biosuite-ultra 4.2.0

BioSuite Ultra - Comprehensive open-source bioinformatics platform with 47 analysis modules, parallel processing, molecular cloning, plasmid maps, and virtual gel electrophoresis

BioSuite Ultra

The most comprehensive open-source bioinformatics platform.

BioSuite Ultra is a full-stack bioinformatics platform with 47 analysis modules, 26 visualization types (123 functions), a cyberpunk GUI, a 99+ option CLI, and SnapGene-killer molecular cloning tools — all in pure Python. No external bioinformatics tools required. 100% free.

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What's New in v4.2.0

• Parallel Processing: Multi-threaded/multi-process execution for all modules
• 100+ Restriction Enzymes: Expanded from 18 to 100+ enzymes
• Better Bayesian Phylogeny: Real MCMC sampling with Jukes-Cantor model
• Improved MD Simulation: Velocity Verlet integrator, Berendsen thermostat
• Bug Fixes: 30+ bug fixes across all modules
• Better Documentation: Comprehensive changelog and improved docs

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🚀 Quick Start

# Install
pip install biosuite-ultra

# Run GUI
python -m biosuite

# Or use Docker
docker pull sahandtkod/biosuite-ultra:latest
docker run -p 8000:8000 sahandtkod/biosuite-ultra

Binder:

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Features

47 Analysis Modules

Domain	Modules	Coverage
Sequence Analysis	FASTA/FASTQ I/O, GC%, translation, reverse complement, ORF finder, primer design, restriction enzymes, codon usage	85%
Alignment	Needleman-Wunsch, Smith-Waterman, BLAST (k-mer), MSA (progressive + Clustal/MUSCLE/MAFFT)	75%
Phylogenetics	p-distance, UPGMA, NJ, ML (RAxML/IQ-TREE), Bayesian (MrBayes + MCMC)	90%
Transcriptomics	CPM/TPM/DESeq2 normalization, differential expression (NB GLM), GO/KEGG enrichment	70%
NGS/Genomics	BAM/VCF parsing, read alignment (BWA/Bowtie2), variant calling, SV/CNV detection	70%
Single-Cell	Scanpy-based scRNA-seq pipeline (QC, normalization, PCA, UMAP, clustering)	85%
Proteins	PDB analysis, ESMFold structure prediction, molecular docking	55%
Epigenomics	Bisulfite methylation, DMR detection, ATAC-seq peak analysis	45%
Metagenomics	K-mer classifier, 16S rRNA pipeline, alpha/beta diversity	70%
Metabolomics	Peak detection, ANOVA, feature alignment, PCA	55%
Population Genetics	HWE, FST, Tajima's D, LD, PCA, nucleotide diversity	75%
CRISPR	Guide RNA design, PAM finding (SpCas9, SaCas9, Cas12a), off-target scoring	75%
Metabolism	Flux balance analysis (FBA), knockout simulation	60%
Machine Learning	Random Forest, SVM, SHAP, cross-validation, feature selection	55%
Workflow	Pipeline builder, batch processor, HTML report generator	85%
GO/Pathways	GO browser, pathway visualization (KEGG-style maps)	65%
GWAS	Chi-squared test, Manhattan/QQ plots, lead SNP detection	75%
Epitope Prediction	T-cell (MHC binding), B-cell (surface propensity), linear epitopes	75%
Molecular Cloning	Plasmid maps, restriction digest, virtual gel, PCR simulation, ligation, Gibson assembly	90%
Parallel Processing	Multi-threaded execution, batch processing, progress tracking	NEW

Molecular Cloning Tools 🧬

BioSuite includes a complete molecular cloning suite — features that SnapGene charges $350/year for:

Tool	Description	SnapGene Equivalent
Restriction Digest	Simulate single/double digests with 100+ enzymes	✅ Same
PCR Simulation	Primer annealing, extension, cycling with Tm calculation	✅ Same
Ligation	Insert:vector ratios, T4 ligase efficiency	✅ Same
Gibson Assembly	Overlap-based cloning design	✅ Same
Plasmid Maps	Circular rendering with annotated features	✅ Same
Virtual Gel	Agarose gel simulation from digest results	✅ Same
Sequence Viewer	Linear display with feature highlighting	✅ Same

All FREE. No subscriptions. No trials. No limits.

