Create github repo for fragalysis documentation (RS)
Send Rachael a list of all github repos (& context) (TD)
Deployment (K8S refactoring)
Major tasks:
Fragalysis stack → kubernetes IN PROGRESS(ISH)FRAGALYSIS QUESTIONS COMING
Plus JupyterHub(?)
Fragment network → kubernetes DONE
Squonk → kubernetes DONE
Galaxy → kubernetes PLANNING
Fragalysis stack CI/CD HOLD
Fragment network CI/CD HOLD
Openshift K8s HOLD
Notes:
Early March for K8S
Don’t need CI/CD for demo on kubernetes – should we hold off for 2/3 months? (Travis vs. Jenkins)
Testing of documentation (Janssen)
Process for AWS exists, but openstack doesn’t (for DLS) – 1 week after start (as long as networking, accessibility etc. work)
Need to discuss Galaxy:
use helm charts instead of playbooks?
Fragalysis questions: Mechanisms for running the data loaders?
Janssen: Scott will have a better idea of wether it will be applicable outside of the Fragalysis scope/use (still investigate)
Pin down date for starting deployment
Long TC for deployment on AWS
Actions:
Follow-up on technology stack questions with Janssen (TD)
Second technology stack meeting - arrange (RS) [week after next]
Send containers to Janssen so they can run through tests (TD) - keep sending
Link Janssen up with Björn for Galaxy deployment
Documentation Repo (for deployment) (RS)
Dates for STFC for deployment (openstack) (TD/AC)
Workflows infrastructure (Galaxy & Squonk)
Major tasks:
Squonk to galaxy link UNKNOWN
Fragalysis to squonk link UNKNOWN
Actions:
Review timeline/roadmap
Jackall
Major tasks:
Scoring method containerised DONE
Finalise docking workflow IN PROGRESS
Insert Bayesian optimisation DISCOVERY
Implement scoring into Galaxy tool UNKNOWN
Docking+scoring workflow in galaxy UNKNOWN
Improve container HOLD
Notes:
Currently putting full workflow together before it goes into squonk/galaxy
Orchestration between layers needs thought
Options should be configurable (e.g. number of poses to dock)
Actions:
Chat to Galaxy guys to include GPU node and configure to target it (TD)
Check current docking workflow (RS) – arrange f2f @SGC meeting for Friday afternoon (RS)
Scope out enumeration step – should we add as galaxy tool? (TD)
Scores and poses into SDF file as output of scoring step (TD)
Fragment Network
Major tasks:
Improve fragmentation algorithm IN PROGRESS
Define data-building workflow IN PROGRESS
Implement API HOLD
Add compounds into network via. API DISCOVER
Notes:
Relational database - being used to index molecules (all datasets that are processed) – it’s where the molecules are stored before the graph network is created
Upper limit (guess) of adding molecules directly into network is ~10,000