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Short description

Towards an e-infrastructure for plant phenotyping

Involved in EOSChub as a EAP.

In recent years, technological progress has been made in plant phenomics (major improvements concerning imaging and sensor technologies). High-throughput plant phenotyping platforms now produce massive datasets involving millions of plant images concerning hundreds of different genotypes at different phenological stages in both field and controlled environments. Networks of sensors also measure environmental conditions in real time. The ongoing robotization of experimental processes foreshadows an explosion in the volume and complexity of the data produced by the different research facilities. There is a need for an integrated and federated solution for data management and data processing.

Type of community

Thematic Services - Plant sciences, agricultural sciences

Community contact

Vincent Nègre, INRA – France, vincent.negre@inra.fr

Interviewer
Date of interview
Meetings
Supporters

Shepherd: Nicolas Cazenave, CINES – France, cazenave@cines.fr


User stories

정보
titleInstruction

Requirements are based on a user story, which is  is an informal, natural language description of one or more features of a software system. User stories are often written from the perspective of an end user or user of a system. Depending on the community, user stories may be written by various stakeholders including clients, users, managers or development team members. They facilitate sensemaking and communication, that is, they help software teams organize their understanding of the system and its context. Please do not confuse user story with system requirements. A user story is an informal description of a feature; a requirement is a formal description of need (See section later).

User stories may follow one of several formats or templates. The most common would be:

"As a <role>, I want <capability> so that <receive benefit>"

"In order to <receive benefit> as a <role>, I want <goal/desire>"

"As <persona>, I want <what?> so that <why?>" where a persona is a fictional stakeholder (e.g. user). A persona may include a name, picture; characteristics, behaviours, attitudes, and a goal which the product should help them achieve.

Example:

“As provider of the Climate gateway I want to empower researchers from academia to interact with datasets stored in the Climate Catalogue, and bring their own applications to analyse this data on remote cloud servers offered via EGI.”


No.

User stories

US1


US2


...



Use cases

정보
titleInstruction

A use case is a list of actions or event steps typically defining the interactions between a role (known in the Unified Modeling Language as an actor) and a system to achieve a goal.

Include in this section any diagrams that could facilitate the understanding of the use cases and their relationships.


..

Step

Description of action

Dependency on 3rd party services (EOSC-hub or other)

UC1

UC2

...

Image Added

The PHIS information system and the Galaxy environment will be deployed on EGI virtual machines. The storage layer is based on the existing FranceGrilles iRODS infrastructure. An authentication layer based on the EGI check-in serviceand a computing layer provided with the EGI Notebooks servicewill be added.


UC2

Image Added

Compared to the previous pilot the storage layer is based on the B2SAFE service supported by the EGI infrastructure.


UC3

Image Added

Compared to the previous pilot the storage layer is based on the Data Hub service supported by the EGI infrastructure.




Requirements

Technical Requirements


정보
titleInstruction

- Requirement number: Use numbers RQ1, RQ2, RQ3, ...
- Requirement title: Use a short but descriptive title. Use the same title in the Jira ticket 'Summary' field
- Link to requirement JIRA ticket: Open a ticket in <this JIRA queue  https://jira.eosc-hub.eu/projects/EOSCWP10/issues/EOSCWP10-4?filter=allopenissues> (click on 'CREATE' button in the middle-top of JIRA)
- Source use case: Refer back to the use cases above (UC1, 2, ...)



Requirement number

Requirement title

Link to Requirement JIRA ticket

Source Use Case

Example

EOSC-hub to provide an FTS data transfer service

Jira
serverEGI JIRA
serverId89b2a620-0cec-34da-8cfe-a343203be114
keyEOSCWP10-21

UC1

RQ1

EGI Cloud Compute & Cloud Container Compute - EGI/CESNET - , EGI/IN2P3



RQ2

EGI Notebook - EGI/EGI.eu



RQ3

B2SAFE - EUDAT/CINES

RQ4EGI DataHub -  EGI/CYFRONET

RQ5Check-in - EGI/GRNET

RQ6B2ACCESS - EUDAT/Juelich

RQ7B2HANDLE - EUDAT/GRNET


Capacity Requirements


EOSC-hub services

Amount of requested resources

Time period

RQ1

CESNET-MCC: 6x4CPUs with 6x32GB RAM (including support for a Oneprovider)

IN2P3-IRES: 2VMs with 32GB RAM for pilot and Oneprovider VM with 8 vCPU, 32GB RAM with SSD


RQ2

EGI: community-deployment for notebooks for 4 concurrent users (2 vCPUs cores, 4GB of RAM and 40GB of storage per notebook)

RQ3

10 TB safe storage

RQ4

10 TB on DataHub Oneprovider, user support


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