diff --git a/.github/scripts/resolve_dockerfile.py b/.github/scripts/resolve_dockerfile.py
new file mode 100644
index 0000000..4b06921
--- /dev/null
+++ b/.github/scripts/resolve_dockerfile.py
@@ -0,0 +1,49 @@
+import sys
+import os
+import requests
+
+from ersilia_pack.parsers import DockerfileInstallParser, YAMLInstallParser
+
+REPO_PATH = os.path.abspath(os.path.join(os.path.dirname(os.path.abspath(__file__)), "../.."))
+PY_VERSION_MAP = {
+    '3.8': 'py38', 
+    '3.9': 'py39',
+    '3.10': 'py310',
+    '3.11': 'py311',
+    '3.12': 'py312'
+}
+model_id = sys.argv[1]
+def resolve_parser():
+    if os.path.exists(os.path.abspath(os.path.join(REPO_PATH, "Dockerfile"))):
+        return DockerfileInstallParser(file_dir=REPO_PATH)
+    elif os.path.exists(os.path.join(REPO_PATH, "install.yml")):
+        return YAMLInstallParser(file_dir=REPO_PATH)
+    else:
+        raise ValueError("No install file found")
+    
+def resolve_python_version(parser):
+    return parser._get_python_version()
+
+def read_dockerfile(parser):
+    commands = parser._get_commands()
+    has_conda = parser._has_conda(commands)
+    if has_conda:
+        file_url = "https://raw.githubusercontent.com/ersilia-os/ersilia/master/dockerfiles/dockerize-ersiliapack/model/Dockerfile.conda"
+    else:
+        file_url = "https://raw.githubusercontent.com/ersilia-os/ersilia/master/dockerfiles/dockerize-ersiliapack/model/Dockerfile.pip"
+    response = requests.get(file_url)
+    return response.text
+
+def write_version_and_model_id(file_content, python_version):
+    python_version = PY_VERSION_MAP[python_version]
+    file_content = file_content.replace("eos_identifier", model_id)
+    lines = file_content.split("\n")
+    lines[0] = lines[0].replace("VERSION", python_version)
+    with open(os.path.join(REPO_PATH, "../", "Dockerfile"), "w") as f:
+        f.write("\n".join(lines))
+
+if __name__ == "__main__":
+    parser = resolve_parser()
+    python_version = resolve_python_version(parser)
+    dockerfile = read_dockerfile(parser)
+    write_version_and_model_id(dockerfile, python_version)
\ No newline at end of file
diff --git a/.github/scripts/verify_model_outcome.py b/.github/scripts/verify_model_outcome.py
new file mode 100644
index 0000000..5021e81
--- /dev/null
+++ b/.github/scripts/verify_model_outcome.py
@@ -0,0 +1,27 @@
+import csv
+
+def check_non_null_outcomes_in_output_csv(csv_file_path):
+    with open(csv_file_path, 'r') as csv_file:
+        csv_reader = csv.reader(csv_file)
+        header = next(csv_reader)
+        row = next(csv_reader)
+        for val in row[2:]: # Skip the first two columns (Inchikey and input)
+            if val not in ['', None]: # Returns if even one outcome is not null
+                return False
+    return True
+
+if __name__ == '__main__':
+    # Read file path from command line
+    import sys
+    if len(sys.argv) < 2:
+        print('Usage: python verify_model_output.py <output_csv_file>')
+        exit(1)
+
+    output_csv_file = sys.argv[1]
+
+    if check_non_null_outcomes_in_output_csv(output_csv_file):
+        # If there are null outcomes, exit with status code 1
+        print('All outcomes are null')
+    else:
+        print('Some outcomes are not null')
+
diff --git a/.github/workflows/json-check.yml b/.github/workflows/json-check.yml
new file mode 100644
index 0000000..22cd701
--- /dev/null
+++ b/.github/workflows/json-check.yml
@@ -0,0 +1,18 @@
+name: json syntax check
+
+on:
+  push:
+    paths:
+      - "**.json"
+  pull_request:
+
+jobs:
+  json-test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: checkout
+        uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # pin@v3.5.2
+
+      - name: json syntax check
+        id: json-yaml-validate
+        uses: GrantBirki/json-yaml-validate@87b2d309a02f4942c5e602183eeea11008a640f9 # pin@v1.4.0
diff --git a/.github/workflows/post-model-upload.yml b/.github/workflows/post-model-upload.yml
new file mode 100644
index 0000000..d33c69f
--- /dev/null
+++ b/.github/workflows/post-model-upload.yml
@@ -0,0 +1,194 @@
+name: Post Model Upload actions
+
+on:
+  workflow_run:
+    workflows: ["Upload model to DockerHub"]
+    types:
+      - completed
+
+jobs:
+  post-model-upload:
+    if: ${{ github.repository != 'ersilia-os/eos-template' }}
+    runs-on: ubuntu-latest
+    steps:
+
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Download arch.txt
+        uses: actions/download-artifact@v4
+        with:
+          name: arch
+          path: .
