BIGNASim database structure and analysis portal for nucleic acids simulation data

Data Manager

Trajectories generated with BIGNASim, especially the ones built from a particular nucleotidic fragment using different trajectories (see metatrajectory help section), can be large files and might require several minutes to be ensembled. To allow an asynchrounous generation of metatrajectories and their subsequent retrieval, BIGNASim implements a data manager. The data manager stores all the trajectories generated in a BIGNASim session. The list of generated trajectories will be updated in the data manager until the browser is closed or the session expired (after some time of inactivity). After that, the workspace containing the list of trajectories can be accessed from a given link, and will be available for one month from the day of their generation. Trajectories are shown in a very intuitive workspace, and can be compressed, downloaded, erased, and sent to the NAFlex flexibility server to further analyse them. Users also have the possibility to download all the generated trajectories in a particular session in a single compressed tar tgz file. The datamanager also lists the trajectories in progress under the label RUNNING. If an error occurs during the process, the job output and error logfile are also uploaded to the workspace to ease the debugging of the job failure.

Data Manager Icons

Workspace icons
Show Trajectory description Show Trajectory description
Download Trajectory Download Trajectory
Compress Trajectory Compress Trajectory.
NAFlex Analyse Trajectory flexibility with NAFlex.
Remove Trajectory Delete Trajectory from the workspace.
Download All Download All trajectories in a compressed tar tgz file.

Persistent link

The persistent link to a list of generated trajectories (workspace) is given in the waiting page shown after submiting a meta-trajectory generation process (see figure below), and can also be directly copied from the browser url bar once the workspace is loaded. This link allows access to the list of trajectories even after the session has been closed or expired. Trajectories will be stored in local disks for a period of up to one month after their generation.