Software demos

SOFTWARE DEMOS
(Friday July 1st, 17:15 – 19:15)

The goal of this session is to present a software tool (program, platform, library, server). Each presenter will be allocated 30′: 15′ of talk / demo, and 15′ for discussions with the audience.

1.
AiiDA, http://www.aiida.net/
Martin Uhrin (martin.uhrin@epfl.ch) and the Nicola Marzari group (http://nccr-marvel.ch/)

AiiDA is a automation tool that makes it trivial to carry out high-throughput calculations locally or on remote resources e.g. run DFT calculations on remote clusters. It’s key strengths are full pro-
and retrospective provenance tracking meaning that a workflow can define a series of steps to be executed, these are then all stored
including inputs and outputs as the workflow executes. This way AiiDA acts as an electronic labbook which can be used to look up the full series of steps that led to a particular result.

2.
MoMA: Molecular Motion Algorithms
Juan Cort├ęs (juan.cortes@laas.fr)

MoMA is a software platform containing molecular modeling tools and robotics-inspired algorithms to sample conformations and to compute transition paths. An application to compute protein-ligand unbinding paths, called MoMA-LigPath, is accessible via a web server (http://moma.laas.fr/) and other applications will be available soon. The demo will illustrate the performance of a method to compute conformational transition paths of peptides.

3.
UnityMol+HiRE-RNA
Samuela Pasquali (samuelapn@gmail.com)

This demo will focus on UnityMol+HiRE-RNA, a software platform to perform interactive molecular dynamic simulations based on a coarse-grained representation of RNA and DNA molecule. My oral presentation will discuss the model employed in the simulation and will present some applications.

4.
SBL: The Structural Bioinformatics Library, http://sbl.inria.fr
Frederic.Cazals@inria.fr

The SBL is a comprehensive in silico environment providing applications answering complex bio-physical problems, in a robust, fast and reproducible way. It targets both end-users with off the self applications, and developers with advanced low level C++ classes. The presentation will emphasize applications dealing with conformational ensembles and energy landscapes (see http://sbl.inria.fr/applications/ Conformational analysis).