Even though each Open Targets release is made globally available in 3 regions, we decided early on to mask this complexity from the user and publish our API from a single URL at https://api.opentargets.io

We achieve this by load balancing our traffic from https://api.opentargets.io to three reverse proxies in three different regions. Here is a tutorial on how to recreate the same setup, using kubernetes on Google Cloud Platform.

taken from https://www.slideshare.net/quintonh/kubernetes-ubernetes-cluster-federation-by-quinton-hoole-google-inc-huawei-tech-talk-20160526-slides/9

Motivation

Publishing our platform to a global audience, we have always strived to maintain a fast and responsive user experience. How fast our webapp is, directly depends on how fast our API


In our latest release of the Open Targets Platform, we have 13 publicly available data sources all integrated in one place to facilitate your drug target identification and prioritisation.

We process this data following a complex and ever changing ETL (Extract, transform, load) pipeline, which right now is composed of 15 steps.

One of the major requirements for our pipeline is that it should work seamlessly in different environments: we want anyone to easily fork our code and host a private version.

Docker containers make our pipeline easily portable. Each step of our pipeline is encapsulated in a container, where…


How to write a beautiful CV, using markdown, css and html instead of LaTeX.

I have previously used LaTeX to typeset my curriculum vitae, as it invariably produces a beautiful looking document. I have now become frustrated at how long it takes me to relearn LaTeX from scratch every time I want to change something. Plus my .tex source file was becoming completely unreadable. In an attempt to clear up the mess, I decided to put all the content in a markdown file and use CSS to style it. The result is markdown-cv, which can be forked and used as a template by anyone who wants to do the same thing.

Don’t get me…


A comparison of open source tools to delete duplicate files

tl;dr

I needed to clean up duplicates photos from my personal library. And because I could not choose which duplicate finder to try, I have decided to test them all. Amongst the free tools that were correct in identifying all duplicates in my test, dupd was the fastest. I ended up using fastdupes, since it did not require any C/C++ compilation on my NAS.

Why a duplicate file finder?

As a parent, my picture collection has mushroomed in size. I do try to save everything in one place and have backups, but it is difficult to keep track of it. Too afraid of losing family memories…


Many users look at our table view, showing which genes are associated to a specific disease:

However, they sometimes want to restrict this view to a list of genes they are interested in, either because they have already focussed their attention on a specific set of targets or because these targets surface in a different experiment.

Good news: our API makes this easy. One can obtain all the data behind the table view using the API and specifically the /public/association/filter call.

Get the data

For instance, to select data for the first 10 targets associated with a particular disease (eg. asthma) we can…


Please note you no longer need an API key. Read our [Discovering drug targets gets faster — our API upgrades to v3](http://blog.opentargets.org/discovering-drug-targets-gets-faster-our-api-upgrades-to-v3/) post to know why.

I’ve got an API key. What happens now?

Accessing our API is easy, free and available to all.

Once you start using it, you will like it so much that you may hit our rate limit. If that happens, do not despair. Email us and ask for an API key. It will consist of an <app_name> and a <secret> combination.

So you’ve got the key, what happens now?

  • Request a token with your credentials using the method /public/auth/request_token
import requests API='https://www.targetvalidation.org/api/latest/' jwt…

Coinciding with release 1.1 of the Target Validation Platform, we are changing our name to Open Targets. Information about Open Targets will now be found on the new site at opentargets.org. However the Target Validation Platform will not be moving and will remain accessible from the usual targetvalidation.org.

As you can see we are also launching a blog. It will contain updates on new releases and more technical details on what happens under the hood of targetvalidation.org.

Features

This release 1.1 contains important new features described in detail in the documentation, most notably:

  • New public REST API: programmatic access to the…

Since release 1.1, the Open Targets Platform, previously known as Target Validation Platform, exposes a public REST API to allow programmatic retrieval of data served at targetvalidation.org. This is the same API that powers our website and gives full access to the data we use to build our Open Targets Platform user interface.

The available methods are divided in to:

  • public — Methods that serve the core set of our data and that we will keep stable and support.
  • private — Methods used by the web app to serve additional data. …

eliseo papa

data scientist, engineer, doctor, geek, dad

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