# mRNAid: mRNA optimization tool
mRNAid is an experimentally validated open-source tool for optimization and visualisation of mRNA molecules. It features
different optimization strategies based on user preferences.
mRNAid is available at: [https://mrnaid.dichlab.org](https://mrnaid.dichlab.org)
More information about the tool and experiments performed for its evaluation is available in the following publication:
> Nikita Vostrosablin, Shuhui Lim, Pooja Gopal, Kveta Brazdilova, Sushmita Parajuli, Xiaona Wei, Anna Gromek,
>Martin Spale, Anja Muzdalo, Constance Yeo, Joanna Wardyn, Petr Mejzlik, Brian Henry, Anthony W Partridge and
>Danny A. Bitton: **mRNAid, an Open-Source Platform for Therapeutic mRNA Design and Optimization Strategies**, 2022
>
>[bioRxiv link](https://www.biorxiv.org/content/10.1101/2022.04.04.486952v1)
You can find brief manual on how to use the tool [here](./usage_manual/Manual.md).
## Command-line interface setup
Install mRNAid with pip:
```bash
pip install mRNAid
```
See help using:
```bash
mrnaid optimize --help
```
Example:
```bash
mrnaid optimize \
--output example.json \
--optimization-criterion codon_usage \
--five-end ATG \
--three-end CGG \
--input-mRNA AGCAGAGAAGGCGGAAGCAGTGGCGTCCGCAGCTGGGGCTTGGCCTGCGGGCGGCCAGCGAAGGTGGCGAAGGCTCCCACTGGATCCAGAGTTTGCCGTCCAAGCAGCCTCGTCTCGGCGCGCAGTGTCTGTGTCCGTCCTCTACCAGCGCCTTGGCTGAGCGGAGTCGTGCGGTTGGTGGGGGAGCCCTGCCCTCCTGGTTCGGCCTCCCCGCGCACTAGAACGATCATGAACTTCTGAAGGGACCCAGCTTTCTTTGTGTGCTCCAAGTGATTTGCACAAATAATAATATATATATTTATTGAAGGAGAGAATCAGAGCAAGTGATAATCAAGTTACTATGAGTCTGCTAAACTGTGAAAACAGCTGTGGATCCAGCCAGTCTGAAAGTGACTGCTGTGTGGCCATGGCCAGCTCCTGTAGCGCTGTAACAAAAGATGATAGTGTGGGTGGAACTGCCAGCACGGGGAACCTCTCCAGCTCATTTATGGAGGAGATCCAGGGATATGATGTAGAGTTTGACCCACCCCTGGAAAGCAAGTATGAATGCCCCATCTGCTTGATGGCATTACGAGAAGCAGTGCAAACGCCATGCGGCCATAGGTTCTGCAAAGCCTGCATCATAAAATCAATAAGGGATGCAGGTCACAAATGTCCAGTTGACAATGAAATACTGCTGGAAAATCAACTATTTCCAGACAATTTTGCAAAACGTGAGATTCTTTCTCTGATGGTGAAATGTCCAAATGAAGGTTGTTTGCACAAGATGGAACTGAGACATCTTGAGGATCATCAAGCACATTGTGAGTTTGCTCTTATGGATTGTCCCCAATGCCAGCGTCCCTTCCAAAAATTCCATATTAATATTCACATTCTGAAGGATTGTCCAAGGAGACAGGTTTCTTGTGACAACTGTGCTGCATCAATGGCATTTGAAGATAAAGAGATCCATGACCAGAACTGTCCTTTGGCAAATGTCATCTGTGAATACTGCAATACTATACTCATCAGAGAACAGATGCCTAATCATTATGATCTAGACTGCCCTACAGCCCCAATTCCATGCACATTCAGTACTTTTGGTTGCCATGAAAAGATGCAGAGGAATCACTTGGCACGCCACCTACAAGAGAACACCCAGTCACACATGAGAATGTTGGCCCAGGCTGTTCATAGTTTGAGCGTTATACCCGACTCTGGGTATATCTCAGAGGTCCGGAATTTCCAGGAAACTATTCACCAGTTAGAGGGTCGCCTTGTAAGACAAGACCATCAAATCCGGGAGCTGACTGCTAAAATGGAAACTCAGAGTATGTATGTAAGTGAGCT
# See all arguments using mrnaid optimize --help
```
The results will be stored in the output JSON file, see example [here](notebooks/01_mRNAid_example_usage.ipynb).
