1. The CLoud Infrastructure for Microbial Bioinformatics
Dr Tom Connor
Cardiff University
Genome Science 2015
@tomrconnor

2. The CLIMB Consortium Are
Professor Mark Pallen (Warwick) and Dr Sam Sheppard (Swansea) – Joint PIs
Professor Mark Achtman (Warwick), Professor Steve Busby 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
Simon Thompson (Birmingham, Project Technical/OpenStack lead), Marius Bakke (Warwick, Systems administrator), Simon Thompson (Swansea, Systems administrator)
* Principal bioinformaticians architecting and designing the system

3. 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

4. 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

5. CLIMB Overview: GS Update
4 sites, running OpenStack
Hardware procured in a three 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

6. Hardware (per site)
2 router/firewalls (capable of routing >80Gb each)
3 Controllers
21x 64 vCore, 512GB RAM nodes
3x 192 vCore, 3TB RAM nodes
~500TB GPFS (local)
4 controllers
Infiniband, with 10Gb failover
~2PB total Ceph (shared)
27x 64TB nodes/site
Cross site replication
10Gb Backbone

7. Overview – 4 sites, (virtually) identical hardware
External clouds
External databases
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 
External clouds
External databases
A single system makes it easy(er)
to share methods and data!

8. 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 2+ nodes with 2+ vCPUs, 2-4GB RAM/vCPU
Also provides for Long Term Hosting (for new or orphan datasets/tools)

9. 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

10. 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 “pro” dashboard online now (intended for bioinformaticians/developers)
“version 1.0” system providing universal access to predefined images starting with the GVL – by Winter 2015 (intended for those who just want a single server with predefined software)

11. Live Demo Dashboard Login: http://birmingham.climb.ac.uk Wiki Login:

12. VMs are already up

13. Users are already using CLIMB to do research

14. 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

15. The CLIMB Consortium Are
Professor Mark Pallen (Warwick) and Dr Sam Sheppard (Swansea) – Joint PIs
Professor Mark Achtman (Warwick), Professor Steve Busby 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
Simon Thompson (Birmingham, Project Technical/OpenStack lead), Marius Bakke (Warwick, Systems administrator), Simon Thompson (Swansea, Systems administrator)
* Principal bioinformaticians architecting and designing the system

16. 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
Already in production, and use by researchers