+          run-id: ${{ github.event.workflow_run.id }}
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Check metadata file
+        id: checkMetadata
+        continue-on-error: true
+        run: |
+          if [[ ! -f metadata.yml ]]; then
+            echo "metadata.yml file not found"
+            exit 1
+          fi
+
+      - name: Update Metadata YAML file with DockerHub info
+        id: updateMetadataYAML
+        if: steps.checkMetadata.outcome == 'success'
+        run: |
+          python3 -c "
+          import yaml
+          with open('metadata.yml', 'r') as f:
+            data = yaml.safe_load(f)
+          print(data)
+          with open('arch.txt', 'r') as f:
+            arch = f.read().rstrip()
+            arch = arch.split(',')
+          data['DockerHub'] = 'https://hub.docker.com/r/ersiliaos/{0}'.format(data['Identifier'])
+          data['Docker Architecture'] = arch
+          with open('metadata.yml', 'w') as f:
+            yaml.dump(data, f, default_flow_style=False, sort_keys=False)
+          "
+          rm arch.txt
+
+      - name: Update Metadata JSON file with DockerHub info
+        id: updateMetadataJSON
+        if: steps.checkMetadata.outcome == 'failure'
+        run: |
+          python3 -c "
+          import json
+          with open('metadata.json', 'r') as f:
+            data = json.load(f)
+          print(data)
+          with open('arch.txt', 'r') as f:
+            arch = f.read().rstrip()
+            arch = arch.split(',')
+          data['DockerHub'] = 'https://hub.docker.com/r/ersiliaos/{0}'.format(data['Identifier'])
+          data['Docker Architecture'] = arch
+          with open('metadata.json', 'w') as f:
+            json.dump(data, f, indent=4)
+          "
+          rm arch.txt
+      
+          
+      - name: Commit and push changes done to the Metadata file
+        uses: actions-js/push@156f2b10c3aa000c44dbe75ea7018f32ae999772 # pin@v1.4
+        with:
+          author_name: "ersilia-bot"
+          author_email: "ersilia-bot@users.noreply.github.com"
+          message: "updating metadata [skip ci]"
+          repository: "ersilia-os/${{ github.event.repository.name }}"
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          amend: true
+          force: true
+
+      # Setup conda
+      - name: Setup conda
+        id: setupConda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          python-version: "3.10.10"
+  
+      # Install ersilia
+      - name: Install dependencies in Conda environment
+        id: installDependenciesInConda
+        run: |
+          conda install gh -c conda-forge
+          python -m pip install git+https://github.com/ersilia-os/ersilia.git
+
+      - name: Update metadata to AirTable
+        id: update-metadata-to-airtable
+        env:
+          USER_NAME: ${{ github.repository_owner }}
+          BRANCH: "main"
+          REPO_NAME: ${{ github.event.repository.name }}
+          AIRTABLE_API_KEY: ${{ secrets.AIRTABLE_API_KEY }}
+        run: |
+          source activate
+          pip install requests pyairtable
+          echo "Updating metadata to AirTable looking at owner: $USER_NAME"
+          wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/airtableops.py
+          python3 airtableops.py airtable-update --user $USER_NAME --repo $REPO_NAME --branch $BRANCH --api-key $AIRTABLE_API_KEY
+          rm airtableops.py
+  
+      - name: sync metadata to S3 JSON
+        id: sync-metadata-to-s3
+        env:
+          AIRTABLE_API_KEY: ${{ secrets.AIRTABLE_API_KEY }}
+          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY }}
+          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+        run: |
+          source activate
+          wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/convert_airtable_to_json.py
+          pip install boto3 requests pyairtable
+          python convert_airtable_to_json.py $AIRTABLE_API_KEY $AWS_ACCESS_KEY_ID $AWS_SECRET_ACCESS_KEY
+          rm convert_airtable_to_json.py
+
+      - name: Update README file
+        id: update-readme-file
+        env:
+          MODEL_ID: ${{ github.event.repository.name }}
+        run: |
+          echo "Updating README file with AirTable metadata for model: $MODEL_ID"
+          wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/airtableops.py
+          python3 airtableops.py readme-update --repo $MODEL_ID --path .
+          rm airtableops.py
+          less README.md
+
+      - name: Commit and push changes done to the README file
+        uses: actions-js/push@156f2b10c3aa000c44dbe75ea7018f32ae999772 # pin@v1.4
+        with:
+          author_name: "ersilia-bot"
+          author_email: "ersilia-bot@users.noreply.github.com"
+          message: "updating readme [skip ci]"
+          repository: "ersilia-os/${{ github.event.repository.name }}"
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          amend: true
+          force: true
+
+      - name: Docker Hub Description
+        uses: peter-evans/dockerhub-description@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+          repository: ersiliaos/${{ github.event.repository.name }}
+          short-description: "Ersilia Model Hub Identifier: ${{ github.event.repository.name }}"
+
+      # Create an issue within the repository to track that this model is ready for testing
+
+      - name: Shuffle assignees
+        id: shuffle
+        run: |
+          export assignees=$(echo "${{ vars.assignees }}" | awk 'BEGIN {FS=","}; {srand();split($0,a,FS); print a[int(rand()*NF+1)]}')
+          echo "$assignees" >> $GITHUB_STEP_SUMMARY
+          echo "shuffled_assignee=$assignees" >> $GITHUB_OUTPUT
+          echo "shuffled_assignee=$assignees" >> $GITHUB_ENV
+
+      - name: Check for existing issue
+        id: check_existing_test_issue
+        run: |
+          gh auth login --with-token <<< ${{ secrets.GITHUB_TOKEN }}
+          issue_number=$(gh issue list --limit 100 --search "${{ vars.test_issue_title }}" --json number --jq '.[0].number')
+          echo "::set-output name=issue_number::$issue_number"
+  
+      - name: Create a Test issue
+        uses: actions-ecosystem/action-create-issue@b63bc2bbacb6a838dfe4a9f70da6665ae0962a49
+        id: create_test_issue 
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          title: ${{ vars.TEST_ISSUE_TITLE }}
+          assignees: |
+            ${{ steps.shuffle.outputs.shuffled_assignee }}
+          body: |
+            This model is a new incorporation to the Ersilia Model Hub or it has been modified. If you are assigned to this issue, please try it out and ensure everything works!
+            To test a model, first clone it in your local system (ideally, from dockerhub) using the CLI commands:
+            ```
+            ersilia -v fetch eosxxxx --from_dockerhub
+            ersilia serve eosxxxx
+            ersilia test
+            ```
+            The test command will automatically check that the model can handle null outputs and whether it produces consistent results. Please copy here the result of the test command. If it passes, simply close the issue as completed. If it fails, please detail at which step and whether you have taken any steps to solve it. Please tag the original model contributor and one of Ersilia's maintainers for support.
+          labels: |
+            test
+        if: steps.check_existing_test_issue.outputs.issue_number == ''
diff --git a/.github/workflows/post2slack.yml b/.github/workflows/post2slack.yml
new file mode 100644
index 0000000..9a77592
--- /dev/null
+++ b/.github/workflows/post2slack.yml
@@ -0,0 +1,17 @@
+name: Send Slack message
+on:
+  issues:
+    types: [opened]
+
+jobs:
+  slack:
+    runs-on: ubuntu-latest
+    steps:
+      - name: post slack
+        uses: slackapi/slack-github-action@v1.23.0
+        env:
+          SLACK_BOT_TOKEN: ${{ secrets.SLACK_TOKEN }}
+        with:
+          slack-message: |
+              "new issue: https://github.com/${{ github.repository }}/issues/${{ github.event.issue.number }} created."
