Question 1

What is Neuron Lab?

Accepted Answer

Neuron Lab is a comprehensive research platform for neurobioinformatics, computational neuroscience, and genomics. It provides 83 analysis modules spanning statistics, machine learning, signal processing, dynamical systems, sequence analysis, and graph tools — plus 7 production bioinformatics pipelines, 3 foundation-model baselines (Neuron-FM), and a built-in AI research assistant. Everything runs on cloud compute with no local setup required.

Question 2

Who is it for?

Accepted Answer

Neuroscientists, bioinformaticians, genomics researchers, clinical labs, computational biology students, and small-to-medium labs that need a single platform for analysis without stitching together notebooks, scripts, and CLI tools. Whether you work with EEG, fMRI, single-cell RNA-seq, whole-genome sequencing, or neural network simulations, Neuron Lab has modules for your workflow.

Question 3

Do I need to know how to code?

Accepted Answer

No. Every module has a parameter form, a plain-language description, and structured outputs (metrics, tables, interactive charts, embeddings, rasters). You can also use sample datasets to explore any module instantly. Coding is entirely optional.

Question 4

How are results computed?

Accepted Answer

All analyses run on a dedicated cloud compute backend (Google Cloud Run). Each module implements its algorithm server-side — from Welch's t-test to Hodgkin-Huxley integration to deep learning classifiers. No third-party statistical services are called. Pipeline jobs run on scalable cloud infrastructure with real-time progress tracking.

Question 5

How many modules are available?

Accepted Answer

83 modules across 12 categories: Statistics & Hypothesis Testing (t-test, ANOVA, chi-square, Mann-Whitney, Kruskal-Wallis, correlation, regression, survival analysis, Bayesian inference, bootstrap, permutation test, effect size), Machine Learning (random forest, SVM, gradient boosting, logistic regression, neural network, k-means, DBSCAN, hierarchical clustering, isolation forest, cross-validation), Signal Processing (EEG spectral analysis, wavelet transform, Fourier transform, bandpass filter, spike sorting, event-related potentials, coherence analysis, phase-amplitude coupling), Dynamical Systems (Hodgkin-Huxley, FitzHugh-Nagumo, Wilson-Cowan, Izhikevich neuron, neural field, mean field, bifurcation analysis, Lotka-Volterra, Morris-Lecar), Dimensionality Reduction (PCA, t-SNE, UMAP, ICA, NMF, factor analysis, MDS, LDA), Sequence & Omics (sequence alignment, motif discovery, gene expression, differential expression, pathway enrichment, variant calling, methylation analysis, single-cell RNA-seq), Network & Graph (community detection, graph metrics, spectral clustering, network motifs, small-world analysis, rich-club detection, connectome analysis), Imaging (image segmentation, cell counting, morphometry, colocalization, deconvolution), and more.

Question 6

What is the AI research assistant?

Accepted Answer

The built-in AI assistant is powered by Google Gemini and helps you interpret results, suggest next analyses, explain statistical concepts, and draft methodology sections. It is context-aware — it can see your current module outputs and suggest relevant follow-up analyses.

Question 7

Can I run modules on my own data?

Accepted Answer

Yes. Upload CSV, TSV, or other supported formats directly in each module's interface. You can also use the built-in sample datasets to test any module before uploading your own data.

Question 8

What output formats are available?

Accepted Answer

Each module produces structured JSON results that render as interactive charts (Recharts), data tables, heatmaps, network graphs, raster plots, or downloadable files. You can export results as CSV or JSON, and visualizations as PNG.

Question 9

What pipelines are available?

Accepted Answer

7 production-grade bioinformatics pipelines: RNA-Seq (differential gene expression, from $50 base + $12/sample), ATAC-Seq (chromatin accessibility, $40 + $8/sample), ChIP-Seq (protein-DNA binding, $40 + $8/sample), Methyl-Seq (DNA methylation profiling, $75 + $18/sample), Sarek (somatic & germline variant calling, $120 + $35/sample), scRNA-Seq (single-cell transcriptomics, $85 + $22/sample), and CUT&RUN (histone modification mapping, $45 + $9/sample).

Question 10

Which organisms are supported?

Accepted Answer

9 reference organisms with pre-configured genome references: Human (GRCh38), Mouse (GRCm39), Rat (mRatBN7.2), Zebrafish (GRCz11), Drosophila (BDGP6), C. elegans (WBcel235), Macaque (Mmul_10), Marmoset (mCalJac1), and Pig (Sscrofa11.1).

Question 11

How does pipeline pricing work?

Accepted Answer

Each pipeline has a base cost plus a per-sample fee. Pricing is standalone per run and separate from monthly subscription plans. You can validate your pipeline configuration (organism, samples, parameters) before submitting. Submitted jobs run on scalable cloud infrastructure with real-time status tracking.

Question 12

How do I submit a pipeline job?