You can also invoke mRNAid directly from Python:
```python
from mrnaid import optimize
optimize(
input_mrna='AGCAGAGAAGGCGGAAGCAGTGGCGTCCGCAGCTGGGGCTTGGCCTGCGGGCGGCCAGCGAAGGTGGCGAAGGCTCCCACTGGATCCAGAGTTTGCCGTCCAAGCAGCCTCGTCTCGGCGCGCAGTGTCTGTGTCCGTCCTCTACCAGCGCCTTGGCTGAGCGGAGTCGTGCGGTTGGTGGGGGAGCCCTGCCCTCCTGGTTCGGCCTCCCCGCGCACTAGAACGATCATGAACTTCTGAAGGGACCCAGCTTTCTTTGTGTGCTCCAAGTGATTTGCACAAATAATAATATATATATTTATTGAAGGAGAGAATCAGAGCAAGTGATAATCAAGTTACTATGAGTCTGCTAAACTGTGAAAACAGCTGTGGATCCAGCCAGTCTGAAAGTGACTGCTGTGTGGCCATGGCCAGCTCCTGTAGCGCTGTAACAAAAGATGATAGTGTGGGTGGAACTGCCAGCACGGGGAACCTCTCCAGCTCATTTATGGAGGAGATCCAGGGATATGATGTAGAGTTTGACCCACCCCTGGAAAGCAAGTATGAATGCCCCATCTGCTTGATGGCATTACGAGAAGCAGTGCAAACGCCATGCGGCCATAGGTTCTGCAAAGCCTGCATCATAAAATCAATAAGGGATGCAGGTCACAAATGTCCAGTTGACAATGAAATACTGCTGGAAAATCAACTATTTCCAGACAATTTTGCAAAACGTGAGATTCTTTCTCTGATGGTGAAATGTCCAAATGAAGGTTGTTTGCACAAGATGGAACTGAGACATCTTGAGGATCATCAAGCACATTGTGAGTTTGCTCTTATGGATTGTCCCCAATGCCAGCGTCCCTTCCAAAAATTCCATATTAATATTCACATTCTGAAGGATTGTCCAAGGAGACAGGTTTCTTGTGACAACTGTGCTGCATCAATGGCATTTGAAGATAAAGAGATCCATGACCAGAACTGTCCTTTGGCAAATGTCATCTGTGAATACTGCAATACTATACTCATCAGAGAACAGATGCCTAATCATTATGATCTAGACTGCCCTACAGCCCCAATTCCATGCACATTCAGTACTTTTGGTTGCCATGAAAAGATGCAGAGGAATCACTTGGCACGCCACCTACAAGAGAACACCCAGTCACACATGAGAATGTTGGCCCAGGCTGTTCATAGTTTGAGCGTTATACCCGACTCTGGGTATATCTCAGAGGTCCGGAATTTCCAGGAAACTATTCACCAGTTAGAGGGTCGCCTTGTAAGACAAGACCATCAAATCCGGGAGCTGACTGCTAAAATGGAAACTCAGAGTATGTATGTAAGTGAGCT',
five_end='ATG',
three_end='CGG',
optimization_criterion='codon_usage',
)
```
See [mrnaid/cli/optimize.py](mrnaid/cli/optimize.py) for all available parameters.
See [notebooks/01_mRNAid_example_usage.ipynb](notebooks/01_mRNAid_example_usage.ipynb) for usage and output format example.
## Local web server setup
If you don't want to use public server you can install this tool locally on your machine.
