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TALOS

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TALOS (Three-dimensional, Algorithmically-Generated Library of Origami Shapes) is a new, free and open-source software package written by FORTRAN 90/95 that enables the automated convertion of 3D computer-generated design files (PLY) into DNA sequences. These DNA sequences can be subsequently synthesized and mixed to fold DNA 6HB based wireframe 3D nanoparticles with high fidelity.

Jun, H., Shepherd, T., Zhang, K., Bricker, W., Li, S., Chiu W., Bathe, M. Automated sequence design of 3D polyhedral wireframe DNA origami with honeycomb edges. ACS Nano, DOI: 10.1021/acsnano.8b08671 (2019)

  • Pure Fortran library for modern Fortran project
  • Free and open source (GNU General Public License, version 3.0)
  • Fully automatic procedure of the sequence design for scaffolded DNA DX-based wireframe lattices
  • Importing PLY file format as an input
  • Exact edge-lengths to design highly asymmetric and irregular shapes
  • JSON output for editing staple paths and sequences from caDNAno
  • 3D visual outputs by UCSF Chimera
  • A library of 240 nanoparticles - 40 geometries, 2 vertex designs, and 3 different edge lengths
  • User-friendly TUI (Text-based User Interface)
  • Online web resources and release packages for Microsoft Windows and Mac OS

Online Portal | Documentation | Pre-compiled Binaries | Compiling Code | Copyrights

Online Portal


http://talos-dna-origami.org/

In addition to the source code and pre-compiled binaries available here, we also offer an online web application with all the functionality found in the downloaded version. By submitting the same inputs (PLY, GEO, IGS, or SVG input CAD files), the web service will return the same file output as the downloaded version.

Documentation

The full software documention for TALOS v1.0 can be downloaded here.

Please find below 3 tutorial movies on how to use TALOS to generate computer aided design files, automate meshing, generate sequences, and review atomic models.

  • The *.csv file generated by TALOS contains final staple sequences.
  • The *.bild and *.json generated by TALOS can be opened by UCSF Chimera and caDNAno.
  • The atomic model (PDB) can be generated by *.cndo file using the atomic model generator written by Dr. Keyao Pan.

Pre-compiled Binaries

Compiling Code

GNU Intel PGI Code size

git clone https://github.com/hmjeon/TALOS.git

Requirements to compile from source:

  • Intel Fortran compiler: Intel Parallel Studio XE 2016, 2017 or 2018
  • Compiling the TALOS sources require Intel Fortran. Free Intel (R) Software Development Tools are available for qualified students, educators, academic researchers and open source contributors, see the details.
  • The Intel Fortran compiler supports all of the features of the Fortran 90, Fortran 95, Fortran 2003 standards and most of Fortran 2008. It also supports some draft Fortran 2018 features.
  • We provide MakeFile which is a simple way to organize code compilation of TALOS.

Copyrights

Author
Dr. Hyungmin Jun ( Personal web | e-mail )

License
TALOS is an open-source software distributed under the GPL license, version 3

Anyone is interest to use, to develop or to contribute to TALOS is always welcome!

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