Overview

Bionomics Lab is a simple research platform for exploring genes, sequences, protein structure, and viral search results.

What the platform does

• Finds biological evidence from trusted sources.
• Shows results with citations so you can see where the information came from.
• Uses plain language so the result is easier to understand.
• Lets you move from a quick lookup to a deeper analysis without changing tools.

Who it is for

• Students who want to learn biology with real examples.
• Teen users who want clear answers without hard jargon.
• Researchers who want a fast way to check evidence before digging deeper.

Main ideas to remember

• Search first, explain second.
• Every important result should be backed by a source.
• If the system is unsure, it should say so.

Example use case

You want to learn what the BRCA1 gene does. You search for BRCA1, look at the sequence and structure modules, and then ask the assistant to explain the results in simple terms.

Getting Started

Use these steps if you are opening the platform for the first time.

1. Start on the Research page

The home page gives a quick overview of the platform and links to the main tools.

2. Open the Platform page

The Platform page contains the live research workspace. You can try the modules, run discovery actions, and chat with the assistant.

3. Pick a module

Choose the module that matches your question:

• info for gene or protein facts
• seq for sequences
• blast for similarity search
• pdb for known structures
• alphafold for predicted structures
• elm for motifs and domains
• virus for virus search by host

4. Read the citations

Always check the citations and uncertainty notes before you use the result in a report or project.

5. Ask the assistant

Use the assistant when you want the evidence explained in simple language.

Example use case

You are writing a school project about a gene. You open the Platform page, run the info module, check the citations, and then ask the assistant to explain what the gene does.

Modules

This platform has seven core modules. Each module focuses on one type of question.

Gene Annotation: info

Use this when you want a short summary of a gene or protein.

Example use case: You search for BRCA1 to learn its main function and key metadata.

Sequence Retrieval: seq

Use this when you want the DNA or protein sequence for a target.

Example use case: You paste a gene name to get the sequence and compare it with another sample.

Homology Search: blast

Use this when you want to compare a sequence against other known sequences.

Example use case: You have a DNA fragment from a sample and want to find the closest match.

Structure Lookup: pdb

Use this when you want an experimentally solved protein structure.

Example use case: You search for a protein before building a report on its shape and known structure.

Structure Prediction: alphafold

Use this when no solved structure is available and you want a predicted 3D model.

Example use case: You want a likely structure for a protein that has not been solved in the lab.

Motif Analysis: elm

Use this when you want to find small functional regions, like domains or signals.

Example use case: You check whether a protein has a nuclear localization signal or another known motif.

Virus Search by Host: virus

Use this when you want to find viruses linked to a host or organism.

Example use case: You search for viruses associated with a host species while preparing a class presentation.

How to choose the right module

• Want a quick fact? Use info.
• Want a sequence? Use seq.
• Want a similar match? Use blast.
• Want a structure? Use pdb or alphafold.
• Want a motif or domain? Use elm.
• Want a virus lookup? Use virus.

Features

The platform includes features that help users move from search to understanding.

Research Playground

The Research Playground lets you run a module with a query and view the result immediately.

Example use case: You test a gene name in info, then switch to seq to see the sequence without leaving the page.

Discovery Workbench

The Discovery Workbench is for looking at normalized discovery responses from the data layer.

Example use case: You compare search terms and IDs to see which records come back first.

AI Research Assistant

The assistant explains results using grounded evidence. It should not guess when the evidence is weak.

Example use case: After finding a result, you ask, "What does this mean in simple terms?" and the assistant answers with citations.

Citations and uncertainty

Every result should show sources and a clear uncertainty note when the data is incomplete or partial.

Example use case: You are unsure whether a result is strong enough for a report, so you check the citations before using it.

Simple navigation

The site keeps the main paths easy to find: Research, Platform, and Docs.

Example use case: A new user can open the docs first, then jump to the Platform page when they are ready to try the tools.

Example workflows

• Learn a gene with info, seq, and the assistant.
• Compare a sample with blast, then verify structure with pdb or alphafold.
• Look for motifs with elm and explain the result in the assistant.
• Search viruses with virus, then save the answer with the citations.

API and Data Flow

The frontend talks to the FastAPI backend. The backend fetches biological data and returns it with citations and uncertainty notes.

What the backend returns

• The module name that answered the request.
• The user query.
• The data payload.
• Citations.
• Uncertainty notes.
• A retrieval timestamp.

Main endpoints

• POST /api/info
• POST /api/seq
• POST /api/blast
• POST /api/pdb
• POST /api/alphafold
• POST /api/elm
• POST /api/virus
• POST /api/assistant/query

Simple data flow

• The user types a query.
• The frontend sends it to the backend.
• The backend gets evidence from gget-based sources.
• The frontend shows the response, citations, and uncertainty.

Good habits

• Check the source before you trust the answer.
• Use the assistant to explain, not to invent facts.
• Treat uncertainty notes as important, not optional.

Example use case

You open the Platform page, run a module, and then read the returned citations before sharing the result with your class or team.

FAQ

Is this platform beginner friendly?

Yes. The docs and UI should stay simple, with clear labels and short explanations.

Do I need to know biology before using it?

No. You can start with a gene name or a simple question, then learn the terms as you go.

What should I check before using a result?

Read the citations and uncertainty notes.

What if I do not know which module to use?

Start with info. If you need more detail, move to seq, blast, pdb, alphafold, elm, or virus.

Example use case

You are not sure which tool fits your question. You read the FAQ, open the module guide, and then choose the best module before running a search.