ChEMBL Resources


Thursday, 3 October 2013

ChEMBL Virtual Machine (a.k.a. myChEMBL)

With last weeks ChEMBL_17 release out of the way, we have had time to revisit our ChEMBL Virtual Machine project. This project, which we now refer to as myChEMBL, is aimed at providing users with a complete and free, easy-to-intstall cheminformatics infrastructure. To achieve this we have provided users with a Ubuntu based virtual machine, which comes with:
  • A PostgreSQL database, preloaded with ChEMBL_17. You will notice some extra tables, which are required to allow the RDkit chemical searching.
  • The latest build of RDkit taken from the RDkit github repo.
  • A web application to allow you to query the ChEMBL database. You can pick up a copy of the web application from Rodrigo Ochoa github repo.
You might now ask How do I get a copy of myChEMBL? And the answer to that is you visit the ChEMBL ftpsite:

To install myChEMBL you will need to use some virtualisation software, such as VirtualBox or VMware Fusion. You will find installation instructions on the ftpsite, which describe how to load myChEMBL into VirtualBox. These will soon appear on this blog - with pictures :)

Get in touch via mail to if you have any myChEMBL questions.

The ChEMBL Team


GrumpyOldMan said...

Excellent idea, although I have downloaded it twice today and both times (Mac OSX Mountain Lion) both Parallels Mounter and VirtualBox have complained about corruption - is the image OK ?

GrumpyOldMan said...

Hmmm, third time lucky, and this time I didn't start with Parallels Mounter. Could it be breaking the VM by any chance ?

John Overington said...

This seems to be a problem with the Apple finder - if you use this to connect to the ftp server, it does not always complete the large download. We have been able to reproduce this behaviour on several machines.


A workaround will be to use command line access to the ftp site, or try another ftp client for the Mac.

GrumpyOldMan said...

Wow, didn't realise I was going to show up as "Grumpy Old Man" ! I just downloaded by clicking on the link in Chrome but you're right, for such a big file an FTP client isn't a bad idea. Cheers !