Infrastructure Roadmap 2022
- Jeffrey Wagner
- Matt Thompson
- David Mobley
List of infrastructure tasks for 2022. Each task should be linked to its Confluence or GitHub page with more information. See also Science Roadmap 2021 .
Labels
Category | Labels |
|---|---|
Priority | high | MEDIUM | LOW |
Effort | high | MEDIUM | LOW |
Status | Not started | In Progress | PROTOTYPE | Completed | BLOCKED | |
Roadmap
Infrastructure tasks | Priority | Effort | Blocking science? | Infrastructure Dependencies | Start date | End/Due date | Status | Driver |
|---|---|---|---|---|---|---|---|---|
Architecture / General infrastructure | ||||||||
95%+ core package uptime and deployment (OpenFF TK, s99F, OpenFFs)
| High | High |
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| Ongoing |
| Completed | @John Chodera @Jeffrey Wagner @Matt Thompson @David Dotson |
Add | High |
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| MEDIUM |
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| @Josh Mitchell |
Refresh , consolidate, and prune OpenFF toolkit examples | MEDIUM |
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| @Josh Mitchell |
SQM AM1 optimization connectivity change handling | MEDIUM |
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| @Jeffrey Wagner @Connor Davel |
| High |
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| @Jeffrey Wagner |
Streamline | MEDIUM |
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| LOW |
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Refactor | Unresolved – Don’t know timeline for adoption – Bring up in leadership/gov board meeting. Infra team will look into completeness of tests/reference values to estimate refactor cost |
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Accept, reject, or request specific feedback for SMIRNOFF spec proposals within 4 weeks of submission | High |
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| @Jeffrey Wagner @David Mobley @John Chodera @Simon Boothroyd |
Automated upstream RC tests | MEDIUM |
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| IN PROGRESS | @Matt Thompson |
“Did I break something else?” tests against | MEDIUM |
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| @Matt Thompson @Jeffrey Wagner |
QCA Standards v3 implementation | High |
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| new qca hire? |
MEDIUM |
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QCA 2D torsiondrive support (may just need to verify that this works) | High |
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High |
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LOW (may increase if found to be blocking) |
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General “reproducible computation” records and data infrastructure | High |
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| Interoperable molecule class |
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| @Simon Boothroyd @Joshua Horton |
Bayesian infrastructure: ML frameworks |
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| Bayesian Fitting | Analytically Differentiable System Object |
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| BLOCKED |
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Off-site charges (support for conversion to other packages) | MEDIUM |
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| Hard to spec without VirtualSite Handler implementation | June 2021 |
| IN PROGRESS | @Matt Thompson |
Define and maintain specific goals for Bespokefit deployability/stability (succeeds on 95% of minidrugbank? In under some set number CPU-hours? Regression test suite incorporated into CI) | High |
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| @Jeffrey Wagner @Matt Thompson @Joshua Horton |
Local torsiondrive executor (default qc, ANI, and XTB - a more formalized version of this command line command in | MEDIUM |
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| @David Dotson |
Interchange: Have ForceField.create_openmm_system either be deprecated or wrap Interchange call | MEDIUM |
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| GBSA suport in Interchange Plugin support in Interchange, and a few months of lead time for scientists who need to port parameterhandler plugins |
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| @Jeffrey Wagner @Matt Thompson |
Interchange: System combination | MEDIUM |
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| PROTOTYPE | @Matt Thompson |
Interchange: AMBER export | High |
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| Biopolymer topologies SMIRNOFF updates |
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| IN PROGRESS | @Matt Thompson |
Interchange: GROMACS export | High |
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| Biopolymer topologies SMIRNOFF updates |
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| PROTOTYPE | @Matt Thompson |
Interchange: OpenMM export | High |
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| PROTOTYPE | @Matt Thompson |
Intercharge: LAMMPS export | LOW |
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| SMIRNOFF updates |
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| @Matt Thompson |
Interchange: ParmEd export | MEDIUM |
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| Biopolymer topologies SMIRNOFF updates |
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| PROTOTYPE (not to be advertised for production use) | @Matt Thompson |
Interchange: AMBER import | MEDIUM |
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| Biopolymer topologies |
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| IN PROGRESS | @Matt Thompson |
Interchange: GROMACS import | LOW |
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| Biopolymer topologies |
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| IN PROGRESS | @Matt Thompson |
Interchange: OpenMM import | LOW |
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| Biopolymer topologies |
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| PROTOTYPE | @Matt Thompson |
Interchange: ParmEd import | MEDIUM |
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| Biopolymer topologies |
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| PROTOTYPE (not to be advertised for production use) | @Matt Thompson |
Interchange: Track parameter provenance on import (ie, hold a single value for shared GAFF parameters) | LOW |
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| Biopolymer topologies |
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| @Matt Thompson |
Interchange: Interfacing with ML-based fitting |
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| Blocked by lack of specification / needs to be broken into more discrete deliverables |
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| BLOCKED | @Matt Thompson |
Interchange: “Book” documentation/user’s guide | MEDIUM |
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| IN PROGRESS PROTOTYPE | @Josh Mitchell@Matt Thompson |
HIGH |
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| June 2020 |
| IN PROGRESS PROTOTYPE | @Matt Thompson @Jeffrey Wagner | |
Remove | MEDIUM |
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| @Jeffrey Wagner |
High |
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| PROTOTYPE IN PROGRESS | @Jeffrey Wagner @Connor Davel | |
Toolkit | ||||||||
HIGH |
| Biopolymer fitting |
| March 2020 |
| PROTOTYPE | @Jeffrey Wagner @Chapin Cavender | |
Polarizability ParameterHandler | LOW |
| Polarizable fitting |
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(Follow up with @Jeffry Setiadi @Michael Gilson to understand long term plans and infrastructure needs) |
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| PROTOTYPE |
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WBOs for improper torsions |
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| Waiting on research results to assign priority |
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A deep dive into toolkit parametrization differences (Josh Fass SMIRKS differences) / Automate complaining about cases where incoming molecule/chemistry is bad/misformatted | ||||||||