European Life Sciences Infrastructure for Biological Information www.elixir-europe.org “BILS-ProteomeXchange integration using EUDAT resources” ELIXIR-Pilot Project Dr. Juan A. Vizcaíno, EMBL-EBI, [email protected]Dr. Fredrik Levander, BILS, [email protected]
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ELIXIR Pilot Actions launched in 2014: Integration of BILS-ProteomeXchange using EUDAT resources
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European Life Sciences Infrastructure for Biological Informationwww.elixir-europe.org
“BILS-ProteomeXchange integration using EUDAT resources”
4. Other files: Optional files:1. QUANT: Quantification related results e. FASTA2. PEAK: Peak list files f. SP_LIBRARY3. GEL: Gel images4. OTHER: Any other file type
Origin: 396 USA224 Germany191 United Kingdom106 Netherlands105 China104 France 94 Switzerland 75 Canada 55 Japan 55 Spain 54 Denmark 52 Sweden 50 Belgium 48 Australia 34 Austria 25 Norway 23 Taiwan 22 India 21 Finland 20 Ireland 20 Italy 16 Brazil 15 Russia 14 Republic of Korea 10 Israel 10 Singapore …
ProteomeXchange: 1,963 datasets up until 1st April, 2015
BILS – Bioinformatics Infrastructure for Life Sciences
• Distributed national research infrastructuresupported by the Swedish Research Council• Coordination with other bioinformatics activities
• BILS provides:• Bioinformatics support (consultancy) • Bioinformatics infrastructure (data and tools)
Computing and storage is provided in collaboration with SNIC
• Bioinformatics network • Nodes at each of the 6 large university cities• Annual workshop• Training• Coordination with other bioinformatics activities
EUDAT• EUDAT aims to contribute to building and operating a
Collaborative Data Infrastructure for European science.
• This involves a suite of co-ordinated and interoperable services for preserving scientific data, and for making them accessible to researchers.
• EUDAT collaborates with research communities across a range of disciplines, from social sciences to environmental science and including molecular biology (as represented by ELIXIR).
• These communities have diverse structures, cultures and scales but also share some common requirements regarding the management of data. http://www.eudat.eu
EUDAT: B2SAFE AND iRODS• B2SAFE aims to provide a software ecosystem for
persistently available data, including persistent identification, abstracted data storage, and reliable automated replication via auditable rules.
• It is built on top of the iRODS data management software (http://irods.org) and integrates a PID system such as the European Persistent Identification Consortium (EPIC - (http://www.pidconsortium.eu) Handle API).
• To integrate the data repositories for MS proteomics data run by BILS (Sweden) and ProteomeXchange (via the PRIDE database, EMBL-EBI, UK), using EUDAT’s B2SAFE software.
• To integrate the data repositories for MS proteomics data run by BILS (Sweden) and ProteomeXchange (via the PRIDE database, EMBL-EBI, UK), using EUDAT’s B2SAFE software.
• This project will also show the potential of collaboration among research infrastructures and e-infrastructures to better manage the data deluge. It will help to evaluate the requirements of such federated systems.
• B2SAFE 3.0.0 (including iRODS 3.3.1) was initially installed at EMBL-EBI.
• However, BILS had moved already to iRODS v4.
• Incompatibility problems were found.
• It was decided to install iRODS 4.0 at the EBI, to solve the incompatibility issue.
• At the time iRODS v4 was not officially supported with iRODS version 4.0.3, so changes were necessary to the original install procedure to accommodate 4.0.3.
Implementation process (2)• EBI and BILS obtained Handle prefixes and made them
available within EPIC. The integration with iRODS was successfully tested.
• The next step was to configure B2SAFE and achieve a test replication of a file from BILS to EBI using the B2SAFE PID creation and file transfer rules.
• Unexpected delays:
• EBI experienced some network issues that affected communications between the EBI and BILS iRODS.
• Two successive bugs were discovered. Both centered on the rule execution engine and prevented B2SAFE from functioning.
• These bugs were solved by EUDAT & iRODs developers.
Implementation process (3)• With workarounds now in place it was possible to manually
trigger a successful replication of a file from BILS to EBI.
• However it became apparent that the authorisation mechanism employed by iRODS in a federation would make the proposed submission workflow difficult to manage in a production environment.
• This means every BILS researcher able to submit data must have a user created for them on the EBI server first. Alternative customised solutions could solve this issue by decoupling the actions of researchers from the replication itself. However this would inevitably add complexity.
• At this point (March 2015) the pilot had overrun (it was expected to last 6 months), with more work required to integrate the B2SAFE replication process with the PRIDE submission pipeline.
• It was decided to halt the process and find an alternative way to achieve the same goals using existing resources.
• A detailed report has been written and has been sent to all the parties involved.
• EMBL-EBI is involved in the EUDAT 2020 project (PI is Steven Newhouse).
• EMBL-EBI will then continue to collaborate with EUDAT, for gaining experience in the use of this software.
• PRIDE will evaluate the situation in the future to decide if the originally envisioned submission pipeline (based on B2SAFE and IRODS) is implemented.
Conclusions• The pilot establishes that the original use case is not the best
application of B2SAFE at the present time. However, the situation will be kept under review by PRIDE.
• This conclusion is not a reflection on B2SAFE per se, indeed B2SAFE and iRODS have been found to be very flexible and are likely to be interesting candidates for other use cases outside of PRIDE elsewhere in EMBL-EBI or ELIXIR.
• In particular, use cases focused on data management within or between data centres (i.e. bipartite collaborations) or environments where mature data submission, curation and archiving solutions do not already exist.
• In addition, we recommend ELIXIR continues to explore EUDAT services and their relevance in ELIXIR use cases.
• Incorporate a fully-functional RESTful interface for iRODS into B2SAFE, that can be used by a client to avoid installing iCommands on the client machine.
• The security model should be adapted to allow anonymous RW to a specified URL.
• If widespread deployment of EUDAT software is expected, effort must be committed by EUDAT 2020 to make the software more easily and quickly deployable by ‘ordinary’ system administrators.