Synthetic Biology Software
AgroNT: tool that analyzes plant DNA sequences to predict gene modifications
BindNet: protein-ligand binding representation learning from fine-grained interactions
BioNetGen: structure-based modeling of biochemical reaction networks
BioCRNplyer: biomolecular chemical reaction network compiler
BioGRID: large database of biological interactions modeled at the molecular level (proteins, genes, chemicals), not at the atomic bond level
BioNetGen: rule based biochemical reaction network
Cello: genetic circuit design using logic gates
COPASI: modeling biochemical reaction networks
COBRA: whole-cell metabolic modeler that you can call as a package (E. Coli, etc)
DNA Chisel: codon optimization and solving sequence constraints
EC-KitY: python toolkit for evolutionary computation that integrates with sci-kit learn
GapMind: maps out carbon utilization pathways for a genome. You can compare how complete each pathway is across your organism and see which are missing entirely in an organism
iBioSim: genetic circuit simulation and analysis
KBase: AWS for systems bio analysis, hosted by the Department of Energy
PoSeiDon: a pipeline to detect significantly positive selected sites and possible recombination events in an alignment of multiple protein-coding sequences
PySB: systems biology modeling in Python
RecombineX: genome engineering toolkit
RBS Calculator: directly outputs a DNA sequence based on a need- if a specific amount of protein is needed, the tool will suggest an RBS design that is accurate within a variance factor of 2.3 (turns this into a reliable tool)
SBML: standardized models for systems biology as a markup language, use it as a data format to describe synthetic biology code
SBOL canvas: genetic circuit schematic building using SBOL
SnapGene: visual plasmid construction + simulation
SpliceVarDB: variant database for splicing
TCellMatch: collection of models to predict which antigens a T-cell receptor will bind, based on single-cell sequence data; test immune design before lab work
TISIGNER-ReactJS: pathway optimization in E Coli
Uniprot/PDB: protein sequence + 3D structure databases
Virtual Metabolic Human: represent metabolic diagram on a chip
SynthBio Tools
Biometra TRobot: PCR machine
Digital to Biological Converter (DBC): a standalone machine that converts any input sequence to its chemical counterpart- DNA, RNA, proteins, viruses (1 → many type converter)
FlowJo: flow cytometry data analysis software (1996)
Gibson Assembly: method for joining/stitching DNA together
JCat: codon optimization tool
PUREexpress: cell free expression system
Sleeping Beauty (SB100): transposase system for stable circuit integration in mouse liver cancer models
SOLO Automated Liquid Handler: high resolution, compact robotic pipettor