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Exabyte.io [7] - a cloud-native integrated platform for nanoscale modeling, supporting simulations at multiple scales, including Density Functional Theory and Molecular Dynamics; JCMsuite – a finite element analysis software for simulating optical properties of nanostructures; LAMMPS – Open source molecular dynamics code
PHP language toolkit with classes for DNA and protein sequence analysis, alignment, database parsing, and other bioinformatics tools Cross-platform: GPL v2 Open Bioinformatics Foundation: Biopython: Python language toolkit Cross-platform: Biopython [2] Open Bioinformatics Foundation: BioRuby: Ruby language toolkit Linux, macOS, Windows [3] GPL ...
Agilent Technologies RFLP Decoder Software, Fish Species; Applied Biosystems GeneMapper; Joint BioEnergy Institute j5; CLC bio CLC DNA Workbench Software; CLC bio CLC Free Workbench Software; CLC bio CLC Sequence Viewer; CLC bio Protein Workbench Software; DNASTAR Lasergene; Geneious; LabVantage Solutions Inc. LabVantage Sapphire; LabVantage ...
Molecular design software; Molecule editor; Quantum chemistry computer programs; List of molecular graphics systems; List of protein structure prediction software; List of sequence alignment software; List of gene prediction software; List of RNA structure prediction software; Comparison of software for molecular mechanics modeling
However, nearly all software meeting the Free Software Definition also meets the Open Source Definition and vice versa. A small fraction of the software that meets either definition is listed here. Some of the open-source applications are also the basis of commercial products, shown in the List of commercial open-source applications and services.
DNADynamo is a general purpose DNA and Protein sequence analysis package that can carry out most of the functions required by a standard research molecular biology laboratory DNA and Protein Sequence viewing, editing and annotating; Contig assembly and chromatogram editing including comparison to a reference sequence to identify mutations
Molecular Dynamics Studio (2016) free open-source multi-scale modeling and simulation program for nano-composites with special support for structural DNA nanotechnology (originally Nanoengineer-1 by Nanorex) Nano-Hive: Nanospace Simulator (2006) free software for modeling nanotech entities
DNA nanotechnology, specifically, is an example of bottom-up molecular self-assembly, in which molecular components spontaneously organize into stable structures; the particular form of these structures is induced by the physical and chemical properties of the components selected by the designers. [19]