### 1. Using docker-compose
The easiest way to run the tool locally is to use `docker`. You will have to install docker first and it should either
contain `docker-compose` utility as a part of the distribution or you will need to
[install it](https://docs.docker.com/compose/install/) separately.
Navigate to the project folder and execute:
```bash
docker-compose up --build
```
The tool will be available at [http://localhost/](http://localhost/)
### 2. Without docker
To be able to run the tool without `docker` you will need to run frontend and backend separately.
#### Backend
You need [Conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/download.html) or one of
the alternatives ([Miniconda](https://docs.conda.io/en/latest/miniconda.html), [Miniforge](https://github.com/conda-forge/miniforge))
being installed.
First, navigate to the `./mrnaid/backend/flask_app/` directory and execute following commands:
```bash
cd ./mrnaid/backend/flask_app/
```
* Create a new virtual environment:
```bash
make env-create
```
* Install redis database
```bash
make redis-install
```
- In separate terminals execute following commands:
1. Start redis server: `make redis-run`
2. Start uwsgi server: `make uwsgi-run`
3. Start celery: `make celery-run`
- After these steps are executed, the job submission is available at the "optimize" API url: http://localhost/api/v1/optimize.
Example of the json submitted to the "optimize" end point:
```json
{
"config": {
"avoided_motifs": ["EcoRI", "UUU"],
"codon_usage_frequency_threshold": 0.1,
"max_GC_content": 0.9,
"min_GC_content": 0.5,
"GC_window_size": 100,
"organism": "m_musculus",
"entropy_window": 30,
"number_of_sequences": 2
},
"dinucleotides": false,
"match_codon_pair": false,
"uridine_depletion": true,
"CAI": false,
"precise_MFE_algorithm": true,
"file_name": "test",
"sequences": {
"five_end_flanking_sequence": "UGAAUUCAGCAAUCU",
"gene_of_interest": "AAUCAAAUAGGGUUAAGUCUAGGAUUGUUAGUCUGCUAAGGUCUGCAGUUACUGUGUCUACUGAUGAUAGUUCGCAUUGACAAU",
"three_end_flanking_sequence": "GC"
}
}
```
- The job execution results are available at: http://localhost/api/v1/status/task-id, where `task-id` should be
replaced with actual task id received after the request is submitted to the "optimize" API
##### Running the tests
To be able to execute tests for backend with pytest, you need to set up following environmental variables in the corresponding
environment:
- PYTHONPATH=..:../common:../flask_app
- LOG_FILE=../flask_app/logs/logs.log
- BACKEND_OBJECTIVES_DATA=../common/objectives/data
Tests can be found in `backend/tests/` directory
#### Frontend
Install [Node.js](https://nodejs.org/en/download/) and [Nginx](https://www.nginx.com/resources/wiki/start/topics/tutorials/install/)
web server.
* Navigate to `frontend` directory
* Build a package:
```bash
npm ci && npm run build
```
* Remove default nginx configurations from nginx system directory
```bash
# location may vary based on your system and installation
rm /etc/nginx/conf.d/default.conf
```
* Replace deleted configs with custom ones
```bash
# target location may vary based on your system and installation
cp ./config/nginx.conf /etc/nginx/conf.d/
```
* Move build files to the corresponding nginx directory
```bash
cp -R ./build/* /usr/share/nginx/html
```
* Restart nginx web server
## Contributing
mRNAid is an open platform, please propose your changes and improvements. This can be done through the [Issues](link)
tab.
