Importing Experiments

When starting with AGROBASE Generation II, you probably have data from previous years, typically in Excel, and would like to import that data.  You can import one or many different experiments from an Excel file, or a multi-location experiment ("trial") with entries ("treatments") across several locations. Imports can also be done with text (CSV), dBASE and a few other file formats, but in this tutorial we will demonstrate the file import with Excel. Any treatments, traits, or locations being imported with the experiment, but not known to the research group will also be automatically updated in the research group. The tutorial will also show how the research tree explorer is then updated.

Duration: 8m57

Importing Treatments

Treatments (or varieties, or hybrids, or entries, etc.) - whatever is planted in an experiment or nursery or is a factor in an experimental design - may be entered into AGROBASE three ways: (1) Import from an external file, such as in Excel, as will be shown in this tutorial (2) Enter directly via the Treatments Viewer on the Research Tree Explorer (3) Indirectly when importing experiments new to the research group, wherein any treatments new to the research group will be automatically added during the import.

Duration: 8m03

Creating Traits

You can create and define traits or "variables" unique to your research program – this is fundamental in order to use AGROBASE Generation II. This tutorial will give the “rules” for valid trait names, their abbreviations, and other attributes. Trait types are numeric, character, date, date time, logical, integer, and double (double precision for numeric data). You can also import a list of traits (File->Import->Traits) and related information from an Excel sheet instead of creating them directly in a research group as in this tutorial. When you import new experiments or nurseries, any new traits can also be added to the research group in the process - you don't have to create them beforehand.

Duration: 6m06

Managing Traits

Traits can be renamed, resized, undergo type conversion (character to numeric, for example), their properties changed, grouped or re-grouped and more. If the same data is stored under two or more different trait names, which is not ideal since a relational database expects unique trait names; you can rectify this by storing the data under one trait name. All these changes will be done globally throughout the entire research group. Whenever trait names are changed, all the experiments, nurseries, means, etc. will display data with the new trait name.

Duration: 7m39

Creating Experiments

This tutorial will demonstrate the creation of experiments via randomizations for the Randomized Complete Block, Split Plot, and Alpha (Generalized Lattice) experimental designs. There are many more types of designs available within AGROBASE Generation II, including some non-replicated designs. In order to create a new experiment, you must first have a list or group of treatments (varieties, factors, hybrids, etc.) to be randomized and at least one location defined within your research group.

Duration: 8m10

Managing Trials

Trials are comprised of experiments at different locations. You can only perform a multi-location analysis of variance, view means across locations, or run genotype x environment analyses from an open trial or trial means. But if you import a trial through separate spreadsheets for the locations, how then do you "cut and paste" the locations together to make a trial? Or when a trial is randomized and later you need to add (or remove) a location, how do you change the trial? This is all done with the Trial Manager, as we will show in this tutorial.

Duration: 4m38

Defining Locations

Location names are required in AGROBASE Generation II. For example, you cannot create an experiment or prepare a nursery without a location name. Location names can refer to sites, environments, or research stations, for example - wherever you will locate or plant an experiment or nursery. Location names can be defined by entering them directly, as shown in this tutorial), by addition to the research automatically upon importing a new experiment or nursery (see tutorials on importing experiments or nurseries), or by importing location names from an Excel sheet.

Duration: 12m47

Importing Data With Special Excel Files: Overview

For experiments or nurseries created or imported into AGROBASE Generation II, there are two main methods to import data into those experiments or nurseries. This tutorial demonstrates the fastest and most efficient method, using special Excel (or Calc for OpenOffice users) files that have the unique plot number from the research group imbedded within the spreadsheet for each record. With a few restrictions on the usage of such spreadsheets, you can then import your data back into the research group with only a few mouse clicks. Even for many experiments at the same time, or an entire location, and many thousands of data points. This is a powerful feature that you will want to use as often as possible.

Duration: 6m26

Importing Data By Relation

You can import data into an experiment, trial or nursery that was created in, or imported into, AGROBASE Generation II. This tutorial will demonstrate an import method that uses an "index" for a relational connection to match the import records with those in the relational database. A typical index would use plot numbers, or the experiment name plus the plot numbers. Fields with data for import must exist in the experiment or nursery. You will also see how to import data by relation for an entire trial, location, or any group of experiments or nurseries. With some planning, you can import many thousands of data points into Generation II and save time using import profiles or templates. See also another tutorial that shows how to use special Excel files for a different import methodology.

Duration: 15m28

Viewing Data

Accessing and viewing your data is done easily from the research tree explorer. You can view experiments, for example, like an open spreadsheet. This tutorial will show you how to adjust the displayed columns or fields, sort, use filters and logical expressions, and many of the other capabilities for viewing data.



Duration: 24m37

Data Transformations I

Inevitably, your data must be transformed or you need to make some calculations. For example, converting yield data as grams per plot to tons per hectare. Data transformations, or calculations, can be achieved several ways. In this tutorial, we will look at the Edit->Transform Field Data tool which works for experiments, nurseries, treatments, parents, populations, crosses, and more. Here, the newly transformed data will be stored in an existing field. This tutorial gives examples of numeric and character data transformations, some commonly used logical expressions and functions, the scope and context of transformations, and also data transformations within labels or reports.



