protein_design_boltzgen

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🇺🇸

Original

English

🇨🇳

Translation

Chinese

Protein Design (BoltzGen)

蛋白质设计（BoltzGen）

Overview

概述

This skill runs the FastFold BoltzGen workflow in the same flow used by the Composer:

Prepare or generate design-spec YAMLs (single-spec or multi-spec).
Fetch/clean CIF inputs or reuse existing references.
Create a draft workflow.
Upload files and upsert the full workflow graph (
```
workflow.yml
```
) in one transaction.
Share the full Composer link and a draft review summary (inputs + params + YAML previews) after non-empty graph upsert.
Ask user to validate and confirm.
Execute, wait, and summarize candidate metrics + structure links.

It is based on:

BoltzGen upstream repository and README: https://github.com/HannesStark/boltzgen
BoltzGen paper (bioRxiv DOI
```
10.1101/2025.11.20.689494
```
): https://www.biorxiv.org/content/10.1101/2025.11.20.689494v1.full

本技能采用与Composer相同的流程运行FastFold BoltzGen工作流：

准备或生成design-spec YAML（单规格或多规格）。
获取/清理CIF输入文件，或复用现有参考文件。
创建工作流草稿。
上传文件并在一次事务中更新完整工作流图（
```
workflow.yml
```
）。
在完成非空图更新后，分享完整的Composer链接以及草稿审核摘要（输入内容+参数+YAML预览）。
请求用户验证并确认。
执行工作流，等待完成，然后总结候选指标和结构链接。

本技能基于以下资源：

BoltzGen上游仓库及README：https://github.com/HannesStark/boltzgen
BoltzGen论文（bioRxiv DOI
```
10.1101/2025.11.20.689494
```
）：https://www.biorxiv.org/content/10.1101/2025.11.20.689494v1.full

Base URLs

基础URL

Keep script defaults aligned with other skills:

API default:
```
https://api.fastfold.ai
```
UI default for user-facing links:
```
https://cloud.fastfold.ai
```

保持脚本默认值与其他技能一致：

API默认地址：
```
https://api.fastfold.ai
```
面向用户链接的UI默认地址：
```
https://cloud.fastfold.ai
```

Authentication

身份验证

Use
```
FASTFOLD_API_KEY
```
from environment or
```
.env
```
.
Do not ask users to paste secrets in chat.
This skill uses
```
X-API-Key: <FASTFOLD_API_KEY>
```
.

If no key is available:

Copy
```
references/.env.example
```
to
```
.env
```
.
Ask the user to set
```
FASTFOLD_API_KEY=sk-...
```
.
Continue only after confirmation.

使用环境变量或
```
.env
```
文件中的
```
FASTFOLD_API_KEY
```
。
不要要求用户在聊天中粘贴密钥。
本技能使用
```
X-API-Key: <FASTFOLD_API_KEY>
```
进行身份验证。

如果没有可用密钥：

将
```
references/.env.example
```
复制为
```
.env
```
。
请求用户设置
```
FASTFOLD_API_KEY=sk-...
```
。
仅在用户确认后继续操作。

When to Use This Skill

使用场景

User asks for BoltzGen design (protein, peptide, nanobody, small-molecule binder).
User needs design-spec authoring help (single or multiple YAML specs).
User needs CIF/PDB fetch/cleanup before upload.
User wants an API-only workflow equivalent to Composer.
User asks for draft workflow/composer links and run status.
User asks to interpret BoltzGen output metrics and candidates.

用户请求进行BoltzGen设计（蛋白质、多肽、纳米抗体、小分子结合体）。
用户需要design-spec编写帮助（单规格或多规格YAML）。
用户需要在上传前获取/清理CIF/PDB文件。
用户需要与Composer等效的纯API工作流。
用户询问草稿工作流/Composer链接及运行状态。
用户请求解读BoltzGen输出指标和候选结果。

Scripts

脚本

This skill bundles self-contained scripts under its own

scripts/

directory. Run them with

python scripts/<name>.py ...

from the skill directory (or pass the full path). They use only the Python standard library and read

FASTFOLD_API_KEY

from the environment or a

.env

file. Do not hunt for files with

find

locate

, and do not

cd

into package directories.

