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RNA structures (DSSR) / Source distribution/Linux packaging
« on: June 10, 2015, 02:46:55 pm »
Dear Xiang Jun,
With a Master student (Pauline Pommeret - Ecole Normale Supérieure/Ecole Polytechnique), we are currently enriching the 3D RNA-specific capabilities of BioPython, to allow users to load PDB files and compute such things as dihedral angle computation, base-pairs annotations...
On this last feature, we would like to include wrappers for DSSR, as your software is clearly gaining popularity within the growing field of RNA structural biology. For this, there are mainly two options:
a) We assume that the software is available/installed, and that some 'standard' path is set (related functions fail with some human readable error message if the executable is not found);
b) DSSR is installed "on demand" if unavailable, ideally using some package manager (for Linux/Mac OS).
Option a. is the quick-and-dirty option, but typical users will tend to stick to whatever tools they are used to (probably RNAView, still very popular despite its increasing obsolescence).
Option b. means that the source code of DSSR must be packaged and regularly updated, but it will make it much easier for users to "give it a shot" and move away from alternatives. Note that most package repositories do not require the license to be "open" (eg Debian non-free packages https://www.debian.org/distrib/packages), and you may retain any IP privileges on the code.
The main constraint on your part with the second option is distributing a source code version of DSSR. From your website, it is not clear if you would oppose such an option (my apologies if I missed something here).
Is a source code distribution (+Linux/MacOS packaging) an option for DSSR?
Best,
Yann
With a Master student (Pauline Pommeret - Ecole Normale Supérieure/Ecole Polytechnique), we are currently enriching the 3D RNA-specific capabilities of BioPython, to allow users to load PDB files and compute such things as dihedral angle computation, base-pairs annotations...
On this last feature, we would like to include wrappers for DSSR, as your software is clearly gaining popularity within the growing field of RNA structural biology. For this, there are mainly two options:
a) We assume that the software is available/installed, and that some 'standard' path is set (related functions fail with some human readable error message if the executable is not found);
b) DSSR is installed "on demand" if unavailable, ideally using some package manager (for Linux/Mac OS).
Option a. is the quick-and-dirty option, but typical users will tend to stick to whatever tools they are used to (probably RNAView, still very popular despite its increasing obsolescence).
Option b. means that the source code of DSSR must be packaged and regularly updated, but it will make it much easier for users to "give it a shot" and move away from alternatives. Note that most package repositories do not require the license to be "open" (eg Debian non-free packages https://www.debian.org/distrib/packages), and you may retain any IP privileges on the code.
The main constraint on your part with the second option is distributing a source code version of DSSR. From your website, it is not clear if you would oppose such an option (my apologies if I missed something here).
Is a source code distribution (+Linux/MacOS packaging) an option for DSSR?
Best,
Yann