presents

An open-source web application to manage the entire data life-cycle of experiments and assays from Experimental Chemistry and related Science disciplines.
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Table of Contents

1. About The Project
   • Built With
2. Getting Started
   • Try the platform
   • Deploy and run the software locally
   • Deploy and run the software locally with Docker
   • Deploy and run the software locally manually
   • Learning how it works
   • Set up a development environment
3. Usage
4. Roadmap
5. Contributing
6. License
7. Contact
8. Acknowledgments

About The Project

The Chemistry electronic notepad (eChempad) platform is a suite of web services oriented to manage the entire data life-cycle of experiments and assays from Experimental Chemistry and related Science disciplines.

Currently, the eChempad platform allows researchers to extract experimentation data from the PerkinElmer Signals Notebook in bulk, enrich them with metadata, and finally publish them into CORA RDR a Dataverse instance maintained by the Consorci de Serveis Universitaris de Catalunya (CSUC).

The eChempad platform appears as an answer to the digitization needs of experimental chemists at Institut Català d'Investigació Química (ICIQ). This platform intends to be an analogous example of the successful platform for Computational Chemistry developed at ICIQ, ioChem-BD.

To know more about other digitalization services at ICIQ, you can check the ICIQ digitalization portal or read the ICIQ digitalization documentation.

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Built With

This section lists any major frameworks/libraries used to bootstrap the eChempad platform:

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Getting Started

Try the platform

To get started, you will probably want to try the software from the official web page echempad.iciq.es. eChempad executes in your browser and does not require any installation.

Check the user guide from the official documentation to know more.

Deploy and run the software locally

With Docker

The fastest way to get a copy up and running in your local machine is using Docker with docker-compose.

Assuming that you have them installed on your machine, use these commands to pull the latest version of the eChempad docker image and postgreSQL to run them in containers:

wget https://raw.githubusercontent.com/ICIQ-DMP/eChempad-public-mirror/master/docker-compose.yaml
sudo docker-compose up -d

Then, open a browser and navigate to the URL http://localhost and eChempad will be displayed and ready to work.

Check the running with Docker guide from the official documentation to know more.

Manually

If you want to run the software locally without using Docker, you may want to check how to install the dependencies of eChempad into your machine and how to compile and run the software manually.

Learning how it works

If you want to understand how eChempad works we recommend that you read the developer guide from the official documentation.

Set up a development environment

If you want to make a contribution to the project or want to debug an error, you will need a functional development environment. This environment involves many tools and utilities in addition to the ones needed to run the software manually.

You can follow this guide from the official documentation to learn how to set up the development environment.

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Usage

Open a browser and navigate to the URL of eChempad. The first thing you will find is the login page:

By default, eChempad has an administrator user with the username eChempad@iciq.es and password chemistry.

Do not forget to change the password of the administrator user if you plan to use your eChempad instance in real scientific production.

After that, you will be received by the home page: .

If you want to retrieve from a Signals Notebook or want to upload to a Dataverse instance, you need to introduce the corresponding API tokens into your user by editing your profile. To do so, click edit profile from the options menu, in the left superior corner of the page:

You will land on the profile page where you can introduce the API tokens in the corresponding fields. Use submit to save your changes:

Then, go back to the home page by clicking the eChempad logo on the superior left corner. You will be back to the home page of eChempad.

Now, you can click the import from Signals Button on the left of the top bar. This will trigger the import of the available resources with the previously introduced API token from Signals. This operation usually takes some minutes, so you will need to have patience. While the operation is running, a loading icon will appear in the page like this:

When the operation ends, the imported resources will appear in the home page. Reload the page if they do not appear. It may look similar to this:

Now, you can edit the metadata of the imported resources by using the form in the inferior right area of the screen. You can also delete the resources that you do not need by clicking the trash button in the same form.

When you are finished editing your data and want to export a resource to Dataverse, you have to select the resource to export and click export to CORA RDR. A loading sign will appear while the operation is running the same as when importing from a Signals Notebook.

When the loading sign disappears, your resources will be available in the CORA RDR Dataverse instance.