## License
Released under MIT License
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"description": "# mRNAid: mRNA optimization tool\n\n\n\nmRNAid is an experimentally validated open-source tool for optimization and visualisation of mRNA molecules. It features\n different optimization strategies based on user preferences.\n\nmRNAid is available at: [https://mrnaid.dichlab.org](https://mrnaid.dichlab.org)\n\nMore information about the tool and experiments performed for its evaluation is available in the following publication:\n\n> Nikita Vostrosablin, Shuhui Lim, Pooja Gopal, Kveta Brazdilova, Sushmita Parajuli, Xiaona Wei, Anna Gromek, \n>Martin Spale, Anja Muzdalo, Constance Yeo, Joanna Wardyn, Petr Mejzlik, Brian Henry, Anthony W Partridge and \n>Danny A. Bitton: **mRNAid, an Open-Source Platform for Therapeutic mRNA Design and Optimization Strategies**, 2022\n> \n>[bioRxiv link](https://www.biorxiv.org/content/10.1101/2022.04.04.486952v1)\n\nYou can find brief manual on how to use the tool [here](./usage_manual/Manual.md).\n\n## Command-line interface setup\n\nInstall mRNAid with pip:\n```bash\npip install mRNAid\n```\n\nSee help using:\n```bash\nmrnaid optimize --help\n```\n\nExample:\n```bash\nmrnaid optimize \\\n --output example.json \\\n --optimization-criterion codon_usage \\\n --five-end ATG \\\n --three-end CGG \\\n --input-mRNA AGCAGAGAAGGCGGAAGCAGTGGCGTCCGCAGCTGGGGCTTGGCCTGCGGGCGGCCAGCGAAGGTGGCGAAGGCTCCCACTGGATCCAGAGTTTGCCGTCCAAGCAGCCTCGTCTCGGCGCGCAGTGTCTGTGTCCGTCCTCTACCAGCGCCTTGGCTGAGCGGAGTCGTGCGGTTGGTGGGGGAGCCCTGCCCTCCTGGTTCGGCCTCCCCGCGCACTAGAACGATCATGAACTTCTGAAGGGACCCAGCTTTCTTTGTGTGCTCCAAGTGATTTGCACAAATAATAATATATATATTTATTGAAGGAGAGAATCAGAGCAAGTGATAATCAAGTTACTATGAGTCTGCTAAACTGTGAAAACAGCTGTGGATCCAGCCAGTCTGAAAGTGACTGCTGTGTGGCCATGGCCAGCTCCTGTAGCGCTGTAACAAAAGATGATAGTGTGGGTGGAACTGCCAGCACGGGGAACCTCTCCAGCTCATTTATGGAGGAGATCCAGGGATATGATGTAGAGTTTGACCCACCCCTGGAAAGCAAGTATGAATGCCCCATCTGCTTGATGGCATTACGAGAAGCAGTGCAAACGCCATGCGGCCATAGGTTCTGCAAAGCCTGCATCATAAAATCAATAAGGGATGCAGGTCACAAATGTCCAGTTGACAATGAAATACTGCTGGAAAATCAACTATTTCCAGACAATTTTGCAAAACGTGAGATTCTTTCTCTGATGGTGAAATGTCCAAATGAAGGTTGTTTGCACAAGATGGAACTGAGACATCTTGAGGATCATCAAGCACATTGTGAGTTTGCTCTTATGGATTGTCCCCAATGCCAGCGTCCCTTCCAAAAATTCCATATTAATATTCACATTCTGAAGGATTGTCCAAGGAGACAGGTTTCTTGTGACAACTGTGCTGCATCAATGGCATTTGAAGATAAAGAGATCCATGACCAGAACTGTCCTTTGGCAAATGTCATCTGTGAATACTGCAATACTATACTCATCAGAGAACAGATGCCTAATCATTATGATCTAGACTGCCCTACAGCCCCAATTCCATGCACATTCAGTACTTTTGGTTGCCATGAAAAGATGCAGAGGAATCACTTGGCACGCCACCTACAAGAGAACACCCAGTCACACATGAGAATGTTGGCCCAGGCTGTTCATAGTTTGAGCGTTATACCCGACTCTGGGTATATCTCAGAGGTCCGGAATTTCCAGGAAACTATTCACCAGTTAGAGGGTCGCCTTGTAAGACAAGACCATCAAATCCGGGAGCTGACTGCTAAAATGGAAACTCAGAGTATGTATGTAAGTGAGCT \n# See all arguments using mrnaid optimize --help\n```\n\nThe results will be stored in the output JSON file, see example [here](notebooks/01_mRNAid_example_usage.ipynb).