Datanator-frontend

Web-based graphical user interface of Datanator, a toolkit for discovering the data needed for modeling the biochemistry of cells.

Contents

• Overview
• Usage and installation
• License
• Development team
• Questions and comments

Overview

A central goal of synthetic biology is to rationally design organisms. Similarly, a central goal of precision medicine is to tailor therapy to each patient based on their unique genome. Many engineering fields use computer-aided design (CAD) tools driven by mechanistic models to efficiently design complex systems such as planes. Analogously, more comprehensive and more predictive models of biological systems, such as whole-cell models, are needed to help bioengineers and physicians design biomachines and medical therapy.

One of the biggest bottlenecks to achieving such models is collecting and aggregating the large amount of data needed for model construction and verification. Due to advances in genomics and increased emphasis on data sharing, there is now extensive data about a wide range of biochemical entities and processes such as data about metabolite concentrations, RNA and protein abundances, and reaction rates. However, it remains difficult to utilize this information for modeling because the data scattered across numerous databases and publications; the data is described using different formats, identifiers, and units; and there are inadequate tools for finding relevant data for modeling a specific biological system in a specific environment.

The Datanator toolkit seeks to address these problems for biochemical modeling by providing investigators an integrated database of molecular data and tools for discovering relevant data for modeling projects and other meta analyses. Please see the About page for more information about the goals and features of Datanator.

The Datanator toolkit is composed of the following packages:

• Datanator: Tools for aggregating and integrating diverse data from diverse sources into a single dataset and searching these datasets
• Datanator-db: MongoDB server for Datanator-data
• Datanator-fulltext-db: ElasticSearch server for Datanator-data
• Datanator-query-python: Tools for querying Datanator-db and Datanator-fulltext-db
• Datanator-rest-api: REST interface for Datanator-query-python
• Datanator-frontend: This package, a web-based graphical user interface to Datanator-db.

This package provides a web-based graphical user interface to Datanator-db. A public, hosted version of the package is freely available at https://datanator.info. The package provides investigators tools for browsing and searching Datanator-db to find data about biochemical entities of interest (e.g., metabolites, proteins, reactions). This includes tools for finding experimental observations from chemically and genetically similar entities (according to structural and sequence similarity) in phylogenetically similar organism (according to the NCBI Taxonomy tree) under similar enviromental conditions (e.g., temperature, pH). The package is implemented using React.

Development, testing, installation, and usage

Users

Use the public, hosted deployment

We recommend that users use the public, hosted version of Datanator-frontend at https://datanator.info.

Tutorial and FAQs

Please see the Help page for a tutorial and FAQs.

Developers

Install and deploy Datanator-frontend locally

We recommend that developers install and run Datanator-frontend locally. Below are instructions for installing and running Datanator-frontend locally.

1. Install git

   apt-get install git

2. Install npm

   curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.35.3/install.sh | bash
   ~/.nvm/nvm.sh install v8.17.0

3. Clone this repository

   git clone https://github.com/karrlab/datanator_frontend

4. Install this package

   cd /path/to/datanator_frontend
   npm install .

5. Launch a server. This will compile the application. As you make changes to the source code, the server will automatically incrementally compile the application and refresh your browser.

   npm start

6. Navigate your browser to http://localhost:3000.

Test Datanator-frontend

1. Run the unit tests

   npm run test-unit-coverage

2. Run the integration tests

   npm run test-integration-run

Lint and pretty print Datanator-frontend

1. Lint CSS

   npm run lint-style

2. Lint JavaScript

   npm run lint-js

3. Lint JSON

   npm run lint-json

4. Lint SVG

   npm run lint-svg

Build Datanator-frontend for deployment

  NODE_ENV=production npm run build

Implementation

Datanator-frontend is implemented as a Single Page Application (SPA) using the following packages:

• React: framework for the application
• Axios: HTTP requests
• history: browser history
• Blueprint: UI components
• Material-UI: UI components
• AG-grid: data tables
• Chart.js: charts
• bruit.io: feedback form
• FontAwesome: icons

The following tools were used to test Datanator-frontend:

• cypress: integration testing
• depcheck: dependency checking
• Enzyme: testing utilities
• ESLint: JavaScript linting
• Jest: unit testing
• jsonlint: JSON linting
• stylelint: CSS/SCSS linting
• svglint: SVG linting