For more examples, please refer to the user guide from the official documentation

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Roadmap

• Frontend addition with ZK
• Change backend to composite structure
• Refactored ACLs
• Create eChempad logo
• Write tests
• Customize license plugins
• Finish API to import / export
• Integrate API abstractions into the front-end
• Create usage example in the readme

See the open issues for a full list of proposed features (and known issues).

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Contributing

This is an open-source project, so any contributions are greatly appreciated ❤. You can start by taking a look to the Developer guide to understand how eChempad works.

If you have an issue or suggestion that would make eChempad better, please open a new issue explaining your inquiry. We will try to satisfy your needs as soon as possible.

If you want to make a contribution to eChempad by yourself, please open a new issue so we can discuss the reach of your contribution. After that, fork the repo, implement your change and create a pull request from your fork to the develop branch. We will merge your changes as soon as possible, so they are available in the next releases of eChempad.

So, for each change that you want to do to eChempad by yourself, you will need to:

1. Fork the repo.
2. Create your Feature Branch (git checkout -b feature/AmazingFeature).
3. Add and commit your Changes (git add src; git commit -am 'Add some AmazingFeature').
4. Push to the Branch (git push origin feature/AmazingFeature).
5. Repeat steps 3 and 4 as many times as you need.
6. Open a pull request from your fork to the develop branch.
7. Repeat steps 3 and 4 if further changes are required.

Do not forget to give the project a star ⭐ on GitHub!

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License

Distributed under the GNU AFFERO GENERAL PUBLIC LICENSE, Version 3. See LICENSE to obtain a copy of the therms of this license. See also LICENSE.md for more information about the licensing state of this project.

This software was developed by Aleix Mariné-Tena using a grant of Personal Técnico de Apoyo (Technical staff for support) with reference PTA2020-019734-I from Ministerio de Ciencia e Innovación from the spanish government.

eChempad ultimately belongs to ICIQ and has the control over the licensing and distribution therms.

Copyright 2020-2023 Institute of Chemical Research of Catalonia (ICIQ)

This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

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Contact

ICIQ data steward & main developer of eChempad: Aleix Mariné-Tena - dmp@iciq.es 📫

You can also reach us on Twitter @ICIQchem.

You can get more information of our work and research on our official web page https://iciq.cat.

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Acknowledgments

eChempad was possible thanks to a grant of Personal Técnico de Apoyo (Technical staff for support) with reference PTA2020-019734-I from Ministerio de Ciencia e Innovación from the spanish government.

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Credits

Institutions involved in the eChempad project

• Institute of Chemical Research of Catalonia (ICIQ): ICIQ, the institution that developed eChempad.
• Catalan University Services Consortium (CSUC): CSUC, the institution that developed CORA RDR, a Dataverse instance to store the data from the catalan scientific research.

People involved in the eChempad development

• Aleix Mariné-Tena (ICIQ): Main developer of eChempad. ICIQ data steward.
• Moisés Álvarez (ICIQ - URV): Main developer of ioChem-BD. Main developer counsellor.
• Dr. Carles Bo (ICIQ): Product owner. Supervisor. Main scientific counsellor and contributor. Research Leader at Bo Group.
• Dra. Imma Escofet (ICIQ): Scientific contributor and counsellor. Group Scientific Coordinator at Ballesté group. Presented examples of integration with Signals in the Open Data Day. Provides real datasets to work with. Explains the needs of researchers of her group towards eChempad and ICIQ digitalization.
• Dra. Gemma Aragay (ICIQ): Scientific contributor. Group Scientific Coordinator at Ballesté group. Explained the needs of researchers of her group towards eChempad and ICIQ digitalization.
• Dra. Sonia Sayalero (ICIQ): Project counsellor. Manager of the Institutional Strengthening Unit at ICIQ. Coordinates the Severo Ochoa program and the development of eChempad. Involved in the data management plan at ICIQ.
• Martin Gumbau (ICIQ): System administrator at ICIQ theoretical groups. Maintains the physical machine used to develop eChempad.
• Angel Mosquera (ICIQ): IT Manager at ICIQ. Provides and maintains the infrastructure to host the eChempad application and other services related with the ICIQ digitalization.