Parallel Processing ⚡

Process large datasets faster with built-in parallel execution:

from biosuite.core.parallel import parallel_map, parallel_gc_content
from biosuite.core.sequence import gc_content

# Process 10,000 sequences in parallel
sequences = ["ATCG...", "GCTA...", ...]  # 10,000 sequences
gc_values = parallel_gc_content(sequences, workers=8)

# Or use the batch processor for large datasets
from biosuite.core.parallel import ParallelBatchProcessor
processor = ParallelBatchProcessor(workers=4)
results = processor.process(gc_content, sequences, batch_size=1000)
print(f"Processed {processor.stats['completed']} sequences in {processor.stats['time']:.1f}s")

100+ Restriction Enzymes 🧪

Full database of Type II restriction enzymes used in molecular biology:

from biosuite.core.utils import RESTRICTION_ENZYMES, RESTRICTION_ENZYMES_SITES

# List all available enzymes
print(f"Available enzymes: {len(RESTRICTION_ENZYMES)}")

# Get enzyme recognition site
site = RESTRICTION_ENZYMES_SITES['EcoRI']  # 'GAATTC'

# Use in restriction digest
from biosuite.core.cloning import simulate_digestion
result = simulate_digestion(plasmid_seq, enzyme='EcoRI')

36+ Visualization Types

Volcano, PCA, Manhattan, MA, Venn, Barplot, Boxplot, Heatmap, Scatter, Time Series, QQ-plot, Clustered Heatmap, Circos, Alignment Viewer, Violin, Raincloud, Ridge, Dot Plot, GSEA, Motif Logo, Sankey, UMAP, Network (PPI/Regulatory/Metabolic), UpSet, Genome Browser, Interactive (Plotly), Sequence Logo, Conservation, Synteny Dotplot, Plasmid Map, Virtual Gel, and more.

Dual-Mode Architecture

Every module follows a consistent pattern:

def analyze(input, ...):
    # Try external tool first (fast)
    if _has_external_tool():
        return _run_external(input, ...), {"engine": "external"}
    # Fall back to pure Python (always works)
    return _run_builtin(input, ...), {"engine": "builtin"}

Cyberpunk GUI

• 29 analysis tabs with scrollable sidebar
• 3 themes: Dark-Green-Cyber, Dark-Purple-Cyber, Light-Blue-Cyber
• Keyboard shortcuts (Ctrl+S, Ctrl+Q, F1, F5, Escape)
• Progress bars for long operations
• Plot history (last 10 plots)
• API key configuration panel
• 15 built-in help guides
• Molecular cloning tab with plasmid viewer

CLI with 99+ Options

Professional CLI menu with organized sections for every analysis type.

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Installation

Via PyPI (recommended)

pip install biosuite-ultra

Install with all optional features

pip install "biosuite-ultra[full]"

Windows Users — If pip install fails on pysam

pysam needs C build tools. Two options:

Option A: Visual Studio Build Tools

1. Download: https://visualstudio.microsoft.com/visual-cpp-build-tools/
2. Run installer → select "Desktop development with C++" → Install
3. Open "x64 Native Tools Command Prompt for VS" (search in Start Menu)
4. Run: pip install pysam

Option B: Use Conda (easier)

1. Install Anaconda: https://anaconda.com/download
2. Run: conda install -c bioconda pysam

From source

git clone https://github.com/sahandtkod-byte/BioSuite-Ultra.git
cd BioSuite-Ultra
pip install -r requirements.txt

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Quick Start

CLI Mode

python run.py

GUI Mode

python run.py --gui

REST API

python -m biosuite.api.server
# Open http://localhost:8000/docs for Swagger UI

Authentication: All endpoints require an X-API-Key header. Admin endpoints (/api/v1/admin/*) additionally require a JWT Authorization: Bearer <token> obtained from /api/v1/admin/login. Requests are rate-limited to 100/minute. See API_GUIDE.md for setup and env vars.

Programmatic API

Basic Sequence Analysis

from biosuite.core.sequence import gc_content, reverse_complement, translate

gc = gc_content("ATCGATCG")  # 50.0
rc = reverse_complement("ATCG")  # "CGAT"
protein = translate("ATGAAATTTTAA")  # "MKF"

Parallel Processing

from biosuite.core.parallel import parallel_align_pairs

# Align 1000 sequence pairs in parallel
pairs = [("ATCG", "ATCG"), ("GCTA", "GCTA"), ...]  # 1000 pairs
results = parallel_align_pairs(pairs, algorithm='needleman_wunsch', workers=8)

Molecular Cloning

from biosuite.core.cloning import simulate_digestion, simulate_pcr

# Restriction digest with 100+ enzymes
result = simulate_digestion(plasmid_seq, enzyme="EcoRI")
print(f"Generated {len(result['fragments'])} fragments")

# PCR simulation
pcr_result = simulate_pcr(template, forward_primer, reverse_primer, cycles=30)
print(f"PCR product: {pcr_result['product_size']} bp")