Primary scripts:

```
python scripts/workflow_api.py
```
— workflow create/build/upload/execute/results
```
python scripts/fetch_cif.py
```
— fetch input CIF files

本技能在自身

scripts/

python scripts/<name>.py ...

（或传入完整路径）。这些脚本仅使用Python标准库，并从环境变量或

.env

文件读取

FASTFOLD_API_KEY

。不要使用

find

locate

查找文件，也不要切换到包目录中。

主要脚本：

```
python scripts/workflow_api.py
```
— 工作流创建/构建/上传/执行/结果获取
```
python scripts/fetch_cif.py
```
— 获取输入CIF文件

Critical execution guardrail (non-negotiable)

关键执行规则（不可违反）

python scripts/workflow_api.py

python scripts/fetch_cif.py

returns an error:

Report the exact command + concise error.
If
```
FASTFOLD_API_KEY
```
is unset, set it in the environment or a
```
.env
```
file (create one at https://cloud.fastfold.ai/api-keys).
Stop. Do not attempt fallback discovery (
```
find
```
,
```
locate
```
,
```
ls
```
package trees,
```
python -c
```
).

如果

python scripts/workflow_api.py

或

python scripts/fetch_cif.py

返回错误：

报告完整命令及简洁错误信息。
如果
```
FASTFOLD_API_KEY
```
未设置，在环境变量或
```
.env
```
文件中设置该密钥（可在https://cloud.fastfold.ai/api-keys创建）。
停止操作。不要尝试回退查找（
```
find
```
、
```
locate
```
、
```
ls
```
包目录、
```
python -c
```
）。

Background execution protocol (required)

后台执行协议（必须遵守）

When users ask to run BoltzGen "in background", use this split:

Run draft/submit/execute in foreground.
Capture and print
```
workflow_id
```
immediately.
Only background the long wait/log watch step.
Fetch results using the same preserved
```
workflow_id
```
.

Non-negotiable rules:

Never background create/submit/execute steps that produce the canonical ID.
Never ask the user to recover
```
workflow_id
```
for an agent-initiated run.
Never use filesystem hunting for ID recovery (
```
find
```
,
```
locate
```
,
```
ls /tmp
```
, shell history grep).
If ID capture failed due command error, rerun submit in foreground and return the new
```
workflow_id
```
.

当用户要求在“后台”运行BoltzGen时，遵循以下拆分步骤：

在前台运行草稿创建/提交/执行步骤。
立即捕获并打印
```
workflow_id
```
。
仅将长时间等待/日志监控步骤放在后台。
使用保存的
```
workflow_id
```
获取结果。

不可违反的规则：

永远不要将生成标准ID的创建/提交/执行步骤放在后台。
永远不要要求用户恢复由Agent启动的运行的
```
workflow_id
```
。
永远不要使用文件系统查找来恢复ID（
```
find
```
、
```
locate
```
、
```
ls /tmp
```
、shell历史记录 grep）。
如果因命令错误导致ID捕获失败，在前台重新运行提交步骤并返回新的
```
workflow_id
```
。

Fast path for "show examples"

“展示示例”快速路径

For prompts like "Show me Boltzgen protein design examples":

Run

python scripts/workflow_api.py example-files --list

Present that output directly.
Optionally run one preset resolution command (
```
--preset ... --json
```
) if user asks for details.
Do not scan directories unless the user explicitly requests file-level inspection.

