A collaborative notebook for comparative genomics

Visit for a GeneNoteBook server running on an example dataset.

Getting started

Install GeneNoteBook using bioconda

> conda install -c bioconda genenotebook

Start a GeneNoteBook daemon on localhost:3000

> genenotebook run

Add your data

> genenotebook add [genome/annotation/...]
Additional options
For additional information on for instance Docker containers, loading transcriptome data, or configuring user accounts, see the full documentation.

Gene Table

Quickly scroll through all genes from multiple organisms and perform custom queries. The Gene Table allows for comparative visualization of Gene Models, Protein Domains and Gene Expression.

Custom queries

Any gene attribute is automatically indexed to allow efficient queries.
Query results can be saved in several canonical file formats like fasta for coding sequences, gff3 for genome annotations and tsv for gene expression levels.

Gene Models

Visualize the exon structure of predicted Gene Models. Explore predicted alternative splicing.

Protein Domains

Visualization of InterProScan predicted protein domains allows for quick assesment of putative protein function.
Links to InterPro based on IDs.


Orthogroup phylogenetic trees visualize evolutionary relationships between genes. Tree labels are hyperlinks to quickly navigate between members of an orthogroup.

Expression levels

Expression level barplots automatically display sample sizes of experiments, as well as error bars representing the standard error.

User profiles

The user profile system allows for configuration of private access to data.

Version history

Every manually changed annotation is tracked in a version history system, so that at any moment unwanted changes can be reverted.