CIP Genebank IT Platform till 2019

1. P a c i f i c C o m m u n i t y ( S P C ) - S U V A F I J I
September, 2019
CIP Genebank IT Platform
Exchange of technologies and best practice in barcoding and data management
Edwin Rojas (CIP)
IT Specialist & GRIN-Global Administrator

2. Agenda: CIP Genebank IT Platform
• CIP Genebank Overview
• CIP Genebank
• Environments
• Process
• LIMS (Laboratory Information Management System)
• Data flows
• Improving the Genebank Data Management
• Use international standards to interoperate with others
• Use best practices to get more efficiencies
• Barcode KIT: Benefits and Components
• Use Cases for Barcode KIT
• In Vitro Collection
• Herbarium Collection
• Cryo and DNA Collection
• Seed Collection
• Clonal Collection in Greenhouse
• Field Collection
• CIP Genebank Platform

3. CIP Genebank Overview
ISO 17025 Accreditation revalidated till 2008 every year
CIP has given the users of the Genebank a visible
assurance of the quality of the germplasm being distributed.
CIP is the custodian of one
the world’s largest in vitro
collection for potato,
sweetpotato and ARTC.
CIP is the custodian of
one of the largest clonal
plant cryobanks.

4. CIP Genebank Overview
Genebank Environments
Cold Chambers/
Laboratories
Greenhouses Fields
Genebank Mobility  Promote Massive Mountains of IT Innovations

5. CIP Genebank Overview
CIP Genebank Process
Outside CIP
Genetic
Material
Client
Inside CIP Genebank
Pathogen
Elimination
Pathogen Tested
Conservation
Distribution
Post Entry
Quarantine
Characterization
Evaluation
Outside CIP
Genebank
Ex situ
In situ
Cryo
Herbarium
DNA
Safety backup
Blackbox
Collection:
Wild species
Landraces
Improved lines
Breeding material

6. CIP Genebank Overview
CIP Genebank Process and LIMS
Outside CIP
Genetic
Material
Client
Inside CIP Genebank
Pathogen
Elimination
Pathogen Tested
Conservation
Distribution
Post Entry
Quarantine
Characterization
Evaluation
Outside CIP
Genebank
LIMS: Laboratory Information System
LIMS: CIPTCL, CIPSER, CIPVIR, CIPGADC, CIPCROSS
GRIN-Global: Public Web GG, Curator Tool + Wizards
Passport and Attributes Search Tool
In Vitro = CIPTCL
Seed = CIPSER
Herbarium = CIPSER
DNA = CIPSER
Cryo = CIPCRYO
Chemical & supplies = CIPKardex
Washing & sterilizing vessels
New CIPGADC
Crossing plants = CIPCROSS
Public Web GRIN-Global
New CIPGADC
CIPTCL
Chemical & supplies = CIPKardex
Washing & sterilizing vessels
In Vitro = CIPTCL
Chemical & supplies = CIPKardex
Washing & sterilizing vessels
CIPVIR = Pathogen tests
CIPGADC
CIPTCL
Chemical & supplies = CIPKardex
Washing & sterilizing vessels
CIPVIR = Pathogen tests
Curator Tool GRIN-Global
In Vitro = CIPTCL
Chemical & supplies = CIPKardex
Washing & sterilizing vessels
In Vitro = CIPTCL
Seed = CIPSER
DNA = CIPSER
Cryo = CIPCRYO
Curator Tool GRIN-Global

7. CIP Genebank Overview
CIP Genebank Dataflow
CIP Genebank Database Other CIP Databases International
Databases
GRIN-Global
Database
Support Database
(LIMS and other data types)
1. FAO WIEWS
2. GLIS
3. EASY-SMTA
4. Genesys-PGR
5. Svalbard Global Seed Vault
1. Finance Database
2. Plant Pathology Database
3. Breeding Database

8. Elevate to international standards the Genebank data management.
Outside the Genebank (Interoperate with others)
Genebank
International Data
Repositories
Recipients /
Institutions
Publication: Data Transfer
Distribution: PGRFA & and data Transfer
• Genesys-PGR
• FAO GLIS
• FAO WIEWS
• EASY-SMTA
• Breeder
• Curator
• Farmer
• Researcher
• MCPD Descriptors
• DOI GLIS
• SMTA
MCPD descriptors: https://www.bioversityinternational.org/e-library/publications/detail/faobioversity-multi-crop-passport-descriptors-v21-mcpd-v21/
Genesys-PGR: https://www.genesys-pgr.org/
FAO GLIS: https://ssl.fao.org/glis/
FAO WIEWS: http://www.fao.org/wiews/background/en/
EASY-SMTA: https://mls.planttreaty.org/itt/

