CassavaBase

Upload an experimental field trial into the database that you have saved on your computer in Excel

Design a completely new experimental field trial in the database

Catalog your available seed inventory into the database

Upload phenotypic data into the database that you have saved on your computer in Excel

Prepare a 96 or 384 well plate for a genotyping experiment

Upload crosses and crossing information into the database

Print barcode labels for my experiment (for your plots or plants or tissue samples in the field, or for your 96 well plate and tissue samples)

Analyze phenotypic performance across trials

Intro
File Formatting
Enter trial information
Trial Linkage
Fix missing accessions problem
Fix missing seedlots problem
Try submitting trial again

This workflow will guide you through uploading a new trial in the database

A field trial represents plots in the field where each plot has a globally unique plot_name, a sequential plot_number that is unique in the trial (e.g. 101, 102, 103 for three separate plots), and an accession_name representing the genotype being tested in that plot. Each plot can belong to different blocks (block_number) and reps (rep_number) depending on the experimental design you are using (e.g. complete block vs augmented design). Each plot can have a row_number and col_number indicating the relative position of the plot in the field.

If a specific accession is a check or control, you can indicate the plots that that accession is planted in as controls using is_a_control.

You can provide the specific seedlot_name planted in each plot, along with the number of seeds (num_seed_per_plot) and/or the weight (g) of seed (weight_gram_seed_per_plot) that were used.

A trial can represent a yield trial, a phenotyping trial, a crossing block, a greenhouse, a nursery, etc.

A plot can have many plants, which the database can track as separate entities, allowing you to record plant level observations and information.
Make sure your experiment is formatted in the right format

Enter information about the experiment and upload your trial layout

File format information
Spreadsheet format

Trial Name:

Breeding Program:

Location:

Trial Type:

Year:

Plot Width (m):

Plot Length (m):

Field Size (ha):

Description:

Design Type:

Upload File:

Is your trial linked with other field trials, genotyping trials, or crossing trials in the database? If you are unsure, you can skip this. This information can be added from the trial detail page after the trial is saved.

Is this trial following-up a previous field trial?:

Select the trial(s) which preceded this trial:

If you go on to collect tissue samples for creating a 96 well plate for genotyping, when adding the genotyping trial (plate layout) to the database you can use plot names or plant names or tissue sample names from this field trial. By doing so, we can create linkage between this field trial and the genotyping plate.

Will this trial be genotyped?:

If you go on to perform crosses on this field trial, each cross can be linked to specific female and male plots. When you upload these crosses we can then automatically link this field trial to the crossing trial in the database.

Will crosses be done on this trial?:
Fixing the missing accession(s) problem
- Accessions tested in your trial must exist in the database prior to adding your trial. The reason for this is that an accession can be tested in many trials and therefore exists as a separate entity in the database. We also want to be careful about adding new accessions into the database because we do not want incorrectly duplicated data.
- When adding accessions into the database, you can use either a list of accessions or an Excel file.
Trial Upload Error Messages
Fixing the missing seedlot(s) problem
- Seedlots tested in your experimental trial must exist in the database prior to adding your trial. The reason for this is that a seedlot can be tested in many trials and therefore exists as a separate entity in the database. We also want to be careful about adding new seedlots into the database because we do not want data to be incorrectly linked to duplicates.
- When adding seedlots into the database, you can upload an Excel file or you can add seedlots one at a time.
Trial Upload Error Messages
Submit your trial again. You should have corrected all errors by now, but if not please take a look at the errors in the red box below. You can continue to modify your file and then click Upload until it works.

There exist these problems in your file:

Finished! Your trial is now in the database

The trial file was uploaded successfully

You may want to proceed to the trial detail page for the trial you just created.
You can print barcodes for the plots or plants or tissue samples in this trial.
You an add phenotypes for the plots or plants in this trial now.

Finished! Your trial is now in the database

The trial file was uploaded successfully

You may want to proceed to the trial detail page for the trial you just created.
You can print barcodes for the plots or plants or tissue samples in this trial.
You an add phenotypes for the plots or plants in this trial now.

