Molecular & Evolutionary Biology Workbench
MolBioCraft is a free, non-commercial desktop workbench for bench and computational biologists. It unites plasmid mapping, restriction digests, 14 cloning simulators, primer & CRISPR design, sequence alignment, phylogenetics, 4-dye Sanger chromatogram assembly, protein biophysics, and Mol* 3D structure visualization in one native window — powered by a 7-crate compiled Rust engine with publication-ready SVG export.
Sequence Map, Cloning, CRISPR, MSA, Phylogeny, Sanger & Mol* 3D
Gibson, Golden Gate, HiFi, In-Fusion, Gateway, TOPO & Virtual Gel
Compiled bioinformatics core with local REST API (127.0.0.1:18420)
Every algorithm cites its primary method in PROVENANCE.md
99 Built-In Sample Documents · 69 Vector Backbones · 98 Modular Vector Parts
MolBioCraft Welcome Hub featuring the Engraved Phoenix of Molecular Life emblem, one-click sample project loader, drag-and-drop multi-format ingestion, and interactive feature/codon/trace previews.
Circular plasmid map and linear sequence view synchronized under one zoom, with restriction sites, ORFs, primers, 3-frame translation, GC and hydropathy tracks, and a construct summary bar.
Sortable, filterable feature and primer table with one-click sequence selection, inline qualifier editing, automatic detection of 74 standard plasmid features, and GFF3 export.
Real-time GenBank, FASTA, EMBL, and GFF3 flatfile inspection and round-trip serialization of the active construct or genome record.
Simulate Restriction-Ligation, Gibson, NEBuilder HiFi, In-Fusion, Golden Gate / MoClo, LIC, SLIC, SLiCE, Yeast HR, TA/GC, TOPO, Gateway BP/LR, annealed oligos, and SOE-PCR beside a darkroom virtual agarose gel.
Browse a curated 69-backbone expression and cloning vector catalog, assemble constructs from 98 standardized modular parts, and run a 9-rule custom vector onboarding QC audit.
SantaLucia + Owczarzy salt-corrected Tm, Zuker/Nussinov hairpin & dimer folding, PCR & multiplex primer design, site-directed mutagenesis, and SpCas9 / LbCas12a CRISPR guide ranking with silent-PAM HDR ssODN donors.
Pairwise Gotoh affine global/local alignment (DNA scoring, BLOSUM62, PAM250), 2D k-mer synteny dotplots, multiple sequence alignment with MacClade/ClustalX conservation coloring, consensus building, and local BLAST.
Neighbor-Joining, UPGMA, and Felsenstein Maximum-Likelihood trees, JC69/K80/HKY85/GTR+Γ model ranking by BIC/AICc, Nei-Gojobori dN/dS, Tajima’s D, RSCU, and rectangular/cladogram/radial tree views.
4-dye ABI (.ab1) and SCF (.scf) capillary chromatogram viewer with Phred Q-scores, Mott quality trimming, heterozygote mixed-peak calling, and multi-read consensus contig assembly with variant calls.
Interactive Mol* 3D viewer for PDB/mmCIF structures with presets, pLDDT/B-factor coloring, Ramachandran plot, and Kabsch SVD Cα superposition (RMSD/TM-score), plus VCF/FASTQ/SAM/BED NGS tools.
ProtParam biophysics (MW, pI, ε280, GRAVY, instability, aliphatic index), Kyte-Doolittle hydropathy, multi-host codon optimization, 13 Bioinformatics Plugins, and an undoable provenance history.
127.0.0.1:18420Automate high-throughput sequence analysis from Python, R, or shell scripts on the same machine via the embedded multi-threaded REST server at http://127.0.0.1:18420/api/v1.
End-to-end construct audit combining GC and homopolymer window scans, in-frame CDS reading-frame verification, unique restriction cutters with Dam/Dcm methylation audit, colony-PCR primer design, and virtual diagnostic gel bands.
Automated early-exon target window identification, SpCas9 and LbCas12a guide RNA specificity/efficiency ranking, golden-gate cloning oligo generation, 120-nt silent-PAM HDR ssODN donor design, and flanking genotyping primers.
Validates ITR-to-ITR and LTR-to-LTR cargo size budgets, screens DNA synthesis onboarding constraints (repeats, extreme GC windows, forbidden motifs), and checks promoter-transgene-polyA cassette orientation.
Computes solubility and isoelectric point (pI) profiles, performs multi-host codon adaptation (E. coli, Yeast, CHO, HEK293), evaluates 5′ mRNA secondary structure folding, and audits affinity tags and protease cleavage sites.
Spliced gene models from GT-AG splice junctions, Kozak consensus starts, and in-frame exon chaining.
Prokaryotic and viral 6-frame coding sequence prediction with Shine-Dalgarno ribosome-binding site scoring.