9. Elevate to international standards the Genebank data management and
use the best practices.
Inside the Genebank (Improve operations)
Quality Management
System (QMS)
Best Practices
Get more efficiency
ISO 17025 : 2017
• Ensure quality results
• Requires data security
• Requires data integrity
• Requires traceability
• Document procedures
• Barcoding labelling in all procedures
• Print with thermal transfer
• Data collection with mobile computers
• GRIN-Global platform
• PDCI
ISO 17025:2017: https://www.iso.org/obp/ui/#iso:std:iso-iec:17025:ed-3:v1:en
GRIN-Global: https://www.grin-global.org/
PDCI: https://doi.org/10.1017/S1479262111000682
Genebank
Improving processes for client satisfaction

10. Barcode KIT
Needs and Benefits to Develop More Efficiencies
• Capture data where activities
occur
• Use mobile computers
• Develop Apps
Improve
Data
Collection
• User barcode Labels
• Labeling all accessions in all
procedures
• Use scanners instead reading
• Use thermal printers instead
writing
Improve
Germplasm
Identification
• Connect online to central
repository
• Use WiFi inside laboratories
• Allow query inventories and status
with related information's
Improve
Germplasm
Tracking and
Monitoring

11. Barcode KIT
Components Evolution
2000
First pilot
In Vitro
2003 Jan
WiFi
in Vitro &
Grrenhouses
2003 Nov
App & Hardware
migration
2004
More Mobile Apps
2005-2006
Improve Hardware
2010
Improve Hardware,
WiFi, barcodes &
more Apps
2012-2015
Extend barcodes
& Mobile to Regions
& Other CG Centers
2016
Pilot GG &
Cross Platform
Apps
2017
Launch GG
2017-2018
Start Android
& TabletPC
CIP Genebank Hardware Platform
30 PocketPC + 5 TabletPC
12 Desktop Barcode Printers
7 Mobile Barcode Printers
7 Handheld Scanners
1 Million Labels per year

12. Mobile
Hardware
Platform
Barcode KIT
Components
Rugged devices supporting IP Norm:
• Complete protection against contact
• Protections from infiltration
• Protection from dust
• Protection from dripping water
• Protection from sprayed water
• Protection from splashed water

13. Barcode KIT
Components - PocketPC
Product: Zebra TC75
• Manufacture: Zebra
• Rugged device with IP65
• Scanner incorporated
• WiFi + Bluetooth
• Camera 13 MP
• GPS
• Android 5 Lollipop or Android 7 Nougat
• CPU 1.8 GHz – 64 bit
• Memory 4 GB RAM/32 GB Flash
• Display 4.7 inches (1280 x 720 MP)
• Cost 3000 USD
• Programmed obsolescence: 5 years

14. Product: Zebra ET50
• Manufacture: Zebra
• Rugged device with IP65
• Scanner incorporated
• WiFi + Bluetooth
• Camera 8 MP
• GPS
• Windows 10
• CPU 1.59 GHz – 64 bit
• Memory 4 GB RAM/64 GB Flash
• Display 8.3 inches (1920 x 1200 MP)
• Cost 3500 USD
• Programmed obsolescence: 5 years
Barcode KIT
Components - TabletPC

15. Product: Handheld Scanner
Manufacture: Zebra
Model: DS6707SR
Classification: IP41
Barcode KIT
Components – Barcode Scanners
Product: Handheld Scanner
Manufacture: Zebra
Model: LS3578-ER
Classification: IP65

16. Product: Mobile Printer
Manufacture: Zebra
Model: ZQ500
Classification: IP54
Print Technology: Direct Thermal
Language Printing: ZPLII, CPCL
Product: Desktop Barcode and RFID Printer
Manufacture: Zebra
Model: Series ZT400
Classification: Rugged metal frame and case for
demanding activities
Print Technology: Direct Thermal or Thermal Transfer
(to produces longlife image stability)
Language Printing: ZPLII, EPL,…
Barcode KIT
Components – Barcode Scanners

17. Use barcode 2D symbologyes: Data Matrix or QR
Data Matrix
A Data Matrix Code is a two-
dimensional (2D) code that consists of
black and white modules. Capacity to
recover 20-30% of data
QR
A QR Code is another type of 2D code
that consists of black modules arranged
in a square pattern on a white
background. Capacity to recover 20-30%
of data
Barcode KIT
Components – Barcode

18. Stick-ins Label
(Pointend end Label)
Self-tie Label
Self Adhesive Label
Barcode KIT
Components – Labels

19. Pre-cut Self
Adhesive Labels
Self-Tie
Labels
Pointed End
Labels
Continue Self
Adhesive Labels
Barcode KIT
Components – One printer model for different label layouts
Pre-cut Self
Adhesive Labels

