DNA and Natural Algorithms Group

Pinned Repositories

ArrheniusInference
A framework with a reduced state space to train the Arrhenius DNA kinetic model
Language:Python4 5 05
FPEI
Parameter estimation for interacting nucleic acid strands modelled as CTMCs, using a fixed path ensemble inference approach
Language:Python21
KinDA
Kinetic DNA strand displacement analyzer
Language:Python8 5 05
multistrand
Multistrand nucleic acid kinetic simulator
Language:C++17 7 510
nuskell
Nucleic acid strand displacement compiler
Language:Python83
peppercompiler
A compiler for DNA circuits and tile systems.
Language:Python3 3 13
peppercornenumerator
domain-level nucleic acid reaction enumeration
Language:Python10 4 06
piperine
Piperine compiles abstract CRNs into DNA sequences and estimates how much the generated DNA implementations may participate in undesired DNA-DNA interactions during experiments.
Language:Python22 5 26
SST-sequence-designer
Sequence designer for single-stranded DNA tiles
Language:Python64
xgrow
Simulator package for algorithmic tile self-assembly models aTAM and kTAM, as a python package.
Language:C34

DNA and Natural Algorithms Group's Repositories

DNA-and-Natural-Algorithms-Group/piperine
Piperine compiles abstract CRNs into DNA sequences and estimates how much the generated DNA implementations may participate in undesired DNA-DNA interactions during experiments.
Language:Python22 5 26
DNA-and-Natural-Algorithms-Group/multistrand
Multistrand nucleic acid kinetic simulator
Language:C++17 7 510
DNA-and-Natural-Algorithms-Group/peppercornenumerator
domain-level nucleic acid reaction enumeration
Language:Python10 4 06
DNA-and-Natural-Algorithms-Group/KinDA
Kinetic DNA strand displacement analyzer
Language:Python8 5 05
DNA-and-Natural-Algorithms-Group/nuskell
Nucleic acid strand displacement compiler
Language:Python83
DNA-and-Natural-Algorithms-Group/SST-sequence-designer
Sequence designer for single-stranded DNA tiles
Language:Python64
DNA-and-Natural-Algorithms-Group/ArrheniusInference
A framework with a reduced state space to train the Arrhenius DNA kinetic model
Language:Python4 5 05
DNA-and-Natural-Algorithms-Group/peppercompiler
A compiler for DNA circuits and tile systems.
Language:Python3 3 13
DNA-and-Natural-Algorithms-Group/xgrow
Simulator package for algorithmic tile self-assembly models aTAM and kTAM, as a python package.
Language:C34
DNA-and-Natural-Algorithms-Group/FPEI
Parameter estimation for interacting nucleic acid strands modelled as CTMCs, using a fixed path ensemble inference approach
Language:Python21
DNA-and-Natural-Algorithms-Group/PathwayElaboration
Predicitng nucleic acid kinetics with the pathway elaboration method
Language:Python2
DNA-and-Natural-Algorithms-Group/stickydesign
A package for designing short orthogonal and isoenergetic DNA sequences, intended for DNA tile sticky ends and often used for toeholds.
Language:Python23
DNA-and-Natural-Algorithms-Group/surface_crns
Package for simulating and displaying chemical reaction networks (CRNs) on a surface.
Language:Python1
DNA-and-Natural-Algorithms-Group/alhambra
A package for designing and working with algorithmic DNA tile systems.
Language:Python03
DNA-and-Natural-Algorithms-Group/crnverifier
Test the correctness of an implementation CRN, or the equivalence of two CRNs.
Language:Python
DNA-and-Natural-Algorithms-Group/dsdobjects
base classes for nucleic acid strand displacement programming
Language:Python