AI-powered adeno-associated virus (AAV) vector design for gene therapy including capsid engineering, promoter selection, and tropism optimization.
日本語の概要は準備中です。原文の説明を表示しています。
MongoDB with Mongoose — schemas, models, aggregation pipelines, migrations, and Atlas connections. Use when designing collections, writing queries, or integrating MongoDB into Node.js/Next.js apps.
インストールする前に、エージェントに与えられる指示の中身を確認できます。
Optimized for current MongoDB server releases, Mongoose 8.x+, Node.js 22+, and TypeScript 5.5+.
Comprehensive guidance for MongoDB database design, Mongoose ODM patterns, and Atlas integration for Node.js/Next.js applications.
Use symptom -> action triggers: when one matches, apply this skill and verify with the protocol below.
Before claiming "skill applied successfully":
// Before
const recipes = await Recipe.find({ author: userId }).populate('author');
// After
const recipes = await Recipe.find({ author: userId, isPublished: true })
.select({ title: 1, slug: 1, createdAt: 1 })
.sort({ createdAt: -1 })
.lean();
Narrows the query shape, avoids unnecessary hydration, and aligns the result with the view model actually needed.
import mongoose from 'mongoose';
const recipeSchema = new mongoose.Schema({
title: {
type: String,
required: [true, 'Title is required'],
trim: true,
maxlength: [200, 'Title cannot exceed 200 characters'],
index: true,
},
slug: {
type: String,
unique: true,
lowercase: true,
},
ingredients: [{
name: { type: String, required: true },
amount: { type: Number, required: true },
unit: { type: String, enum: ['g', 'kg', 'ml', 'l', 'cup', 'tbsp', 'tsp', 'piece'] },
}],
author: {
type: mongoose.Schema.Types.ObjectId,
ref: 'User',
required: true,
index: true,
},
tags: [{ type: String, lowercase: true, trim: true }],
isPublished: { type: Boolean, default: false },
}, {
timestamps: true,
toJSON: { virtuals: true },
toObject: { virtuals: true },
});
// Indexes for common queries
recipeSchema.index({ title: 'text', tags: 'text' });
recipeSchema.index({ author: 1, createdAt: -1 });
// Virtual fields
recipeSchema.virtual('ingredientCount').get(function() {
return this.ingredients.length;
});
// Pre-save middleware
recipeSchema.pre('save', function(next) {
if (this.isModified('title')) {
this.slug = this.title.toLowerCase().replace(/[^a-z0-9]+/g, '-');
}
next();
});
export const Recipe = mongoose.models.Recipe || mongoose.model('Recipe', recipeSchema);
required, type, and validation rulestimestamps: true for automatic createdAt/updatedAtenum for fields with fixed valuesclass RecipeRepository {
async findAll(filter = {}, options = {}) {
const { page = 1, limit = 20, sort = '-createdAt', populate = '' } = options;
const skip = (page - 1) * limit;
const [recipes, total] = await Promise.all([
Recipe.find(filter)
.sort(sort)
.skip(skip)
.limit(limit)
.populate(populate)
.lean(),
Recipe.countDocuments(filter),
]);
return {
data: recipes,
pagination: {
page,
limit,
total,
pages: Math.ceil(total / limit),
},
};
}
async findById(id) {
return Recipe.findById(id).populate('author', 'name avatar').lean();
}
async create(data) {
const recipe = new Recipe(data);
return recipe.save();
}
async update(id, data) {
return Recipe.findByIdAndUpdate(id, data, {
new: true,
runValidators: true,
});
}
async delete(id) {
return Recipe.findByIdAndDelete(id);
}
async search(query, options = {}) {
return this.findAll(
{ $text: { $search: query } },
{ ...options, sort: { score: { $meta: 'textScore' } } }
);
}
}
export const recipeRepository = new RecipeRepository();
// Group recipes by tag with counts
const tagStats = await Recipe.aggregate([
{ $match: { isPublished: true } },
{ $unwind: '$tags' },
{ $group: { _id: '$tags', count: { $sum: 1 } } },
{ $sort: { count: -1 } },
{ $limit: 20 },
]);
// Author statistics with lookup
const authorStats = await Recipe.aggregate([
{ $group: {
_id: '$author',
recipeCount: { $sum: 1 },
avgRating: { $avg: '$rating' },
}},
{ $lookup: {
from: 'users',
localField: '_id',
foreignField: '_id',
as: 'authorInfo',
}},
{ $unwind: '$authorInfo' },
{ $project: {
name: '$authorInfo.name',
recipeCount: 1,
avgRating: { $round: ['$avgRating', 1] },
}},
{ $sort: { recipeCount: -1 } },
]);
// Date-based analytics
const monthlyRecipes = await Recipe.aggregate([
{ $match: { createdAt: { $gte: new Date('2024-01-01') } } },
{ $group: {
_id: { $dateToString: { format: '%Y-%m', date: '$createdAt' } },
count: { $sum: 1 },
}},
{ $sort: { _id: 1 } },
]);
import mongoose from 'mongoose';
const MONGODB_URI = process.env.MONGODB_URI;
if (!MONGODB_URI) {
throw new Error('MONGODB_URI environment variable is not defined');
}
let cached = global.mongoose;
if (!cached) {
cached = global.mongoose = { conn: null, promise: null };
}
export async function connectDB() {
if (cached.conn) return cached.conn;
if (!cached.promise) {
cached.promise = mongoose.connect(MONGODB_URI, {
bufferCommands: false,
});
}
cached.conn = await cached.promise;
return cached.conn;
}
bufferCommands: false for explicit error handlingmaxPoolSize for productionretryWrites=true&w=majorityconst userSchema = new mongoose.Schema({
schemaVersion: { type: Number, default: 2 },
// ... fields
});
userSchema.pre('save', function(next) {
if (this.schemaVersion < 2) {
// Migrate old fields to new format
this.schemaVersion = 2;
}
next();
});
async function migrateUsers() {
const batchSize = 100;
let processed = 0;
let batch;
do {
batch = await User.find({ schemaVersion: { $lt: 2 } }).limit(batchSize);
for (const user of batch) {
user.schemaVersion = 2;
await user.save();
processed++;
}
console.log(`Migrated ${processed} users`);
} while (batch.length === batchSize);
}
.lean() for read-only queries (returns plain objects, 5-10x faster).select() to return only needed fields$project early in aggregation to reduce working set$lookup in high-frequency queries; denormalize insteadexplain() to analyze query performance| Issue | Solution |
|---|---|
| Slow queries | Add indexes, use .lean(), check with explain() |
| Connection timeouts | Check Atlas network access, increase pool size |
| Validation errors | Review schema constraints, check middleware order |
| Duplicate key errors | Ensure unique indexes, handle with try/catch |
| Memory issues | Use cursors for large datasets, limit batch sizes |
This skill is written to stay usable across GitHub Copilot, Claude Code, and Codex.