File organization

This repository is organized as follows:

• config/: React configuration
• integration-tests/:
  • fixtures/: fixtures for the integration tests
  • plugins/: cypress configuration
  • support/: cypress configuration
  • tests/: integration tests implemented using cypress and organized parallel to the source code
• public/: static files such as the favicon and sitemap
• scripts/: scripts for managing the application such as starting and stopping a test server
• src/
  • components/ - common components used by multiple pages
  • ErrorDialog/ - dialog for displaying errors
  • FeedbackForm/ - form to collected feedback from users
  • Footer/ - footer on the bottom of each webpage
  • Header/ - header on the top of each webpage
  • SearchForm/ - search form on homepage and in the header
  • scenes/ - code to render the individual webpages
  • Home/ - the home page
  • SearchResults/ - page which display the results of a search
  • BiochemicalEntityDetails/ - the pages which display metadata and experimental observations about a biochemical entity
  • About/ - page with general information about Datanator such as the motivation for the application and the team which implemented it
  • Help/ - page with a tutorial and FAQs
  • Stats/ - page which summarizes the contents of Datanator's database
  • Error404/ - page which is displayed when a user requests and undefined route
  • services/
  • __tests__/ - unit tests implemented using Jest
  • utils/ - miscellaneous helper functions (e.g. removing duplicates, formatting numbers in scientific notation, etc.)
  • colors.scss: common colors for the application
  • index.js: entrypoint for the application which handles all routes
  • index.scss: commmon styles for the application
  • index.mobile.scss: styles for mobile devices
  • react-app-env.d.ts: React configuration
  • setupTests.js: Jest configuration
• .env: default environment variables
• CODE_OF_CONDUCT: code of conduct
• cypress.json: cypress configuration
• LICENSE: license
• LICENSE-THIRD-PARTY: summary of the licenses of the dependencies
• package.json: package configuration
• README: overview of the application

Organization of the CSS styles

• The common styles used by multiple components and scenes are contained in src/index.scss.
• The styles for individual components and scenes are defined in separated files within the directories in which the components and scenes are defined (e.g., src/scenes/Home/Home.scss). The styles for the individual components and scenes are isolated from each other through the use of unique CSS classes for each component/scene.

Naming conventions

Datanator-frontend uses the following naming conventions:

• Directory, file, and class names: UpperCamelCase
• Variable and method namse: lowerCamelCase
• CSS class names: lower-hyphen-case

Development and deployment workflow

1. Create a Git new branch
2. Commit code to the new branch
3. Push the branch to GitHub
4. GitHub will automatically trigger CircleCI to run the unit test, integration tests, and other static analyses
5. Use Coveralls to review the coverage of the tests
6. As needed, add additional tests and fix any failing tests
7. Once the new code passes the tests and has high coverage, create a pull request to merge the new branch into the master branch
8. One of the main developers will review the pull request and request changes as necessary
9. Once any necessary changes have been made, one of the main developers will approve the pull request
10. GitHub will automatically trigger CircleCI to run the unit test, integration tests, and other static analyses for the master branch
11. Once the CircleCI build succeeds, https://datanator.info will automatically be updated to the latest revision of the master branch

Contributing to Datanator

We welcome contributions to Datanator via Git pull requests. Please contact the developers to coordinate potential contributions, and please see above for information about how to submit pull requests.

License

This package is released under the MIT license. The licenses of the third party dependencies are summarized in LICENSE-THIRD-PARTY.

Citing Datanator

Roth YD, Lian Z, Pochiraju S, Shaikh B & Karr JR. Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior. bioRxiv, 2020.08.06.240051 (2020). DOI: 10.1101/2020.08.06.240051.

Development team

This package was developed by the Karr Lab at the Icahn School of Medicine at Mount Sinai in New York by the following individuals:

• Yosef Roth
• Yang Lian
• Jonathan Karr
• Saahith Pochiraju
• Bilal Shaikh
• Balazs Szigeti

Questions and comments

Please submit an issue, or contact the Karr Lab with any questions or comments.

Acknowledgements

Datanator was developed with support from the Center for Reproducible Biomedical Modeling from the National Institute of Bioimaging and Bioengineering and the National Institute of General Medical Sciences of the National Institutes of Health and the National Science Foundation (awards P41EB023912 and R35GM119771).