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Formaticon Documentation

Your complete guide for using the Cellformatica  AI-powered tools for bioscience research - from submitting general unstructured tasks to AI scientist (write a paper, perform data analysis or literature research)  to running preconfigured instruments (interpret a candidate target list or generate a rich  analysis of a gene set ) .

What is Formaticon?

Formaticon is an AI-driven bioscience research platform developed by Cellformatica. It combines large language models with systematic literature retrieval, pathway analysis, and structured report generation to help researchers answer scientific questions at scale. Whether you need to screen hundreds of genes against a hypothesis, generate a multi-section analytical report, or commission a fully autonomous deep-research pipeline, Formaticon delivers publication-ready outputs, complete with code, figures, hypotheses, PRISMA-compliant search protocols, and formatted references.

Three ways to do research

🤖

Bioscientist Agent

Describe any open-ended research question or task. The autonomous pipeline searches, reasons, hypothesizes, and delivers a full PDF/DOCX white paper.

Best foR RevieW, research & white papers, DATA ANALYSIS,PEER REVIEW.
🔬

Batch Query

Screen a list of entities — genes, drugs, diseases, cell types — against a research question. Get an interactive ranked table and scatter plot.

Best for INTERPRETING large entity lists
📄

Gene module analysis   

Submit a focused gene list and research question. Receive a multi-section narrative report with regulatory network analysis, figures, and references.

Best for DEEP ANALYSIS OF targeted gene sets

Quick start

  1. Create an account Register at formaticon.cellformatica.com/register with your name, email, phone, and a password. Then log in.
  2. Add credits Each run consumes credits based on AI compute used. Open your Profile page and follow the billing link to purchase credits via Stripe.
  3. Choose a workflow Use the table below or the navigation to choose: Batch Query for entity screening, Detailed Report for a curated gene set, or Bioscientist Agent for open-ended deep research.
  4. Fill in the form and submit Enter your research question and any required inputs (entity list, gene list, or a detailed task description). Review the cost estimate, then confirm.
  5. Wait for results Batch Queries typically complete in a few minutes. Detailed Reports take 30–90 minutes. Bioscientist Agent tasks run for 1–2.5 hours. You can monitor status in real time.
  6. Download and share View your results in the browser, download PDF and DOCX files, export CSVs, and share results with colleagues via a secure access-token link.

Choosing the right workflow

Criterion Batch Query Gene module analysis  Bioscientist Agent
Input Question + entity list (genes, drugs, diseases, etc.) Question + gene list (<30 genes) Open-ended question or research task (+ optional files)
Output Ranked table + scatter plot + CSV PDF/DOCX multi-section report PDF/DOCX white paper + figures + hypotheses + PRISMA
Runtime A few minutes 30–90 minutes 1–2.5 hours
Best for Screening many candidates against one question Narrative causal analysis of a curated gene set Systematic reviews, white papers, exploratory deep research
Downloads CSV PDF, DOCX PDF, DOCX, figures, session log, RIS references

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