\n\nYou can also invoke mRNAid directly from Python:\n```python\nfrom mrnaid import optimize\n\noptimize(\n input_mrna='AGCAGAGAAGGCGGAAGCAGTGGCGTCCGCAGCTGGGGCTTGGCCTGCGGGCGGCCAGCGAAGGTGGCGAAGGCTCCCACTGGATCCAGAGTTTGCCGTCCAAGCAGCCTCGTCTCGGCGCGCAGTGTCTGTGTCCGTCCTCTACCAGCGCCTTGGCTGAGCGGAGTCGTGCGGTTGGTGGGGGAGCCCTGCCCTCCTGGTTCGGCCTCCCCGCGCACTAGAACGATCATGAACTTCTGAAGGGACCCAGCTTTCTTTGTGTGCTCCAAGTGATTTGCACAAATAATAATATATATATTTATTGAAGGAGAGAATCAGAGCAAGTGATAATCAAGTTACTATGAGTCTGCTAAACTGTGAAAACAGCTGTGGATCCAGCCAGTCTGAAAGTGACTGCTGTGTGGCCATGGCCAGCTCCTGTAGCGCTGTAACAAAAGATGATAGTGTGGGTGGAACTGCCAGCACGGGGAACCTCTCCAGCTCATTTATGGAGGAGATCCAGGGATATGATGTAGAGTTTGACCCACCCCTGGAAAGCAAGTATGAATGCCCCATCTGCTTGATGGCATTACGAGAAGCAGTGCAAACGCCATGCGGCCATAGGTTCTGCAAAGCCTGCATCATAAAATCAATAAGGGATGCAGGTCACAAATGTCCAGTTGACAATGAAATACTGCTGGAAAATCAACTATTTCCAGACAATTTTGCAAAACGTGAGATTCTTTCTCTGATGGTGAAATGTCCAAATGAAGGTTGTTTGCACAAGATGGAACTGAGACATCTTGAGGATCATCAAGCACATTGTGAGTTTGCTCTTATGGATTGTCCCCAATGCCAGCGTCCCTTCCAAAAATTCCATATTAATATTCACATTCTGAAGGATTGTCCAAGGAGACAGGTTTCTTGTGACAACTGTGCTGCATCAATGGCATTTGAAGATAAAGAGATCCATGACCAGAACTGTCCTTTGGCAAATGTCATCTGTGAATACTGCAATACTATACTCATCAGAGAACAGATGCCTAATCATTATGATCTAGACTGCCCTACAGCCCCAATTCCATGCACATTCAGTACTTTTGGTTGCCATGAAAAGATGCAGAGGAATCACTTGGCACGCCACCTACAAGAGAACACCCAGTCACACATGAGAATGTTGGCCCAGGCTGTTCATAGTTTGAGCGTTATACCCGACTCTGGGTATATCTCAGAGGTCCGGAATTTCCAGGAAACTATTCACCAGTTAGAGGGTCGCCTTGTAAGACAAGACCATCAAATCCGGGAGCTGACTGCTAAAATGGAAACTCAGAGTATGTATGTAAGTGAGCT',\n five_end='ATG',\n three_end='CGG',\n optimization_criterion='codon_usage',\n)\n```\n\nSee [mrnaid/cli/optimize.py](mrnaid/cli/optimize.py) for all available parameters.\n\nSee [notebooks/01_mRNAid_example_usage.ipynb](notebooks/01_mRNAid_example_usage.ipynb) for usage and output format example.\n\n## Local web server setup\n\nIf you don't want to use public server you can install this tool locally on your machine.\n\n### 1. Using docker-compose\n\nThe easiest way to run the tool locally is to use `docker`. You will have to install docker first and it should either\ncontain `docker-compose` utility as a part of the distribution or you will need to \n[install it](https://docs.docker.com/compose/install/) separately.\n\nNavigate to the project folder and execute:\n\n\n```bash\ndocker-compose up --build\n```\n\nThe tool will be available at [http://localhost/](http://localhost/)\n\n### 2. Without docker\n\nTo be able to run the tool without `docker` you will need to run frontend and backend separately.\n\n#### Backend\n\nYou need [Conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/download.html) or one of \nthe alternatives ([Miniconda](https://docs.conda.io/en/latest/miniconda.html), [Miniforge](https://github.com/conda-forge/miniforge)) \nbeing installed.