluster analysis, then generates new queries, retrieves candidates, and presents them for human review. Use iteratively after an initial collection exists.

Research Swarm

Multi-angle parallel research. Attacks a question from 3-5 perspectives simultaneously, then synthesizes findings. Use when "research this topic", "deep dive on", "research swarm", "investigate from multiple angles", "I need to understand X thoroughly".

Scientific Computing

Version Compatibility

Statistical testing for differentially abundant proteins between conditions. Covers preprocessing (log2 transformation, normalization), limma and DEqMS workflows with empirical Bayes moderation, fold change shrinkage for accurate effect size estimation, and Python alternatives. Use when identifying proteins with significant abundance changes between experimental groups.

Computational Chemistry

Version Compatibility

Detects circadian and ultradian rhythms in time-series omics data using CosinorPy cosinor models, MetaCycle (JTK_CYCLE, ARSER), and RAIN non-parametric tests. Fits cosine models to estimate phase and amplitude, tests rhythmicity significance at pre-specified periods. Use when testing for 24-hour or other known-period oscillations in circadian, feeding-fasting, or light-dark cycle experiments. Not for unknown-period discovery (see temporal-genomics/periodicity-detection).

Computational Chemistry

Forcefield Selection

为不同分子体系（蛋白质、脂质膜、有机小分子、碳水化合物等）选择合适的力场和水模型。使用此技能来获取 MD 模拟中的力场推荐，包括蛋白质、核酸、脂质、有机小分子、碳水化合物、无机离子等体系。当用户需要为特定体系选择力场或询问力场相关问题时调用此技能。

Computational Chemistry

Role

Transforms the agent into a computational molecular biologist capable of designing, verifying, and exporting DNA cloning strategies using pydna. Use this skill whenever the user mentions DNA cloning, plasmid construction, plasmid design, Gibson assembly, Golden Gate assembly, PCR primer design, restriction enzyme digestion, molecular cloning workflows, GenBank files (.gb), or wants to simulate biological assemblies. Also trigger for mentions of pydna, OpenCloning JSON, Addgene plasmids, or any request to design primers, digest vectors, or assemble DNA fragments.

Antibody Humanizer

Humanize murine antibody sequences using CDR grafting and framework optimization to reduce immunogenicity while preserving antigen binding. Predicts optimal human germline frameworks and identifies critical back-mutations for therapeutic antibody development.

GeorgeDoors8880

Computational Chemistry

Crispr Screen Analyzer

Process CRISPR screening data to identify essential genes and hit candidates. Performs quality control, statistical analysis (RRA), and hit calling for pooled CRISPR screens including viability screens and drug resistance/sensitivity studies.

GeorgeDoors8880

Eln Template Creator

Generate standardized experiment templates for Electronic Laboratory Notebooks

GeorgeDoors8880

Mouse Colony Planner

Calculate breeding timelines and cage requirements for transgenic mouse colonies

GeorgeDoors8880

Motif Logo Generator

Generate publication-quality sequence logos for DNA or protein motifs.

GeorgeDoors8880

Paper Fetcher

Fetch academic papers from Sci-Hub given a DOI. Automatically downloads PDFs and saves them to research/papers/ with clean filenames. Use when the user provides a DOI or requests a paper from PubMed.

GeorgeDoors8880

Science Research Writing

Draft, revise, and diagnose English scientific writing for manuscript sections, review-style synthesis, lay summaries, and reviewer-facing revisions. Use when Codex needs to turn notes or rough text into journal-style research prose, align a section with its expected rhetorical moves, improve sentence-level choices such as tense, voice, hedging, cohesion, causality, and terminology consistency, or package research writing for adjacent scholarly formats.

Paperbanana Lite

Generate publication-quality academic methodology diagrams and statistical plots from text descriptions using a multi-agent Gemini pipeline. Use when the user wants to create scientific figures, methodology diagrams, architecture diagrams, or statistical plots for academic papers. Triggers on requests like "generate a diagram", "create a methodology figure", "make a plot for my paper", or "illustrate this architecture".