Open Science Prize Proposal

Antidote: An open platform for data-driven drug discovery applications

George Papadatos, Michal Nowotka, Nathan Brown, Greg Landrum and Patrick Walters

Executive Summary

Vision: we propose Antidote, an open source, state-of-the-art, end-to-end platform which enables the complete life cycle of compound data acquisition, curation, storage, querying, mining, dissemination and reuse for chemoinformatics and drug discovery applications. Specifically, Antidote combines open chemical, pharmacological and chemogenomics data and analogous in-house data with open source chemoinformatics and data science and mining tools, along with interactive demos, tutorials, documentation and drug discovery use-cases in a free, accessible and intuitive platform. We envisage that this will catalyse and facilitate

Academic drug discovery via easy access to standardised infrastructure, data and use-cases;
Accessibility and dissemination of modern informatics and computational applications for data-driven drug discovery to all levels of the scientific community;
Interactive teaching and learning of chemoinformatics and data mining concepts and applications;
Reproducibility and sharing of research methodologies and outcomes; and
Synergy and collaborations between different institutions and domain experts outside drug discovery.

Implementation: As an existing early-stage prototype, we use myChEMBL, which was co-developed by members of our team at the EBI. myChEMBL is a virtual machine which hosts the ChEMBL database and a number of data analysis tools. We plan to heavily extend and scale-up myChEMBL by combining existing open data content, open source data mining and analytics technologies, as well as user-friendly data curation and querying web platforms and applications built by members of our team. Importantly, the resulting platform will be modular, scalable and accessible via several deployment methods.

Audience: We envisage that Antidote will become a widely adopted data analysis and reuse platform among researchers of diverse backgrounds and experience, ranging from students to experts and from wet-lab scientists to computational ones. Particularly, we expect that Antidote will become indispensable to institutions with limited resources, such as academia, not-for-profit organisations, and research institutes in developing economies.

Installing Antidote using Virtual Box

Installing the Antidote prototype (myChEMBL) using Virtual Box is the default option for most users. You will need to:

Install Virtual Box.
Download myChEMBL disk image, this will download the latest version of myChEMBL by default; if you want to get different one, check the archive. The file containing the myChEMBL image is quite large (several GBs), so you may want to make sure you have a stable internet connection. You may also want to use a download manager (or FTP program) in order to be able to restore the process in case your internet connection drops. Finally, you have to check the location where the file is saved, this is usually your system-defined Downloads folder.
Once your copy of the myChEMBL image is downloaded, you have to unpack it. You can do it by double-clicking on the file icon if you have the archive utilities installed in your system. On Unix systems you can do it from the command line by executing:
```
tar -zxvf ubuntu.vmdk.tar.gz
```
in the Downloads folder.
Create a Virtual Machine. Start the VirtualBox application and click on the New button to create a new VM, and then Next.
Enter a name such as mychembl, and choose Linux as the “Operating system”, and Ubuntu as the “Version”.
In the next screen, set the memory to 1024 MB (or more if your host computer has more than 4GB).
Continue to the next screen and choose “Use existing hard disk”. Now click on the button (a folder icon) to browse to where you saved the ubuntu.vmdk file. Select this file, press Next and Create.
Now bootup the VM by clicking the Start (green arrow) button. Once the myChEMBL system finish booting, you can navigate your browser to http://localhost:8000 and start using it.

Installing Antidote using Docker

Docker is a new open-source project that automates the deployment of distributed applications. It takes advantage of the new cool features of modern Linux kernels in order to run virtual containers, thus avoiding the overhead of starting and maintaining virtual machines.

In contrast to virtual machines, which emulate virtual hardware, Docker containers employ the kernel of the host machine so they don’t require or include the whole operating system. While still separated from the host, they only add a very thin level of abstraction.

Docker deployment is aimed at advanced users but it has the best performance.

Please note that the following instructiona is for the Linux operating system only. If you plan to use Antidote on other operating systems (such as OS X or Windows), we suggest the Vagrant or Virtual Box methods.

In order to install Antidote (myChEMBL) using Docker you have to:

Install Docker. For Linux the easiest way to do this is to invoke the following command:
```
wget -qO- https://get.docker.com/ | sh
```
Once you have Docker installed in your system, all you have to do is:
- Download the myChEMBL image
- Uncompress
- Load the image into docker
- Run it
You can do it all from your terminal by executing following commands:

install mychembl

                                  ~
                                  $$
                                  wget http://ftp.ebi.ac.uk/pub/databases/chembl/VM/Docker/mychembl_20_ubuntu_docker.tar.gz
                                

                                  ~
                                  $$
                                  gunzip mychembl_20_ubuntu_docker.tar.gz
                                

                                  ~
                                  $$
                                  docker load < mychembl_20_ubuntu_docker.tar
                                

                                  ~
                                  $$
                                  docker run -p 2222:22 -p 80:80 -p 9612:9612 -t -i chembl/mychembl_20_ubuntu /usr/local/bin/supervisord
                                

                                  # => Now browse to http://localhost
                                

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