Detects direct-repeat and spacer arrays across bacterial and archaeal genomic sequences.
Identifies 1–6 bp short tandem repeat (STR/SSR) tracts with copy number and repeat purity metrics.
Computes haplotype groups, haplotype diversity, segregating sites, and Shannon entropy across alignments.
Assigns taxonomic lineage from oligonucleotide k-mer signatures, dinucleotide odds ratios, and barcode motifs.
Evaluates clade distinctiveness, reciprocal monophyly, and intra/interspecific barcoding-gap distributions.
Scans conserved functional motifs (P-loop, zinc fingers, EF-hand, kinase loop), secondary structure, and B-cell epitopes.
Predicts hydropathy-window transmembrane helices, positive-inside orientation, and N-terminal signal-peptide cleavage.
Performs Illumina, Nextera, Nanopore, and PacBio adapter removal alongside Phred sliding-window quality trimming.
Maps collinear syntenic blocks, inversions, and rearrangements between two complete genome sequences.
Generates ready-to-submit SLURM / PBS cluster job scripts for large-scale phylogenetic tree searches.
Orchestrates MAFFT, Clustal Omega, Minimap2, Bowtie2, IQ-TREE 2, RAxML-NG, FastTree, PhyML, MrBayes, SPAdes, and Flye when installed.
| Code | Plugin | What It Does |
|---|---|---|
| PLG-01 | Eukaryotic Gene Predictor | Spliced gene models from GT-AG splice junctions, Kozak consensus starts, and in-frame exon chaining. |
| PLG-02 | Microbial Gene Predictor | Prokaryotic and viral 6-frame coding sequence prediction with Shine-Dalgarno ribosome-binding site scoring. |
| PLG-03 | CRISPR Repeat Array Finder | Detects direct-repeat and spacer arrays across bacterial and archaeal genomic sequences. |
| PLG-04 | Microsatellite & Tandem Repeats | Identifies 1–6 bp short tandem repeat (STR/SSR) tracts with copy number and repeat purity metrics. |
| PLG-05 | Haplotype & Allele Partitioner | Computes haplotype groups, haplotype diversity, segregating sites, and Shannon entropy across alignments. |
| PLG-06 | Taxonomic Sequence Classifier | Assigns taxonomic lineage from oligonucleotide k-mer signatures, dinucleotide odds ratios, and barcode motifs. |
| PLG-07 | Species Delimitation | Evaluates clade distinctiveness, reciprocal monophyly, and intra/interspecific barcoding-gap distributions. |
| PLG-08 | Protein Domains & Epitopes | Scans conserved functional motifs (P-loop, zinc fingers, EF-hand, kinase loop), secondary structure, and B-cell epitopes. |
| PLG-09 | Transmembrane & Signal Topology | Predicts hydropathy-window transmembrane helices, positive-inside orientation, and N-terminal signal-peptide cleavage. |
| PLG-10 | Adapter & Quality Read Trimmer | Performs Illumina, Nextera, Nanopore, and PacBio adapter removal alongside Phred sliding-window quality trimming. |
| PLG-11 | Whole-Genome Synteny Blocks | Maps collinear syntenic blocks, inversions, and rearrangements between two complete genome sequences. |
| PLG-12 | HPC Phylogeny Job Builder | Generates ready-to-submit SLURM / PBS cluster job scripts for large-scale phylogenetic tree searches. |
| PLG-13 | External CLI Suite Runner | Orchestrates MAFFT, Clustal Omega, Minimap2, Bowtie2, IQ-TREE 2, RAxML-NG, FastTree, PhyML, MrBayes, SPAdes, and Flye when installed. |
arm64 + x86_64 · macOS 11+
Universal macOS disk image (.dmg) containing native Apple Silicon and Intel binaries in a single MolBioCraft.app bundle.
Drag MolBioCraft.app to Applications. On first launch, Control-click > Open, or run:
xattr -dr com.apple.quarantine /Applications/MolBioCraft.app
x86_64 · Windows 10 / 11
Standard Windows MSI installer package for system deployment, plus a standalone zero-install Portable .exe executable.
If Microsoft Defender SmartScreen prompts on first launch, click "More info" -> "Run anyway". Or deploy via CLI:
msiexec /i MolBioCraft-1.0.0-Windows-x64.msi
x86_64 / amd64 · Ubuntu 22.04+ & Debian 12+
Native ELF x86_64 Debian package built with WebKitGTK 4.1 and GTK 3 desktop integration.
