Tools
Here you can find accessible computational and laboratory workflow tools designed to streamline day-to-day analysis and workflows.
Bioinformatics Tools
Structural Modeling
Protenix-v2
Biomolecular Structure Prediction · Proteins, Nucleic Acids & Small MoleculesGoogle Colab notebooks providing single-sequence and high-throughput batch structure prediction powered by ByteDance's Protenix-v2, an open-source all-atom biomolecular modeling system. Predicts structures of proteins, DNA, RNA, and small-molecule ligand complexes.
OpenDDE
Drug Design Engine · Macromolecular Modeling & Structure GenerationGoogle Colab notebooks providing single-run and batch modeling via OpenDDE (Open-Source Drug Design Engine) by Aureka Research, tailored for macromolecular complex modeling, binding interface prediction, and structure-based discovery workflows.
Binder Design
RFdiffusion3
De Novo Binder Design · All-Atom Biomolecular InteractionsGoogle Colab pipeline implementing RFdiffusion3 for de novo design of high-affinity protein binders against specified molecular targets. Generates complementary binder backbones conditioned on target structures with full atom-level accuracy.
Genome Annotation
OrionGeno
Deep Learning Genome Annotation · Ab Initio Gene Model PredictionGoogle Colab notebook deploying OrionGeno for accurate ab initio eukaryotic gene prediction directly from genomic FASTA sequences. Utilizes modern deep learning to resolve exon-intron boundaries and complex genomic architecture.
Tiberius
End-to-End Deep Learning & HMM · Eukaryotic Gene FindingGoogle Colab notebook running Tiberius, an end-to-end gene prediction framework that couples convolutional neural networks and transformer layers with a differentiable Hidden Markov Model (HMM) for rapid, accurate eukaryotic genome annotation.
Lab Workflows
cloneBench
Assembly Planner · Golden Gate & Restriction-LigationAn interactive planner for Golden Gate and Type IIS restriction-ligation cloning. Calculates exact pipetting volumes for plasmid preps based on measured concentrations and molar ratios relative to the destination vector.
Features automated Type IIS recognition site auditing across circular sequences, water make-up calculations, shared master mix pooling with configurable excess, part inventory tracking across multi-tube runs, and a quick dilution calculator (C1·V1 = C2·V2).
prepBench
Dilution Planner · Bacterial Culture & OD600 NormalizationAn interactive bench tool designed for bacterial dilution planning and OD600 normalization. Calculates exact neat culture and buffer volumes needed to normalize bacterial suspensions to target densities.
Supports single-strain dilutions and multi-strain co-culture combinations, tracks construct metadata (strains, plasmids, tags, antibiotics, stock locations), accounts for pipetting dead volume, and exports formatted run sheets for the bench.