\n\nFirst, navigate to the `./mrnaid/backend/flask_app/` directory and execute following commands:\n\n```bash\ncd ./mrnaid/backend/flask_app/\n```\n\n* Create a new virtual environment:\n\n```bash\nmake env-create\n```\n\n* Install redis database\n\n```bash\nmake redis-install\n```\n\n- In separate terminals execute following commands:\n 1. Start redis server: `make redis-run`\n 2. Start uwsgi server: `make uwsgi-run`\n 3. Start celery: `make celery-run`\n\n- After these steps are executed, the job submission is available at the \"optimize\" API url: http://localhost/api/v1/optimize.\nExample of the json submitted to the \"optimize\" end point:\n\n```json\n{\n \"config\": {\n \"avoided_motifs\": [\"EcoRI\", \"UUU\"],\n \"codon_usage_frequency_threshold\": 0.1,\n\t\"max_GC_content\": 0.9,\n\t\"min_GC_content\": 0.5,\n\t\"GC_window_size\": 100,\n\t\"organism\": \"m_musculus\",\n\t\"entropy_window\": 30,\n \"number_of_sequences\": 2\n },\n \"dinucleotides\": false, \n \"match_codon_pair\": false,\n \"uridine_depletion\": true,\n \"CAI\": false,\n \"precise_MFE_algorithm\": true,\n \"file_name\": \"test\",\n \"sequences\": {\n \"five_end_flanking_sequence\": \"UGAAUUCAGCAAUCU\",\n \"gene_of_interest\": \"AAUCAAAUAGGGUUAAGUCUAGGAUUGUUAGUCUGCUAAGGUCUGCAGUUACUGUGUCUACUGAUGAUAGUUCGCAUUGACAAU\",\n \"three_end_flanking_sequence\": \"GC\"\n }\n}\n```\n\n- The job execution results are available at: http://localhost/api/v1/status/task-id, where `task-id` should be \nreplaced with actual task id received after the request is submitted to the \"optimize\" API\n\n\n\n\n \n##### Running the tests\n\nTo be able to execute tests for backend with pytest, you need to set up following environmental variables in the corresponding\nenvironment:\n\n- PYTHONPATH=..:../common:../flask_app\n- LOG_FILE=../flask_app/logs/logs.log\n- BACKEND_OBJECTIVES_DATA=../common/objectives/data\n\nTests can be found in `backend/tests/` directory\n\n#### Frontend\n\nInstall [Node.js](https://nodejs.org/en/download/) and [Nginx](https://www.nginx.com/resources/wiki/start/topics/tutorials/install/) \nweb server.\n\n* Navigate to `frontend` directory\n* Build a package:\n\n```bash\nnpm ci && npm run build\n```\n\n* Remove default nginx configurations from nginx system directory\n\n```bash\n# location may vary based on your system and installation\nrm /etc/nginx/conf.d/default.conf\n```\n\n* Replace deleted configs with custom ones\n```bash\n# target location may vary based on your system and installation\ncp ./config/nginx.conf /etc/nginx/conf.d/\n```\n\n* Move build files to the corresponding nginx directory\n```bash\ncp -R ./build/* /usr/share/nginx/html\n```\n\n* Restart nginx web server\n\n\n\n## Contributing\n\nmRNAid is an open platform, please propose your changes and improvements. This can be done through the [Issues](link)\ntab.\n## License\n\nReleased under MIT License\n\n",
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