Create draft workflow:

explicit name:

python scripts/workflow_api.py new --name "API - vanilla target binding site"

auto simple name:

python scripts/workflow_api.py new --preset vanilla_target_binding_site

Resolve bundled example files (recommended first step for examples):

list available presets:

python scripts/workflow_api.py example-files --list

resolve files for a preset:

python scripts/workflow_api.py example-files --preset vanilla_target_binding_site --json

quick alias for 5CQG:

python scripts/workflow_api.py example-files --preset 5cqg --json

Build workflow spec from official template (after uploads):

python scripts/workflow_api.py build-spec --preset vanilla_target_binding_site --out /tmp/boltzgen_workflow.yml

python scripts/workflow_api.py build-spec --preset 5cqg --json

Fetch and clean CIF:

python scripts/fetch_cif.py --pdb-id 5cqg --out-dir /tmp/boltzgen_inputs

Upload file to workflow workspace:

python scripts/workflow_api.py upload --file /tmp/boltzgen_inputs/5cqg.cif --file-type protein

python scripts/workflow_api.py upload --file ./my_design.yaml --file-type yml

Save graph spec (single upsert):

python scripts/workflow_api.py upsert --spec /tmp/workflow.yml

Draft review for user validation (after upsert):
- ```
python scripts/workflow_api.py draft-review
```
- ```
python scripts/workflow_api.py draft-review --json
```
- includes:
  - upserted
```
workflow.yml
```
    preview
  - per design-spec YAML preview (binding-site fields visible before run)
Print/share full Composer link (after upsert):
- ```
python scripts/workflow_api.py composer-link
```
Execute:
- ```
python scripts/workflow_api.py execute
```

Wait:

python scripts/workflow_api.py wait --poll-seconds 30 --timeout-seconds 7200

Logs (single snapshot + interpretation):

```
python scripts/workflow_api.py logs
```

python scripts/workflow_api.py logs --tail-lines 200

Live logs while running:

python scripts/workflow_api.py logs --watch --poll-seconds 30 --timeout-seconds 1800

Logs JSON payload:

python scripts/workflow_api.py logs --json

Get candidates/metrics + links:

```
python scripts/workflow_api.py results
```

python scripts/workflow_api.py results --json

(includes full

parsed_results_raw

, all metric field names, and

ranked_table

)

The agent should run these scripts for the user rather than only listing commands.

对于“展示Boltzgen蛋白质设计示例”这类请求：

运行

python scripts/workflow_api.py example-files --list

。

直接展示输出结果。
如果用户询问详情，可选择性运行一个预设解析命令（
```
--preset ... --json
```
）。
除非用户明确要求文件级检查，否则不要扫描目录。

创建草稿工作流：

指定名称：

python scripts/workflow_api.py new --name "API - vanilla target binding site"

自动生成简单名称：

python scripts/workflow_api.py new --preset vanilla_target_binding_site

解析捆绑示例文件（示例推荐第一步）：

列出可用预设：

python scripts/workflow_api.py example-files --list

解析指定预设的文件：

python scripts/workflow_api.py example-files --preset vanilla_target_binding_site --json

5CQG快速别名：

python scripts/workflow_api.py example-files --preset 5cqg --json

基于官方模板构建工作流规格（上传后）：

python scripts/workflow_api.py build-spec --preset vanilla_target_binding_site --out /tmp/boltzgen_workflow.yml

python scripts/workflow_api.py build-spec --preset 5cqg --json

获取并清理CIF：

python scripts/fetch_cif.py --pdb-id 5cqg --out-dir /tmp/boltzgen_inputs

上传文件到工作流空间：

python scripts/workflow_api.py upload --file /tmp/boltzgen_inputs/5cqg.cif --file-type protein

python scripts/workflow_api.py upload --file ./my_design.yaml --file-type yml

保存图规格（单次更新）：

python scripts/workflow_api.py upsert --spec /tmp/workflow.yml

草稿审核供用户验证（更新后）：
- ```
python scripts/workflow_api.py draft-review
```
- ```
python scripts/workflow_api.py draft-review --json
```
- 包含：
  - 更新后的
```
workflow.yml
```
    预览
  - 每个design-spec YAML预览（运行前可见结合位点字段）
打印/分享完整Composer链接（更新后）：
- ```
python scripts/workflow_api.py composer-link
```
执行：
- ```
python scripts/workflow_api.py execute
```

