Skip to main content

Posts

Showing posts from June, 2014

Meeting - EMBL-EBI/Wellcome Trust Workshop on Resources for Computational Drug Discovery

It's that time of year again, when we advertise our fun and engaging course on computational drug discovery. This year it is held on the 17th to 21st November 2014, at the Wellcome Trust Genome Campus, Hinxton, Cambs UK.
This workshop provides participants with the underlying principles of computational chemical biology and addresses how these methods are applied in the field of drug discovery. It will explore approaches to accessing data, combining different data types and introduce the tools available to assist analysis work. Practical sessions will guide participants in retrieving and analysing chemogenomic, proteomic and metabolomic data for target analysis.
Target Audience This workshop is suitable for both academic and industrial researchers interested in drug discovery from a range of biological disciplines. An undergraduate level of biology is essential and participants should have a basic understanding of UNIX, programming and running simple scripts (such as python).
Syllabus…

myChEMBL on Bare Metal

myChEMBL is distributed as a Virtual Machine (VM), which is good because you can treat it like another file on your filesystem. It can be transmitted, copied, renamed, deleted, etc. The myChEMBL VM behaves like a sandbox, so software installed there can't harm your computer.

But there are sometimes costs associated with using a VM, for example VMs are usually several percent slower than the host they are running on. There are also a number of scenarios where using a VM may not optimal or even possible, for example:
You just want to enrich your existing machine with chemistry-related software The only machine you have is itself virtual - VM provisioning software often prevents you from installing a VM within a VMWhen performance is critical In these cases you may not want the whole myChEMBL VM, only the software that it ships with.

Fortunately we have a script, that automates the process of creating our customized VM. But not only that - we keep it publicly available along with all…

How to install myChEMBL using two Vagrant commands

TL;DRinstall Vagrant and VirtualBoxrun vagrant init chembl/myChEMBL && vagrant upwait a bit... go to http://127.0.0.1:8000/enjoy!
What have I just done?
Vagrant is a tool for building and deploying complete development environments and myChEMBL 18 now supports installation via Vagrant. We achieved this by first creating a myChEMBL Vagrant Box, which we then register on the Vagrant Cloud. This then allows users to install myChEMBL on there local system using two simple commands*:

vagrant init chembl/myChEMBL
vagrant up


*assumes you have vagrant installed

It's that simple! After you type this into your system console, the expected output should be similar to the one below:




What are those two commands doing?
The first command initializes the current directory to be a Vagrant environment by creating an initial Vagrantfile and prepopulates the config.vm.box setting in the created Vagrantfile. This happens immediately. This command should be executed only once.

The second one, wh…

A python client for accessing ChEMBL web services

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 data via webservices…

New Drug Approvals 2014 - Pt. X - Albiglutide (Eperzan™ or Tanzeum™)

Wikipedia: Albiglutide ChEMBLCHEMBL2107841
On April 15th the FDA approved Tanzeum (albiglutide) subcutaneous injection to improve glycemic control, along with diet and exercise, in adults with type 2 diabetes.
Type II diabetesType II diabetes is a metabolic disorder that is characterized by high blood sugar (hyperglycemia) due to insulin resistance or relative lack of insulin. The disease affects millions of patient world-wide and can lead to long-term complications if the blood levels are not lowered in the patients: heart diseases, strokes and kidney failure.

Albiglutide The drug is a dipeptidyl peptidase-4-resistant glucagon-like peptide-1 dimer fused to human albumin.
Schematic representation of the albiglutide (EMA)
Mode of action Traditionally, a decrease in the glucose blood level of affected patients is triggered using insulin injections. One alternative mechanism consists at indirectly stimulating insulin release using a glucagon-like peptide-1 (GLP-1) or an analogue of the c…

Recruitment: Two Biological Data Manager positions within the team

We have two positions in the group currently open, both working on bioassay data aspects of the ChEMBL database. One is funded by a Wellcome Trust Grant, and the other under funding from the newly established EMBL-EBI/Sanger Center/GSK Center for Therapeutic Target Validation (CTTV). These are both great opportunities to work in a fun group committed to working on Open Data to help drug discovery.
Curating and organising bioactivity data in the ChEMBL database in a structured way. Mapping measured bioactivity data from the scientific literature to other biological entities (proteins, cell-lines etc) using a variety of biological resources and ontologies. Storing the information in the ChEMBL database in a structured format. Implementing curation pipelines for data from complex and phenotypic assays such as those from cell-based and whole organism studies. Manually checking and annotating data by reference to the original data sources. Developing semi-automated processes for identifying and…

myChEMBL LaunchPad......Launched!

We are pleased to announce that the latest myChEMBL release (based on ChEMBL_18), is available to download. For users not familiar with myChEMBL, the aim of the project is to create an open platform, which combines public domain bioactivity data with open source web, database and cheminformatics technologies. More details about the project can be found in this paper and more details about a recent award it helped pick up can be found here.
Like the previous release, once you have installed the myChEMBL virtual machine, you will have access to an Ubuntu linux machine which comes preloaded with the ChEMBL data in a RDKit enabled PostgreSQL database and the original myChEMBL web application. We have added a lot of new features and enhancements to the new myChEMBL release, which include: A local copy the ChEMBL Web Services, which uses the local PostgreSQL database as a backend.A suite of interactive tutorials, created using IPython Notebooks. Topics covered include introductory material us…