Create github repo for fragalysis documentation (TD)
Send Rachael a list of all github repos (& context) (TD)
Deployment (K8S refactoring)
Major tasks:
Fragalysis stack → kubernetes PLANNING
Fragment network → kubernetes DONE
Squonk → kubernetes DONE
Galaxy → kubernetes DISCOVER
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 kubernetes deployment (separate budgeting)
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)
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