ChEMBL Resources

Resources:
ChEMBL
|
SureChEMBL
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ChEMBL-NTD
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ChEMBL-Malaria
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The SARfaris: GPCR, Kinase, ADME
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UniChem
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DrugEBIlity
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ECBD

Tuesday, 14 July 2015

myChEMBL 20 has landed




We are very pleased to announce that the latest myChEMBL release, based on the ChEMBL 20 database, is now available to download. In addition to the ChEMBL upgrade, you will also find a number of changes and new features:


  • Updates in system and Python libraries, including the iPython notebook server
  • Upgrade in the web services (data and utils) to match the new functionality provided by the main ChEMBL ones
  • Current stable version of RDKit (2015.03)
  • Two brand new notebooks, namely an RDKit tutorial and a tutorial on SureChEMBL data mining, increasing the total number of notebooks to 14
  • Updates in several other iPython notebooks and the KNIME workflow, in order to take advantage of the new data, models and web services functionality
  • Several bug fixes
  • A CentOS 7 VM version, in addition to the existing Ubuntu 14.04 one
  • New virtualisation technologies, as explained in the section below


Lots of flavours

dipping case3.JPG

This new myChEMBL release is technical feature-rich, as we’ve decided to focus on providing a  variety of myChEMBL boxes and image formats via different distribution channels:

  1. New CentOS-based distribution - as requested by many users, we now provide a CentOS-based image, along with the existing Ubuntu one. CentOS is a Linux distribution that is focused on security and enterprise-class computing. It’s free and widely used in industry so no further introduction is needed. Our box is based on the latest stable version 7. One thing worth noting is that CentOS-based images are significantly smaller than Ubuntu ones.
  2. Different image formats - in addition to the standard vmdk images now available for Ubuntu and CentOS, we also provide other image formats. Although VMDK is an open format, it’s mainly used by proprietary software, such as vSphere. We decided to support free and open-source hypevisors as well, so this is why we are now publishing QEMU compatible qcow2 format. To help even more, we are providing a generic raw disk image dumps in img format which can then be converted to any other specific format to provide support for other virtualisation platforms. In fact, we used img files to generate qqow2 by running qemu-img convert -f raw -O qcow2 ubuntu.img ubuntu.qcow2
  3. Distribution channels - the traditional way to get myChEMBL image is to visit our FTP page. You can find there compressed images of our Ubuntu and CentOS myChEMBL distributions in different image formats. If you want to save time creating and configuring your Virtual Machine from scratch, you can use Vagrant instead of FTP. If you have Vagrant already installed, all you need to do is to open the terminal and type:
    vagrant init chembl/mychembl_20_ubuntu && vagrant up or:
    vagrant init chembl/mychembl_20_centos && vagrant up
    depending on the version you would like to use.
  4. An additional cool new feature is docker support but, since docker is a quite new technology, we would like to dedicate a separate blog post to this topic - so come back soon for exciting details.


Installation

There are now several different ways for installing myChEMBL:

  1. Follow the instructions in the INSTALL file on the ftpsite. This will import the myChEMBL VM into VirtualBox.
  2. Use Vagrant to install myChEMBL. See  point 3 in the section above.
  3. Bare metal - if you have a clean Ubuntu or CentOS box with root access and want to install myChEMBL software directly, then you may run:
    wget https://raw.githubusercontent.com/chembl/mychembl/master/bootstrap.sh && chmod +x bootstrap.sh && bash bootstrap.sh
    for Ubuntu or:
    wget https://github.com/chembl/mychembl/blob/master/bootstrap_centOS.sh && chmod +x bootstrap_centOS.sh && bash bootstrap_centOS.sh
    for CentOS.
  4. Instructions for Docker will be released #soon in a coming blog post.

As usual, the full codebase lives on GitHub


Publications and webinars

myChEMBL is reported and documented in two Open Access publications, namely here and here. In case you're new to myChEMBL, there is also a recorded webinar and its associated slides here


Future plans

The myChEMBL resource is an evolving system and we are always interested in new open source projects, tools and notebooks. Please get in touch if you have any suggestions or questions.



The myChEMBL team

3 comments:

Gerard JP van Westen said...

CentOS based myChembl is brilliant.. ! To bad i have just finished installing remus... :(

Maciek Wójcikowski said...

Hey, why won't you use qcow2's compression instead of tar.gz? You wouldn't need to decompress it and save some more disk space. I had a blog post about using myCHEMBL in KVM about a year or so, and the compression worked like a charm. The initial image was roughly the same size as tarball, but functional. It will grow over time. I don't know how big is the performance hit, although for light usage there was no difference at all. For reference see http://maciek.wojcikowski.pl/2014/06/mychembl-running-on-kvm/

kott said...

Thank you Maciek, we will use qcow2 compression for myChEMBL 21.