Duration: 15m25

Data Transformations II:Using Calculated Traits

The first tutorial on data transformations covered the Edit->Transform Field Data method which directly replaced the contents of a data field. In this tutorial, we will show you how to create and use calculated traits, wherein data from other fields is used in calculations to store the new values in the new calculated traits. Calculated traits are computed every time an experiment or nursery is opened. So, if any of the data used in the calculated trait has been changed, correct and updated values will appear for the calculated traits.



Duration: 13m16

Planting Plans

Experiments, trials and nurseries are eventually planted in the field in plots, or maybe in a greenhouse in pots. The entries or genotypes are typically assigned to plot (or pot) numbers and often referenced by ranges (groups of plot planted side by side) and rows (or "columns" of plots perpendicular to ranges). The experiment planting plan tool generates field or plot plans, seed packet planting lists, and more, for laying out and planting experiments and nurseries.

Duration: 25m53

Perennial Experiments or Nurseries

Data might be taken over several or many years from the same plots, such as in tree crops or forage breeding or evaluation trials. Such experiments are "perennial" since the research involves perennial, instead of annual, crops. This tutorial will show how such experiments (or nurseries) are created or converted in AGROBASE Generation II. You will also see how such data is displayed and an example of the analysis and storage of means.


Duration: 10m45

Subsamples

You might want to take repeated observations for a plot, or data on individual plants in a plot or head-row in an experiment or a nursery with populations under development. Perhaps you need to compute not only the average or total for a sub-sample, but the variance, skew, kurtosis, and more. This tutorial will demonstrate how to create, manage, and use the sub-sampling capability.

Duration: 14m04

Grouping Genotypes - Part I

Genotypes, whether treatments (hybrids, varieties, cultivars, clones, polycrosses), parents, or populations, must be grouped for the most efficient use of AGROBASE Generation II. When randomizing a yield trial, for example, it is best to have the entries already in a group to quickly complete the process. Or, you might want to group selected lines or group parents for planning a series of crosses. Grouping will save time later, as well as help develop and customize the relational database around your research program. This tutorial will demonstrate the grouping tools from the research tree explorer main nodes, as well as using "drag and drop" and other tools right on the research tree explorer itself. Please be sure to see Part II as well.

Duration: 18m01

Grouping Genotypes - Part II

This tutorial continues from the "Grouping Genotypes - Part I" tutorial. Please watch that tutorial first. This tutorial will focus on some advanced topics - single field query, grouping by selection index, and grouping from means. You will also see where to group crosses, when further organization is required.

Duration: 10m28

Importing Parents

Treatments (hybrids, cultivars, etc.) or populations can be converted to parents, or appear also as parents for crossing in AGROBASE Generation II. However, in this tutorial we will show how new parental genotypes are initially imported. We will also show how you can subsequently import more data on parents already in the software system.

Duration: 8m17

Creating Crosses - Method 1

You can create crosses in AGROBASE Generation II three different ways. This tutorial will show the simplest way, where you just use a list of females and possibly females often referenced from a crossing block or pots in a greenhouse. This approach is quite flexible, but doesn't reference individual plants and uses only the most common breeding methods. For crosses involving more breeding methods and tracing individual female and male plants if needed, you would perform the crosses within a nursery.

Duration: 15m08

Managing Crosses

Once crosses are created, they must be managed. That can involve grouping, deleting, or moving some or all crosses to another group or grouping of crosses. Ultimately, you must “confirm” crosses so that they become populations, which means that seed exists from a cross. The most frequent path is Crosses->Populations->Nursery. But remember, any genotype might appear in Generation II simultaneously as a treatment, parent, or population.

Duration: 11m05

Selfing Nursery

Typically in self-pollinating crops, populations are grown out, selections made, and the next Fn (filial) generation is planted out. When selfing and developing segregating populations is the primary purpose for a nursery, then the steps in this tutorial should be followed. However, AGROBASE Generation II is flexible such that you can even do crossing and other types of breeding events right within a nursery.    

Duration: 4m52

Crossing Nursery

When developing hybrids, a crossing nursery is often required to either make hybrids initially, or "re-make" the hybrids for more seed. Some breeders refer to such a nursery as a "pollination nursery" or a "crossing block". Often, several rows of females are planted for every row of a male parent in a hybrid cross, to maximize the amount of seed produced for hybrids per seeded area. This tutorial shows the capabilities in Generation II to create such a nursery with field layouts to facilitate pollination.

Duration: 19m15

Segregating Populations

Developing segregating populations, or population advancement, typical for self-pollinating crops, is accomplished from within a nursery. One or many records (sub-populations) will be written in the database for the next generation, or the next clone level. For flexibility, you can define one or more methods for deriving the new names for the sub-populations. Population advancement can even be done on individual plants.

Duration: 18m11