CIP – RIU selected activities Information systems for crop and genebank data management Edwin Rojas, Reinhard Simon ICIS workshop 2006, CIMMYT.

CIP – RIU selected activities

Information systems for crop and genebank data management

Edwin Rojas, Reinhard Simon

ICIS workshop 2006, CIMMYT

Adopted from: W. Busch:Max und Moritz, 1865

Problematic situation Hypothesis Data capture

Data/information management Analytical processing Standardized reports

Publication for diverse uses/uptake

Research

Research informatics

The Research Informatics story

Presentation to CIP annual meeting 2004Reinhard Simon

Selected activities

• Workflows• CIPSTATIONS• CIPPEX• CIPSTAT• LIMS for molecular marker lab and “quality” lab• CIPTCL• DIVA-GIS• Data warehouse for access and quality control• Software development and collaboration tools• Outlook – harmonization with ICIS database schemes and

tools

Workflows

• Workflow motor: (Edwin teniamos un slide aqui de esto? Si no – use el siguinte como ejemplo.)

+MS

Request

Process: Distribution

Scientist

Revise

Prepare Documents

If In-Vitro Plants

Request Propgation If Tubers

ADU IVU Inv.ADU HQUSENASA

Revise Documentation

If Hybrid True Seed

If cuttings (Only for Ipomoea)

Prepare DocumentsAnd Package

. MTA – (designated, no designated)

. Permiso de importación

. Condiciones fitosanitarias

SupplyPlantlets

Treat Seed Supply Plantlets

Check ELISA NASH Results

Request Phytosanitary Certificate

Send Documents And Package

Application

Sign MTA

If Tubers

If Hybrid True SeedIf Available

If no Available

VerifyAvailability

Lab.ADU

A

RequestExport

A

If Black Box

Curator

If TrueSeedReserve True Seed

Register in Distribution Database

A

Deliver Material

Propagated

GADC

Approve

NationalDistribution

A

B

InternationalDistribution

NacionalDistribution

B

AB

AB

AB

AB

B

Reject

International Distribution

Reserve True Seed Hybrid

Reserve Tuber

Check ELISA NASH Results

Receive Phytosanitary Certificate

AB

NotifyMaterial

Send Materials to ADU

Request Reserve

CIPSTATIONS

CIPPEX

• Based on tool for project management (PHProjekt)

• Phenotype data management inspired by ICIS

• Genotype data management inspired by GERMINATE

Project and experiment management:

PHProject

CIP databases:passport, charact, eval.

data

CIP-WorkflowEngine

Resource scheduler:MRBS

Breeding data:adaptations from

ICIS

Molecular data:adaptations from

Germinate

ExperimentalDesign

Input parameters

Add Factors

Add Variables

Field Book

Analysis Modules

Diagram of the Experimental Design & Analysis Generator Module for the CIP-PEX System

Statistical GISDataware

House

Experimental Map

–RCBD–Plot Design–Lattice….

RegisterExperiment

CentralDatabase

Data Capture

Presentation to CIP annual meeting 2004Reinhard Simon

Potato Sweet potato ARTC

LIM

AJU

NIN

In vitro Chamber

Cold Chamber for Seeds

Cold Chamber for Tubers

Greenhouses

Field

CIP Mobile/Barcode Infrastructure Status 2005-12Barcode Pockets LAN Wireless

In vitroChamber

Greenhouses

Field

Storage Room

Areas

Notes: The barcode includes the use of labels, thermal printers and reader guns. The symbol “ – ” means that the specific crop does not are the respective facility.

Pending

Pending

Pending

Pending Pending

Design completed (by ITU)

Pending

Pending Pending

Pending Pending Pending Pending Pending Pending

Pending Pending Pending

Pending Pending Pending

Pending

Pending

Pending

Pending Pending Pending

Pending Pending Pending

Pending Pending Pending

Pending Pending PendingPending

Pending Pending

Pending

Pending Pending

2000

First Pilot in In vitro Potato

2003 January

InfrastructureDesign for all In vitro & Greenhouse

2003 November

Infrastructurefor all In vitro & Lima-Greenhouse

2004

Applications

2005

Improve Infrastructureand Wireless Covertures (from

11MB to 54 MB)

Pending

Laboratories (Molecular/Processing)

Pending Pending

PendingPending Pending Pending Pending PendingPending

Pending Pending Pending

PendingLaboratories Pending Pending Pending

Pending

Pending Pending

CentralDatabase

Environment Experiment Data Capture with Mobile Device

Performance IndicatorsIn-Vitro Genebank Activities

Barcode and Mobile Solution Technologies

Prior to Implementation Technologies

Locate a material by any staff 5 seconds 3600 seconds

Create a list for a “grid” of 15 entries 30 seconds 90 seconds

Print 90 labels for a “grid” 20 seconds 120 seconds

Clients request germplasm availability for distribution

10 seconds (by on-line web) 1 or 2 days (by email)

Inventory report for stock and locations

1.5 weeks by 2 staff 6 weeks by 2 staff

Migration to barcode100% of germplasm use autoadhesive

labeled with barcode identification100% of germplasm used paper

labeled and eye identification

CIPSTAT

• Web interface for users (via web forms) and software (via WSDL web services) to statistical routines

• Statistical routines packaged in a library ‘Agricolae’ written in R

• Presently access to 29 routines covering frequently used at CIP for experimental planning and analysis

CIPSTAT – screenshot

CIPSTAT – screenshot

Interface for tools via WSDL – e.g. Taverna

CIPPEX – LIMS molecular data

CIPTCL – LIMS for GR

In vitro – quality check

DIVA-GIS overview

Data warehouse

• MS based solution for genebank and GADC

• OS based solution for breeding experiments (and others)

Data warehouse –CIP intranet

Data warehouse – examples from

OS solution• Edwin: lista

Software development practices

• Use of RUP documents for planning and documentation

• Languages: VB/.NET; Java, PHP, R, SAS, (JavaScript, Delphi, Perl, C, C++, Fortran, Python)

• Standardized on Eclipse editors for Java, PHP, C, R

• (use of Tortoise for CVS access for VB, etc)

• Use of CVS and Subversion for all software development

• JIRA (Issue management), Confluence (Wiki)

• Evaluating: Tools for automating builds and software development quality control

Outlook

• Stronger collaboration with ICIS team for better harmonization of tools developed at CIP for potato and sweetpotato data management

• Statistical quality control tools for process management

• Integration of ontologies for data capture and quality control