Modelling/simulation tools use case, MoDEL_CNS API

[adamhospital]

New Use Case

Aspect	Detail
Summary	C1997 (Platforms providing web-access to molecular level tools for guiding systems level modelling)
Usecase Group	Molecular Level
Expert	Adam Hospital, Aurélien Luciani (IRB Barcelona)
Scientific User	Interested in MD simulation data
Deadline	M22
Target audience	New users of molecular modelling/simulation tools
Target interface	GUI and notebooks (latter for tutorials)
HPC Requirements	none
Dependencies	nglview
Nominal runtime	Minutes

Use case: Extracting relevant information from atomistic Molecular Dynamics trajectories of relevant signal transduction proteins using MoDEL_CNS API

Use case with several useful examples of how to extract, play, store, and visualize information from the atomistic MD trajectories stored in the MoDEL_CNS database.

Mandatory features

• Getting a list of the MD simulations stored in the database and publicly available.
• Programmatically download trajectories information:
  • Snapshot, ensemble – time selection.
  • Macromolecule regions, residues or atoms – structure selection.
• Programmatically download analysis information:
  • RMSd, Rgyr, SASA, Atom/Residue fluctuation, Principal component Analysis, etc.
• Represent trajectory information in a 3D-visualizer (NGLview).
• Represent analysis information with data visualizer (matplotlib).

Important features

• Visualize the trajectory information using nglview jupyter widget.
• Visualize the data information from the analysis using matplotlib jupyter widget

To do

• [x] Create the jupyter notebook with all the required dependencies.
• [ ] Prepare scientifically relevant examples of data retrieval and representation.
• [ ] Write markdown cells with information about the workflow and the different steps.
• [ ] Make the notebook publicly available.

[alex4200]

Still in progress, but delayed as Aurélien left the group two months ago. Might be moved to SGA3