By default, Assemble2 uses RNA algorithms and RNA data to automate several steps (2D structure prediction, 3D refinement, 3D modules search,…). The default configuration of Assemble2 is to use the algorithms and data made available through a database and a bunch of Web services hosted at http://arn-ibmc.in2p3.fr/api/. The main advantage is that you have nothing to configure, you just need an internet connection. But if your data are large, some steps like 3D annotation and 3D modules search could be slow.
The current release (1.0 beta1) allows you to deploy your own local server with PyRNA. But the installation of a local server can be cumbersome for untrained people (mainly due to the installation of dependencies). Consequently, i have added to the upcoming release the ability to install everything on your own computer for a direct communication with Assemble2, without any server to handle the requests. Your copy of Assemble2 will connect directly the database and the algorithms. With this option, the installation of PyRNA is not anymore necessary.
If several copies of Assemble2 are running in your laboratory, the installation of a local server remains the best strategy. Choose your flavor and don’t hesitate to contact me for support.