EGI-Engage:WP6 (SA2) Knowledge Commons

EGI-Engage project:	Main page	WP1(NA1)	WP3(JRA1)	WP5(SA1)	PMB	Deliverables and Milestones	Quality Plan	Risk Plan	Data Plan
	Roles and responsibilities	WP2(NA2)	WP4(JRA2)	WP6(SA2)	AMB	Software and services	Metrics	Project Office	Procedures

WP leader: Gergely Sipos/EGI.eu at SZTAKI

WP contact: egi-engage-wp6@mailman.egi.eu

Objective

WP6 (SA2) coordinates the provisioning of services for scientific communities and supports the co-design, co-development and dissemination of new community-specific e-Infrastructure services. These services will support novice and semi-experienced user communities as well as members of the long-tail of sciences to become active and self-sufficient users of e-Infrastructure solutions. In addition, some of the services will support mature e-Infrastructure communities in taking their production experiments on distributed computing and data infrastructures to the next level. The work package includes dedicated tasks for eight Competence Centres (CCs) to support high-impact Research Infrastructures/communities by joint development of customised services for these based on core EGI capabilities, by user engagement and training. Two of the CCs (BBMRI and EISCAT_3D) are supported by both EGI and EUDAT within the Horizon2020 programme. The work package also contributes to fostering open science, and nurturing smaller or less structured research groups by providing training and direct technical support to them. Specific objectives of WP6 are: 

1. Identify and support communities and users from EGI and its partners;
2. Facilitate the integration of scientific applications with EGI’s e-Infrastructure services;
3. Co-design and co-develop services for sustainable, structured scientific communities;
4. Promote and support the uptake of new services within scientific communities;
5. Provide a training framework, foundational training services and domain specific training events for scientific communities, EGI members and partners.
   

Tasks and contacts

Task	Name	Task Leader	Deputy/Technical	Task members' email list
SA2.1	Training	Gergely.Sipos AT egi.eu
SA2.2	Technical User Support
SA2.3	ELIXIR	Tommi Nyrönen tommi.nyronen AT csc.fi
SA2.4	BBMRI	Petr Holub  petr.holub AT bbmri-eric.eu
SA2.5	MoBrain	Alexandre M.J.J. Bonvin a.m.j.j.bonvin AT uu.nl
SA2.6	DARIAH	Karolj Skala skala AT irb.hr	Zoltán Farkas zoltan.farkas AT sztaki.mta.hu
SA2.7	LifeWatch	Jesus Marco de Lucas marco AT ifca.unican.es
SA2.8	EISCAT_3D	Ingemar Häggström ingemar.haggstrom AT eiscat.se
SA2.9	EPOS	Daniele Bailo daniele.bailo AT ingv.it	Mariusz Sterzel m.sterzel AT cyfronet.pl
SA2.10	Disaster Mitigation	Eric Yen Eric.Yen AT twgrid.org	Simon Lin Simon.Lin AT twgrid.org

Involved partners

• EGI.eu   
• OEAW   
• VLIZ   
• CESNET   
• FRAN HOFER   
• GWDG
• CSIC   
• CSC   
• CNRS    
• INRA   
• GRNET   
• SRCE
• MTA SZTAKI   
• INFN   
• CIRMMP   
• IRCCS FBF   
• SURF sara   
• CYFRONET
• LIP   
• ICETA   
• SNIC   
• STFC   
• BBMRI ERIC   
• EMBL
• EISCAT  
• GNUBILA   
• UI (OSG)   
• AS   
• ASTI   
• ITB
• KISTI   
• UPM   
• NSTDA
  

Task descriptions

TASK SA2.1 Training

Lead: EGI.eu, M1 – M30)

Estimated task effort: 37PM
This task provides coordination to training activities across EGI, and a framework to develop, integrate and deliver training content and events customised for various audiences. The task will connect training activities of the CCs, NGIs and external projects, and will strive to maximise their effectiveness and impact across e-Infrastructure communities. A plan of join training activities with EUDAT will be defined at PM12 and PM24. The foundational services to be provided by the task are:

1. Operating an up to date section in the EGI website about training events resources;
2. Develop generic training content for customised courses prepared by CCs, NGIs and scientific communities;
3. Contribute to the setup and delivery of tutorials at high-impact events organised by CCs, the NGIs, scientific communities and partner projects.