+          channel-id: ${{ secrets.SLACK_CHANNEL_TESTER }}
diff --git a/.github/workflows/test-model-pr.yml b/.github/workflows/test-model-pr.yml
new file mode 100644
index 0000000..a76fb5c
--- /dev/null
+++ b/.github/workflows/test-model-pr.yml
@@ -0,0 +1,79 @@
+name: Model Test on PR
+
+on: 
+  pull_request:
+
+jobs:
+  test:
+    if: github.repository != 'ersilia-os/eos-template'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # pin@v3.5.2
+        with:
+          lfs: true
+
+# This might stop working in the future, so we need to keep an eye on it
+      - name: Free Disk Space (Ubuntu)
+        uses: jlumbroso/free-disk-space@main
+        with:
+          # this might remove tools that are actually needed,
+          # if set to "true" but frees about 6 GB
+          tool-cache: true
+          
+          # all of these default to true, but feel free to set to
+          # "false" if necessary for your workflow
+          android: true
+          dotnet: true
+          haskell: true
+          large-packages: true
+          swap-storage: true
+
+      - name: Add conda to system path
+        run: echo $CONDA/bin >> $GITHUB_PATH
+      
+      - name: Source conda
+        run: source $CONDA/etc/profile.d/conda.sh
+        
+      - name: Set Python to 3.10.10
+        run:
+         conda install -y python=3.10.10 
+      
+      - name: Install dependencies
+        run: |
+          source activate
+          conda init
+          conda install git-lfs -c conda-forge
+          git-lfs install
+          conda install gh -c conda-forge
+
+      - name: Install ersilia
+        run: |
+          source activate
+          python --version
+          echo "After conda init"
+          conda init
+          python -m pip install git+https://github.com/ersilia-os/ersilia.git
+  
+      - name: Predict output
+        env:
+          MODEL_ID: ${{ github.event.repository.name }}
+        uses: nick-fields/retry@v3
+        with:
+          timeout_minutes: 10
+          max_attempts: 3
+          command: |
+            source activate
+            echo "Sample model id selected: $MODEL_ID"
+            ersilia -v fetch $MODEL_ID --from_dir .
+            ersilia -v serve $MODEL_ID
+            ersilia example -n 5 -f input.csv --predefined
+            ersilia -v api -i input.csv
+            ersilia close
+          
+      - name: Upload log output
+        if: always()
+        uses: actions/upload-artifact@83fd05a356d7e2593de66fc9913b3002723633cb #pin v3.1.1
+        with:
+          name: debug-logs
+          retention-days: 14
+          path: /home/runner/eos/*.log
diff --git a/.github/workflows/test-model.yml b/.github/workflows/test-model.yml
new file mode 100644
index 0000000..db5ce34
--- /dev/null
+++ b/.github/workflows/test-model.yml
@@ -0,0 +1,155 @@
+name: Model test on push
+
+on:
+  push: 
+    branches: ['main']
+  workflow_dispatch:
+
+jobs:
+  test:
+    if: github.repository != 'ersilia-os/eos-template'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout persist credentials
+        uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # pin@v3.5.2
+        with:
+          persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token
+          fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
+          lfs: 'true'
+          
+# This might stop working in the future, so we need to keep an eye on it
+      - name: Free Disk Space (Ubuntu)
+        uses: jlumbroso/free-disk-space@main
+        with:
+          # this might remove tools that are actually needed,
+          # if set to "true" but frees about 6 GB
+          tool-cache: true
+          
+          # all of these default to true, but feel free to set to
+          # "false" if necessary for your workflow
+          android: true
+          dotnet: true
+          haskell: true
+          large-packages: true
+          swap-storage: true
+
+      - name: Add conda to system path
+        run: echo $CONDA/bin >> $GITHUB_PATH
+      
+      - name: Source conda
+        run: source $CONDA/etc/profile.d/conda.sh
+
+      - name: Set Python to 3.10.10
+        run:
+         conda install -y python=3.10.10 
+         
+      - name: Install dependencies
+        run: |
+          source activate
+          conda init
+          conda install git-lfs -c conda-forge
+          git-lfs install
+          conda install gh -c conda-forge
+
+      - name: Install ersilia
+        run: |
+          source activate
+          python --version
+          echo "After conda init"
+          conda init
+          python -m pip install git+https://github.com/ersilia-os/ersilia.git
+  
+      - name: Update metadata to AirTable
+        id: update-metadata-to-airtable
+        env:
+          USER_NAME: ${{ github.repository_owner }}
+          BRANCH: "main"
+          REPO_NAME: ${{ github.event.repository.name }}
+          AIRTABLE_API_KEY: ${{ secrets.AIRTABLE_API_KEY }}
+        uses: nick-fields/retry@v3
+        with:
+          timeout_minutes: 10
+          max_attempts: 3
+          command: |
+            source activate
+            pip install requests pyairtable
+            echo "Updating metadata to AirTable looking at owner: $USER_NAME"
+            wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/airtableops.py
+            python3 airtableops.py airtable-update --user $USER_NAME --repo $REPO_NAME --branch $BRANCH --api-key $AIRTABLE_API_KEY
+            rm airtableops.py
+
+      - name: sync metadata to S3 JSON
+        id: sync-metadata-to-s3
+        env:
+          AIRTABLE_API_KEY: ${{ secrets.AIRTABLE_API_KEY }}
+          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY }}
+          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+        run: |
+          source activate
+          wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/convert_airtable_to_json.py
+          pip install boto3 requests pyairtable
+          python convert_airtable_to_json.py $AIRTABLE_API_KEY $AWS_ACCESS_KEY_ID $AWS_SECRET_ACCESS_KEY
+          rm convert_airtable_to_json.py
+
+      - name: Update README file
+        id: update-readme-file
+        env:
+          MODEL_ID: ${{ github.event.repository.name }}
+        run: |
+          source activate
+          echo "Updating README file with AirTable metadata for model: $MODEL_ID"
+          wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/airtableops.py
+          python3 airtableops.py readme-update --repo $MODEL_ID --path .
+          rm airtableops.py
+          less README.md
+
+      - name: Commit and push changes done to the README file
+        uses: actions-js/push@156f2b10c3aa000c44dbe75ea7018f32ae999772 # pin@v1.4
+        with:
+          author_name: "ersilia-bot"
+          author_email: "ersilia-bot@users.noreply.github.com"
+          message: "updating readme [skip ci]"
+          repository: "ersilia-os/${{ github.event.repository.name }}"
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          amend: true
+          force: true
+      
+      - name: Fetch model
+        env:
+          MODEL_ID: ${{ github.event.repository.name }}
+        run: |
+            source activate
+            ersilia -v fetch $MODEL_ID --from_dir .
