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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

Instruction

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

As an IT architect, I contribute to provide an european e-infrastructure for high throughput plant phenotyping data management. Such an objective will not be possible without the support and services offered by EGI fundation.


The open-source Phenotyping Hybrid Information System PHIS (Neveu et al. 2019 New Phytologist, 221: 588–601) has been proposed to organize these data and make them accessible and reusable to a larger scientific community.


Three use cases have been proposed to explore which EGI services are the most appropriate to support an european plant phenotyping e-infrastructure.



...



Use cases

Instruction

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

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 service and a computing layer provided with the EGI Notebooks service will be added.


UC2

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


UC3

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




Requirements

Technical Requirements


Instruction

- 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

Services

Link to Requirement JIRA ticket

Source Use Case

Example

EOSC-hub to provide an FTS data transfer service


EOSCWP10-21 - Getting issue details... STATUS

UC1

RQ1

Deploy virtual machines :
CESNET-MCC (or other sites if more performant), vo.emphasisproject.eu: 1VM ; 4CPUs with 32GB RAM; 80GB of storage for the system + 100GB of additionnal storage (Mongodb)

EGI cloud compute

EOSCSO-702 - Getting issue details... STATUS

UC1

RQ2

Install PHIS information system on the VMs

PHIS team


UC1

RQ3

Connect iRODS data with PHIS IS

PHIS team


UC1
RQ4

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

EGI

EOSCSO-703 - Getting issue details... STATUS

UC1
RQ5

Data available in Notebooks

PHIS team
UC1
RQ6

Deploy Galaxy environnements

4 concurrent users

Galaxy.eu

EOSCSO-704 - Getting issue details... STATUS

UC1
RQ7

Provide persistent identifier to the data

B2HANDLE EUDAT/GRNET

EOSCSO-705 - Getting issue details... STATUS

UC1
RQ8

Federated authentification should be integrated within PHIS IS.

check-in EGI/GRNET

EOSCSO-706 - Getting issue details... STATUS

UC1

RQ9

Deploy virtual machines :
CESNET-MCC (or other sites if more performant), including support with B2HANDLE vo.emphasisproject.eu: 1VM ; 4CPUs with 32GB RAM; 80GB of storage for the system + 100GB of additionnal storage (Mongodb)

EGI cloud compute

EOSCSO-709 - Getting issue details... STATUS

UC2
RQ10

Install PHIS information system on the VMs

PHIS team


UC2
RQ11

Provide 10TB of storage in B2SAFE

B2SAFE – EUDAT/CINES

+ other location for replication ?

EOSCSO-710 - Getting issue details... STATUS

UC2
RQ12

Connect PHIS IS with B2SAFE

B2CONNECT – EUDAT/Juelich

PHIS team


UC2
RQ13

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

EGI

EOSCSO-711 - Getting issue details... STATUS

UC2
RQ14

Provide persistent identifier to the data

B2HANDLE EUDAT/GRNET

EOSCSO-712 - Getting issue details... STATUS

UC2
RQ15

Data available in Notebooks

PHIS team


UC2
RQ16

Deploy Galaxy environnements

4 concurrent users

EGI

EOSCSO-713 - Getting issue details... STATUS

UC2

RQ17

Provide virtual machines :

IN2P3-IRES

vo.emphasisproject.eu
- 1VM  for PHIS IS; 4CPUs with 32GB RAM; 80GB of storage for the system + 100GB of additionnal storage (Mongodb)

- Oneprovider VM with 8

vCPU, 32GB RAM with SSD

EGI cloud compute

EOSCSO-714 - Getting issue details... STATUS

EOSCSO-715 - Getting issue details... STATUS

UC3
RQ18

Install PHIS information system on the VMs

PHIS team


UC3
RQ19

Provide 10TB of storage in EGI DataHub

EGI

https://jira.egi.eu/browse/EOSCSO-719UC3
RQ20

Support to Connect PHIS IS EGI DataHub

EGI


UC3
RQ21

Provide persistent identifier to the data

B2HANDLE EUDAT/GRNET

EOSCSO-717 - Getting issue details... STATUS

UC3
RQ22

Deploy Jupyter Notebook :
community-deployment for notebooks for 4 concurrent users (2 vCPUs

cores, 4GB of RAM and 40GB of storage per notebook)

EGI

EOSCSO-717 - Getting issue details... STATUS

UC3
RQ23

Data available in Notebooks

PHIS team


UC3
RQ24

Deploy Galaxy environnements

4 concurrent users

EGI

EOSCSO-718 - Getting issue details... STATUS

UC3