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Protein Mining
作者
majiajia0529
· GitHub ↗
· v1.0.0
· MIT-0
243
总下载
0
收藏
1
当前安装
1
版本数
在 OpenClaw 中安装
/install protein-mining
功能描述
自动化蛋白质挖掘完整流程，从文献调研到潜在蛋白确定，生成可发表的学术成果
安全使用建议
This skill describes a legitimate, heavy bioinformatics pipeline but the metadata is incomplete: it declares only three binaries while the instructions require many more tools (CD-HIT, TrimAl, PAML, CAFE, AlphaFold/ColabFold, Foldseek, PyMOL, Python packages, etc.) and it mentions a 'protein-mining' CLI that is not provided. Before installing or running it: (1) confirm where the 'protein-mining' executable comes from and obtain a trustworthy install method or source code; (2) ensure all required bioinformatics binaries are installed from verified projects (not random URLs); (3) be aware that using AlphaFold/ColabFold or Google Colab may send sequence data to third-party services — avoid submitting sensitive sequences; (4) run the workflow in an isolated environment (container/VM) if you will allow the agent to invoke commands autonomously; (5) ask the author for an explicit install script, dependency list, and provenance for the CLI. If you cannot verify those, treat the skill as untrusted and do not let it run commands on sensitive systems or data.
功能分析
Type: OpenClaw Skill
Name: protein-mining
Version: 1.0.0
The protein-mining skill bundle describes a legitimate bioinformatics workflow for automated protein discovery and analysis. It outlines a 7-module process involving literature review, sequence collection, HMM modeling, and phylogenetic analysis using standard scientific tools like MAFFT, HMMER, and IQ-TREE. There are no signs of malicious code, data exfiltration, or prompt injection; the instructions are strictly aligned with the stated purpose of computational biology research.
能力评估
Purpose & Capability
The described pipeline (MSA, HMM, phylogeny, AlphaFold, Foldseek, etc.) matches the stated purpose, but the registry 'requires.bins' lists only mafft, hmmbuild, iqtree while the SKILL.md lists many additional dependencies (CD-HIT, TrimAl, PAML, CAFE, AlphaFold2/ColabFold, Foldseek, PyMOL, etc.). The usage examples also reference a 'protein-mining' CLI that is not provided or declared. This mismatch suggests the skill assumes external software/environment setup that is not documented in metadata.
Instruction Scope
The SKILL.md outlines expected runtime actions (literature search, downloading sequences from UniProt/NCBI, running alignment/HMM/phylogeny and AlphaFold), all of which are relevant to the task. It does not instruct reading unrelated local files or accessing secrets, but it implicitly requires network access to public databases and potentially third-party services (e.g., ColabFold/AlphaFold on remote GPU instances). There are no explicit instructions to transmit data to unknown endpoints, but using Colab/third-party services can result in data leaving the local environment.
Install Mechanism
There is no install spec (instruction-only skill), so nothing is written to disk by the skill itself. That reduces immediate supply-chain risk. However, because the skill expects many external tools and an undocumented 'protein-mining' CLI, the user must manually install/trust these binaries from outside sources.
Credentials
The skill requests no environment variables or credentials, which is appropriate. However, SKILL.md expects use of external services (AlphaFold/ColabFold) that often require accounts or tokens in practice; those are not declared. Also heavy compute/GPU access will be required for structure prediction but this is a resource, not a secret.
Persistence & Privilege
The skill is not always-enabled and is user-invocable; it does not request persistent system privileges or modify other skills. Autonomous invocation is permitted (platform default) but not combined with other high-risk flags.
如何使用
- 确保已安装 OpenClaw（本地或 Docker 部署）
- 在对话框中输入安装命令：
/install protein-mining - 安装完成后，直接呼叫该 Skill 的名称或使用
/protein-mining触发 - 根据 Skill 的参数说明提供必要输入，即可获得结构化输出
版本历史
v1.0.0
- Initial release of the protein-mining skill for automated, end-to-end protein mining workflows.
- Covers literature survey, sequence collection and QC, HMM profile construction, cross-species searches, structure-based search (Foldseek), phylogenetic analysis, and candidate prioritization.
- Each module generates publication-ready data files, visualizations, and summary reports.
- Requires key bioinformatics software tools including MAFFT, hmmbuild, and IQ-TREE.
- Workflow and technical requirements detailed for seamless academic application.
元数据
常见问题
Protein Mining 是什么？
自动化蛋白质挖掘完整流程，从文献调研到潜在蛋白确定，生成可发表的学术成果. 它是一个面向 Claude Code / OpenClaw 的 AI Agent Skill 插件，目前累计下载 243 次。
如何安装 Protein Mining？
在 OpenClaw 或 Claude Code 对话框中运行命令「/install protein-mining」即可一键安装，无需额外配置。
Protein Mining 是免费的吗？
是的，Protein Mining 完全免费，采用 MIT-0 许可证，可自由下载、安装和使用。
Protein Mining 支持哪些平台？
Protein Mining 跨平台运行，可在任意部署了 OpenClaw / Claude Code 的环境中使用（cross-platform）。
谁开发了 Protein Mining？
由 majiajia0529（@majiajia0529）开发并维护，当前版本 v1.0.0。
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