CRISPR Guide Design

from biosuite.core.crispr import design_guides

result = design_guides(target_sequence, pam_type='SpCas9', guide_length=20)
for guide in result.guides[:5]:
    print(f"{guide.sequence} (score={guide.score:.3f})")

Differential Expression

from biosuite.core.expression import differential_expression

result = differential_expression(counts_df, conditions=['ctrl', 'ctrl', 'treat', 'treat'])
print(f"Up-regulated: {result['num_upregulated']}")
print(f"Down-regulated: {result['num_downregulated']}")

Plasmid Maps

from biosuite.plotting.plasmid_map import create_sample_plasmid, draw_plasmid

fig = create_sample_plasmid()
fig.savefig("pUC19_map.png", dpi=150)

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Architecture

BioSuite-Ultra/
├── biosuite/                  # Main package (84 files, 26,000+ lines)
│   ├── core/                    # 45 analysis modules
│   │   ├── parallel.py          # Parallel processing utilities
│   │   ├── sequence.py          # FASTA/FASTQ I/O, GC%, translation
│   │   ├── alignment.py         # NW/SW alignment, MSA
│   │   ├── blast.py             # Sequence similarity search
│   │   ├── assembly.py          # Genome assembly
│   │   ├── ngs.py               # NGS analysis (BAM/VCF)
│   │   ├── crispr.py            # CRISPR guide design
│   │   ├── cloning.py           # Molecular cloning
│   │   ├── expression.py        # Differential expression
│   │   ├── databases.py         # Database searches
│   │   ├── ...                  # 35+ more modules
│   │   └── utils.py             # Shared utilities (100+ enzymes)
│   ├── plotting/                # 13 visualization modules
│   ├── gui/                     # Cyberpunk GUI (29 tabs)
│   ├── cli/                     # CLI menu (99+ options)
│   ├── api/                     # REST API (42+ endpoints)
│   └── notebook/                # Jupyter integration
├── tests/                       # 1,089+ tests
├── examples/                    # 8 tutorials + 5 notebooks
├── docs/                        # Sphinx documentation
├── run.py                       # Entry point
├── pyproject.toml               # Package configuration
├── Dockerfile                   # Multi-stage Docker build
├── docker-compose.yml           # Multi-service Docker Compose
└── CHANGELOG.md                 # Version history

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Dependencies

Core (required)

numpy>=1.24, pandas>=2.0, matplotlib>=3.7, seaborn>=0.12
scipy>=1.10, scikit-learn>=1.3, customtkinter>=5.2
tqdm>=4.65, biopython>=1.81, networkx>=3.0, plotly>=5.0

Optional (for specific modules)

goatools>=1.3, gseapy>=1.0, cutadapt>=4.0
scanpy>=1.9, anndata>=0.9, scikit-bio>=0.5
shap>=0.42, statsmodels>=0.14, umap-learn>=0.5
fastapi>=0.100, uvicorn>=0.23

External Tools (optional, for speed)

BLAST+, Clustal Omega, MUSCLE, MAFFT
BWA, Bowtie2, FreeBayes, MACS2
RAxML, IQ-TREE, MrBayes
SPAdes, MEGAHIT, Kraken2
AutoDock Vina, OpenMM

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Testing

# Run all tests
python -m pytest tests/ -v

# Run with coverage
python -m pytest tests/ --cov=biosuite --cov-report=html

# Run parallel tests
python -m pytest tests/ -n auto

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Docker

# Build and run CLI
docker-compose up biosuite

# Build and run REST API
docker-compose up biosuite-api

# Build and run Jupyter
docker-compose up jupyter

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Contributing

See CONTRIBUTING.md for guidelines.

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License

MIT License - see LICENSE for details.

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Citation

If you use BioSuite Ultra in your research, please cite:

@software{biosuite2026,
  author = {Sahand Touri},
  title = {BioSuite Ultra: Comprehensive Open-Source Bioinformatics Platform},
  year = {2026},
  version = {4.2.0},
  doi = {10.5281/zenodo.21256296},
  url = {https://github.com/sahandtkod-byte/BioSuite-Ultra}
}

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Links

• GitHub: https://github.com/sahandtkod-byte/BioSuite-Ultra
• DOI: https://doi.org/10.5281/zenodo.21256296
• PyPI: https://pypi.org/project/biosuite-ultra/
• Issues: https://github.com/sahandtkod-byte/BioSuite-Ultra/issues
• JOSSPaper: https://joss.theoj.org/papers/6efd11d9995ddc82d5d76403c32a4a2d

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Contributors

We thank the following people for their contributions to BioSuite Ultra:

• Faiz Mulla (@faizmullaa) — India — REST API authentication and rate limiting