Hi all,
I am hoping for some assistance. I (the researcher) would like to know whether it is possible and how to go about building a Jupyter Notebook that a collaborator could load in their web browser to view results? We're working remotely, so there are no shared machines.
First of all, I've performed some MD simulations using Gromacs. I then load up Jupyter Notebook on my machine, import the MDAnalysis Python package and performs some analysis that depends on those trajectory files generated by Gromacs (.trr/.xtc/.pdb).
The problem I face is that I want my collaborator to see the analysis of results (MDAnalysis) and even parts of a trajectory-of-interest using NGLViewer. (1) How does one (a) host a Jupyter Notebook for the collaborator to view/interact with? (2) If I was to upload a short Gromacs trajectory (e.g., a trajectory file that has been reduced to display a rare event/transition event) to somewhere like Google Drive, can the NGLViewer look for remote files?
Thanks
Anthony
Hi,
As a partial answer, it is relatively easy to run a Jupiter Notebook on a server or shared machine and access them remotely (I run my notebooks on my workstation (where I save all of my larger trajectories and can perform computational, more demanding analysis), but I access and modify them on my laptop).
This work fairly easy:
( 0. Set up a passwordless ssh connection to the server )
1. server: jupyter notebook --no-browser --port 8889
2. client: ssh -N -f -L localhost:8888:localhost:8889 server
Afterward, type http://localhost:8888/ in your preferred browser and you can access the notebooks. Also, multiple users can access the same notebook (at the same time).
In principle, you could run a Notebook server on your personal computer and allowing access to your collaborator, but this requires things like a static IP, allowing ssh connection to your computer, maybe requiring to setup a VPN. This is perhaps not the best/safest approach.
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