feat: 1.1.0 release (#191)

--------- Co-authored-by: AoyuQC <[email protected]> Co-authored-by: Fan Su <[email protected]> Co-authored-by: cuihubin <[email protected]> Co-authored-by: Nihir Chadderwala <[email protected]> Co-authored-by: jag-p <[email protected]> Co-authored-by: lxy-z <[email protected]> Co-authored-by: cocojs <[email protected]> Co-authored-by: l xy <[email protected]> Co-authored-by: Renata Wong <[email protected]> Co-authored-by: rrxie <[email protected]>
awslabs · Jun 26, 2023 · 54afc1b · 54afc1b
1 parent aebf504
commit 54afc1b
Show file tree

Hide file tree

Showing 610 changed files with 41,111 additions and 20,803 deletions.
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -1,10 +1,9 @@
 ---
 name: Bug report
 about: Create a report to help us improve
-title: ''
+title: ""
 labels: bug
-assignees: ''
-
+assignees: ""
 ---
 
 **Describe the bug**
@@ -17,9 +16,10 @@ Steps to reproduce the behavior.
 A clear and concise description of what you expected to happen.
 
 **Please complete the following information about the solution:**
-- [ ] Version: [e.g. v1.0.0]
 
-To get the version of the solution, you can look at the description of the created CloudFormation stack. For example, "_(SO8027) Quantum Computing Exploration for Drug Discovery on AWS (Version **v1.0.0**)_". 
+- [ ] Version: [e.g. v1.1.0]
+
+To get the version of the solution, you can look at the description of the created CloudFormation stack. For example, "_(SO8027) Quantum Computing Exploration for Drug Discovery on AWS (Version **v1.1.0**)_".
 
 - [ ] Region: [e.g. us-west-2]
 - [ ] Was the solution modified from the version published on this repository?

diff --git a/.github/workflows/cfn-nag.yml b/.github/workflows/cfn-nag.yml
@@ -9,13 +9,13 @@ jobs:
       CI: 'true'
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           ref: '${{ github.event.pull_request.head.ref }}'
           repository: '${{ github.event.pull_request.head.repo.full_name }}'
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
         with:
-          node-version: '14'
+          node-version: '18.x'
       - name: Install dependencies
         run: |
           cd source/

diff --git a/.github/workflows/eslint.yml b/.github/workflows/eslint.yml
@@ -9,13 +9,13 @@ jobs:
       CI: 'true'
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           ref: '${{ github.event.pull_request.head.ref }}'
           repository: '${{ github.event.pull_request.head.repo.full_name }}'
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
         with:
-          node-version: '14'
+          node-version: '18.x'
       - name: Install dependencies
         run: |
           cd source/

diff --git a/.github/workflows/test-python.yml b/.github/workflows/test-python.yml
@@ -19,7 +19,6 @@ jobs:
       - name: Install dependencies
         run: |
           cd source/src/cdk
-          pip3 install -r requirements.txt
           pip3 install -U pytest
           pip3 install moto==3.0.5
 

diff --git a/.gitignore b/.gitignore
@@ -21,3 +21,8 @@ __pycache__
 .ipynb_checkpoints
 .idea
 
+nohup.out
+
+# json
+molecular-unfolding-hybrid-jobs.json
+source/src/notebook/healthcare-and-life-sciences/**/*.json
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,13 +1,34 @@
 # Change Log
+
 All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.1.0] - 2023-06-25
+
+### Fix
+
+- Restructure the architecture, decouple the user notebook code and the underlying system code
+- Simplify the architecture design and eliminate the batch and quickSight functions
+- Add the SNS mail subscription function to ensure that the job running results reach the user in time
+- Remove VPC to reduce user cost
+- Add new scenarios support
+
+## [1.0.2] - 2023-04-19
+
+### Fix
+
+- [source]: reslove the issue caused by S3 policy change
+
 ## [1.0.1] - 2022-07-01
+
 ### Fix
+
 - [notebook]: pin the source code in experimental notebook
 
 ## [1.0.0] - 2022-05-20
+
 ### Added
+
 - All files, initial version
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -6,24 +6,23 @@ documentation, we greatly value feedback and contributions from our community.
 Please read through this document before submitting any issues or pull requests to ensure we have all the necessary
 information to effectively respond to your bug report or contribution.
 
-
 ## Reporting Bugs/Feature Requests
 
 We welcome you to use the GitHub issue tracker to report bugs or suggest features.
 