+            FOLDER="$HOME/eos/repository/$MODEL_ID"
+            if [ ! -d "$FOLDER" ]; then
+              echo "Error: Folder '$FOLDER' does not exist." >&2
+              exit 1
+            fi
+
+      - name: Generate input and run model
+        env:
+          MODEL_ID: ${{ github.event.repository.name }}
+        run: |
+            source activate
+            ersilia -v serve $MODEL_ID
+            ersilia example -n 5 -f input.csv --predefined
+            ersilia -v run -i "input.csv" -o "output.csv"
+            ersilia close
+            cat output.csv
+      
+      - name: Test output
+        run: |
+            output=$(python .github/scripts/verify_model_outcome.py output.csv)
+            if echo "$output" | grep -q "All outcomes are null"; then
+              echo "Error in model outcome, aborting test"
+              exit 1
+            fi
+            rm output.csv
+
+      - name: Upload log output
+        if: always()
+        uses: actions/upload-artifact@83fd05a356d7e2593de66fc9913b3002723633cb #pin v3.1.1
+        with:
+          name: debug-logs
+          retention-days: 14
+          path: /home/runner/eos/*.log
diff --git a/.github/workflows/upload-bentoml.yml b/.github/workflows/upload-bentoml.yml
new file mode 100644
index 0000000..456876a
--- /dev/null
+++ b/.github/workflows/upload-bentoml.yml
@@ -0,0 +1,142 @@
+name: Upload BentoML Dockerized Model with or without Multi-stage Conda Pack
+
+on:
+  workflow_call:
+    inputs:
+      version:
+        required: true
+        type: string
+
+jobs:
+  build-bentoml-image:
+    if: ${{ github.repository != 'ersilia-os/eos-template' }}
+    runs-on: ubuntu-latest
+    steps:
+
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Check if we can use this workflow
+        run: |
+          if [[ -f install.yml ]]; then
+            echo "This workflow is not supported for this repository"
+            exit 1
+          fi
+      
+      # https://github.com/docker/setup-qemu-action
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+      
+      # https://github.com/docker/setup-buildx-action
+      - name: Set up Docker Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v3
+    
+      # log in to dockerhub
+      - name: Login to Docker Hub
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+
+      # This might stop working in the future, so we need to keep an eye on it
+      - name: Free Disk Space (Ubuntu)
+        uses: jlumbroso/free-disk-space@main
+        with:
+          # this might remove tools that are actually needed,
+          # if set to "true" but frees about 6 GB
+          tool-cache: true
+          
+          # all of these default to true, but feel free to set to
+          # "false" if necessary for your workflow
+          android: true
+          dotnet: true
+          haskell: true
+          large-packages: true
+          swap-storage: true
+
+      - name: Setup conda
+        id: setupConda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          python-version: "3.10.10"
+
+      - name: Install dependencies in Conda environment
+        id: installDependenciesInConda
+        run: |
+          conda install git-lfs -c conda-forge
+          git-lfs install
+          conda install gh -c conda-forge
+          python -m pip install git+https://github.com/ersilia-os/ersilia.git
+
+      - name: Generate the  Dockerfile
+        id: generateDockerfile
+        env:
+          REPO_NAME: ${{ github.event.repository.name }}
+          VERSION: ${{ inputs.version}}
+        run: |
+          wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/place_a_dockerfile_in_current_eos_repo.py
+          python -m pip install requests
+          python place_a_dockerfile_in_current_eos_repo.py $REPO_NAME $VERSION
+          rm place_a_dockerfile_in_current_eos_repo.py
+
+      # We cannot tag it as anything other than latest because 
+      # ersilia cli only looks for the 'latest' tag
+      - name: Build only  AMD64 Image for Testing
+        id: buildForTest
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          load: true
+          tags: ersiliaos/${{ github.event.repository.name }}:latest
+          
+      # TODO This is very hacky, maybe we want to use the ersilia test command in the future for this
+      - name: Test built image
+        id: testBuiltImage
+        env:
+          PULL_IMAGE: n
+          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          AWS_DEFAULT_REGION: us-east-1
+        run: |
+          ersilia -v fetch ${{ github.event.repository.name }} --from_dockerhub
+          ersilia -v serve ${{ github.event.repository.name }} --track #Added --track here
+          ersilia example -n 1 -f input.csv --predefined
+          ersilia -v run -i "input.csv" -o "output.csv"
+          ersilia close
+          output=$(python .github/scripts/verify_model_outcome.py output.csv)
+          if echo "$output" | grep -q "All outcomes are null"; then
+            echo "Error in model outcome, aborting build"
+            exit 1
+          fi
+          rm output.csv
+
+      - name: Build and push
+        id: buildMultiple
+        continue-on-error: true
+        uses: docker/build-push-action@v6.7.0
+        timeout-minutes: 45
+        with:
+          context: .
+          platforms: linux/amd64,linux/arm64
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ersiliaos/${{ github.event.repository.name }}:latest
+          
+      - name: Set build failure output
+        id: buildCheck
+        run: |
+          if [[ "${{ steps.buildMultiple.outcome }}" == "failure" ]]; then
+            echo "::set-output name=failed::true"
+            echo "AMD64" > arch.txt 
+          else
+            echo "::set-output name=failed::false"
+            echo "AMD64,ARM64" > arch.txt
+          fi
+      
+      - name: Upload arch.txt
+        uses: actions/upload-artifact@v4
+        with:
+          name: arch
+          path: arch.txt
diff --git a/.github/workflows/upload-ersilia-pack.yml b/.github/workflows/upload-ersilia-pack.yml
new file mode 100644
index 0000000..fe4bd5c
--- /dev/null
+++ b/.github/workflows/upload-ersilia-pack.yml
@@ -0,0 +1,122 @@
+name: Upload Ersilia Pack Dockerized Model
+
+on:
+  workflow_call:
+
+jobs:
+  build-ersilia-pack-image:
+    if: ${{ github.repository != 'ersilia-os/eos-template' }}
+    runs-on: ubuntu-latest
+    steps:
+    
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+
+      - run: git lfs pull
+      # https://github.com/docker/setup-qemu-action
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+      
+      # https://github.com/docker/setup-buildx-action
+      - name: Set up Docker Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v3
+    
+      # log in to dockerhub
+      - name: Login to Docker Hub
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+      
+      # This might stop working in the future, so we need to keep an eye on it
+      - name: Free Disk Space (Ubuntu)
+        uses: jlumbroso/free-disk-space@main
+        with:
+          # this might remove tools that are actually needed,
+          # if set to "true" but frees about 6 GB
+          tool-cache: true
+          
+          # all of these default to true, but feel free to set to
+          # "false" if necessary for your workflow