Accepted Answer

Use the Pipeline Wizard: select your pipeline type, choose an organism preset, configure parameters, upload your data, and submit. The system validates your configuration before submission and provides real-time progress updates as the job runs.

Question 13

What is Neuron-FM?

Accepted Answer

Neuron-FM is our catalog of foundation-model baselines for three data domains: single-cell transcriptomics, neural signals, and brain connectomes. The current release uses parameter-free representations (PCA / spectral embeddings + nearest-centroid or k-means) that reproduce competitive baselines from the recent literature.

Question 14

Which downstream tasks are supported?

Accepted Answer

Cell-type annotation and clustering for scRNA-seq (Cell Atlas FM), dynamical-state classification and embedding for EEG/electrophysiology (Neural Signal FM), and community detection on brain connectomes (Connectome FM).

Question 15

Can I run Neuron-FM on my own data?

Accepted Answer

Yes. Attach a compatible dataset or use the built-in synthetic demo data when launching any foundation model.

Question 16

What kinds of data can I upload?

Accepted Answer

Numeric matrices, count tables, gene expression data, sequences, spike trains, EEG/signal recordings, adjacency matrices, VCF files, FASTQ references, and signal windows in common text formats (CSV/TSV). Each module page lists its accepted input types and provides sample datasets.

Question 17

Where is my data stored?

Accepted Answer

Uploaded datasets and analysis results are stored in a private cloud storage bucket scoped to your account. Metadata is stored in a database with row-level security so that only you (and collaborators you explicitly invite) can access your data. Data is retained for 30 days after your last activity.

Question 18

Is my data used to train models?

Accepted Answer

No. Your uploads are only used to run the analyses you launch. We do not train foundation models or any other models on user data.

Question 19

Can I delete my data?

Accepted Answer

Yes. Datasets, projects, and analysis results can be deleted from the corresponding page. Deletion removes the underlying storage object and all associated database rows.

Question 20

How do I create an account?

Accepted Answer

Sign up with email and password on the Sign in page. A profile is created automatically the first time you sign in. You can start using all 83 modules and the AI assistant immediately.

Question 21

Is there a free plan?

Accepted Answer

Yes. The Free plan gives you access to all 83 analysis modules and the AI assistant for evaluation and small projects. Paid plans add higher usage limits, priority compute, and pipeline access. Pipeline jobs are priced separately per run.

Question 22

How is usage measured?

Accepted Answer

Usage is measured by the number of analyses launched, pipeline jobs submitted, AI assistant queries, and the size of stored datasets. Detailed limits per plan are on the Pricing page.

Question 23

How does pipeline billing work?

Accepted Answer

Pipeline jobs are billed per run at a fixed base cost plus a per-sample fee. This is separate from your monthly plan. You can see the exact cost before submitting any pipeline job.

Question 24

How are accounts protected?

Accepted Answer

Passwords are handled by a managed authentication service (Supabase Auth); the platform never sees plaintext passwords. Sessions use short-lived access tokens and rotating refresh tokens. All communication between the frontend and backend is encrypted via HTTPS.

Question 25

Who can see my data?

Accepted Answer

Only you. Every user-scoped table has row-level security policies keyed on your authenticated user ID. The compute backend uses API-key authentication, and all server operations verify roles server-side.

Question 26

Is the platform compliant with research data regulations?

Accepted Answer

Neuron Lab follows industry best practices for data security: encryption in transit (TLS), isolated per-user storage, row-level security, and no cross-user data sharing. For institutions requiring formal compliance documentation (HIPAA BAA, DPA), please contact us about our Enterprise plan.

Question 27

How do I report a security issue?

Accepted Answer

Please email support@neuron-lab.online with a description and reproduction steps. We aim to acknowledge reports within one business day.

Question 28

What technology stack powers Neuron Lab?

Accepted Answer

The frontend is built with React, TypeScript, and TailwindCSS, hosted on Vercel. The compute backend runs on Google Cloud Run (Python/FastAPI) with auto-scaling. Data is stored in Supabase (PostgreSQL) with Google Cloud Storage for file uploads. This architecture means zero cold-start costs when the platform is idle.

Question 29

Can I use Neuron Lab offline?

Accepted Answer

No. Neuron Lab is a cloud-based platform. All computations run on the server to ensure reproducibility and to handle large datasets that would be impractical to process locally.

Question 30

Are there API endpoints I can call programmatically?

Accepted Answer

The compute backend exposes a RESTful API for all 83 modules. Programmatic access is available on paid plans. Contact us for API documentation and integration details.

Question 31

What browsers are supported?

Accepted Answer

Neuron Lab works in all modern browsers: Chrome, Firefox, Safari, and Edge. We recommend the latest version of Chrome or Firefox for the best experience with interactive charts and visualizations.

Frequently asked questions

About Neuron Lab

Modules & capabilities

Bioinformatics pipelines

Foundation models (Neuron-FM)

Data & privacy

Accounts, billing & pricing

Security & compliance

Technical details