-When filing an issue, please check [existing open](https://github.com/awslabs/cdk-solution-init-pkg/issues), or [recently closed](https://github.com/awslabs/cdk-solution-init-pkg/issues?utf8=%E2%9C%93&q=is%3Aissue%20is%3Aclosed%20), issues to make sure somebody else hasn't already
+When filing an issue, please check [existing open](https://github.com/awslabs/quantum-computing-exploration-for-drug-discovery-on-aws/issues), or [recently closed](https://github.com/awslabs/quantum-computing-exploration-for-drug-discovery-on-aws/issues?utf8=%E2%9C%93&q=is%3Aissue%20is%3Aclosed%20), issues to make sure somebody else hasn't already
 reported the issue. Please try to include as much information as you can. Details like these are incredibly useful:
 
-* A reproducible test case or series of steps
-* The version of our code being used
-* Any modifications you've made relevant to the bug
-* Anything unusual about your environment or deployment
-
+- A reproducible test case or series of steps
+- The version of our code being used
+- Any modifications you've made relevant to the bug
+- Anything unusual about your environment or deployment
 
 ## Contributing via Pull Requests
+
 Contributions via pull requests are much appreciated. Before sending us a pull request, please ensure that:
 
-1. You are working against the latest source on the *master* branch.
+1. You are working against the latest source on the _master_ branch.
 2. You check existing open, and recently merged, pull requests to make sure someone else hasn't addressed the problem already.
 3. You open an issue to discuss any significant work - we would hate for your time to be wasted.
 
@@ -40,23 +39,22 @@ To send us a pull request, please:
 GitHub provides additional document on [forking a repository](https://help.github.com/articles/fork-a-repo/) and
 [creating a pull request](https://help.github.com/articles/creating-a-pull-request/).
 
-
 ## Finding contributions to work on
-Looking at the existing issues is a great way to find something to contribute on. As our projects, by default, use the default GitHub issue labels ((enhancement/bug/duplicate/help wanted/invalid/question/wontfix), looking at any ['help wanted'](https://github.com/awslabs/cdk-solution-init-pkg/labels/help%20wanted) issues is a great place to start.
 
+Looking at the existing issues is a great way to find something to contribute on. As our projects, by default, use the default GitHub issue labels (enhancement/bug/duplicate/help wanted/invalid/question/wontfix), looking at any ['help wanted'](https://github.com/awslabs/quantum-computing-exploration-for-drug-discovery-on-aws/labels/help%20wanted/labels/help%20wanted) issues is a great place to start.
 
 ## Code of Conduct
+
 This project has adopted the [Amazon Open Source Code of Conduct](https://aws.github.io/code-of-conduct).
 For more information see the [Code of Conduct FAQ](https://aws.github.io/code-of-conduct-faq) or contact
 [email protected] with any additional questions or comments.
 
-
 ## Security issue notifications
-If you discover a potential security issue in this project we ask that you notify AWS/Amazon Security via our [vulnerability reporting page](http://aws.amazon.com/security/vulnerability-reporting/). Please do **not** create a public GitHub issue.
 
+If you discover a potential security issue in this project we ask that you notify AWS/Amazon Security via our [vulnerability reporting page](http://aws.amazon.com/security/vulnerability-reporting/). Please do **not** create a public GitHub issue.
 
 ## Licensing
 
-See the [LICENSE](https://github.com/awslabs/cdk-solution-init-pkg/blob/master/LICENSE) file for our project's licensing. We will ask you to confirm the licensing of your contribution.
+See the [LICENSE](https://github.com/awslabs/quantum-computing-exploration-for-drug-discovery-on-aws/blob/main/LICENSE.txt) file for our project's licensing. We will ask you to confirm the licensing of your contribution.
 
 We may ask you to sign a [Contributor License Agreement (CLA)](http://en.wikipedia.org/wiki/Contributor_License_Agreement) for larger changes.
diff --git a/NOTICE.txt b/NOTICE.txt
@@ -1,5 +1,11 @@
 Quantum Computing Exploration for Drug Discovery on AWS
+
 Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
+Licensed under the Apache License Version 2.0 (the "License"). You may not use this file except
+in compliance with the License. A copy of the License is located at http://www.apache.org/licenses/
+or in the "license" file accompanying this file. This file is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, express or implied. See the License for the
+specific language governing permissions and limitations under the License.
 
