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titleRoadmap%20Planner
hashc94780fe44ab13aa9299d971f522ade9
Expand
titleProject management

Actions:

  •  Share time spreadsheets (TD)
  •  Create github repo for fragalysis documentation (TD)
  •  Send Rachael a list of all github repos (& context) (TD)
Expand
titleDeployment (K8S refactoring)

Major tasks:

  • Fragalysis stack → kubernetes

    Status
    colourRed
    titleplanning

  • Fragment network → kubernetes

    Status
    colourGreen
    titleDONE

  • Squonk → kubernetes

    Status
    colourGreen
    titleDONE

  • Galaxy → kubernetes

    Status
    colourPurple
    titlediscover

  • Fragalysis stack CI/CD

    Status
    titleHOLD

  • Fragment network CI/CD

    Status
    titleHOLD

  • Openshift K8s

    Status
    titleHOLD

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)

...

Expand
titleJackall

Major tasks:

  1. Scoring method containerised

    Status
    colourGreen
    titleDONE

  2. Finalise docking workflow

    Status
    colourYellow
    titlein progress

  3. Insert Bayesian optimisation

    Status
    colourPurple
    titlediscovery

  4. Implement scoring into Galaxy tool

    Status
    titleunknown

  5. Docking+scoring workflow in galaxy

    Status
    titleunknown

  6. Improve container

    Status
    titleHOLD

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)
Expand
titleFragment Network

Major tasks:

  1. Improve fragmentation algorithm

    Status
    colourYellow
    titlein progress

  2. Define data-building workflow

    Status
    colourYellow
    titlein progress

  3. Implement API

    Status
    titleHOLD

  4. Add compounds into network via. API

    Status
    colourPurple
    titleDiscover

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