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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[1.12.7] - 2024-03-14

1.12.7 Fixed

  • Updated S3 location for reference data

[1.12.6] - 2023-12-08

1.12.6 Changed

  • Remove jax from notebook requirements

[1.12.5] - 2023-09-05

1.12.5 Changed

  • Update AlphaFold to version v2.3.2

[1.12.4] - 2023-08-29

1.12.4 Changed

  • Removed VPC configuration for Lambda-based custom resources to better support bring-you-own-VPC

[1.12.3] - 2023-08-8

1.12.3 Fixed

  • Updated scipy version in JackHMMER container in response to Dependabot alert.

[1.12.2] - 2023-08-7

1.12.2 Added

  • Optional p4d compute environment and job queue
  • Deployment script for updating existing stacks

1.12.2 Changed

  • Updating the cfn stack will now restart the CodeBuild jobs for all module containers

[1.12.1] - 2023-07-26

1.12.1 Fixed

  • Fixed bug in miniconda version for OpenFold, ESMFold, and NextFlow container images.

1.12.1 Changed

  • Updated ESMFold container to match Amazon HealthOmics implementation and improve run outputs.

[1.12.0] - 2023-07-19

1.12.0 Fixed

  • Due to a lack of ARM in the HMMER package, reverting all non-accelerated jobs back to x86 architecture.

[1.11.0] - 2023-07-06

1.11.0 Added

  • Support for running AlphaFold jobs on non-accelerated instance types by setting gpu=0 and submitting job to the CPUOnDemandJobQueue.
  • Support for passing a dictionary of environment variables to AlphaFold jobs.
  • Support for c/m/r6i instance types in the CPU on-demand compute environment.
  • Support for c/m/r7g instance types on the Graviton on-demand and spot compute environments.
  • Added model version information to README.

[1.10.4] - 2023-06-12

1.10.4 Changed

  • Updated AlphaFold CUDA version to 11.6

1.10.4 Fixed

  • Fixed bug causing hhsearch errors on g5 instance types

[1.10.3] - 2023-06-07

1.10.3 Fixed

  • Fixed bug preventing load of nested stacks.

[1.10.2] - 2023-06-06

1.10.2 Changed

  • Added additional error handling to batchfold package.

[1.10.1] - 2023-05-31

1.10.1 Fixed

  • Added paginators to boto3 calls in batchfold environment class to address issue with deploying multiple stacks.

[1.10.0] - 2023-05-25

1.10.0 Added

  • Added support for NextFlow

[1.9.0] - 2023-04-21

1.9.0 Added

  • Added support for RFDiffusion

1.9.0 Changed

  • Removed deprecated notebook for RFDesign
  • Update ProteinMPNN container and job definition to use accelerated instance types.
  • Add new option to ProteinMPNN inference script to remove the input sequence from the output

1.9.0 Fixed

  • Fixed bug with ESMFold metric logging for multiple sequence inputs.

[1.8.0] - 2023-04-10

1.8.0 Added

  • Added support for DiffDock
  • Added ECR URIs as outputs to the CloudFormation template

1.8.0 Fixed

  • Fixed typo in the pip install cell of the AlphaFold-Multimer notebook
  • Updated version of py3Dmol to address structure visualization issue in JupyterLab

[1.7.2] - 2023-03-21

1.7.2 Fixed

  • Pin base image for ProteinMPNN and download containers.

[1.7.1] - 2023-02-21

1.7.1 Fixed

  • Check for AWSServiceRoleForEC2Spot and AWSServiceRoleForEC2SpotFleet service-linked roles before creating duplicates

[1.7.0] - 2023-02-21

1.7.0 Added

  • Updated AlphaFold version to 2.3.1
  • Added support for OmegaFold release 2 models
  • Moved reference data to S3 for faster stack provisioning

[1.6.2] - 2023-02-10

1.6.2 Fixed

  • Pinned commit of OmegaFold repository

[1.6.1] - 2022-12-27

1.6.1 Fixed

  • Fixed issue with ESMFold Dockerfile

[1.6.0] - 2022-12-1

1.6.0 Added

  • Added support for ProteinMPNN jobs.

1.6.0 Changed

  • Incorporated ProteinMPNN into protein design notebook.
  • Added list of supported algorithms to README index.

[1.5.1] - 2022-11-30

1.5.1 Fixed

  • Fixed ESMFold issue with malformed fasta headers
  • Pinned ESMFold dependencies

[1.5.0] - 2022-11-18

1.5.0 Added

  • Added support for ESMFold jobs.

[1.4.0] - 2022-11-18

1.4.0 Added

  • Added support for RFDesign hallucination and inpainting jobs.

[1.3.0] - 2022-10-12

1.3.0 Added

  • Added default support for multi-AZ deployments.
  • Added an S3 data repository to FSx for Lustre deployment to back up reference data.

1.3.0 Fixed

  • Added exception handling for invalid JackHMMER db_preset values.

1.3.0 Changed

  • Improved clarity of prep_databases.py script.
  • Removed Batch compute environments for amd instance types.
  • Moved S3 resource to root CloudFormation stack and updated retention policy
  • Updated cost estimates.

[1.2.0] - 2022-10-12

1.2.0 Added

  • Support for the OmegaFold LLM-based protein folding algorithm.

1.2.0 Fixed

  • Resolved issue with plotting protein structures on SageMaker Notebook instances.

1.2.0 Changed

  • Update AlphaFold version to v2.2.4.
  • Added nbhelper functions to BatchFold package
  • Improved README

[1.1.0] - 2022-09-19

1.1.0 Changed

  • Refactor code to make algorithms more modular. This will make it easier to add new ones!

[1.0.0] - 2022-09-08

1.0.0 Added

  • Initial Release