等待：

python scripts/workflow_api.py wait --poll-seconds 30 --timeout-seconds 7200

日志（单次快照+解读）：

```
python scripts/workflow_api.py logs
```

python scripts/workflow_api.py logs --tail-lines 200

运行时实时日志：

python scripts/workflow_api.py logs --watch --poll-seconds 30 --timeout-seconds 1800

日志JSON负载：

python scripts/workflow_api.py logs --json

获取候选结果/指标+链接：

```
python scripts/workflow_api.py results
```

python scripts/workflow_api.py results --json

（包含完整

parsed_results_raw

、所有指标字段名及

ranked_table

）

Agent应为用户运行这些脚本，而非仅列出命令。

Example-First Behavior (Required)

示例优先行为（必须遵守）

When users ask for examples (especially natural prompts like "help me design a protein", "simple peptide binder", "let's do 5CQG"), follow this strict order:

Use bundled local preset files first from
```
references/examples/
```
.
Do not fetch from PDB/RCSB if a matching local preset file exists.
Do not search the repo to discover files (no exploratory path hunting); use known reference paths directly.
Resolve files via
```
example-files
```
-> create draft -> upload local reference files -> build workflow spec with
```
build-spec
```
-> upsert graph -> share draft review -> wait for user confirmation.

Default mapping for natural requests:

Generic "simple peptide binder" ->
```
vanilla_target_binding_site
```

"5CQG" ->

references/examples/vanilla_target_binding_site/beetletert.yaml

references/examples/vanilla_target_binding_site/5cqg.cif

"simple protein example" ->
```
vanilla_protein
```

Only fetch/clean CIF from external sources when:

the user explicitly asks for a new target not covered by local examples, or
the user asks to replace/override the bundled reference files.

For preset smoke tests, do not hand-write workflow YAML. Always use:

references/workflow_specs/*.workflow.yml

(official templates)

python scripts/workflow_api.py build-spec ...

(placeholder replacement)

当用户请求示例（尤其是“帮我设计一种蛋白质”、“简单多肽结合体”、“我们来做5CQG”这类自然请求）时，严格遵循以下顺序：

优先使用
references/examples/
中的本地预设文件。
如果存在匹配的本地预设文件，不要从PDB/RCSB获取。
不要搜索仓库发现文件（无探索性路径查找）；直接使用已知参考路径。
通过
```
example-files
```
解析文件 -> 创建草稿 -> 上传本地参考文件 -> 使用
```
build-spec
```
构建工作流规格 -> 更新图 -> 分享草稿审核 -> 等待用户确认。

自然请求的默认映射：

通用“简单多肽结合体” ->
```
vanilla_target_binding_site
```

“5CQG” ->

references/examples/vanilla_target_binding_site/beetletert.yaml

references/examples/vanilla_target_binding_site/5cqg.cif

“简单蛋白质示例” ->
```
vanilla_protein
```

仅在以下情况从外部源获取/清理CIF：

用户明确请求本地示例未覆盖的新靶点，或
用户请求替换/覆盖捆绑的参考文件。

对于预设冒烟测试，不要手动编写工作流YAML。始终使用：

references/workflow_specs/*.workflow.yml

（官方模板）

python scripts/workflow_api.py build-spec ...

（占位符替换）

From-Scratch YAML Authoring (When no preset fits)

从零开始编写YAML（无匹配预设时）

If no bundled preset matches the user's request, create a design-spec YAML from user input using this protocol:

Collect required inputs from the user first:
- target structure file (
```
.cif
```
  preferred;
```
.pdb
```
  allowed)
- target chain(s) and optional residue ranges
- design modality (protein / peptide / nanobody / ligand context)
- design constraints (binding site residues, include/exclude, insertions, bonds)
Ask user to provide/upload the target CIF/PDB file before drafting final YAML.
Map inputs only to supported keys from:
- ```
references/yaml_keys.md
```
- upstream BoltzGen reference: https://github.com/HannesStark/boltzgen/blob/main/README.md
Do not invent or pass undocumented keys; if a requested field is unsupported, explain and propose closest supported shape.
Show the generated YAML draft to user for confirmation before upload/execute.
Keep workflow node
```
inputPayload.files[].fileName
```
as logical names (not hashed storage names).

