Web, Core Bioinformatics and Software Action Team

Informatics and Digital Solutions

The Wellcome Sanger Institute is a world-leading genomics research institute. Our work helps improve human health and understand life on Earth. Underpinning much of this work is a reliance on the Institute’s Informatics and Digital Solutions (IDS) presence and web technologies to store, interpret and make available genomic research data sets to the scientific community world-wide. Core Software Services (CSS) ensures the Wellcome Sanger Institute research data are made available through the use of web technologies to the external scientific community and the public in a timely fashion in accordance with the Institute’s strategic plans and funding.

CSS likewise supports the Wellcome Genome Campus itself, for which we provide its web presence and on campus bespoke IT requirements. Wellcome Connecting Science, the programme which supports teaching, learning; courses and conferences as well as on Campus venue facilities, is also provided with its web presence and bespoke IT requirements by the CSS.

How we work

CSS is a team within IDS, a department of about 140 people where we work very closely with other teams in IDS: Database administrators (DBAs); Infrastructure Management; Informatics Support Group; Data Centre; Project Management Group; Pipelines Group; Service Delivery; Service Desk.  

We are a very large Linux house specialising in Ubuntu as our Operating System of choice and have access to a dedicated 800Kw rated data centre on campus  split into four data halls; with additional data centre provisioning in AWS and other cloud providers.

In terms of general website development we tend to use well supported frontend frameworks such as Vue.js, Node.js and React.  We use SASS for our CSS and adhere to a standards compliant approach to all our web development.

For backend functionality we utilise various scripting languages including PERL, Python and PHP to generate bespoke web functionality for our large scientific datasets.

Regarding web content management systems we use WordPress as our CMS of choice, pre-rendering the web content during publishing. This removes the need for PHP and databases, thus making these websites very fast to render and very secure.

We support a number of Database types including MySQL, Postgres and to a lesser degree Oracle.  NoSQL options are also available; such as MongoDB.  For database provisioning, replication and backup we work closely with our DBA colleagues.

Our virtual machine (VM) infrastructure runs on either VMware, for most robust and repeatable websites we provide.  We also use Images running on OpenStack for more of the research and development resources we provide.  In both cases we work closely with our Platform infrastructure colleagues who provide us with over 500 VMs on both platforms.

Our development strategy tends to a standard Sandbox, Development, Staging and live setup with the live service having multiple VMs to give resilience to each web service.  The live servers sit behind Traffic managers that also manage aspects of security and load balancing. 

We take security very seriously and use professional applications and tools to continually monitor and test the security of all our websites (of which there are 160 domains along with a further 180 subdomains).

On Campus there are approximately 300 software developers, working on various aspects of genomics, some of whom specialise in web technologies as a means to share their data sets.  Being an academic institute this often means upcoming and niche web frameworks are chosen.  One part of CSS’ role is to work with these developers and optimise their web code for use at scale, with resilience and repeatability in mind as well as ensuring it conforms to web security standards.  

To support further the genomics software developers on campus we also maintain and administer large bioinformatics databases which are critical to the work of these software developers.  Many of these databases are Terabytes in size, so by providing these as a central resource allows the developers to concentrate on their primary goals.

We also support other core requirements of the Campus such as Matomo for web analytics;  Solr for website searching capabilities; management of cookies and cookie policies; website monitoring; VM and network monitoring.

In summary the team has a very broad and interesting software/web/IT remit across the Campus and is key to many aspects of work on Campus and its key deliverables.