Plant Science

Katmandoo Workshop

5th March 2008

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Why have Database monitoring

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System with no regular monitoring program

GenotypesFor example Encore,EncEncrEncore_1Encore_1 _F7ENC_1_F7EN-1

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KatmandooA biosciences data management system

• This introduction has been set up as a guide to help you start using Katmandoo

• It will show you how to add and operate some of the operations in Katmandoo, however it is not a complete user guide but an introduction to the management and Field trial data storage system.

• It does not cover all the different tools and options that Katmandoo has.

• To read a more detailed induction please refer to the Help Menu, “Using Katmandoo” a “Quick Start Guide” and the “Reference”

• To enter/import data into Katmandoo the data has to be entered in a certain order so as to enable the data to be stored correctly.

• Some of the data required is only required to be added once at the original setup of the system.

• The general hierarchy order that the data must be added is set out in the Task menu guide.

• The aim of the Quick Start Guide is to work through the order of steps and items that must be added to set

• up and import a designed trial sample measurement and let you export all the relevant data.

• This will give you a general introduction to some of the main features in Katmandoo.

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Login screen

• Enables each user to be setup with own password and security level

• Select Different Data bases• Connect up to MSSQL Server

Two Databases installed • Katmandoo2: is the main starting database with some data

already setup• KatmandooDemo: Used for training purpose

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Main Menu“Finding your way around”

• The Main Menu Bar of Katmandoo with Task, Record, View, Tools, Windows and Help menu items

Navigators• Contact Navigator • Site Navigator • Genotype Navigator • Trial Navigator • Trial AOV Navigator • Quick Search

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Sub System• Sub-system is used in Katmandoo to logically partition data in the

database, typically this would correspond to functional work areas.

Note : Make sure you select a source subsystem when updating new subsystem

Following are some suggestions onlyProject Name

Sub-system Names

Plant Agronomy Barley Agronomy, Canola Agronomy, Lupin Agronomy,

  Wheat Agronomy, Wheat Chemistry etc

Biometric Consulting Pig Trial, Fruit Fly etc

Mango breeding Mangoes, post_harvest_testing

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Adding an Organisation

An organisation is defined as group of company with which contacts or sources of seed are associated

• Depending upon the table it is used, it identifies different type of organisation

• E.g. NSW DPI or DPI&F

Table Name What is Organisation used for?

Trial Unit (Design) Organisation is as sample supplier for the trial units of the trial.

Genotype Organisation is used as Origin of the genotype i.e. the Organisation which owns the genotype.

Contact Organisation is the employer of the contact in this table.

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Location and Virtual Columns

Location

• Location in Katmandoo, it is the location of site, Contact or Meteorology Station

• location information used in Katmandoo are based on the Australia Post Code database

• The location table has a record for Unknown Location

• The Location Latitude and Location Longitude are used by the navigators to perform map-based search in the database

• Useful web Link http://www.ga.gov.au/map/names/

Virtual Columns

• The virtual column, is a Column that is not part of the database structure, it is “a user” added column

Validation rule

• The system uses the validation rule of the column to validate data of each column before storing into the database

Note When updating system Virtual Columns will have to remove “Region” from Met Group Name.

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Contact

• Contact can be Site Manager, Co-operator, Trial Manager, District Agronomist, Laboratory Officer, Research Scientist, Breeder, Biometrician (Analyst) or any who performs tasks which are stored in Katmandoo.

• A contact can be both Site Manager as well as Trial Manager.• A contact can be used as a responsibility or audit trail for the trial or data• The contact table has a record for Unknown Contact (Last Name = Unknown

and First Name = xxxx) which can be used when the contact information is not available, however is best to set up the appropriate contact when available.

Note; Edit Mary Smith Location

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System User, Add System User

• The users are uniquely identified by their user name ( login name) which the user must use along with the password to access Katmandoo.

• User name is case-sensitive and can be up to 16 characters.• Can have Alpha Numeric (A-Z and 0-9) characters only, it must

have at least one Alpha character and one Numeric characters• Recent information such as Logout Time, Sub-system Name etc

are saved as user preference• In Katmandoo, Authorised System Resource is used to grant

security level to system groups to access the system resources.• It defines which users, can have permission to use or edit which

system resources.

Note: Update Authorised System Group for selected user, select System group.

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Trial

Trial is a comparative experiment established to test the effectiveness of various treatments.

There are following three parts of trial information stored in the database.• Trial type identifies a type of trial that are done to evaluate the

genotype. (Genotype and Crop Genus must be added prior to trial data being added)

• Trial Header information (such as Site, Year, Trial Type, Trial Number, Trial Manager etc) of the trial is stored in this part of the database.

• Trial Design: This part stores information (such as treatment, design parameters) of each trial unit of the trial.

• Sample Measurement: This part stores sample measurement of each trial unit (i.e. trial design) of the trial.

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Crop Genus

• Genus is defined in Katmandoo as a taxonomic category ranking below a family and above species and generally consisting of a group of species exhibiting similar characteristics

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Genotype

• In Katmandoo Genotype uniquely identifies each individual organism in the database based on combination of Genus, Genotype Name and Selection History.

• Genotype Name uniquely identifies a genotype and it can not be changed once the genotype has dependant data

• Genotype Name is checked in the Genotype Alias table to ensure that it does not exist as an alias.

• Genotype and Pedigree management system PBMASS

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Trial Type

• Trial type identifies a type of trial that are done to evaluate the genotype. It is defined for each Sub-systems.

• It can be a “Characterisation” trial

• A generation stage trial, S1 S2 S3

• Or a certain type of Pathogen trial

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Trial Header information, Site and Site year data

• Site is defined in Katmandoo as the place or location where the trial or experiment is conducted.

• It can be a farm, research station or laboratory etc which are identified by Site Type.

• Site Year, is the year which the trial was carried out. If this is not define the current year is used

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Trial Design

• Stores information of the unit position Rep and Genotype.

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Virtual Columns Data Trial design

• If require other design parameters can be user added columns or virtual columns.

• As default, Column, Row and block are not added as system column.

• We will add these as Virtual columns.

• Import Trial Design

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Import Trial Sample Measurement Data

• The Sample measurement table stores the measured data for an individual trial unit (sampling unit) for a given sample type and variates.

• Traits which have been measured must be added to the system before we can import sample measurements.

• Use a standard set of traits

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Import Traits and Trait Validation Rules

• The Trait is an attribute of the Trial.

• It is a measured quantity of the individual trial unit (sampling unit) for a given sample.

• Each Trait can have its own validation rule.

• Can be Sub system dependant

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Wispy Veil Nebula

The interplay of interstellar gas and a supernova led to the formation of the Veil nebula seen here.Also known as NGC 6992, the Veil nebula sits about 2,000 light-years from Earth in a region known as the Cygnus Loop.As ejecta from the supernova moved through space, it flattened clouds of gas and dust to form the intricate, colourful structures seen here.This image was obtained by Jean-Charles Cuillandre using the CFH12K CCD mosaic camera and the Canada-France-Hawaii Telescope, atop Mauna Kea in Hawaii.