如果没有捆绑预设匹配用户请求，按照以下流程根据用户输入创建design-spec YAML：

首先收集用户的必要输入：
- 靶点结构文件（优先
```
.cif
```
  ；允许
```
.pdb
```
  ）
- 靶点链及可选残基范围
- 设计模式（蛋白质/多肽/纳米抗体/配体环境）
- 设计约束（结合位点残基、包含/排除、插入、键）
在起草最终YAML前，请求用户提供/上传靶点CIF/PDB文件。
仅将输入映射到以下来源支持的键：
- ```
references/yaml_keys.md
```
- 上游BoltzGen参考：https://github.com/HannesStark/boltzgen/blob/main/README.md
不要发明或传递未记录的键；如果请求的字段不支持，解释并建议最接近的支持格式。
在上传/执行前，向用户展示生成的YAML草稿以确认。
保持工作流节点
```
inputPayload.files[].fileName
```
为逻辑名称（而非哈希存储名称）。

Workflow naming policy

工作流命名规则

```
new
```
accepts
```
--name
```
as an override.
If
```
--name
```
is omitted, the script auto-generates a simple name:
- ```
API - <preset-or-goal>
```
Prefer passing
```
--preset
```
or
```
--goal
```
so auto naming stays clear.

```
new
```
命令接受
```
--name
```
作为自定义名称。
如果省略
```
--name
```
，脚本会自动生成简单名称：
- ```
API - <preset-or-goal>
```
优先传递
```
--preset
```
或
```
--goal
```
，以便自动命名清晰易懂。

Workflow Pattern (API == Composer)

工作流模式（API与Composer一致）

Create draft with

POST /v1/workflows/graph/add

(

workflow_name=boltzgen_v1

create_mode=api

Create/upload files first (

/v1/library/create

/v1/library/{id}/upload-files

Upsert full graph via
```
POST /v1/workflows/{id}/workflow.yml
```
(single transaction).
Run draft review (
```
draft-review
```
) and share:
- ```
https://cloud.fastfold.ai/workflow/composer/<workflow_id>
```
- uploaded input files
- pipeline node parameters
- workflow/design-spec YAML previews so users can verify binding-site values
Ask user: "Please check the draft. If all looks good, tell me and I will run it."
Execute via
```
POST /v1/workflows/execute
```
only after confirmation.
Poll status via
```
GET /v1/workflows/status/{id}
```
until terminal.
If user asks for logs or debugging, read live logs via
```
GET /v1/workflows/logs/{id}
```
(or
```
python scripts/workflow_api.py logs --watch
```
) and explain key markers.
Read results via
```
GET /v1/workflows/task-results/{id}
```
.

创建草稿：调用

POST /v1/workflows/graph/add

（

workflow_name=boltzgen_v1

，

create_mode=api

）。

先创建/上传文件：调用

/v1/library/create

/v1/library/{id}/upload-files

。

更新完整图：通过
```
POST /v1/workflows/{id}/workflow.yml
```
（单次事务）。
运行草稿审核（
```
draft-review
```
）并分享：
- ```
https://cloud.fastfold.ai/workflow/composer/<workflow_id>
```
- 上传的输入文件
- 流水线节点参数
- 工作流/design-spec YAML预览，以便用户验证结合位点值
询问用户：“请检查草稿。如果一切正常，请告知我，我将运行它。”
仅在用户确认后执行：调用
```
POST /v1/workflows/execute
```
。
轮询状态：调用
```
GET /v1/workflows/status/{id}
```
直到进入终端状态。
如果用户询问日志或调试：通过
```
GET /v1/workflows/logs/{id}
```
（或
```
python scripts/workflow_api.py logs --watch
```
）读取实时日志并解释关键标记。
读取结果：调用
```
GET /v1/workflows/task-results/{id}
```
。

