Viewers

Which file types open in a BioBase viewer, and the limits every viewer shares.

Select a file in the file explorer to open it in a pane. Research formats open in a viewer, and other text files open in the editor.

File type	Extensions	Opens in
Genome tracks	.bed, .gff, .gff3, .gtf, .vcf, .wig, .bedgraph	Genome viewer
Sequences	.fa, .fasta, .fna, .ffn, .faa, .frn	Sequence viewer
Molecular structures	.pdb, .cif, .mmcif, .sdf, .mol, .mol2, .xyz	Structure viewer
Spreadsheets	.xlsx, .xls	Spreadsheet viewer
CSV and TSV	.csv, .tsv	Table view in the editor
NumPy arrays	.npy, .npz	Array viewer
HDF5 and AnnData	.h5, .hdf5, .h5ad	HDF5 viewer
R objects	.rds, .RData, .rda	R object viewer
Python pickles	.pkl, .pickle, .joblib	Pickle viewer
Charts	.json files holding a Vega-Lite spec	Chart viewer
HTML reports	.html, .htm	Report viewer
Word documents	.docx	Document viewer
PDF	.pdf	PDF viewer
Images	.png, .jpg, .jpeg, .gif, .webp, .svg, .bmp, .ico	Image viewer

A .json file that isn’t a chart spec shows as plain text.

Preview and Source

A text-based research file, such as a FASTA, BED or HTML file, opens in Preview. Select Source to edit it as text. Preview redraws from your unsaved edits. Binary formats open in Preview only.

How BioBase picks a viewer

BioBase reads the first bytes of a binary file, so PNG, JPEG, GIF and WebP images, HDF5 files, NumPy arrays, uncompressed R objects and pickles written with protocol 2 or later open in the right viewer under any extension. A .json or .html file opens as a chart or a report when its contents are a Vega-Lite spec or an HTML document. Every other format opens by its extension.

Size limits

Files	Largest file that previews
Research formats in the viewers	25 MB
PDFs and images	50 MB
CSV, TSV and other text files	50 MB

A larger file shows “Unable to load file” with its size and the limit. Open it in another application.

Messages

“BioBase cannot display this format. Open the file in a compatible application.” BioBase has no viewer for the format. This covers legacy .doc files, compressed files such as .csv.gz, .xz and .bz2 (a gzip-compressed R object opens), BAM, CRAM, bigWig, bigBed and any other binary format BioBase doesn’t recognize. An unrecognized binary file larger than 25 MB shows a binary-file notice instead. FASTQ and GenBank files open as text in the editor.

“This file is password protected. Remove the password in the application that created it, then open the unprotected copy here.” The workbook or document is sealed with a password, and BioBase never asks for it. A password-protected PDF reads “This PDF is password-protected” instead.

“This file is empty.” The file has no content.

The selected sheet, sequence view and genome assembly reset each time a file opens.