Find open-source science resources

SeqBench is a browser-based workbench of 82 tools for molecular cloning, primer design and sequence analysis: nearest-neighbour melting temperature, oligo dimer and hairpin screening, in-silico PCR, site-directed mutagenesis, restriction mapping, Gibson, Golden Gate and restriction-ligation assembly simulation, plasmid annotation and backbone identification, CRISPR gRNA, HDR donor and base editing design, codon optimisation and CAI, pairwise and multiple alignment, RNA secondary structure, protein properties, Sanger ab1 traces, HGVS conversion and variant annotation. It verifies constructs as well as designing them: re-deriving an assembly from its stated parts and diffing it against the claimed product, aligning sequencing reads back onto a claimed reference, and scoring Golden Gate overhang sets against published ligation-fidelity data. Batch FASTA processing, multi-tool workflows, a conversational tool-calling interface (SeqBench-GPT), a REST API and an MCP server are included.

Browser-based viewer for Sanger sequencing chromatograms in AB1/ABIF and SCF format, and for the .srd raw files of the Nanofor-05 capillary sequencer, converted to ABIF as they open. Shows raw and analysed traces, base calls (called or edited), per-base quality and the full ABIF directory, and puts two reads side by side with their tag tables aligned. A read aligns against a pasted or loaded reference, which reports identity, mismatches, indels and the ends that did not align, and flips the strand when the read is on the other one. End trimming (modified Mott or sliding window) has draggable handles, motif search is IUPAC-aware and finds primers, and QC metrics copy out as CSV. Drag on a trace to select a base range, then copy it as FASTA, zoom to it or export just that region. Exports the read as FASTA, FASTQ, .qual or ABIF and the chromatogram as a high-resolution PNG. Open files are kept as local sessions. Runs entirely in the browser — files are never uploaded.

BioCalculator is a mobile toolkit for biology and laboratory calculations. It consolidates calculators and preparation guides for molecular biology, microbiology, virology, stock solutions, buffers, dilutions, unit conversions, and TCID50 endpoint dilution workflows for students and lab professionals.

Browser-based tool to open almost any file that carries sequence — FASTA, FASTQ, GenBank, EMBL, Swiss-Prot, AB1/ABIF, SCF, Clustal, Stockholm, PHYLIP, NEXUS, MSF, PIR, MEGA, GFF3, SAM, BAM, GFA, PDB and ACE — see every sequence inside, pick the ones you want, and save them as FASTA. The format is detected from the file content, not from the extension, so unlabelled or misnamed files still open, and gzip-compressed files are unpacked in place. Records can be filtered by length, name, GC or sequence type, reverse-complemented, transcribed DNA↔RNA or translated to protein, deduplicated and reordered before saving. Runs entirely in the browser — files are never uploaded.

Browser-based viewer for GenBank and GenPept records — .gb, .gbk, .gbff, .gp and plain GenBank text. Renders an interactive linear and circular feature map, including circular plasmid maps, alongside the annotated source text and the nucleotide/protein sequence. Translates CDS features using the record's own genetic code and translation qualifiers, flags where the stored /translation disagrees with a plain translation, and adds optional computed layers: ORF prediction and restriction-site mapping. Drag a range in the sequence band to select it, then copy that stretch — either strand, as DNA or as protein, plain or FASTA. Filters features by type, handles multi-record files, and keeps open records as local sessions, so a closed tab can be picked up where it was left. Runs entirely in the browser — files are never uploaded.

Browser-based viewer that maps sequencing reads onto one short reference — an amplicon, gene or plasmid. Reads open as Sanger AB1/ABIF, SCF, FASTA, FASTQ or a SAM somebody else already mapped (gzipped files are unpacked in place); the reference as FASTA, GenBank or a read. Both read orientations are tried automatically. The pileup reports per-position depth, where reads disagree with the target, and the consensus — phred-weighted for capillary reads, which keep their chromatogram under the letters. An optional protein lane translates target and consensus side by side. Reads are placed by minimap2 compiled to WebAssembly, or by the built-in aligner. One read or the whole alignment saves as FASTA. Runs entirely in the browser — files are never uploaded.