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Interoperability and scalability with microservices in science

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Microservices have emerged as a modern interpretation of service-oriented architectures where processes are small and communicate over a network using lightweight protocols to fulfill a goal.

In this talk I will present our work on microservices, and how they can be used to empower interoperable and scalable analysis services and pipelines in virtual infrastructures on cloud computing resources.

I will also give examples and experiences from the PhenoMeNal H2020 project where a developer community in metabolomics is moving to such architecture.

Published in: Science
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Interoperability and scalability with microservices in science

  1. 1. Interoperability and scalability with microservices Ola Spjuth <ola.spjuth@farmbio.uu.se> Science for Life Laboratory Uppsala University
  2. 2. Service-Oriented Architectures (SOA) in the life sciences • Standardize – Agree on e.g. interfaces, data formats, protocols etc. • Decompose and compartmentalize – Experts (scientists) should provide services – do one thing and do it well – Achieve interoperability by exposing data and tools as Web services • Integrate – Users should access and integrate remote services API Scientist service Scientist consume
  3. 3. Service-Oriented Architectures (SOA) in the life sciences, ~2005 Scientist downtime API changed Not maintained Difficult to sustain, unreliable solutions API API API
  4. 4. Cloud Computing • Cloud computing offers advantages over contemporary e-infrastructures in the life sciences – On-demand elastic resources and services – No up-front costs, pay-per-use • A lot of businesses (and software development) moving into the cloud – Vibrant ecosystem of frameworks and tools, including for big data • High potential for science
  5. 5. Virtual Machines and Containers Virtual machines • Package entire systems (heavy) • Completely isolated • Suitable in cloud environments Containers: • Share OS • Smaller, faster, portable • Docker! 5
  6. 6. MicroServices • Similar to Web services: Decompose functionality into smaller, loosely coupled services communicating via API – “Do one thing and do it well” • Preferably smaller, light-weight and fast to instantiate on demand • Easy to replace, language-agnostic – Suitable for loosely coupled teams (which we have in science) – Portable - easy to deploy and scale – Maximize agility for developers • Suitable to deploy as containers in cloud environments
  7. 7. Scaling microservices 7 http://martinfowler.com/articles/microservices.html
  8. 8. 8 Shipping containers?
  9. 9. Orchestrating containers 9
  10. 10. Kubernetes: Orchestrating containers • A declarative language for launching containers • Start, stop, update, and manage a cluster of machines running containers in a consistent and maintainable way • Origin: Google • Suitable for microservices Containers Scheduled and packed containers on nodes
  11. 11. Virtual Research Environment (VRE) • Virtual (online) environments for research – Easy and user-friendly access to computational resources, tools and data, commonly for a scientific domain • Multi-tenant VRE – log into shared system • Private VRE – Deploy on your favorite cloud provider 11
  12. 12. • Horizon 2020-project, €8 M, 2015-2018 – “standardized e-infrastructure for the processing, analysis and information- mining of the massive amount of medical molecular phenotyping and genotyping data generated by metabolomics applications.” • Enable users to provision their own virtual infrastructure (VRE) – Public cloud, private cloud, local servers – Easy access to compatible tools exposed as microservices – Will in minutes set up and configure a complete data-center (compute nodes, storage, networks, DNS, firewall etc) – Can achieve high-availability, scalability and fault tolerance • Use modern and established tools and frameworks supported by industry – Reduce risk and improve sustainability • Offer an agile and scalable environment to use, and a straightforward platform to extend http://phenomenal-h2020.eu/
  13. 13. Users should not see this…
  14. 14. Deployment and user access Launch on reference installation Launch on public cloud Private VRE
  15. 15. In-house deployment scenarios MRC-NIHR Phenome Centre • Medium-sized IT-infrastructure • Dedicated IT- personnel • Users: ICL staff Hospital environment • Dedicated server • No IT-personnel • User: Clinical researcher Private VRE
  16. 16. Build and test tools, images, infrastructure Docker Hub PhenoMeNal Jenkins PhenoMeNal Container Hub Development: Container lifecycle Source code repositories
  17. 17. Two proof of concepts so far Kultima group Pablo Moreno
  18. 18. Implications • Improve sustainability – Not dependent on specific data centers • Improve reliability and security – Users can run their own service environments (VREs) within isolated environments – High-availability and fault tolerance • Scalability – Deploy in elastic environments • Agile development – Automate “from develop to deploy” • Agile science – Simple access to discoverable, scalable tools on elastic compute resources with no up-front costs • NB: Many problems of interoperability remains! – Data – APIs – etc. 19
  19. 19. Ongoing research on VREs 20 Data federation Compute federation Privacy preservation Workflows Big Data frameworks Data management and modeling
  20. 20. Acknowledgements Pharmb.io Wesley Schaal Maris Lapins Jonathan Alvarsson Arvid Berg Samuel Lampa Marco Capuccini Martin Dahlö Valentin Georgiev Anders Larsson Polina Georgiev Staffan Arvidsson Laeeq Ahmed 21 AstraZeneca Lars Carlsson Ernst Ahlberg-Helgee University Vienna David Kreil Maciej Kańduła SNIC Cloud Salman Toor Andreas Hellander Caramba.clinic Kim Kultima Stephanie Herman Payam Emami ToxHQ team

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