===== Basics =====

==== Overview ====
[[https://www.openondemand.org/|OOD (Open OnDemand)]], which runs the web-portal, can be seen as a superset of JupyterHub. It is a web application that allows you to submit Slurm jobs, access compute node shells, manage your files, run interactive applications (e.g., JupyterLab) and web applications (e.g., TensorBoard). The portal is minimal and contains only a few advanced pages (Monitoring tab, in particular), so feel free to explore them!

==== Enabling an Environment in JupyterLab ====
For Python Conda environments:
<code>conda install -n <ENVIRONMENT> -y conda-forge::ipykernel</code>

For R Conda environments:
<code>conda install -n <ENVIRONMENT> -y r::r-irkernel</code>

==== Installation of NGLview ====
<code>conda install -n <ENVIRONMENT> -c conda-forge -y nglview=3.1.4 "setuptools<80"</code>

==== Installation of Isolde ====

To install Isolde run //chimerax// via remote desktop (Apps ---> [[https://portal.darwin.bioeng.ru/pun/sys/dashboard/batch_connect/sys/bc_desktop/TrinityX/session_contexts/new|Remote Desktop]]) and then in the command line inside ChimeraX run:
<code>
toolshed install /opt/chimerax/chimerax_clipper-0.26.1-cp311-cp311-linux_x86_64.whl
toolshed install /opt/chimerax/chimerax_isolde-1.11.1-cp311-cp311-linux_x86_64.whl
</code>


==== Changing Password ====
Portal (=SSH) password can be changed in Utilities ---> [[https://portal.darwin.bioeng.ru/pun/sys/trinity_passwd|PASSWD]].