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openBIS
- 1. Offering a cloud-based data management platform via a national Swiss marketplace Alex Upton ETH Scientific IT Services
- 2. ETH Scientific IT Services • Complex process that requires tracking and linking different types of information Materials/samples Protocols/ SOPs Raw data Title Date Materials Methods Analysis Results Experimental description/notes Processed data Results Code Analysis notebooks • There are several possible ways of doing this. Electronic Laboratory Notebooks (ELNs) and Laboratory Information Management System (LIMS) offer an all-in-one solution. ETH Scientific IT Services (SIS) develop their own platform, openBIS. How to manage complex research data?
- 3. openBIS openBIS is an integrated: Inventory management system Notebook Data management system Samples Protocols Experiment Description Raw Data Analysis Scripts Results Laboratory Notebook & Inventory Manager ETH Scientific IT Services Title Date Materials Methods Analysis Results
- 4. Samples Protocols Experiment Description Raw Data Analysis Scripts Results Laboratory Notebook & Inventory Manager All entities can be connected to each other, so it is possible to have the full history of published (and unpublished) results. ETH Scientific IT Services Inventory management system Notebook Data management system Title Date Materials Methods Analysis Results openBIS
- 5. ETH Scientific IT Services @ETH: • SIS provides openBIS as a service to research groups Outside ETH: • Universities and non-for-profit organisations can download openBIS free of charge, but they need to install and maintain it • SIS offers support and maintenance contracts for companies (and Universities, if required) • In Switzerland, SIS can provide support to Swiss academics via national projects such as EnhanceR openBIS deployment
- 6. The EnhanceR project • ETH-SIS is part of EnhanceR (www.EnhanceR.ch), which offers research IT support to the entire Swiss academic community through ‘support projects’ • EnhanceR does this by federating specialist Research IT groups at various academic institutions across Switzerland (shown on map below) ETH Scientific IT Services • Through EnhanceR, SIS successfully completed proof of concept for using openBIS to manage telescope camera components built by UniGe particle physics Science IT Support S3IT Vital-IT Competence Centre in Bioinformatics and Computational Biology ETH Scientific IT Services
- 7. • Good data management is a prerequisite for making data FAIR (Findable, Accessible, Interoperable, Reusable) • Running a data management platform requires dedicated IT resources and skills; • Different groups also tend to have different computing setups (no one-size- fits-all) • Some universities and small start-up companies do not always have these computational resources and skills • As such, we would like to offer a cloud version of openBIS for the Swiss academic community, fully maintained by ETH-SIS for users outside ETH ETH Scientific IT Services Why a cloud-based data management service?
- 8. • SWITCH is planning to offer a marketplace for Swiss universities and educational institutions - the Community Service Hub • The marketplace consists of a platform where providers can offer products and/or services and end-users can see what is available and select what they need (similar to Google store or Apple store) • SWITCH ran a pilot from July to December 2017 with a limited number of providers/partners (= end-users). SIS participated as a provider offering openBIS ETH Scientific IT Services Community Service Hub
- 9. • Integration with edu-ID allowed Swiss academic users to log into the pilot marketplace without having to create separate account • Automatic notification about requests allowed rapid provisioning, configuration and deployment by ETH-SIS of new servers on SWITCHengines infrastructure (using Ansible). • ETH-SIS currently exploring further developing the cloud-based openBIS service offering to the Swiss research community through a future project with partners from different institutes (proposal submitted) • This includes improving the interoperability of openBIS with existing and planned solutions for data publication and long-term preservation, thereby supporting the complete data life-cycle ETH Scientific IT Services Pilot evaluation and next steps
- 10. • SIS members involved in this PoC: Bernd Rinn, Caterina Barillari, Cristian Scurtescu • SWITCH partners for PoC: Sebastian Sigloch, Cristoph Graf • SWITCHengines support: Simon Leinen • EnhanceR project: www.EnhanceR.ch, @eScienceCH • DLCM project: www.DLCM.ch ETH Scientific IT Services Acknowledgements
Editor's Notes
- Overview of openBIS ELN-LIMS Supporting researchers deploy openBIS Rationale for cloud based version of openBIS and example to illustrate this need Community Service Hub pilot
- Need to keep track of different information: -materials and samples used in the lab -standard protocols (experimental or computational) -raw data -processed data -analysed data -code used for processing/analysis -analysis notebooks (if used) All this info has to come together when experiments/computations are described and everything must be referenced and documented to have the full history of what was done and enable reproducibility
- All entities can be connected to each other, so it is possible to have the full history of published (and unpublished) results.
- Current openBIS ELN-LIMS deployment - At ETH: SIS provides the openBIS ELN-LIMS as a service to research groups. We have a subscription model for institutes/departments. The ELN is included in the subscription price for groups belonging to these departments. Other groups have to pay for the support. Outside ETH: openBIS can be downloaded free of charge for universities and non-for-profit organisations For companies, we usually offer contracts for support and maintenance (available also for universities, if requested)
- Some examples of research IT support include: Code development - Creation or improvement of code for scientific services and applications. Updating, adding features, fixing bugs and other coding tasks. Would you like to take your old code and update it to take advantage of newer technology? Perhaps you would like to share it with the research community by making it available as e.g. an R package… Data analysis – Do you have data which you would love to analyse, but don’t have the necessary computational tools or experience available to do it? We can assist with the analysis of research data which requires specialist technical platforms and pipelines or human skills. Porting & Migration – Perhaps you need more computing power to carry out your analysis? We can aid you by taking your research applications and services and moving them to new infrastructures, such as cluster, HPC and cloud, giving you the extra oomph required.
- SWITCHengines chosen because it is the cloud infrastructure provided to Swiss academics by SWITCH, all data is stored in Switzerland (Zurich and Lausanne)