TASK SA2.2 Technical User Support

(Lead: CSIC, M1 – M30)

Estimated task effort: 48PM
This task operates a distributed user support team across multiple NGIs to provide technical support to the integration of domain-specific applications with EGI platforms. The support will include, for example, integration of scientific code with EGI cloud and HTC platforms, workflow development, development of community gateways or resource allocation. The effort will be focused on new communities coming from scientific disciplines that do not have dedicated EGI Competence Centres and lack sufficient support within the NGIs. The task will result in community-specific systems underpinned by resources and generic e-Infrastructure services from the NGIs and new communities.

TASK SA2.3 ELIXIR

(Lead: CSC, M6 – M24)

Estimated task effort: 36.5PM
ELIXIR is a pan-European RI supported by 17 European governments united in a vision to build a sustainable European infrastructure for biological information, supporting life science research and its translation to medicine, agriculture, bioindustries and society. Members of the ELIXIR CC will select key life science use case workflows between partners that are representative of many in the community and will have high impact for scientist end-users and use these as drivers to develop demonstrators that will assess the use of EGI cloud resources for tool and/or data services recognised within the ELIXIR community. The CC will also create best practices materials for life science service providers using the experience gained in those tasks and organise events to facilitate discussions between e-Infrastructure and life science communities. The goal is that by the end of the two-year effort ELIXIR service providers feel motivated to use Big Data tools coming from e-Infrastructures, and that e-Infrastructure providers have established processes to support particular life science data analyses. OSG, as an associate partner will organise collaborative discussions co-located with existing events to discuss life science drivers for virtual organisations and research groups.

TASK SA2.4 BBMRI

Lead: SURFsara, M1 – M24)

Estimated task effort: 29PM
Thousands of biobanks in Europe have been collecting data, samples and images of millions of individuals in different stages of their lives, during disease and after recovery. Biobanking is currently evolving from local repositories to a pan-European RI the BBMRI-ERIC. The BBMRI CC facilitates the implementation of big data storage in combination with data analysis and data federation by integrating technologies from community projects, EGI and other e-Infrastructures. The CC will capture requirements and provide technology demonstrators to:

• Increase biobank interoperability and data discovery in BBMRI community by providing a secure and standard way to share biobank high-throughput data.
• Provide biobanking community with a federated infrastructure for big data storage and intensive data analysis.
• Facilitate the efficient use of bio-resources by supporting visibility and sharing, while also respecting the protection level required by owners of the data and samples.
• Facilitate the efficient use of economic resources in BBMRI by providing a common infrastructure for storage and processing of big data.

OSG, as an associated partner will provide interoperability mechanisms for the virtual organisations of the BBMRI competence centre to use OSG resources, and will organise a joint information sharing workshop to discuss interoperability and new technologies that may affect international resource sharing.

TASK SA2.5 MoBrain

(Lead: SURFsara/BCBR, M1 – M30)

Estimated task effort: 59.5PM
The MoBrain CC will lower barriers for scientists to access modern e-Science solutions to simulate life science processes from micro to macro-scales. The CC will build on grid- and cloud-based infrastructures and on the existing expertise available within WeNMR/INSTRUCT and NeuGrid4You. The CC will integrate molecular structural biology and medical imaging services, e.g. Scipion , and data and will kick-start the development of a larger, integrated, global science virtual research environment for life and brain scientists worldwide. The task will deliver a MoBrain integrated infrastructure based on a variety of e-Infrastructure solutions, including grid, cloud and accelerated computing systems accessible through cloud interfaces and a virtual research environment to serve translational research from molecule to brain.

TASK SA2.6 DARIAH

(Lead partner: SRCE/RBI, M1 – M30)

Estimated task effort: 62.5PM
The DARIAH CC aims to widen the usage of the e-Infrastructures for Arts and Humanities research. The CC will develop and provide a workflow-based science gateway based on the generic-purpose WS-PGRADE and gLibrary technologies, adapted and tailored to the needs of users coming from the field of Arts and Humanities. The gateway will provide access and compute services for data residing in distributed grid and cloud storages. The gateway will be validated and enriched with the ‘Multi-Source Distributed Real-Time Search and Information Retrieval’ application (SIR). The CC will engage with Arts and Humanities communities to attract more applications and users to the gateway.

TASK SA2.7 LifeWatch

(Lead partner: CSIC, M1 – M30)

Estimated task effort: 60PM
The goal of the LifeWatch EGI CC is to capture and address the requirements of Biodiversity and Ecosystems research communities. To achieve this the CC will

1. deploy cloud and GPGPU based e-Infrastructure services required to support data management, data processing and modelling for Ecological Observatories,
2. explore possibilities to increase the participation of citizens in data-intensive biodiversity research,
3. facilitate the adoption and exploitation of the EGI infrastructure by the LifeWatch user community.
   

