Skip to main content

myChEMBL 20 has landed

By



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
Labels:

Comments

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

14 July 2015 at 14:42
Unknown 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/
22 July 2015 at 09:21
kott said…
Thank you Maciek, we will use qcow2 compression for myChEMBL 21.
23 July 2015 at 16:41
Post a Comment

Popular posts from this blog

PKIS data in ChEMBL

By Anonymous
The Protein Kinase Inhibitor Set (PKIS) made available by GSK was recently mentioned on  In the Pipeline .  In collaboration with GSK, we are making the data being generated on these compounds available via  the ChEMBL database.  We are also creating a portal for the compound set, where the structures can be browsed and downloaded, direct links to the data are provided and useful information can be posted. A preliminary version is available  here : feedback would be appreciated. The data generated on the PKIS set and deposited in ChEMBL may be downloaded in CSV format here  (note that the Luciferase dataset described in the recent PLoS paper will be in the next release of ChEMBL). Alternatively, to view the data in the ChEMBL web interface, follow these steps: On the home page, enter 'GSK_PKIS' in the search box and click on the 'Assays' button... On the 'Please select...' menu on the right, choose 'Display Bioactivities'...
Post a Comment
Read more

A python client for accessing ChEMBL web services

By
Motivation The CheMBL Web Services provide simple reliable programmatic access to the data stored in ChEMBL database. RESTful API approaches are quite easy to master in most languages but still require writing a few lines of code. Additionally, it can be a challenging task to write a nontrivial application using REST without any examples. These factors were the motivation for us to write a small client library for accessing web services from Python. Why Python? We choose this language because Python has become extremely popular (and still growing in use) in scientific applications; there are several Open Source chemical toolkits available in this language, and so the wealth of ChEMBL resources and functionality of those toolkits can be easily combined. Moreover, Python is a very web-friendly language and we wanted to show how easy complex resource acquisition can be expressed in Python. Reinventing the wheel? There are already some libraries providing access to ChEMBL d
1 comment
Read more

Release of ChEMBL 33

By
We are pleased to announce the release of ChEMBL 33! This fresh release comes with a few new data soures and also some new features: we added bioactivity data for understudied SLC targets from the RESOLUTE project and included a flag for Natural Products and for Chemical Probes. An annotation for the ACTION_TYPE of a measurement was included for approx. 270 K bioactivities. We also time-stamped every document in ChEMBL with their CREATION_DATE! Have fun playing around with ChEMBL 33 over the summer and please send feedback via chembl-help@ebi.ac.uk .   ChEMBL database version ChEMBL 33 release notes ___________________________________________ # This version of the database, prepared on 31/05/2023 contains:      2,399,743 compounds (of which 2,372,674 have mol files)      3,051,613 compound records (non-unique compounds)        20,334,684 activities         1,610,596 assays      15,398 targets      88,630 documents BioAssay Data Sources:    Number Assays:    Number
Post a Comment
Read more

Chemistry and Nature

By
  As the Great Big Green Week (UK) draws to a close, so does EMBL-EBI’s own Sustainability week. The Wellcome Genome Campus held events in the areas of recycling, energy use, and biodiversity. The ChEMBL team was keen to get involved and we developed our own Nature Trail event highlighting some of the bioactive compounds from the flora and fauna found on-site, and elsewhere. Our favourite examples include the sensation of mint and chilli and the glorious smell of rain! The full Nature Trail can be made available for external Public Engagement events upon request . Databases, such as ChEMBL , are large stores of structured data, including genetic, biological, and chemistry data for life sciences research. Data on the natural world is often held by wildlife organisations; this can be used to research biodiversity and species decline. Various Citizen Science initiatives mean that everyone can get involved in submitting nature records. So why not join in with the Butterfly Conservation’s B
Post a Comment
Read more

Accessing SureChEMBL data in bulk

By
It is the peak of the summer (at least in this hemisphere) and many of our readers/users will be on holiday, perhaps on an island enjoying the sea. Luckily, for the rest of us there is still the 'sea' of SureChEMBL data that awaits to be enjoyed and explored for hidden 'treasures' (let me know if I pushed this analogy too far). See here and  here for a reminder of SureChEMBL is and what it does.  This wealth of (big) data can be accessed via the SureChEMBL interface , where users can submit quite sophisticated and granular queries by combining: i) Lucene fields against full-text and bibliographic metadata and ii) advanced structure query features against the annotated compound corpus. Examples of such queries will be the topic of a future post. Once the search results are back, users can browse through and export the chemistry from the patent(s) of interest. In addition to this functionality, we've been receiving user requests for  local (behind the
Post a Comment
Read more