1. Microbial Bioinformatics in the
cloud
Introducing CLIMB
Dr Tom Connor
Cardiff University
Biological Cloud Computing Workshop
www.climb.ac.uk
@tomrconnor ; @mrcclimb
2. Overview
• Background
• View from a newly
minted academic
Bioinformatician at a
“regular” University
– Bioinformatics needs
and challenges
• Introducing CLIMB
3. Big Data
Wave 1 Wave 2 Wave 3
2005-
09
1989-
97
2003-
07
1992-
2002
1993-98
1975-86
1937-611966-71
1967-89
1969-73
1969-81
1981-85
1974
1986-87
1969-73
Adapted from Mutreja, Kim, Thomson, Connor et al, Nature, 2011
Population genomics; using genomics to reconstruct the
global spread of pathogens
Bioinformatics; developing new approaches to analyse
massive datasets
From Marttinen, Hanage, Croucher,
Connor, Harris, Bentley and
Corander, Nucleic Acids Res. 2011
From Cheng, Connor, Sirén, Aanensen,
Corander, MBE, 2013
Grand challenges; fighting antimicrobial resistance
From Fookes et al, PLoS Pathogens 2011
From Reuter, Connor et al, PNAS 2014
From Okoro, Kingsley, Connor et al.
Nature Genetics 2012
From He et al, Nature Genetics
2013
From Dziva, Hauser, Connor et al,
I&I, 2013
Pathogen genomics: understanding how pathogens
evolve
4. About Me
• 2006-2010 - PhD at
Imperial; Population
Genetics / Molecular
Epidemiology of
bacterial pathogens
• 2010-2012 - Post-Doc,
Wellcome Trust Sanger
Institute; Pathogen
Genomics
• 2012 – present Lecturer
then Senior Lecturer,
Cardiff University
Hanage, Fraser, Tang, Connor, Corander, Science, 2009
5. Building bioinformatics capacity
• When I arrived at Cardiff, I
had the joy of working
out how I was going to do
my research in a new
place
• How to get
scripts/software installed
• Where to install
scripts/software
• And I had to do this
mostly on my own
• Not an unusual story
6. Key Challenges
• Infrastructure
– Storage
– HTC capacity
• Portability of software
• Portability of datasets
• But, we do have the
University
Supercomputer….
7. Advanced Research Computing @
Cardiff (ARCCA)
• 2048 core HPC cluster
• Second hand ~868
Westmere core “HTC”
partition
• 8 ‘large memory’ 128GB
nodes
• Lustre file system (scratch,
nominally unlimited, but
50TB total space initially)
• NFS /home mount (50GB
maximum quota)
