The ChEMBL-og

Just a reminder that we are currently looking for a Web Application Developer to join the ChEMBL team at EMBL-EBI. The closing date for this vacancy is 4th Oct, so hurry and apply! The role is primarily to develop a series of web-based applications and interfaces for the ChEMBL chemogenomic resources. The role also involves the development, maintenance and documentation of these tools, and supporting their usage within the EBI and externally. It will also involve some requirement gathering and use-case development. Experience of Python and JavaScript is required as is experience of working with web frameworks such as Django. A sound knowledge of relational databases (primarily Oracle), SQL PL/SQL, REST and HTTP protocol is also a requirement. Experience of contributing to open software projects and documenting them on GitHub for example is desirable. Applicants should have a good understanding of best practice in software engineering, rapid development cycle work, have...

To celebrate the 1000th post, we've decided to take a journey back in time. So, what you see above is a timeline* showing the most important blog posts published on the ChEMBL blog. The posts delineate major events and milestones in the group’s 7-year history and highlight the contributions and impact to the community. Posts on ChEMBL updates, publications, innovative software applications and popular resources are all included there. We hope you will enjoy skimming through it as much as we did. If you have any favourite blog post published here, let us know in the comments. Just remember that this journey continues; here’s to the next chiliad of exciting blog posts! The ChEMBL team. * The timeline was prepared using the excellent timelineJS library by knightlab.com .

We’re co-organising a KNIME chemoinformatics workshop at the EBI on Monday 5th October. This is a regular meeting that takes place the day before the biannual  UK-QSAR meeting . There will be informal discussions on the current and future state of the KNIME chemoinformatics nodes , along with updates by the community and the KNIME guys. There will also be talks on the integration of KNIME with the ChEMBL resources and the Open PHACTS platform.   More details and agenda here ; to register, fill in your details here . George 999

We would like to announce the recent release of two online training resources for ChEMBL and UniChem. For ChEMBL, we   have developed  ‘ChEMBL: Exploring bioactive drug-like molecules’ , which will walk you through how to use the interface, step-by-step. It tackles topics such as target searching, compound searching, web services and data downloads. The course also gives you a chance to test your knowledge throughout. Additionally, Jon Chambers has created the ' UniChem: Quick Tour ' course. This course will give users a basic understanding of UniChem and the benefits it can bring to navigating small molecule resources. It will also walk you through how to conduct simple searches using UniChem and the UniChem Connectivity Search feature. I'd also like to remind you that we store recordings of our past webinars, in case you missed them. You can access these anytime and they can be found here: ...

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 ...

TL;DR: In his excellent blog post , Matt Swain described the implementation of compound similarity searches in MongoDB . Unfortunately, Matt's approach had suboptimal ( polynomial ) time complexity with respect to decreasing similarity thresholds, which renders unsuitable for production environments. In this article, we improve on the method by enhancing it with Locality Sensitive Hashing algorithm, which significantly reduces query time and outperforms RDKit PostgreSQL cartridge . myChEMBL 21 - NoSQL edition    Given that NoSQL technologies applied to computational chemistry and cheminformatics are gaining traction and popularity, we decided to include a taster in future myChEMBL releases. Two especially appealing technologies are Neo4j and MongoDB . The former is a graph database and the latter is a BSON document storage. We would like to provide IPython notebook -based tutorials explaining how to use this software to deal with common cheminformat...