BScOR: Beam Scaffolded Origami Routing

INTRODUCTION

The program bscor is a pipeline of executables for routing polyhedal (version 0.1) and flat meshes (since version 1.0) and relaxing a physical cylinderical model of the mesh so that the mesh can be assembled from DNA at the nanoscale. The original source code for the physical relaxation is found in the repository https://github.com/gardell/scaffold-routing-rectification. The original relaxation code only supported polyhedral meshes; a clone which supports flat meshes is included here. The research related to bscor pipeline and its companion Maya vhelix plugin (http://www.vhelix.net/) are the following:

1. For bscor v0.1 for polyhedral meshes only: http://www.nature.com/nature/journal/v523/n7561/full/nature14586.html
2. For bscor v1.0 also supporting flat meshes: http://onlinelibrary.wiley.com/doi/10.1002/anie.201602446/fullhttp://onlinelibrary.wiley.com/doi/10.1002/anie.201602446/full

INSTALLATION

Download a release package from the releases page in the Git repository. Copy the parent directory to your desired location. To access the binaries and the batch file from other locations, you can pad your BSCoR location to the path environment variable.

USAGE

bscor.bat model_ply_file [scale]

The intended usecase of bscor is as follows:

1. The user builds a 3D polyhedral (topologically equivalent to sphere) or 2D flat mesh in a 3d modelling software such as Maya. Maya is also needed to import the DNA model using vHelix.
2. The resulting model is exported in a standard format (e.g. vrml, obj, stl) which can then be converted into PLY (e.g. using meshconv).
3. The user then opens a command window and goes to the bscor installation directory
4. The user then runs the command bscor.bat octahedron.ply, where octahedron.ply is the filename of target PLY model. Optionally, the user can specify a scale parameter as in bscor.bat octahedron.ply 10, for scaling the model by 10.
5. If the execution was successful, bscor provides an inputfile.rpoly output.
6. If the execution was unsuccesful, the user can troubleshoot the problem from the error messages output by bscor.
7. The resulting rpoly can be imported into maya in with the vhelix plugin for Maya. vhelix can be downloaded and installed from vhelix.net.
8. In vhelix, further processing of the DNA strands composing the target polyhedra can be done. Desired sequences can be applied to the DNA strands in vhelix.

The coordinates in the PLY file are assumed to be in nanometer. Models exported from maya may have small dimensions in this unit. That is, the models may not be feasible to implement using DNA. BSCoR provides an optional argument to set the scale of the model. For instance, to scale the octahedron model by 2 for rendering in DNA, execute bscor.bat octahedron.ply 2 from the command line.

LIST OF FILES as of version 1.0

The following files must be present in the installation:

• bscor.bat
• ply_to_dimacs.exe
• postman_tour.exe
• Atrail_search.exe
• Atrail_verify.exe
• ply_to_embedding.exe
• make_embedding_eulerian.exe
• scaffold-routing-rectification.exe
• PhysX3_x64.dll
• PhysX3Common_x64.dll
• octahedron.ply

NOTES ON BUILDING FROM SOURCE CODE

To build the pipeline from source, you will need the boost graph library (tested on BGL 1.57.0) and LEMON C++ combinatorial optimization library (tested on LEMON 1.3.1.) You will then need to update the library locations in additional includes settings of the project based on your library installation directories.