diff --git a/CHANGELOG.md b/CHANGELOG.md index 1be0dfc..9cfb181 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 --- +## [1.13.4] - 2025-12-29 + +### 1.13.4 Fixed + +- Fixed broken links and added region information to README + +--- + ## [1.13.3] - 2025-10-14 ### 1.13.3 Updates diff --git a/README.md b/README.md index 974297f..e9af6ff 100644 --- a/README.md +++ b/README.md @@ -3,6 +3,9 @@ > [!IMPORTANT] > The examples provided in this repository are for experimental and educational purposes only. They demonstrate concepts and techniques but are not intended for direct use in production environments. +> [!IMPORTANT] +> The CloudFormation templates included in this repository only support deployment to the us-east-1, and us-east-2, eu-west-1, eu-west-2, eu-central-1, and ap-southwest-1 regions. For additional options, please refer to the [Drug Discovery Workflows for AWS HealthOmics](https://github.com/aws-samples/drug-discovery-workflows) project. + ## Contents 1. [Overview](#1-overview) @@ -16,10 +19,10 @@ 4.2. [AlphaFold](#42-alphafold) 4.3. [OpenFold](#43-openfold) 4.4. [OmegaFold](#44-omegafold) - 4.5. [ESMFold](#46-esmfold) - 4.6. [ProteinMPNN](#47-proteinmpnn) - 4.7. [DiffDock](#48-diffdock) - 4.8. [RFDiffusion](#49-rfdiffusion) + 4.5. [ESMFold](#45-esmfold) + 4.6. [ProteinMPNN](#46-proteinmpnn) + 4.7. [DiffDock](#47-diffdock) + 4.8. [RFDiffusion](#48-rfdiffusion) 5. [Architecture Details](#5-architecture-details) 5.1. [Stack Creation Details](#51-stack-creation-details) 5.2. [Cost](#52-cost) @@ -43,18 +46,11 @@ This repository includes the CloudFormation template, Jupyter Notebook, and supp ## 2. Quick Start -1. Choose **Launch Stack** and (if prompted) log into your AWS account: - - | Region | Launch URL | - | ------ | ---------- | - | eu-west-1 | [![Launch Stack](imgs/LaunchStack.jpg)](https://eu-west-1.console.aws.amazon.com/cloudformation/home#/stacks/create/review?templateURL=https://5d1a4b76751b4c8a994ce96bafd91ec9-eu-west-1.s3.amazonaws.com/main/batch-protein-folding-cfn-packaged.yaml) | - | eu-west-2 | [![Launch Stack](imgs/LaunchStack.jpg)](https://eu-west-2.console.aws.amazon.com/cloudformation/home#/stacks/create/review?templateURL=https://5d1a4b76751b4c8a994ce96bafd91ec9-eu-west-2.s3.amazonaws.com/main/batch-protein-folding-cfn-packaged.yaml) | - | eu-central-1 | [![Launch Stack](imgs/LaunchStack.jpg)](https://eu-central-1.console.aws.amazon.com/cloudformation/home#/stacks/create/review?templateURL=https://5d1a4b76751b4c8a994ce96bafd91ec9-eu-central-1.s3.amazonaws.com/main/batch-protein-folding-cfn-packaged.yaml) | - | ap-southeast-1 | [![Launch Stack](imgs/LaunchStack.jpg)](https://ap-southeast-1.console.aws.amazon.com/cloudformation/home#/stacks/create/review?templateURL=https://5d1a4b76751b4c8a994ce96bafd91ec9-ap-southeast-1.s3.amazonaws.com/main/batch-protein-folding-cfn-packaged.yaml) | - | us-east-1 | [![Launch Stack](imgs/LaunchStack.jpg)](https://us-east-1.console.aws.amazon.com/cloudformation/home#/stacks/create/review?templateURL=https://5d1a4b76751b4c8a994ce96bafd91ec9-us-east-1.s3.amazonaws.com/main/batch-protein-folding-cfn-packaged.yaml) | - | us-west-2 | [![Launch Stack](imgs/LaunchStack.jpg)](https://us-west-2.console.aws.amazon.com/cloudformation/home#/stacks/create/review?templateURL=https://5d1a4b76751b4c8a994ce96bafd91ec9-us-west-2.s3.amazonaws.com/main/batch-protein-folding-cfn-packaged.yaml) | +NOTE: This procedure only supports the following AWS regions: eu-west-1, eu-west-2, eu-central-1, ap-southwest-1, us-east-1, and us-east-2 -2. For **Stack Name**, enter a value unique to your account and region. Also update the *DeploymentRegion** parameter with the name of your current AWS region. Leave the other parameters as their default values and select **Next**. +1. Choose **Launch Stack** and (if prompted) log into your AWS account: + [![Launch Stack](imgs/LaunchStack.jpg)](https://console.aws.amazon.com/cloudformation/home#/stacks/create/review?templateURL=https://aws-hcls-ml.s3.amazonaws.com/main/batch-protein-folding-cfn-packaged.yaml) +2. For **Stack Name**, enter a value unique to your account and region. Leave the other parameters as their default values and select **Next**. ![Provide a stack name](imgs/name.png) 3. Select **I acknowledge that AWS CloudFormation might create IAM resources with custom names**. 4. Choose **Create stack**. @@ -113,9 +109,9 @@ Please visit [https://github.com/EddyRivasLab/hmmer](https://github.com/EddyRiva ### 4.2. AlphaFold -Please visit [https://github.com/deepmind/alphafold](https://github.com/deepmind/alphafold) for more information about the AlphaFold2 algorithm. +[Version 2.3.2](https://github.com/deepmind/alphafold/releases/tag/v2.3.2) from 4/5/2023. -Due to updates to the OpenMM module, GPU-accelerated relaxation is no longer available. All alphafold jobs now default to `use_gpu_relax=False`. +Please visit [https://github.com/deepmind/alphafold](https://github.com/deepmind/alphafold) for more information about the AlphaFold2 algorithm. The original AlphaFold 2 citation is