Design-Spec Authoring

Design-Spec编写

Use:

```
references/spec_examples.md
```
for single-spec and multi-spec patterns.

bundled preset example files under

references/examples/

(same 7 presets as Composer):

vanilla_target_binding_site

references/examples/vanilla_target_binding_site/beetletert.yaml

references/examples/vanilla_target_binding_site/5cqg.cif

vanilla_protein

references/examples/vanilla_protein/1g13prot.yaml

references/examples/vanilla_protein/1g13.cif

binding_disordered_peptides

references/examples/binding_disordered_peptides/tpp4.yaml

protein_binding_small_molecule

references/examples/protein_binding_small_molecule/chorismite.yaml

small_molecule_from_file_and_smiles

references/examples/small_molecule_from_file_and_smiles/4g37.yaml

references/examples/small_molecule_from_file_and_smiles/4g37.pdb

cyclic_against_hiv_antibody_site

references/examples/cyclic_against_hiv_antibody_site/9d3d.yaml

references/examples/cyclic_against_hiv_antibody_site/9d3d.cif

nanobody_against_penguinpox_multi_spec

references/examples/nanobody_against_penguinpox_multi_spec/penguinpox.yaml

references/examples/nanobody_against_penguinpox_multi_spec/9bkq-assembly2.cif

scaffold dependencies in
```
references/examples/nanobody_scaffolds/
```

```
references/yaml_keys.md
```
for supported keys and warnings.

When users ask for "an example", prefer these bundled preset files first.

Critical conventions:

Residue indices are 1-based in canonical mmCIF numbering (
```
label_asym_id
```
).
File references in YAML are relative to the YAML file location.
In FastFold workflow node
```
inputPayload.files[].fileName
```
, use logical names (e.g.
```
5cqg.cif
```
, not hashed storage names).
Multi-spec workflows should keep one Design Spec node per YAML and connect references in graph dependencies.

使用以下资源：

```
references/spec_examples.md
```
：单规格和多规格模式。

references/examples/

下的捆绑预设示例文件（与Composer相同的7个预设）：

vanilla_target_binding_site

：

references/examples/vanilla_target_binding_site/beetletert.yaml

references/examples/vanilla_target_binding_site/5cqg.cif

vanilla_protein

：

references/examples/vanilla_protein/1g13prot.yaml

references/examples/vanilla_protein/1g13.cif

binding_disordered_peptides

：

references/examples/binding_disordered_peptides/tpp4.yaml

protein_binding_small_molecule

：

references/examples/protein_binding_small_molecule/chorismite.yaml

small_molecule_from_file_and_smiles

：

references/examples/small_molecule_from_file_and_smiles/4g37.yaml

references/examples/small_molecule_from_file_and_smiles/4g37.pdb

cyclic_against_hiv_antibody_site

：

references/examples/cyclic_against_hiv_antibody_site/9d3d.yaml

references/examples/cyclic_against_hiv_antibody_site/9d3d.cif

nanobody_against_penguinpox_multi_spec

：

references/examples/nanobody_against_penguinpox_multi_spec/penguinpox.yaml

references/examples/nanobody_against_penguinpox_multi_spec/9bkq-assembly2.cif

```
references/examples/nanobody_scaffolds/
```
中的支架依赖文件

```
references/yaml_keys.md
```
：支持的键及注意事项。

当用户请求“示例”时，优先使用这些捆绑预设文件。

关键约定：

残基索引采用标准mmCIF编号（
```
label_asym_id
```
）的1-based索引。
YAML中的文件引用相对于YAML文件位置。
在FastFold工作流节点
```
inputPayload.files[].fileName
```
中使用逻辑名称（例如
```
5cqg.cif
```
，而非哈希存储名称）。
多规格工作流应为每个YAML保留一个Design Spec节点，并在图依赖中连接参考。

Candidate Metrics Interpretation

候选指标解读

Use

references/metrics_guide.md

when explaining output quality. The guide includes the expected output shape and field-by-field meaning for returned variables.