20. Stick-ins Label
(Pointend end Label)
Self-tie Label
Self Adhesive LabelProduct: Ribbon Wax (20USD)
Model: 5319 PERFORMANCE
Manufacture: Zebra Product: Ribbon Wax/Resin, 3200 PERFORMANCE (35USD)
Product: Ribbon Resin, 5095 PERFORMANCE (65USD)
Manufacture: Zebra
Product: Ribbon Wax (20USD)
Model: 5319 PERFORMANCE
Manufacture: Zebra
Barcode KIT
Components – Ribbon

21. Use Cases for Mobile Apps - Germplasm Collections
In Vitro Conservation
- Print instead writing on labels to eliminate pen-based procedures
- Scan instead reading labels to eliminate delays and reduce human errors

22. Use Cases for Mobile Apps - Germplasm Collections
In Vitro Conservation

23. Use Cases for Mobile Apps - Germplasm Collections
In Vitro Conservation
Validate that In one row of the rack exists only one clone.
Detailed Specifications:
https://research.cip.cgiar.org/confluence/x/HAEBBQ

24. Use Cases for Mobile Apps - Germplasm Collections
Cryo Conservation

25. Product: Synthetic Label
Manufacture: Zebra
Print method: Direct Thermal without Ribbon
Use Cases for Mobile Apps - Germplasm Collections
Cryo Conservation

26. Product: Label 8000T Cryocool (350 labels to 100USD)
Manufacture: Zebra
Print method: Thermal transfer
Detailed Specifications:
https://research.cip.cgiar.org/confluence/x/FwCn
Use Cases for Mobile Apps - Germplasm Collections
Cryo Conservation

27. Product: Label 8000T Cryocool (350 labels to 100USD)
Manufacture: Zebra
Print method: Thermal transfer
Polypropylene label with a cold-temp permanent acrylic
adhesive that offers extremely low-temperature performance down to -320° F.
Cryogenic applications involving a deep freezing process; medical labs, hospitals.
Use Cases for Mobile Apps - Germplasm Collections
DNA Conservation

28. Use Cases for Mobile Apps - Germplasm Collections
Herbarium Collection

29. Use Cases for Mobile Apps - Germplasm Collections
Herbarium Collection

30. Use Cases for Mobile Apps - Germplasm Collections
Seed Collection

31. Use Cases for Mobile Apps - Germplasm Collections
Clonal Collection in Greenhouses
Detailed Specifications:
https://research.cip.cgiar.org/confluence/x/WQEBBQ

32. Use Cases for Mobile Apps - Germplasm Collections
Crossing Plants in Greenhouses for Wild Crops

33. Use Cases for Mobile Apps - Germplasm Collections
Field Collection

34. Use Cases for Mobile Apps – Laboratory Support
Chemicals and supplies Management

35. Use Cases for Mobile Apps – Laboratory Support
Chemicals and supplies Management

36. Use Cases for Mobile Apps – Laboratory Support
Chemicals and supplies Management

37. Use Cases for Mobile Apps – Laboratory Support
Laboratory Space Reservation & Washing Tube Stocks

38. Use Cases for Mobile Apps – Laboratory Support
Laboratory Space Reservation & Washing Tube Stocks

39. CIP Genebank IT Platform
Repositories
Identification
Components
Data Systems
Types
Data System
Groups
Genebank CIP Genebank
In-House
Systems
Reporting
LIMS Core
Process
LIMS Support
Process
GRIN-Global
System
Core Process
Barcode Labels, Mobile Computers, Mobile Apps, Printer/Scanners, WiFi
Other Databases
(Internal, National, Regional
and International)
Genebank Databases
GRIN-Global Corporate

40. CIP Genebank IT Platform
GRIN-Global Data Types

41. CIP Genebank IT Platform
GRIN-Global Modules
Curator Tool
(PC)
Search Tool
(PC)
Public Website
(Browse)
Admin Tool
(PC)
Updater Tool
(PC)
Web Server
Database Server

42. CIP Genebank IT Platform
In-House LIMS
In Vitro
Collection
(CIPTCL)
Cryo Collection
Chemical &
Supplies
(CIP-Kardex)
Washing &
Sterilizing
Genebank Database
Crossing
Plants
(CIPCROSS)

43. The International Potato Center (known by its Spanish acronym CIP) is
a research-for-development organization with a focus on potato, sweetpotato,
and Andean roots and tubers. CIP is dedicated to delivering sustainable
science-based solutions to the pressing world issues of hunger, poverty,
gender equity, climate change and the preservation of our Earth’s fragile
biodiversity and natural resources.
www.cipotato.org
CIP is a member of CGIAR
CGIAR is a global agriculture research partnership for a food secure future. Its
science is carried out by the 15 research centers who are members of the
CGIAR Consortium in collaboration with hundreds of partner organizations.
www.cgiar.org