• Freely available to University
Researchers
8. …. So the first thing I did was to buy
myself some servers
• Large HPC clusters often don’t
meet our needs
• Bioinformaticians aren’t the
ideal HPC users
– Disruptive software needs
– Disruptive usage patterns
– Disruptive storage needs
• Setting up our “own” system
seems the most intuitive way
to ensure that you have
something that works
9. Biologists often end up working in silos
• As a discipline we have probably been
taught to think in terms of ‘labs’,
‘groups’ and ‘experiments’ being wet
work
• We build capacity and teams locally,
and those are the resources that we
use every day
• For bioinformaticians this means we
are likely to develop our solutions
locally first, building a local group and
local capacity
• Our software, data set storage, LIMS
etc are usually bespoke
• Because our software/data is locally
stored/setup – it is often less portable
than wet lab methods / approaches
• Bioinformaticians should be working
differently
10. Key Challenges Overall
• We need systems that allow us to rapidly and easily share
complete systems, from the perspective of both novice users and
experienced developers
• We need to develop systems to share complete datasets, rather
than forcing users to install loads of bits of software to
reconstitute the development environment we used, or forcing
us to become proper software developers
• We need to lower the barrier to access for for research scientists
with a limited understanding of UNIX/Computer Science
• We need a system that allows us to train users on systems that
they will then be able to use when they go home
• We need to understand the needs of individual fields
• We need to integrate activities across these needs, to avoid
reinventing the wheel
11. The cloud
• All of the infrastructure
issues are much easier when
tackled at scale
• This concept led to Amazon,
followed by others, offering
Cloud services
• A cloud infrastructure
provides a mechanism to
share systems/software and
data, at scale
• Let someone else do the
admin etc, and all you have
to worry about is running
the software
12. Why not use a commercial cloud?
• We often want lots of RAM – Amazon
max flavour size is ~250GB
• Prices are high ($1200/month for
~250GB RAM flavour)
• Storage costs also high – 1TB on Amazon
S3 costs $30/month (our current costs
are £7/month)
• Additionally Amazon isn’t designed to
facilitate sharing of data etc between
different people who have VMs
• There are possible issues around T&C’s,
governance etc
• Even if we overcome these, often these
services are too hard for novice users to
make use of
13. Needs
• Core infrastructure now to
take advantage of new
technologies
• Systems to easily share data
• Repositories that can make
tools/methods/data
available rapidly and easily
• Better use of the existing
RCUK/University server
estate
• To change the view of
Biologists about working in
silos
14. Introducing the CLoud Infrastructure
for Microbial Bioinformatics (CLIMB)
• MRC funded project to
develop Cloud
Infrastructure for microbial
bioinformatics
• ~£4M of hardware, capable
of supporting >1000
individual virtual servers
• Providing a core, national
cyberinfrastructure for
Microbial Bioinformatics
15. The CLIMB Consortium Are
• Professor Mark Pallen (Warwick) and Dr Sam
Sheppard (Swansea) – Joint PIs
• Professor Mark Achtman (Warwick), Professor
SteveBusby FRS (Birmingham), Dr Tom
Connor (Cardiff)*, Professor Tim Walsh
(Cardiff), Dr Robin Howe (Public Health Wales)
– Co-Is
• Dr Nick Loman (Birmingham)* and Dr Chris
Quince (Warwick) ; MRC Research Fellows
* Principal bioinformaticians architecting and designing the system
16. The CLoud Infrastructure for Microbial
Bioinformatics (climb.ac.uk)
• We are creating A one stop shop
for Microbial Bioinformatics
– Public/private cloud for use by
UK academics
– Standardised cloud images that
implement key pipelines
– Storage repository for
data/images that are made
available online and within our
system, anywhere (‘eduroam
for microbial genomics’)
• We will provide access to
other databases from within
the system
• As well as providing a place to
support orphan databases and
tools
17. System Outline
• 4 sites
• Connected over Janet
• Different sizes of VM available; personal, standard, large memory, huge memory
• Able to support >1,000 VMs simultaneously (1:1 vCPUs/vRAM : CPUs/RAM)
• 7-8PB of object storage across 4 sites (~2-3PB usable with erasure coding)
• 4-500TB of local high performance storage per site
• A single system, with common log in, and between site data replication
• System has been designed to enable the addition of extra nodes / Universities
18. CLIMB Overview
• 4 sites, running OpenStack
• Hardware procured in a two
stage process
• IBM/OCF provided
compute, Dell/redhat
provided storage
• Networks provided by
Brocade
• Are defining a reference
architecture to enable
other sites to trivially be
added
20. Overview – 4 sites, (virtually) identical
hardware
Each site is connected to the
others over VPN tunnels.
Sites can be easily added.
System can use free router
software and commodity
hardware, pay for-software
or dedicated router/firewalls
Our intention is for the system
to be presented to users as a
single system, with single login,
via Shibboleth.
We are currently working on that
bit
A single system makes it easy(er)
to share methods and data!
External clouds
External databases
External clouds
External databases
21. Flavours
• User configurable, with standard
flavours
• Regular; up to 8 vCPUs, 64GB
RAM
• xlarge; up to 16 vCPUs, 256GB
RAM
• Huge; up to 192 vCPUs, 3TB
RAM
• System also supports a scalable
virtual cluster (large
embarrassingly parallel projects)
– 2+ nodes with 2+ vCPUs, 2-4GB
RAM/vCPU
• Also provides for Long Term
Hosting (for orphan
datasets/tools)
22. Access
• Microbial researchers will be
able to access the system
through one of two ways
– Externally, via federated access
system, login via .ac.uk user
login in first instance, later
(hopefully) open to anyone
who uses shibboleth
– Internally, via user accounts
setup by consortium for
collaborators
• Researchers will be able to
provision up a set number of
VMs
23. Where are we now?
• Computational hardware was procured by March 2015 (~6 month process)
• Ahead of schedule - system is now online and in use for research
• Adopting two models for access
– Access for registered users to core OpenStack system online now
– “version 1.0” system providing universal access to predefined images starting
with the GVL – Autumn 2015
26. Challenges
• Future Planning (CLIMB will run for 5 years,
then what?)
• Cross-Cloud Integration
• Not reinventing the wheel
• Standardising software stacks for .ac.uk clouds
• Being able to embrace new technologies
• Meeting cloud development needs
27. The Sequencing Iceberg
All of the sequencing platforms available
now make producing large genomics
datasets relatively cheap and easy
However, the major costs and difficulties
do not lie with the generation of data,
they lie with the pre-requisites for storing
and analysing that data
Informatics expertise
Storage availability
Appropriate HTC capacity
These are
interlinked,
and
expensive
28. Iceberg breaking with the Cloud?
• It is a mechanism for sharing servers
– Clouds remove the need for hardware
maintenance and support
– Storage, compute, networking are most
expensive when bought one by one; building a
large system represents better value for
money
• Sharing servers means you can have
standardised systems, simplifying the process
of installing and maintaining software
– It provides a mechanism for software/data
reuse as well as sharing
– Also makes training easier; you can use the
system you trained on, once you get back
home
• Sharing servers also makes training easier;
you can use the system you trained on, once
you get back home
29. CLIMB Next Steps – and future needs
• New images/analytics tools (GVL!)
• Integration of datasets
• Expanding our userbase
• Collaboration with other cloud services
• Integrating with databases
• Integrating with other clouds
• Developing new sites
• Developing the system to meet the
needs of our users
• Developing policy
• Defining and developing security policy
• Developing/setting up federated access
• Possibly looking at capacity to burst out
or accept bursts from other resources
• Developing our training programme
and outreach
30. Cloud Infrastructure for Microbial
Bioinformatics
• A multi site system to provide a one-stop-bioinformatics-shop, designed
specifically to support Microbial researchers
• For both Bioinformaticians and wet lab scientists
• Combines hardware with training
• Free, simple interface, easy to use
• Common login
• Easy data and method sharing
• Already have multiple users from across UK academia and healthcare
31. The CLIMB Consortium Are
• Professor Mark Pallen (Warwick) and Dr Sam
Sheppard (Swansea) – Joint PIs
• Professor Mark Achtman (Warwick), Professor
SteveBusby FRS (Birmingham), Dr Tom
Connor (Cardiff)*, Professor Tim Walsh
(Cardiff), Dr Robin Howe (Public Health Wales)
– Co-Is
• Dr Nick Loman (Birmingham)* and Dr Chris
Quince (Warwick) ; MRC Research Fellows
* Principal bioinformaticians architecting and designing the system
32. CLoud Infrastructure for Microbial
Bioinformatics (CLIMB)
• MRC funded project to
develop Cloud
Infrastructure for
microbial bioinformatics
• ~£4M of hardware,
capable of supporting
>1000 individual virtual
servers
• Amazon/Google cloud for
Academics
