myChEMBL 19 Released

We are very pleased to announce that the latest myChEMBL release, based on the ChEMBL 19 database, is now available to download. In addition to the extra data, you will also find a number a great new features. So what's new then?

More core chemoinformatics tools

We have included OSRA (Optical Structure Recognition), which is useful for extracting compound structures from images. OSRA can be accessed from the command line or by very convenient web interface, provided by Beaker (described below). We've also added OpenBabel - another great open source cheminformatics toolkit. This means you can now experiment with both RDKit and OpenBabel and use whichever you prefer.

ChEMBL Beaker

myChEMBL now ships with a local instance the ChEMBL Beaker service. For those not familiar with Beaker, the service provides users with an array of chemoinformatics utilities via a RESTful API. Under the hood, Beaker is using RDKit and OSRA to carry out its methods. With the addition of Beaker in myChEMBL, users can now carry out the following tasks in secure local environment:

Convert chemical structure bewteen multiple formats
Extract compound information from images and pdfs
Generate compound images in raster (png) and vector (svg) forms
Generate HTML5 ready representation of compound structure
Generate compound fingerprints
Generate compound descriptors
Identify Maximum Common Substructure
Compound standardisation
Lots of more calculations

New IPython notebooks

We have written a number of new IPyhthon notebooks, which focus on a range of cheminformatics and bioinformatic topics. The topics covered by the new notebooks include:

Introduction on how to use ChEMBL Beaker
Using the Django ORM to query the ChEMBL database
Introduction to BLAST and creation of a simple Druggability Score
Introduction to machine learning
Analysis of SureChEMBL data, focused on identifying the MCS core identified in a patent
Extraction and analysis of ChEMBL ADME data

We have also updated the underlying Ubuntu VM to 14.04 LTS, which also required us to make a number of changes the myChEMBL installation. To see how these changes and new additions have effected a bare metal installation of myChEMBL, head over the myChEMBL github repository.

Installation

There are 2 different ways we recommend for installing myChEMBL:

Follow the instructions in the INSTALL file on the ftpsite. This will import the myChEMBL VM into VirtualBox
Use Vagrant to install myChEMBL. See this earlier blogpost for more details, but the command to run is:

vagrant init chembl/myChEMBL && vagrant up

If you already have myChEMBL_18 installed via Vagrant, instead of running 'vagrant box update', we strongly recommend running:

vagrant box remove chembl/myChEMBL

vagrant init chembl/myChEMBL && vagrant up

Future plans

The myChEMBL resource is an evolving system and we are always looking to add new open source projects, tools and notebooks. We would be really interested to hear from users about what they would like to see in future myChEMBL releases, so please get in touch if you have any suggestions. (Just so you know, we already have a couple of ideas for myChEMBL 20).

We hope you find this myChEMBL update useful and if you spot any issues or have any questions let us know.

The myChEMBL Team

Comments

Unknown said…

Any troubleshooting section, I am one of those having issues with the network thingi in the virtualbox.

I followed the instruction, but cant access the http://IP adress?

24 October 2014 at 20:48

Mark Davies said…

Hi Jörg,

Sorry to hear you are having problems with the install. If you have time maybe you could send some more details to 'mychembl at ebi.ac.uk'. One thing we did notice recently, which caused a similar issue to what you describe was the 'Adapter Type' in the Advanced network settings was set to a server version - it should be changed to the desktop equivalent, something like 'Intel PRO/1000 MT Desktop'.

Thanks

Mark

27 October 2014 at 20:13

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