+          android: true
+          dotnet: true
+          haskell: true
+          large-packages: true
+          swap-storage: true
+      
+      # Install ersilia-pack, requests, and ersilia to test the built image with ersilia CLI
+      - name: Setup Python for Ersilia Pack
+        id: setupPythonForErsiliaPack
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3
+        with:
+          python-version: '3.10'
+
+      - name: Install ersilia-pack and generate the right Dockerfile
+        env:
+          REPO_NAME: ${{ github.event.repository.name }}
+        run: |
+          python -m pip install git+https://github.com/ersilia-os/ersilia-pack.git
+          python -m pip install requests
+          python -m pip install git+https://github.com/ersilia-os/ersilia.git
+          python .github/scripts/resolve_dockerfile.py $REPO_NAME
+
+      - name: Build only AMD64 Image for Testing
+        id: buildForTestErsiliaPack
+        uses: docker/build-push-action@v6.7.0
+        with:
+          context: ../ # We need to go back to the root directory to find the Dockerfile and copy the model repository
+          load: true
+          tags: ersiliaos/${{ github.event.repository.name }}:latest
+
+      - name: Test built image
+        id: testBuiltImageErsiliaPack
+        env:
+          PULL_IMAGE: n
+          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          AWS_DEFAULT_REGION: us-east-1
+        if: steps.buildForTestErsiliaPack.outcome == 'success'
+        run: |
+          ersilia -v fetch ${{ github.event.repository.name }} --from_dockerhub
+          ersilia -v serve ${{ github.event.repository.name }} --track #Added --track here
+          ersilia example -n 1 -f input.csv --predefined
+          ersilia -v run -i "input.csv" -o "output.csv" 
+          ersilia close
+          output=$(python .github/scripts/verify_model_outcome.py output.csv)
+          if echo "$output" | grep -q "All outcomes are null"; then
+            echo "Error in model outcome, aborting build"
+            exit 1
+          fi
+          rm output.csv
+
+      - name: Build and push
+        id: buildMultiple
+        continue-on-error: true
+        uses: docker/build-push-action@v6.7.0
+        timeout-minutes: 45
+        with:
+          context: ../
+          platforms: linux/amd64,linux/arm64
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ersiliaos/${{ github.event.repository.name }}:latest
+          
+      - name: Set build failure output
+        id: buildCheck
+        run: |
+          if [[ "${{ steps.buildMultiple.outcome }}" == "failure" ]]; then
+            echo "::set-output name=failed::true"
+            echo "AMD64" > arch.txt 
+          else
+            echo "::set-output name=failed::false"
+            echo "AMD64,ARM64" > arch.txt
+          fi
+      
+      - name: Upload arch.txt
+        uses: actions/upload-artifact@v4
+        with:
+          name: arch
+          path: arch.txt
diff --git a/.github/workflows/upload-model-to-dockerhub.yml b/.github/workflows/upload-model-to-dockerhub.yml
new file mode 100644
index 0000000..e272e93
--- /dev/null
+++ b/.github/workflows/upload-model-to-dockerhub.yml
@@ -0,0 +1,29 @@
+name: Upload model to DockerHub
+on:
+  workflow_dispatch:
+  
+  workflow_run:
+    workflows: ["Upload model to S3"]
+    types:
+      - completed
+  
+jobs:
+  upload-ersilia-pack:
+    uses: ./.github/workflows/upload-ersilia-pack.yml
+    secrets: inherit
+
+  upload-multi-stage-condapack:
+    needs: [upload-ersilia-pack]
+    if: ${{ failure() }}
+    uses: ./.github/workflows/upload-bentoml.yml
+    secrets: inherit
+    with:
+      version: multistage-condapack
+
+  upload-legacy-bentoml:
+    needs: [upload-multi-stage-condapack]
+    if: ${{ failure() }}
+    uses: ./.github/workflows/upload-bentoml.yml
+    secrets: inherit
+    with:
+      version: legacy-bentoml
diff --git a/.github/workflows/upload-model-to-s3.yml b/.github/workflows/upload-model-to-s3.yml
new file mode 100644
index 0000000..f3a48d5
--- /dev/null
+++ b/.github/workflows/upload-model-to-s3.yml
@@ -0,0 +1,156 @@
+name: Upload model to S3
+on:
+  workflow_dispatch:
+  
+  workflow_run:
+    workflows: ["Model test on push"]
+    types:
+      - completed
+  
+jobs:
+  upload_model_to_s3:
+    if: ${{ github.repository != 'ersilia-os/eos-template' && github.event.workflow_run.conclusion == 'success' }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout persist credentials
+        uses: actions/checkout@master
+        with:
+          persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token
+          fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
+          lfs: 'true'
+            
+      - name: Add conda to system path
+        run: echo $CONDA/bin >> $GITHUB_PATH
+      
+      - name: Source conda
+        run: source $CONDA/etc/profile.d/conda.sh
+
+      - name: Set Python to 3.10.10
+        run:
+         conda install -y python=3.10.10 
+      
+      - name: Install dependencies
+        run: |
+          source activate
+          conda init
+          conda install git-lfs -c conda-forge
+          git-lfs install
+          conda install gh -c conda-forge
+          
+      - name: Install ersilia
+        run: |
+          source activate
+          python --version
+          echo "After conda init"
+          conda init
+          python -m pip install git+https://github.com/ersilia-os/ersilia.git
+                  
+      - name: Check metadata file
+        id: checkMetadata
+        continue-on-error: true
+        run: |
+          if [[ ! -f metadata.yml ]]; then
+            echo "metadata.yml file not found"
+            exit 1
+          fi
+
+      - name: Update Metadata JSON file with DockerHub info
+        if: steps.checkMetadata.outcome == 'failure'
+        id: UpdateMetadataJSON
+        run: |
+          python3 -c "
+          import json
+          with open('metadata.json', 'r') as f:
+             data = json.load(f)
+          data['S3'] = 'https://ersilia-models-zipped.s3.eu-central-1.amazonaws.com/{0}.zip'.format(data['Identifier'])
+          with open('metadata.json', 'w') as f:
+             json.dump(data, f, indent=4)
+          "
+
+      - name: Update Metadata YAML file with DockerHub info
+        if: steps.checkMetadata.outcome == 'success'
+        id: UpdateMetadataYAML
+        run: |
+          python3 -c "
+          import yaml
+          with open('metadata.yml', 'r') as f:
+             data = yaml.safe_load(f)
+          data['S3'] = 'https://ersilia-models-zipped.s3.eu-central-1.amazonaws.com/{0}.zip'.format(data['Identifier'])
+          with open('metadata.yml', 'w') as f:
+             yaml.dump(data, f, default_flow_style=False, sort_keys=False)
+          "
+          
+      - name: Commit and push changes done to the Metadata JSON file
+        uses: actions-js/push@156f2b10c3aa000c44dbe75ea7018f32ae999772 # pin@v1.4
+        with:
+          author_name: "ersilia-bot"
+          author_email: "ersilia-bot@users.noreply.github.com"
+          message: "updating metadata [skip ci]"
+          repository: "ersilia-os/${{ github.event.repository.name }}"
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          amend: true
+          force: true
+
+      - name: Update metadata to AirTable
