dsh-biodsh

dsh-biodsh

中文 | English

BioDSH for DeepSeek Harness: a bundle that adds a BioDSH agent preset for bioinformatics work. Your other presets are not changed.

The BioDSH preset is the standard preset of your dsh release plus:

Part · What it does BioDSH persona · Answers for doctors and wet-lab scientists, in the user's language; keeps raw data untouched; reports what was actually computed. BioDSH skills · 17 validated BioDSH workflows in the session skill catalog: single-cell QC, clustering, annotation and treatment response; bulk RNA-seq limma-voom; survival (KM, Cox), regression with robust SEs and ANOVA designs, each checked against R; workflow building, and more. Skill library · 2000+ community bioinformatics, clinical and data skills. Kept out of the catalog so it stays small and cacheable; the model searches it with the skill_library tool, and you can still run any of them with /name. Skill selection · On each new message, a model reads the whole catalog (BioDSH skills and library) and injects the one or two skills that fit the request, in the same form as /name. Convergence guard · In a long turn, asks the agent to wrap up (480 s, or 40 steps) and then to answer without tools (780 s, or 60 steps); ends a turn past 80 steps.

Install

Requires DeepSeek Harness 0.2.1 or later and pnpm on PATH (dsh's plugin manager runs pnpm).

• Command line

dsh plugin --profile web add dsh-biodsh

• Web UI: open Plugins, choose Install, enter dsh-biodsh.
• Ask the agent (Creator mode): "install the dsh-biodsh bundle".

Restart dsh after installing, then pick BioDSH in the agent preset menu, or make it the default:

# ~/.dsh/cordis.patch.yml
- id: agent-preset-registry
  config:
    default: biodsh

BioDSH (PTC) (biodsh-ptc) is the same preset with programmatic tool calling, like dsh's own ptc preset: the model calls tools from one program per step, so writing a script, running it and checking its output take one step instead of three. On 15 development tasks it cut the median from 23 to 16 steps and from 129 s to 97 s at the same accuracy.

Configure

The bundle adds a settings namespace biodsh (a Host row, so you never edit the preset itself). Change it in ~/.dsh/settings.yaml, on the Settings page, or with settings.mutate; most fields apply to the next step without a restart.

# ~/.dsh/settings.yaml
biodsh:
  selectProvider: deepseek-official   # skill selection model; empty = same route as the agent
  selectModel: deepseek-flash
  selectMaxInject: 2
  guardSoftSeconds: 480               # ask to wrap up (time is the main signal; steps are a backstop)
  guardSoftSteps: 40
  guardHardSeconds: 780               # ask for a final answer without tools
  guardHardSteps: 60
  guardMaxSteps: 80                   # end the turn (0 = no cap)
  library: true                       # 2000+ skill library and the skill_library tool (restart to apply)

Versions

A dsh agent preset restates its full plugin list, so each dsh-biodsh release is built against one dsh release (dshTarget in package.json) by scripts/build.mjs, which copies the standard preset of that release and changes only the persona and the three BioDSH rows. scripts/install-test.mjs installs a build through dsh's own plugin manager in a fresh home and runs a real turn on the preset.

Licenses

BioDSH code and skills: MIT. Skills under skills/library come from community repositories and keep their own licenses; see each skill's folder.

中文说明

为 DeepSeek Harness 增加一个 BioDSH 智能体预设，用于生信分析。你原有的预设不受影响。

BioDSH 预设 = 你当前 dsh 版本的标准预设，再加上：

• BioDSH 人设：面向医生和湿实验科学家，跟随用户语言作答，不改原始数据，如实报告实际算了什么。
• BioDSH 官方技能：17 个经过验证的流程（单细胞质控/聚类/注释/治疗响应、bulk RNA-seq limma-voom、生存分析 KM/Cox、稳健标准误回归、方差分析设计等，统计类均与 R 逐项对照），出现在会话技能目录里。
• 技能库：2000+ 社区技能，不放进目录（目录保持小而稳定，利于缓存）。模型用 skill_library 工具检索，你也可以用 /技能名 直接调用。
• 技能精选：每条新消息，用模型对照全部技能选出最合适的一两个，以 /name 同样的形式注入。
• 收敛护栏：长任务到 480 秒（或 40 步）先提醒收尾，780 秒（或 60 步）要求直接作答；超过 80 步停止本轮。

设置：在 ~/.dsh/settings.yaml 写 biodsh: 一段（字段见上方英文说明），或在设置页修改，大多数改动下一步就生效。

安装：需要 DeepSeek Harness 0.2.1 及以上，并且 PATH 里有 pnpm。

• 命令行：dsh plugin --profile web add dsh-biodsh
• 网页：「插件」→「安装」，输入 dsh-biodsh

装好后重启 dsh，在智能体预设菜单里选 BioDSH，或按上面的 YAML 设为默认。

BioDSH (PTC)（biodsh-ptc）是同一预设加上程序化工具调用（同 dsh 自带的 ptc 预设）：模型每步写一段程序来调用工具，写脚本、运行、检查输出一步完成。在 15 道开发题上，步数中位数从 23 降到 16，耗时从 129 秒降到 97 秒，正确率不变。