 **********************
 THIRD PARTY COMPONENTS
@@ -25,14 +31,22 @@ typescript under the Apache License 2.0
 ts-jest under the Massachusetts Institute of Technology (MIT) license
 ts-node under the Massachusetts Institute of Technology (MIT) license
 jest under the Massachusetts Institute of Technology (MIT) license
+mustache under the Massachusetts Institute of Technology (MIT) license
+
 
 numpy under the BSD License (BSD)
 dimod under the Apache Software License (Apache 2.0)
 networkx under the BSD License
 dwave-ocean-sdk under the Apache Software License (Apache 2.0)
 biopandas under the BSD License (BSD 3-Clause)
-dwave-ocean-sdk under the Apache Software License (Apache 2.0)
 amazon-braket-sdk under the Apache Software License (Apache License 2.0)
 amazon-braket-ocean-plugin under the Apache Software License (Apache License 2.0)
 py3Dmol under the MIT License (MIT)
-ipywidgets under the BSD License (BSD)
+ipywidgets under the BSD License (BSD)
+boto3 under the Apache Software License (Apache 2.0)
+Cython under the Apache Software License (Apache 2.0)
+altair under the BSD License (BSD)
+setproctitle under the GPL-3.0 License
+source-map-support under the MIT license
+cdk-nag under the Apache-2.0 License
+fs under the ISC License
diff --git a/README.md b/README.md
@@ -2,89 +2,77 @@
 
 ## Overview
 
-Quantum Computing Exploration for Drug Discovery on AWS (abbrev. QCEDD), an open-sourced solution customers can launch to design and run computational studies in the area of drug discovery, e.g. molecular docking and protein folding. With this solution, customers can design and load new, or existing algorithms, into Jupyter notebooks, then orchestrate the classical and quantum compute resources using AWS Batch and AWS Step Functions. Due to its design, customers are free to scale their classical simulations by launching a performant HPC resource instead of  a single EC2 instance. At the same time customer’s quantum experiments benefit from the growing number of quantum resources available through the Amazon Braket service.
+Quantum Computing Exploration for Drug Discovery on AWS is an open-source solution that allows researchers and quantum computing advocates to design and run computational studies in the field of drug discovery. With this solution, you can access quantum computers via the Amazon Braket service. The Amazon Braket Hybrid Job feature allows you to use classical computing and quantum computing resources to evaluate experiment values such as cost, time, and performance. The solution comes with built-in sample code for certain drug discovery problems, such as molecular docking, protein folding, RNA folding, and retrosynthetic planning, to help you get started with quantum computing in the field.
 
 The overall architecture is shown as below:
 
 ![architecture](./docs/en/images/architecture.png)
 
-This solution deploys the Amazon CloudFormation template in your 
-AWS Cloud account and provides three URLs. One for **Visualization**.
-The others provide user with two approaches to study drug discovery 
-problems: **Notebook Experiment** and **Batch Evaluation**:
-
-* Notebook Experiment
-
-The solution deploys the notebook for user to study different drug discovery 
-problems. 
-These problems will be studied using classical computing or quantum 
-computing.
-
-* Batch Evaluation
-
-The solution provides user the way to evaluate a particular problem based 
-on different computing resources , classical computing or quantum computing. 
-For example, for the problem of molecular unfolding, the performance difference 
-between quantum annealer and simulated annealer can be compared.
-
-* Visualization
-
-The solution provides user the way to visualize the comparing results of 
-batch evaluation (e.g. performance, time)
-
-For detailed description of architecture, please refer to the 
+For detailed description of architecture, please refer to the
 [Architecture Page](https://awslabs.github.io/quantum-computing-exploration-for-drug-discovery-on-aws/en/architecture/)
 