+        id: update-metadata-to-airtable
+        env:
+          USER_NAME: ${{ github.repository_owner }}
+          BRANCH: "main"
+          REPO_NAME: ${{ github.event.repository.name }}
+          AIRTABLE_API_KEY: ${{ secrets.AIRTABLE_API_KEY }}
+        run: |
+          source activate
+          pip install requests pyairtable
+          echo "Updating metadata to AirTable looking at owner: $USER_NAME"
+          wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/airtableops.py
+          python3 airtableops.py airtable-update --user $USER_NAME --repo $REPO_NAME --branch $BRANCH --api-key $AIRTABLE_API_KEY
+          rm airtableops.py
+
+      - name: sync metadata to S3 JSON
+        id: sync-metadata-to-s3
+        env:
+          AIRTABLE_API_KEY: ${{ secrets.AIRTABLE_API_KEY }}
+          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY }}
+          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+        run: |
+          source activate
+          wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/convert_airtable_to_json.py
+          pip install boto3 requests pyairtable
+          python convert_airtable_to_json.py $AIRTABLE_API_KEY $AWS_ACCESS_KEY_ID $AWS_SECRET_ACCESS_KEY
+          rm convert_airtable_to_json.py
+          
+      - name: Update README file
+        id: update-readme-file
+        env:
+          MODEL_ID: ${{ github.event.repository.name }}
+        run: |
+          source activate
+          echo "Updating README file with AirTable metadata for model: $MODEL_ID"
+          wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/airtableops.py
+          python3 airtableops.py readme-update --repo $MODEL_ID --path .
+          rm airtableops.py
+          less README.md
+
+      - name: Commit and push changes done to the README file
+        uses: actions-js/push@156f2b10c3aa000c44dbe75ea7018f32ae999772 # pin@v1.4
+        with:
+          author_name: "ersilia-bot"
+          author_email: "ersilia-bot@users.noreply.github.com"
+          message: "updating readme [skip ci]"
+          repository: "ersilia-os/${{ github.event.repository.name }}"
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          amend: true
+          force: true
+
+      - name: Upload model to S3
+        id: upload-model-to-s3
+        env:
+          REPO_NAME: ${{ github.event.repository.name }}
+          AWS_ACCESS_KEY: ${{ secrets.AWS_ACCESS_KEY }}
+          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+        run: |
+          source activate
+          echo "Uploading model to S3 bucket"
+          wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/upload_model_to_s3.py
+          python3 upload_model_to_s3.py $REPO_NAME $AWS_ACCESS_KEY $AWS_SECRET_ACCESS_KEY .
+          rm upload_model_to_s3.py
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..809fa6e
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,130 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+/data.h5
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..6aeb811
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,7 @@
+FROM bentoml/model-server:0.11.0-py310
+
+RUN pip install numpy==1.26.4
+RUN pip install rdkit==2022.9.5
+
+WORKDIR /repo
+COPY . /repo
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..f288702
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,674 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
+  The GNU General Public License is a free, copyleft license for
+software and other kinds of works.
+
+  The licenses for most software and other practical works are designed
+to take away your freedom to share and change the works.  By contrast,
+the GNU General Public License is intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains free
+software for all its users.  We, the Free Software Foundation, use the
+GNU General Public License for most of our software; it applies also to
+any other work released this way by its authors.  You can apply it to
+your programs, too.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+them if you wish), that you receive source code or can get it if you
+want it, that you can change the software or use pieces of it in new
+free programs, and that you know you can do these things.
+
+  To protect your rights, we need to prevent others from denying you
+these rights or asking you to surrender the rights.  Therefore, you have
+certain responsibilities if you distribute copies of the software, or if
+you modify it: responsibilities to respect the freedom of others.
+
+  For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must pass on to the recipients the same
+freedoms that you received.  You must make sure that they, too, receive
+or can get the source code.  And you must show them these terms so they
+know their rights.
+
+  Developers that use the GNU GPL protect your rights with two steps:
+(1) assert copyright on the software, and (2) offer you this License
+giving you legal permission to copy, distribute and/or modify it.
+
+  For the developers' and authors' protection, the GPL clearly explains
+that there is no warranty for this free software.  For both users' and
+authors' sake, the GPL requires that modified versions be marked as
+changed, so that their problems will not be attributed erroneously to
+authors of previous versions.
+
+  Some devices are designed to deny users access to install or run
+modified versions of the software inside them, although the manufacturer
+can do so.  This is fundamentally incompatible with the aim of
+protecting users' freedom to change the software.  The systematic
+pattern of such abuse occurs in the area of products for individuals to
+use, which is precisely where it is most unacceptable.  Therefore, we
+have designed this version of the GPL to prohibit the practice for those
+products.  If such problems arise substantially in other domains, we
+stand ready to extend this provision to those domains in future versions
+of the GPL, as needed to protect the freedom of users.
+
+  Finally, every program is threatened constantly by software patents.
+States should not allow patents to restrict development and use of
+software on general-purpose computers, but in those that do, we wish to
+avoid the special danger that patents applied to a free program could
+make it effectively proprietary.  To prevent this, the GPL assures that
+patents cannot be used to render the program non-free.
+
+  The precise terms and conditions for copying, distribution and
+modification follow.
+
+                       TERMS AND CONDITIONS
+
+  0. Definitions.
+
+  "This License" refers to version 3 of the GNU General Public License.
+
+  "Copyright" also means copyright-like laws that apply to other kinds of
+works, such as semiconductor masks.
+
+  "The Program" refers to any copyrightable work licensed under this
+License.  Each licensee is addressed as "you".  "Licensees" and
+"recipients" may be individuals or organizations.
+
+  To "modify" a work means to copy from or adapt all or part of the work
+in a fashion requiring copyright permission, other than the making of an
+exact copy.  The resulting work is called a "modified version" of the
+earlier work or a work "based on" the earlier work.
+
+  A "covered work" means either the unmodified Program or a work based
+on the Program.
