https://darwin.bioeng.ru/ 2026-04-16T12:31:49+00:00 https://darwin.bioeng.ru/ https://darwin.bioeng.ru/lib/exe/fetch.php?media=favicon.ico text/html 2026-04-11T20:06:30+00:00 localadmin (localadmin@undisclosed.example.com) https://darwin.bioeng.ru/doku.php?id=application_guides:alphafold3&rev=1775937990&do=diff Warning Do not share model weights, they are protected by a license! Starting a Job 1. Create a working directory with two subfolders: input and output 2. Place your JSON input file into the input folder (input format documentation). Example: { "name": "2PV7", "sequences": [ { "protein": { "id": ["A", "B"], "sequence": "GMRESYANENQFGFKTINSDIHKIVIVGGYGKLGGLFARYLRASGYPISILDREDWAVAESILANADVVIVSVPINLTLETIERLKPYLTENMLLADLTSVKREPLAKMLEVHTGAVLGLHPMFGADIASMAKQVVVRCDGRFPE… text/html 2026-04-09T11:11:00+00:00 localadmin (localadmin@undisclosed.example.com) https://darwin.bioeng.ru/doku.php?id=portal_guides:basics&rev=1775733060&do=diff Basics Overview 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! text/html 2026-04-09T08:59:35+00:00 Anonymous (anonymous@undisclosed.example.com) https://darwin.bioeng.ru/doku.php?id=portal_guides:slurm&rev=1775725175&do=diff Slurm Job Submission Slurm jobs can be submitted through a Job Composer app inside Slurm tab. This provides a graphical alternative to submitting jobs from the command line or from environments such as JupyterLab. Job script examples can be taken from Templates. Requeueing is disabled in the text/html 2026-04-09T08:45:18+00:00 localadmin (localadmin@undisclosed.example.com) https://darwin.bioeng.ru/doku.php?id=application_guides:alphafold3_guide&rev=1775724318&do=diff AlphaFold 3 To run AlphaFold3 on Darwin you need JSON file with querry, other resources are prepared: * AF3 Apptainer image: /opt/shared_soft/alphafold3/alphafold3_v301.sif * Model weights: /opt/shared_soft/alphafold3/af3model/af3.bin (do not share!) text/html 2026-04-09T08:33:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://darwin.bioeng.ru/doku.php?id=portal_guides:advanced&rev=1775723593&do=diff Advanced Creating Shared Entities Shared environments, modules and binaries can be created by any user inside corresponding directories: * /opt/shared_envs * /opt/shared_modules * /opt/shared_soft These directories have a sticky bit, i.e. everyone can use everything inside, but only the creators can modify their files. text/html 2026-04-09T08:26:30+00:00 localadmin (localadmin@undisclosed.example.com) https://darwin.bioeng.ru/doku.php?id=usage_guides:alphafold3&rev=1775723190&do=diff AlphaFold3 To run AlphaFold3 on Darwin you need four things: * AF3 Apptainer image: /opt/shared_soft/alphafold3/alphafold3_v301.sif * Model weights: /opt/shared_soft/alphafold3/af3model/af3.bin * Databases: /opt/shared_soft/alphafold3/db/ * text/html 2026-04-08T20:11:44+00:00 localadmin (localadmin@undisclosed.example.com) https://darwin.bioeng.ru/doku.php?id=usage_guides&rev=1775679104&do=diff Guides for usage applied software text/html 2026-03-13T22:21:16+00:00 localadmin (localadmin@undisclosed.example.com) https://darwin.bioeng.ru/doku.php?image=cluster_ha.svg&ns=0&rev=1773440476&tab_details=history&media_do=diff&do=media <img src="https://darwin.bioeng.ru/lib/exe/fetch.php?w=500&amp;h=500&amp;tok=fd4890&amp;media=cluster_ha.svg" alt="cluster_ha.svg" loading="lazy" width="500" height="500" />