Install the .deb package with automatic dependency resolution using apt:
sudo apt install ./MolBioCraft-1.0.0-Linux-x86_64.deb
GenBank (.gb, .gbk), FASTA (.fasta, .fa, .fna, .faa), EMBL (.embl), GFF3 (.gff3)
Applied Biosystems ABI (.ab1), Standard Chromatogram Format (.scf)
Clustal (.aln), FASTA, PHYLIP (.phy), NEXUS (.nex), Newick (.nwk, .tre)
Protein Data Bank (.pdb), Crystallographic Information Framework (.cif, .mmcif)
Variant Call Format (.vcf), FASTQ (.fastq, .fq), SAM (.sam), BED (.bed)
MolBioCraft Session (.mbc), Exportable Preferences (.mbcprefs.json)
molbiocraft-coreNucleotide/amino-acid alphabets, intervals, thermodynamic tables, and provenance graph
molbiocraft-formatsZero-copy parsers & serializers for GenBank, EMBL, FASTA, GFF3, ABI .ab1, SCF, PDB/mmCIF, VCF/SAM/BED
molbiocraft-alignGotoh affine pairwise alignment, 2D k-mer dotplots, POA / MSA consensus, and local seed-and-extend search
molbiocraft-phyloNJ, UPGMA, Felsenstein pruning ML, JC69/K80/HKY85/GTR+Γ substitution models, dN/dS, Tajima’s D
molbiocraft-cloningREBASE digest engine, 14 cloning simulators, SantaLucia/Owczarzy Tm, Zuker folding, SpCas9/LbCas12a CRISPR
molbiocraft-proteinProtParam biophysics, Kyte-Doolittle hydropathy, Lupas coiled-coils, TM helices, Kabsch SVD superposition
molbiocraft-wasmWebAssembly bridge exposing deterministic Rust execution to the React 18 / TypeScript studio interface
| Workbench Action | macOS | Windows & Linux |
|---|---|---|
| Quick Command Navigator | ⌘K | Ctrl+K |
| Find in Sequence / Search Tools | ⌘F / ⇧⌘F | Ctrl+F / Ctrl+Shift+F |
| New DNA / RNA / Protein Sequence | ⌘N | Ctrl+N |
| Open .mbc Workbench Session | ⌘O | Ctrl+O |
| Save / Save As .mbc Session | ⌘S / ⇧⌘S | Ctrl+S / Ctrl+Shift+S |
| Import Sequence Files / Clipboard | ⌘I / ⇧⌘I | Ctrl+I / Ctrl+Shift+I |
| Clone Insert into Vector | ⇧⌘C | Ctrl+Shift+C |
| Reverse Complement Active Construct | ⇧⌘R | Ctrl+Shift+R |
| Toggle Left Project Explorer | ⌘B | Ctrl+B |
| Toggle Right Inspector Panel | ⌥⌘I | Ctrl+Alt+I |
| Switch Scientific Studios (1–9) | ⌘1 … ⌘9 | Ctrl+1 … Ctrl+9 |
| Open Preferences | ⌘, | Ctrl+, |
Clone the repository to compile the 7-crate Rust workspace to WebAssembly, run the full reference-oracle test suite, or package native desktop installers.
git clone https://github.com/manbaritone/MolBioCraft.git cd MolBioCraft npm install npm run wasm:build # compile 7-crate Rust engine to WebAssembly npm run dev # launch workbench interface in browser cargo test --workspace # run full Rust bioinformatics test suite npm run package:installers # build native universal desktop installer
Built by Bundit Boonyarit with AI coding agents governed by SDLC Studio (DarrenBenson/sdlc-studio) — a spec-first, TDD operating system for AI agents.
reconcile --verify): Verified via cargo test & Vitest.Enforces a strict No Reverse Engineering Anything (No REA) clean-room policy — never inspecting or copying commercial software.
Every algorithm and parser is implemented from peer-reviewed papers and public specifications, validated against open reference oracles.
.ab1 & wwPDB.PROVENANCE.md)Every scientific equation, primary journal citation, Rust crate path, and reference oracle is documented in the repository.
Open-source specification-driven TDD workflow, compaction-safe state tracking, and independent 5-leg review gate for AI coding agents.
SCAN TO SUPPORT ☕Every contribution helps keep MolBioCraft free, offline-first, and continuously updated for students, bench biologists, and academic labs worldwide.
If you use MolBioCraft to design constructs, simulate gels, align sequences, infer phylogenetic trees, or prepare publication figures, please cite:
@software{Boonyarit_MolBioCraft,
author = {{Bundit Boonyarit}},
license = {CC-BY-NC-4.0},
month = oct,
title = {{MolBioCraft: A cross-platform bioinformatics workbench for sequence analysis in molecular biology and evolutionary biology research}},
url = {https://github.com/manbaritone/MolBioCraft},
version = {1.0.0},
year = {2026}
}Report bugs, request new cloning simulators or file format parsers on github.com/manbaritone/MolBioCraft/issues, or join community Q&A and workflow discussions on github.com/manbaritone/MolBioCraft/discussions.