$CODEX_HOME/skills/mongodb-mongoose and restart Codex after major changes.Preferred MCP Server: MongoDB MCP
SKILL.md, bundled references or scripts, and manual verification. Show the exact commands, evidence, and final checks you used before concluding."mongosh, MongoDB Atlas UI, local schema files, and Mongoose model inspection when the MCP server is unavailable.まだレビューはありません。使ってみた感想をお寄せください。
概要と使いどころ
AI-powered adeno-associated virus (AAV) vector design for gene therapy including capsid engineering, promoter selection, and tropism optimization.
日本語の概要は準備中です。原文の説明を表示しています。
Improve the clarity and voice of AI-assisted academic writing (papers, theses, rebuttals) and
日本語の概要は準備中です。原文の説明を表示しています。
12-agent academic paper writing pipeline. 11 modes (full/plan/outline/revision/revision-coach/abstract/lit-review/format-convert/citation-check/disclosure/rebuttal-audit). 6 paper types, 5 citation formats, bilingual abstracts, LaTeX/DOCX-via-Pandoc/PDF output. Style Calibration + Writing Quality Check + Anti-Patterns with IRON RULE markers. Triggers: write paper, academic paper, guide my paper, parse reviews, audit my rebuttal, check my response draft, AI disclosure, 寫論文, 學術論文, 引導我寫論文, 審查意見, 評估回覆, 논문 작성, 초록 작성, 논문 수정, 논문 계획을 도와줘, 심사 의견 반영, 답변서 점검, AI 사용 고지.
日本語の概要は準備中です。原文の説明を表示しています。
Systematic writing framework for philosophy and interdisciplinary academic papers from optimized outline to submission-ready manuscript. Use when users want to: (1) write a paper from a detailed outline, (2) ensure quality control during writing, (3) maintain consistency across chapters, (4) prepare a submission-ready manuscript, or (5) systematically execute a planned paper. Triggered by phrases like 'write the paper from this outline,' 'compose the full manuscript,' 'execute the outline,' or when users have completed strategic planning (academic-paper-strategist skill) and are ready to write. Takes optimized outline as input; outputs complete manuscript with iterative quality checks.
日本語の概要は準備中です。原文の説明を表示しています。
Multi-perspective academic paper review with dynamic reviewer personas. Runs a 5-seat, role-separated review panel (Journal-Fit Reviewer + 3 peer-review roles + Devil's Advocate) with field-specific expertise; role separation is not a claim of independent error processes. Supports full review, re-review (verification), quick assessment, methodology focus, Socratic guided, and calibration modes. Triggers on: review paper, peer review, manuscript review, referee report, review my paper, critique paper, simulate review, editorial review, calibrate reviewer, reviewer calibration, measure reviewer accuracy, 審查論文, 論文審查, 模擬審查, 同儕審查, 幫我審這篇, 以審查人角度評估, 審查者校準, 논문 심사, 동료 심사, 모의 심사, 심사자 관점에서 평가, 심사자 보정.
日本語の概要は準備中です。原文の説明を表示しています。
Systematic strategic planning framework for philosophy and interdisciplinary academic papers targeting preprint platforms (PhilArchive, arXiv, PhilSci-Archive). Use when users want to: (1) plan a paper on a specific topic, (2) identify research gaps and assess originality, (3) develop optimized paper outlines, (4) prepare for preprint submission, or (5) understand platform requirements and writing standards. Triggered by phrases like 'plan a paper on,' 'help me design a paper about,' 'identify research gaps in,' 'is this idea original,' or when users need structured research planning. The skill guides through three phases: Platform Analysis (identifying target venue and studying sample papers), Theoretical Framework (AI-driven literature search and gap identification), and Outline Optimization (structured design with reviewer-perspective self-assessment). Each phase includes quality evaluation standards and validation checkpoints.
日本語の概要は準備中です。原文の説明を表示しています。