+
+  To "propagate" a work means to do anything with it that, without
+permission, would make you directly or secondarily liable for
+infringement under applicable copyright law, except executing it on a
+computer or modifying a private copy.  Propagation includes copying,
+distribution (with or without modification), making available to the
+public, and in some countries other activities as well.
+
+  To "convey" a work means any kind of propagation that enables other
+parties to make or receive copies.  Mere interaction with a user through
+a computer network, with no transfer of a copy, is not conveying.
+
+  An interactive user interface displays "Appropriate Legal Notices"
+to the extent that it includes a convenient and prominently visible
+feature that (1) displays an appropriate copyright notice, and (2)
+tells the user that there is no warranty for the work (except to the
+extent that warranties are provided), that licensees may convey the
+work under this License, and how to view a copy of this License.  If
+the interface presents a list of user commands or options, such as a
+menu, a prominent item in the list meets this criterion.
+
+  1. Source Code.
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diff --git a/README.md b/README.md
new file mode 100644
index 0000000..7b6785a
--- /dev/null
+++ b/README.md
@@ -0,0 +1,45 @@
+# Morgan counts fingerprints
+
+The Morgan Fingerprints, or extended connectivity fingerprints (ECFP4) are one of the most widely used molecular representations. They are circular representations (from an atom, search the atoms around with a radius n) and can have thousands of features. This implementation uses the RDKit package and is done with radius 3 and 2048 dimensions.
+
+## Identifiers
+
+* EOS model ID: `eos5axz`
+* Slug: `morgan-counts`
+
+## Characteristics
+
+* Input: `Compound`
+* Input Shape: `Single`
+* Task: `Representation`
+* Output: `Descriptor`
+* Output Type: `Integer`
+* Output Shape: `List`
+* Interpretation: Vector representation of a molecule
+
+## References
+
+* [Publication](https://www.rdkit.org/docs/RDKit_Book.html)
+* [Source Code](https://github.com/rdkit/rdkit)
+* Ersilia contributor: [miquelduranfrigola](https://github.com/miquelduranfrigola)
+
+## Ersilia model URLs
+* [GitHub](https://github.com/ersilia-os/eos5axz)
+* [AWS S3](https://ersilia-models-zipped.s3.eu-central-1.amazonaws.com/eos5axz.zip)
+* [DockerHub](https://hub.docker.com/r/ersiliaos/eos5axz) (AMD64, ARM64)
+
+## Citation
+
+If you use this model, please cite the [original authors](https://www.rdkit.org/docs/RDKit_Book.html) of the model and the [Ersilia Model Hub](https://github.com/ersilia-os/ersilia/blob/master/CITATION.cff).
+
+## License
+
+This package is licensed under a GPL-3.0 license. The model contained within this package is licensed under a BSD-3.0 license.
+
+Notice: Ersilia grants access to these models 'as is' provided by the original authors, please refer to the original code repository and/or publication if you use the model in your research.
+
+## About Us
+
+The [Ersilia Open Source Initiative](https://ersilia.io) is a Non Profit Organization ([1192266](https://register-of-charities.charitycommission.gov.uk/charity-search/-/charity-details/5170657/full-print)) with the mission is to equip labs, universities and clinics in LMIC with AI/ML tools for infectious disease research.
+
+[Help us](https://www.ersilia.io/donate) achieve our mission!
\ No newline at end of file
diff --git a/metadata.json b/metadata.json
new file mode 100644
index 0000000..303d278
--- /dev/null
+++ b/metadata.json
@@ -0,0 +1,37 @@
+{
+    "Identifier": "eos5axz",
+    "Slug": "morgan-counts",
+    "Status": "Ready",
+    "Title": "Morgan counts fingerprints",
+    "Description": "The Morgan Fingerprints, or extended connectivity fingerprints (ECFP4) are one of the most widely used molecular representations. They are circular representations (from an atom, search the atoms around with a radius n) and can have thousands of features. This implementation uses the RDKit package and is done with radius 3 and 2048 dimensions.\n",
+    "Mode": "Pretrained",
+    "Input": [
+        "Compound"
+    ],
+    "Input Shape": "Single",
+    "Task": [
+        "Representation"
+    ],
+    "Output": [
+        "Descriptor"
+    ],
+    "Output Type": [
+        "Integer"
+    ],
+    "Output Shape": "List",
+    "Interpretation": "Vector representation of a molecule",
+    "Tag": [
+        "Fingerprint",
+        "Descriptor"
+    ],
+    "Publication": "https://www.rdkit.org/docs/RDKit_Book.html",
+    "Source Code": "https://github.com/rdkit/rdkit",
+    "License": "BSD-3.0",
+    "Contributor": "miquelduranfrigola",
+    "S3": "https://ersilia-models-zipped.s3.eu-central-1.amazonaws.com/eos5axz.zip",
+    "DockerHub": "https://hub.docker.com/r/ersiliaos/eos5axz",
+    "Docker Architecture": [
+        "AMD64",
+        "ARM64"
+    ]
+}
\ No newline at end of file
diff --git a/model/checkpoints/README.md b/model/checkpoints/README.md
new file mode 100644
index 0000000..926034c
--- /dev/null
+++ b/model/checkpoints/README.md
@@ -0,0 +1 @@
+# Model Pretrained Parameters
diff --git a/model/framework/code/main.py b/model/framework/code/main.py
new file mode 100644
index 0000000..1f9eb5e
--- /dev/null
+++ b/model/framework/code/main.py
@@ -0,0 +1,55 @@
+# imports
+import os
+import csv
+import sys
+
+from rdkit import Chem
+from rdkit.Chem import rdMolDescriptors as rd
+import numpy as np
+
+# parse arguments
+input_file = sys.argv[1]
+output_file = sys.argv[2]
+
+# current file directory
+root = os.path.dirname(os.path.abspath(__file__))
+
+RADIUS = 3
+NBITS = 2048
+
+
+def clip_sparse(vect, nbits):
+    l = [0] * nbits
+    for i, v in vect.GetNonzeroElements().items():
+        l[i] = v if v < 255 else 255
+    return
+
+def morganfp(mol):
+    v = rd.GetHashedMorganFingerprint(mol, radius=RADIUS, nBits=NBITS)
+    return clip_sparse(v, NBITS)
+
+# read SMILES from .csv file, assuming one column with header
+with open(input_file, "r") as f:
+    reader = csv.reader(f)
+    next(reader)  # skip header
+    smiles_list = [r[0] for r in reader]
+
+# run model
+
+outputs = list(
+    map(