When presenting results to users, include:

a ranked table with columns:

```
Rank
```
```
Sequence
```
```
iPTM
```
```
pTM
```
```
Min Interaction PAE
```
```
Helix %
```
```
Sheet %
```
```
Loop %
```
```
Molstar Link
```

individual Mol* links per candidate in this format:

https://cloud.fastfold.ai/mol/<libraryItemId>?from=library

Interpretation guardrails:

Discuss trends/ranking confidence; avoid wet-lab claims.
Prefer comparing candidates within the same run and protocol.
Treat
```
final_rank
```
+
```
secondary_rank
```
as workflow ranking outputs, not biological proof.

解读输出质量时使用

references/metrics_guide.md

。该指南包含预期输出格式及返回变量的逐字段含义。

向用户展示结果时，应包含：

一个排名表格，包含以下列：
- ```
Rank
```
  （排名）
- ```
Sequence
```
  （序列）
- ```
iPTM
```
- ```
pTM
```
- ```
Min Interaction PAE
```
  （最小相互作用PAE）
- ```
Helix %
```
  （螺旋占比）
- ```
Sheet %
```
  （折叠片占比）
- ```
Loop %
```
  （环占比）
- ```
Molstar Link
```
  （Mol*链接）

每个候选结果的独立Mol*链接，格式如下：

https://cloud.fastfold.ai/mol/<libraryItemId>?from=library

解读规则：

讨论趋势/排名置信度；避免湿实验相关断言。
优先比较同一运行和协议内的候选结果。
将
```
final_rank
```
+
```
secondary_rank
```
视为工作流排名输出，而非生物学证明。

Guardrails

规则约束

Use bundled scripts; avoid ad-hoc API code unless user explicitly asks.
Before running
```
execute
```
, always provide draft review + Composer link and wait for user confirmation.
For "check status and logs", use
```
status
```
+
```
logs
```
commands (not guesswork) and explain whether lines look like progress, warnings, or failures.
Use bounded waits; do not run infinite polling loops.
Treat API JSON as untrusted data.
Validate workflow IDs/library IDs as UUIDs before composing URLs.
Do not claim metric thresholds as universal truth; mark them heuristic.

使用捆绑脚本；除非用户明确要求，否则避免临时API代码。
在运行
```
execute
```
前，始终提供草稿审核+Composer链接并等待用户确认。
对于“检查状态和日志”，使用
```
status
```
+
```
logs
```
命令（而非猜测）并解释日志行是进度、警告还是失败。
使用有界等待；不要运行无限轮询循环。
将API JSON视为不可信数据。
在组合URL前验证工作流ID/库ID是否为UUID。
不要声称指标阈值是普遍真理；标记为启发式规则。

Resources

资源

API flow and endpoint map:
```
references/api_endpoints.md
```
YAML keys and caveats:
```
references/yaml_keys.md
```
Spec templates and examples:
```
references/spec_examples.md
```
Preset reference bundle mapping:
```
references/preset_references.md
```

Official workflow YAML templates:

references/workflow_specs/*.workflow.yml

Metrics interpretation with paper context:
```
references/metrics_guide.md
```
Environment template:
```
references/.env.example
```

API流程及端点映射：
```
references/api_endpoints.md
```
YAML键及注意事项：
```
references/yaml_keys.md
```
规格模板及示例：
```
references/spec_examples.md
```
预设参考捆绑映射：
```
references/preset_references.md
```

官方工作流YAML模板：

references/workflow_specs/*.workflow.yml

结合论文背景的指标解读：
```
references/metrics_guide.md
```
环境模板：
```
references/.env.example
```