Annual Scientific Report 2015

Web production
Rodrigo Lopez
Systems infrastructure
Petteri Jokinen
• Indexed over 1.5 billion data records from EMBL-EBI
data resources;
• Handled more than 150 million job requests via Job
Dispatcher (36% increase over 2014);
• Hosted approximately 13 000 distinct sequence libraries,
primarily in the ENA, UniProt and Ensembl Genomes;
• Managed FTP and Aspera traffic, which totalled 148.1
Petebytes;
• Improved the EBI Search, which is used in 20 EMBL-EBI
data resources, by reducing its memory footprint through
virtualisation and gaining efficiencies in its core Lucene
libraries;
• Participated in 14 outreach and training events.
• Upgraded the core network links in Hinxton from 10 to 40
Gigabits per second;
• Re-implemented the vault firewall for the EGA using
a software approach, substantially improving system
performance;
• Rebuilt the EMBL-EBI compute clusters’ General Parallel
File System, to improve the high-speed file access.
• Enabled internal users to run Docker containers, resulting in
improved efficiency and more consistent performance;
• Deployed a Lustre (Linux Cluster) for the Functional
Annotation of Animal Genomes project;
• Maintained EMBL-EBI’s growing compute infrastructure,
now based on ~30 000 Central Processing Unit (CPU) cores
Web development
Brendan Vaughan
• Launched an integrated events portal;
• Redesigned the Training Programme web pages, helping
users find events of interest easily;
• Re-engineered the global EMBL-EBI website to be responsive
on mobile devices;
• Designed and launched a fully functional, UX-driven Target
Validation Platform;
• Moved the platform, Open Targets website and Intranet to
an Embassy Cloud workspace;
• Created a dedicated Technical Services information portal;
• Upgraded or moved 14 Drupal6 websites and portals;
• Provided User Experience Research consultation to teams
and groups across the institute.
Systems applications
Andy Cafferkey
• Deployed a new Delphix based infratructure for our
databases across our distributed data centres. This work
was recognized with a ‘Best Data Centre Project of the Year’
award at the Computer Weekly European User Awards 2015.
• Maintained 2000 virtual machines, with 100% uptime;
• Commissioned and maintained a new OpenStack
infrastructure for Embassy Cloud;
• Contributed to the operation of eMedLab project;
• Supported the 950 client devices in use by EMBL-EBI
internal users across OSX, Windows and Linux platforms;
• Began to join the Embassy Cloud with the European Grid
Infrastructure as part of the ELIXIR-Excelerate;
• Consolidated all database instances to virtual machines on
a shared infrastructure, reducing the data-centre capacity
required for databases.
Administration
Mark Green
In 2015 all of the Administration sub-teams examined
processes and procedures in their immediate areas and
in activities that contribute to the overall development
of EMBL-EBI and EMBL. This led to improvements
that are deeply appreciated by those whom
administration serves.
• Established the Strategic Project Management Office, which
supports on-going infrastructure projects;
• Contracted and contributed to a large-scale, independent
analysis of the economic impact of the institute, and
finalised the report for distribution;
• Initiated a Project Management Network to support project
coordinators in teams throughout the institute;
• Introduced flexible working arrangements for EMBL-EBI
staff;
• Managed a nearly 20% increase in recruitment;
• Welcomed a member of the EMBL Budget Office to
EMBL-EBI, improving the coordination of Finance
activities with the EMBL Grants Office.
2015 EMBL-EBI Annual Scientific Report 45