TASK SA2.8 EISCAT_3D

(Leader: EISCAT, M1 – M30)

Estimated task effort: 28PM
The design of the next generation incoherent scatter radar system, EISCAT_3D introduces significant challenges in handling large-scale experimental data which will be massively generated at great speeds and volumes. The CC will build an e-Infrastructure to meet the requirements of the EISCAT_3D data system, will support the EISCAT science community in their acquisition, curation, access to and processing of the data, and will train data scientists who can explore new approaches to solve problems via new data-centric way of conceptualising, organising and carrying out research activities.

TASK SA2.9 EPOS

(Leader: INFN/INGV, M16 – M30)

Estimated task effort: 30.5PM
The task will operate a CC to drive the future design of the use of grid and cloud for the integrated solid Earth Sciences research as part of the European Plate Observing System (EPOS). The CC will

1. identify and validate authentication and authorisation services,
2. will test cloud resources and usage models,
3. provide knowledge transfer services between e-Infrastructure and EPOS communities.
   

TASK SA2.10 Disaster Mitigation

(Leader: AS, M1 – M30)

Estimated task effort: 60PM
The objective of the this CC is to make available customised IT services to support the climate and disaster mitigation researchers to gain a deeper understanding of the most serious natural disasters that affect Asia (e.g. earthquakes, tsunamis, typhoons) and to mitigate multi-hazards via data-intensive, e-Science techniques and collaborations. The task strongly builds on experts from the Asia-Pacific region who will create virtual research environments with embedded services and simulations that enable the sharing of disaster-related data, tools, applications and knowledge among field-workers, scientists, and e-Infrastructure experts, shortening the time they can respond to natural disasters. The CC will have two associated partners, the Leibniz Supercomputing Centre (LRZ, Germany) and University of St. Andrews (UStA, UK) to connect the activities with related projects and initiatives in Europe.

Deliverables

The following gives an overview of deliverables scheduled

Code	Title	Delivery PM	Delivery CM	Delivered date	Status
D6.1	Assisted pattern recognition tools integrated with EGI for citizen science (OTHER)	M09
D6.2	Data repository for DARIAH (OTHER)	M11
D6.3	Production portal for EISCAT_3D (OTHER)	M12
D6.4	Fully integrated MoBrain web portal (OTHER)	M12
D6.5	Final version of Multi-Source Distributed Real-Time Search and Information Retrieval application (OTHER)	M12
D6.6	Data flow handler and basic R tools to integrate and process data from Ecological Observatories on EGI (DEM)	M12
D6.7	Implementation and evaluation of AMBER and/or GROMACS (R)	M13
D6.8	Analysis of requirements on biobank and study workflows (R)	M14
D6.9	web portals for tsunami wave propagation simulations and for WRF-based weather simulation (OTHER)	M14
D6.10	Infrastructure tests and best usage practices for life science service providers (R)	M15
D6.11	Security toolset release for BBMRI-ERIC (OTHER)	M15
D6.12	GPGPU-enabled web portal(s) for MoBrain (OTHER)	M16
D6.13	EPOS EGI pilot incorporating data retrieval, transfer and linkage (DEM)	M18
D6.14	Scipion cloud deployment for MoBrain (OTHER)	M21
D6.15	Demonstrator for ELIXIR workflows implemented in the EGI Federated cloud (DEM)	M24
D6.16	Evaluated cloud environment and demonstrator of analysis workflow for biobank studies (DEM)	M24
D6.17	Production level gateway for Arts and Humanities (OTHER)	M24
D6.18	Report on the installed LifeWatch applications and their usage record (R)	M24
D6.19	EPOS EGI pilot integrating computational resources and services (DEM)	M24
D6.20	Application of the simulation portals for scientific scenario in disaster mitigation (DEM)	M24
D6.21	Second version of enhanced portal for EISCAT_3D (OTHER)	M28
D6.22	Design larger scale multi-hazards simulation attempting to reduce the uncertainty of climate change assessment (DEM)	M29
D6.23	Report on evaluation of EPOS EGI pilot studies (R)	M30

Milestones

The following gives an overview of milestones scheduled

Milestone	Title	Lead-Task	Delivery PM	Delivery CM	Delivered	Status
M6.1	Joint training program for the first period is agreed		M03
M6.2	Security and privacy requirements and secure storage architectural design are agreed		M06
M6.3	Life science requirements analysis and driver use case(s) with implementation roadmap are agreed		M12
M6.4	EPOS requirements analysis and outline of pilot use cases are agreed		M12
M6.5	Joint training program for the second period is agreed		M15

Internal Documents

• Competence centres main page