โ† AI Tools
Bio AIIntermediate

PromptBio

Life science-focused agentic AI platform โ€” for automated experimentation, literature search, and drug discovery.

PromptBio is a life science-specialized agentic AI platform established in 2023 in Pleasanton, California, USA, and fully relaunched in June 2026. Researchers can input scientific questions in natural language, and the platform automatically completes the entire process, from data exploration to pipeline execution, statistical analysis, visualization, and report generation, all within a single environment. Similar to how GPT understands and generates any text, PromptBio's core architecture, the Chief Scientific Orchestrator (CSO), automatically configures and executes appropriate analysis pipelines for any biological data, from bulk RNA-seq to single-cell RNA-seq and multi-omics integrated data. Under the CSO, three modules โ€“ PromptGenie (a human-in-the-loop multi-agent system), DiscoverFlow (an end-to-end automated workflow), and ToolsGenie (dynamic code generation for custom analysis) โ€“ collaborate organically, and a graph-based workflow engine manages data dependencies. Traditional bioinformatics analysis involves high technical barriers, such as R/Python scripting, command-line pipeline configuration, and cluster job management, which has hindered researchers' essential scientific thinking. In reality, even running DESeq2 can take half a day due to environment setup. PromptBio addresses this by simply asking, "What do you want to know?" in natural language, and the agent handles the rest of the technical processes. The division of labor within PromptGenie, where the DataAgent collects data from public databases, the OmicsAgent executes pre-validated pipelines, the AnalysisAgent performs statistical interpretation, and the QAgent handles interactive summarization and visualization, provides domain expertise fundamentally different from a single LLM chatbot. In addition, MLGenie automatically builds machine learning-based biomarker prediction models, and Omics Tools and Analysis Tools handle standardized omics pipelines and downstream statistical analysis, respectively, ensuring the depth of the analysis. Researchers at early adopter institutions such as UCSF, Northeastern University, and the South African CSIR have reported approximately a 30% reduction in analysis time compared to previous methods. For example, if a researcher requests, "Perform differential gene expression analysis followed by pathway enrichment analysis" on RNA-seq data from cancer patients, PromptGenie automatically generates and organizes a reproducible report, including DESeq2-based analysis, Gene Ontology/KEGG pathway enrichment, volcano plots, and heat map visualizations. Using DiscoverFlow, multi-omics workflows that integrate transcriptomics, proteomics, and metabolomics can be executed without code, and ToolsGenie dynamically generates executable Python/R code when custom analysis not included in standard pipelines is required. As a cloud-based SaaS, it is accessible on GCP, AWS, and Azure, and supports automatic scaling of GPU clusters to handle large datasets. It is also noteworthy that PromptBio has released its own benchmark (PromptBio-Bench), consisting of 244 expert-curated tasks, to provide a standard for evaluating the performance of LLM-based bioinformatics agents.

๐Ÿ’ป System Requirements

๐Ÿง RAM

Not required on the client side. Server-side GPU cluster automatically scales (no user management required).

๐Ÿ’พStorage

Minimal storage required on the client side. Data uploads and analysis results are managed in cloud storage.

โšก Installation

### 4-1. Quick Start (SaaS Platform)

```
1. Visit https://platform.promptbio.ai
2. Create a free trial account
3. Enter your analysis question in natural language โ†’ The agent automatically configures and executes the pipeline
```

### 4-2. Open-Source Benchmark (promptbio-bench)

```bash
git clone https://github.com/PromptBio/promptbio-bench.git
cd promptbio-bench
pip install -r requirements.txt
# Execute the task to evaluate 244 bioinformatics agents
```

### 4-3. pyNullstrap (Statistical Tool)

```bash
git clone https://github.com/PromptBio/pyNullstrap.git
cd pyNullstrap
pip install -e .
# Feature selection based on FDR control (Python implementation of the Nullstrap method)
```

๐Ÿงฌ Bio Use Cases

๐Ÿ”ฌ

Multi-omics Biomarker Discovery

Upload RNA-seq and proteomics data, and request in natural language to "identify differentially expressed genes and biomarker candidates between disease and control groups." PromptGenie's OmicsAgent executes an automated pipeline: DESeq2 differential expression analysis โ†’ AnalysisAgent performs Gene Ontology/KEGG pathway enrichment โ†’ MLGenie builds a biomarker prediction model. Based on early adopters at UCSF, this reduces analysis time by approximately 30% compared to manual methods.

๐Ÿงฌ

Single-Cell Transcriptomics Clustering and Cell Type Annotation

Submit scRNA-seq data with the prompt: "Cluster cells by type and identify marker genes." DataAgent performs data preprocessing (QC, normalization), OmicsAgent performs dimensionality reduction (PCA/UMAP) + clustering (Leiden), and QAgent interactively provides UMAP visualization and a heatmap of marker genes for each cluster. This allows users to obtain Scanpy-level analysis results without writing code.

๐Ÿ’Š

Novel Drug Target Exploration through Literature Mining

When requesting to "extract the latest potential therapeutic targets for a specific disease from the literature," the CSO deploys a literature search agent to perform large-scale scans of PubMed/bioRxiv โ†’ extract gene-disease relationships โ†’ and automatically cross-validate the omics expression patterns of candidate targets using DiscoverFlow. This compresses the traditionally weeks-long literature review + data validation cycle into just a few days.

๐Ÿ“„ Official Docs๐Ÿ™ GitHub

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