+This solution deploys the Amazon CloudFormation template in your
+AWS Cloud account and provides the URL for Notebook Experiment about drug discovery problems. 
+
 ## Pre-built Examples for Drug Discovery[<sup>1,</sup>](#more-example)[<sup>2</sup>](#data)
+
 <table border='1' style="text-align: center">
     <tr>
         <td><B>Problem Name</B></td>
-        <td><B>Methods</td>
-        <td colspan='2'><B>Function</td>
-        <td><B>Dataset</td>
+        <td><B>Method</td>
         <td><B>Reference</td>
+    </tr>
     <tr>
+        <td>Molecular Unfolding </td>
+        <td>QUBO</td>
+        <td><a href="https://arxiv.org/abs/2107.13607">Quantum Molecular Unfolding(2021)</a></td>
+    </tr>
     <tr>
-        <td rowspan='4'>Molecular Unfolding </td>
-        <td rowspan='4'>QUBO</td>
-        <td><span>single solver</span></td>
-        <td><span>&#10004;</span></td>
-        <td rowspan='4'><a href="https://www.rcsb.org/ligand/117">117 mol2</a></td>
-        <td rowspan='4'><a href="https://arxiv.org/abs/2107.13607">Quantum Molecular Unfolding(2021)</a></td>
+        <td rowspan='2'>RNA folding</td>
+        <td rowspan='2'>QUBO</td>
+        <td ><span><a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010032">RNA folding using quantum computers(2022)</a></span></td>
+    </tr>
     <tr>
+        <td ><span><a href="https://github.com/XanaduAI/QHack2022/issues/114">QHack 2022 winner</a></span></td>
+    </tr>
     <tr>
-        <td><span>qbsolv</span></td>
-        <td><span><span></td>
+        <td rowspan='5'>Protein folding</td>
+        <td rowspan='2'>Quantum Walk</td>
+        <td ><span><a href="https://iopscience.iop.org/article/10.1088/2058-9565/ac4f2f">QFold: quantum walk and deep learning to solve protein folding(2022)</a></span></td>
+    </tr>
     <tr>
+        <td ><span><a href="https://github.com/roberCO/QFold">Roberto Campos's Implementation</a></span></td>
+    </tr>
     <tr>
-        <td rowspan='4'>RNA Folding</td>
-        <td rowspan='4'>QUBO</td>
-        <td><span>single solver</span></td>
-        <td><span>&#10004;</span></td>
-        <td rowspan='4'><a href="http://bprna.cgrb.oregonstate.edu/">bpRNA-1m</a></td>
-        <td ><span><a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010032">RNA folding using quantum computers(2022)</a></span></td>
+        <td>VQE</td>
+        <td >--</td>
+    </tr>
     <tr>
+        <td rowspan='2'>Grover's Algorithm</td>
+        <td ><span><a href="https://ieeexplore.ieee.org/document/9374469">Quantum Speedup for Protein Structure Prediction(2022)</a></span></td>
+    </tr>
     <tr>
-        <td><span>qbsolv</span></td>
-        <td><span><span></td>
-        <td ><span><a href="https://github.com/XanaduAI/QHack2022/issues/114">QHack 2022 winner</a></span></td>
+        <td ><span><a href="https://github.com/renatawong/quantum-protein-structure-prediction">Roberto Campos's Implementation</a></span></td>
+    </tr>
     <tr>
+        <td >Retrosynthetic Planning</td>
+        <td >Quantum Reinforcement Learning</td>
+        <td ><span><a href="https://pubs.acs.org/doi/10.1021/acscentsci.9b00055">Learning Retrosynthetic Planning through Simulated Experience(2019)</a></span></td>
+    </tr>
 </table>
 
 <div id='more-example'></div>
 1.More examples to be added with continuous update
-<div id='data'></div>
-2.All the data in the solution follow the CC0 License
 
 ## File Structure
 
 Upon successfully cloning the repository into your local development environment, you will see the following file structure in your editor:
 
 ```
-├── CHANGELOG.md                  [Change log file]    
-├── CODE_OF_CONDUCT.md            [Code of conduct file] 
-├── CONTRIBUTING.md               [Contribution guide] 
-├── LICENSE                       [LICENSE for this solution] 
+├── CHANGELOG.md                  [Change log file]
+├── CODE_OF_CONDUCT.md            [Code of conduct file]
+├── CONTRIBUTING.md               [Contribution guide]
+├── LICENSE                       [LICENSE for this solution]
 ├── NOTICE                        [Notice for 3rd-party libraries]
 ├── README.md                     [Read me file]
 ├── docs                          [Solution's document]
@@ -100,21 +88,22 @@ Upon successfully cloning the repository into your local development environment
     ├── package-lock.json
     ├── package.json
     ├── src                       [Solution's source code]
-    │   ├── main.ts
-    │   ├── molecular-unfolding
-    │   │   ├── batch-images      
-    │   │   ├── cdk
-    │   │   ├── lambda
-    │   │   ├── molecular_unfolding.ipynb
-    │   │   ├── molecule-data
-    │   │   ├── requirements.txt
-    │   │   └── utility
+    │   ├── cdk
+    │   ├── notebook
+    │   │   └── healthcare-and-life-sciences
+    │   │       ├── a-1-molecular-unfolding-quadratic-unconstrained-binary-optimization
+    │   │       ├── b-1-folding-quadratic-unconstrained-binary-optimization
+    │   │       ├── c-1-rna-folding-quadratic-unconstrained-binary-optimization
+    │   │       ├── c-2-protein-folding-variational-quantum-eigensolver
+    │   │       ├── c-3-protein-folding-grover-search
+    │   │       └── d-1-retrosynthetic-planning-quantum-reinforcement-learning 
     │   └── stack.ts
-    ├── test                      [Solution's unit test code]             
+    ├── test                      [Solution's unit test code]
     ├── tsconfig.jest.json
     ├── tsconfig.json
     └── version.json
 ```
+
 ## Deploy From Source
 
 Refer to [prerequisites and deployment](source/README.md)
@@ -130,9 +119,10 @@ chmod +x ./run-all-tests.sh
 ./run-all-tests.sh
 
 ```
-***
 
-## Documents 
+---
+
+## Documents
 
 - [Github latest page](https://awslabs.github.io/quantum-computing-exploration-for-drug-discovery-on-aws/en/)