Actions:

• Share time spreadsheets (TD)
• Create github repo for fragalysis documentation (RS)
• Send Rachael a list of all github repos (& context) (TD)

Major tasks:

• Fragalysis stack → kubernetes

  • Backend neo4j

  • Deploy JupyterHub (ORN version)

  • Switch to postgres

  • Fragalysis backend to Fragment Network by API

• Fragment network → kubernetes

• Squonk → kubernetes

• Galaxy → kubernetes

• Migrating Verne to K8s

• Fragalysis stack CI/CD

• Fragment network CI/CD

• Openshift K8s

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

• M2M/Janssen can deploy - can run playbook, entering version that deploys stack to cluster

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)

Major tasks:

• Squonk to galaxy link

• Fragalysis to squonk link

Actions:

• Review timeline/roadmap

Major tasks:

1. Scoring method containerised

2. Finalise docking workflow

3. Insert Bayesian optimisation

4. Implement scoring into Galaxy tool

5. Docking+scoring workflow in galaxy

6. Improve container

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)

Major tasks:

1. Improve fragmentation algorithm

2. Define data-building workflow

3. Implement API

4. Add compounds into network via. API

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