+        lambda x: np.array(morganfp(Chem.MolFromSmiles(x)), dtype=np.uint8), smiles_list
+    )
+)
+
+# check input and output have the same length
+input_len = len(smiles_list)
+output_len = len(outputs)
+assert input_len == output_len
+
+# write output in a .csv file
+with open(output_file, "w") as f:
+    writer = csv.writer(f)
+    writer.writerow(["value"])  # header
+    for o in outputs:
+        writer.writerow(o)
diff --git a/model/framework/examples/input.csv b/model/framework/examples/input.csv
new file mode 100644
index 0000000..291598b
--- /dev/null
+++ b/model/framework/examples/input.csv
@@ -0,0 +1,2 @@
+smiles
+CCCC
\ No newline at end of file
diff --git a/model/framework/examples/output.csv b/model/framework/examples/output.csv
new file mode 100644
index 0000000..9fb7d08
--- /dev/null
+++ b/model/framework/examples/output.csv
@@ -0,0 +1,2 @@
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diff --git a/model/framework/run.sh b/model/framework/run.sh
new file mode 100644
index 0000000..3f33f76
--- /dev/null
+++ b/model/framework/run.sh
@@ -0,0 +1 @@
+python $1/code/main.py $2 $3
diff --git a/pack.py b/pack.py
new file mode 100644
index 0000000..172416e
--- /dev/null
+++ b/pack.py
@@ -0,0 +1,6 @@
+from src.service import Service
+
+
+service = Service()
+service.pack("model", None)
+service.save()
diff --git a/src/LICENSE b/src/LICENSE
new file mode 100644
index 0000000..a44b4f5
--- /dev/null
+++ b/src/LICENSE
@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2006-2015, Rational Discovery LLC, Greg Landrum, and Julie Penzotti and others
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/src/service.py b/src/service.py
new file mode 100644
index 0000000..96a7481
--- /dev/null
+++ b/src/service.py
@@ -0,0 +1,139 @@
+from typing import List
+
+from bentoml import BentoService, api, artifacts
+from bentoml.adapters import JsonInput
+from bentoml.types import JsonSerializable
+from bentoml.service import BentoServiceArtifact
+
+import pickle
+import os
+import shutil
+import tempfile
+import subprocess
+import csv
+
+CHECKPOINTS_BASEDIR = "checkpoints"
+FRAMEWORK_BASEDIR = "framework"
+
+
+def load_model(framework_dir, checkpoints_dir):
+    mdl = Model()
+    mdl.load(framework_dir, checkpoints_dir)
+    return mdl
+
+
+def Float(x):
+    try:
+        return float(x)
+    except:
+        return None
+
+
+class Model(object):
+    def __init__(self):
+        self.DATA_FILE = "_data.csv"
+        self.OUTPUT_FILE = "_output.csv"
+        self.RUN_FILE = "_run.sh"
+        self.LOG_FILE = "run.log"
+
+    def load(self, framework_dir, checkpoints_dir):
+        self.framework_dir = framework_dir
+        self.checkpoints_dir = checkpoints_dir
+
+    def set_checkpoints_dir(self, dest):
+        self.checkpoints_dir = os.path.abspath(dest)
+
+    def set_framework_dir(self, dest):
+        self.framework_dir = os.path.abspath(dest)
+
+    def run(self, input_list):
+        tmp_folder = tempfile.mkdtemp(prefix="eos-")
+        data_file = os.path.join(tmp_folder, self.DATA_FILE)
+        output_file = os.path.join(tmp_folder, self.OUTPUT_FILE)
+        log_file = os.path.join(tmp_folder, self.LOG_FILE)
+        with open(data_file, "w") as f:
+            f.write("input" + os.linesep)
+            for inp in input_list:
+                f.write(inp + os.linesep)
+        run_file = os.path.join(tmp_folder, self.RUN_FILE)
+        with open(run_file, "w") as f:
+            lines = [
+                "bash {0}/run.sh {0} {1} {2}".format(
+                    self.framework_dir, data_file, output_file
+                )
+            ]
+            f.write(os.linesep.join(lines))
+        cmd = "bash {0}".format(run_file)
+        with open(log_file, "w") as fp:
+            subprocess.Popen(
+                cmd, stdout=fp, stderr=fp, shell=True, env=os.environ
+            ).wait()
+        with open(output_file, "r") as f:
+            reader = csv.reader(f)
+            h = next(reader)
+            R = []
+            for r in reader:
+                R += [
+                    {"outcome": [Float(x) for x in r]}
+                ]  # <-- EDIT: Modify according to type of output (Float, String...)
+        meta = {"outcome": h}
+        result = {"result": R, "meta": meta}
+        shutil.rmtree(tmp_folder)
+        return result
+
+
+class Artifact(BentoServiceArtifact):
+    def __init__(self, name):
+        super(Artifact, self).__init__(name)
+        self._model = None
+        self._extension = ".pkl"
+
+    def _copy_checkpoints(self, base_path):
+        src_folder = self._model.checkpoints_dir
+        dst_folder = os.path.join(base_path, "checkpoints")
+        if os.path.exists(dst_folder):
+            os.rmdir(dst_folder)
+        shutil.copytree(src_folder, dst_folder)
+
+    def _copy_framework(self, base_path):
+        src_folder = self._model.framework_dir
+        dst_folder = os.path.join(base_path, "framework")
+        if os.path.exists(dst_folder):
+            os.rmdir(dst_folder)
+        shutil.copytree(src_folder, dst_folder)
+
+    def _model_file_path(self, base_path):
+        return os.path.join(base_path, self.name + self._extension)
+
+    def pack(self, model):
+        self._model = model
+        return self
+
+    def load(self, path):
+        model_file_path = self._model_file_path(path)
+        model = pickle.load(open(model_file_path, "rb"))
+        model.set_checkpoints_dir(
+            os.path.join(os.path.dirname(model_file_path), "checkpoints")
+        )
+        model.set_framework_dir(
+            os.path.join(os.path.dirname(model_file_path), "framework")
+        )
+        return self.pack(model)
+
+    def get(self):
+        return self._model
+
+    def save(self, dst):
+        self._copy_checkpoints(dst)
+        self._copy_framework(dst)
+        pickle.dump(self._model, open(self._model_file_path(dst), "wb"))
+
+
+@artifacts([Artifact("model")])
+class Service(BentoService):
+    @api(input=JsonInput(), batch=True)
+    def run(self, input: List[JsonSerializable]):
+        input = input[0]
+        input_list = [inp["input"] for inp in input]
+        output = self.artifacts.model.run(input_list)
+        return [output]