Trials may be uploaded in an Excel file (.xls)
(.xlsx format not supported)

Header:
The first row (header) must contain the following:

plot_name	accession_name	plot_number	block_number	is_a_control	rep_number	range_number	row_number	col_number	seedlot_name	num_seed_per_plot	weight_gram_seed_per_plot

Header as a string:

plot_name,accession_name,plot_number,block_number,is_a_control,rep_number,range_number,row_number,col_number,seedlot_name,num_seed_per_plot,weight_gram_seed_per_plot

Required fields:

plot_name (must be unique across entire database. this is often a concatenation of the trial name, the accession name, and the plot number.)
accession_name (must exist in the database. this is the accession being tested in the plot.)
plot_number (a sequential number for the plot in the field (e.g. 1001, 1002, 2001, 2002). these numbers should be unique for the trial.)
block_number (a design parameter indicating which block the plot is in)

Optional fields:

is_a_control (type 1 in this field if the plot is a control, otherwise leave blank. generally you will have accessions that are controls, so you shuold indicate the plots that that accession is in as a control.)
rep_number (replicate number, numeric)
range_number (range number. often synonymous with col_number, numeric)
row_number (row number. if the field is a grid, this represents the y coordinate, numeric, required for field map generation. the top left plot shuold be row 1, column 1)
col_number (column number. if the field is a grid, this represents the x coordinate. sometimes called range_number, numeric, required for field map generation. the top left plot shuold be row 1, column 1)
seedlot_name (the seedlot from where the planted seed originated. must exist in the database)
num_seed_per_plot (number seeds per plot. seed is transferred from seedlot mentioned in seedlot_name. numeric)
weight_gram_seed_per_plot (weight in gram of seeds in plot. seed is transferred from seedlot mentioned in seedlot name. numeric)

Treatments:

treatment columns (additional column(s) that specify the name of a treatment (e.g. inoculated, drought, etc). the value for each plot should be 1 if the treatment was applied or empty.)

Background:

Partially replicated designs have some treatments that are unreplicated and rely on replicated treatments to make the trial analysable. The design were described in Cullis et al. (2006). It is recommended that at least 20% of the experimental units are occupied by replicated treatments. The aim of these experiments is usually to select promising treatments from a set of replicated and unreplicated test treatments, with check and quality standard treatments providing the necessary replication overall to give a valid experiment. DiGGer (Coombes, 2002) was used to implement this design. DiGGer is a flexible tool for creating experimental designs that are efficient for specified blocking and correlation patterns. DiGGer package (http://www.austatgen.org/files/software/downloads) is an add-on for the statistical computing language and environment R (R Development Core Team, 2009).

Design Parameters:

The parameters will consider a sample partially replicated design trial with 200 unreplicated accessions, 119 accessions replicated 4 times, 26 rows in design, 26 columns in design, bock sequence of 13 by 2 (13, 2) i.e 2 blocks with each having 13 rows; sub-block sequence of block of 13 by 1 (13, 1) i.e 1 sub-block with each having 13 rows in each block.

List of Unreplicated Accession: You're expected to provide the list of unreplicated accessions in this selectbox. E.g. is a list of 200 accessions.
List of Replicated Accession: List of replicated accessions should be provided in this selectbox. E.g. is a list of 119 accessions.
Number of rows in design: Provide the number of rows you want to have in the design. E.g. 26 number of rows.
Number of Columns in Design: Provide the number of columns you want to have in the design. E.g. 26 number of columns.
Number of Times Replicated Accessions are Replicated: Provide the number of times you want the replicated accessions to be replicated. E.g. 4
Block Sequence: The block sequence should reflect the blocking structure of your design. E.g. (13, 2), meaning the design has 2 blocks and each block has 13 rows.
Sub-block Sequence: The sub-block sequence should reflect the sub-blocking structure of your design. E.g. (13, 1), meaning the design has 1 sub-block (column) and each sub-block has 13 rows.

NOTE:

The product of the number of rows and columns in the design should equal the total number of plots. The sum of the unreplicated accessions and the replicated accessions (given the number of times it was replicated) should equal the total number of plots.: The product of the number of rows and columns in the design should equal the total number of plots.; The sum of the unreplicated accessions and the replicated accessions (given the number of times it was replicated) should equal the total number of plots.

This is for uploading a pre-existing genotyping plate layout.
File must be Excel file (.xls)
(.xlsx format not supported)

Header:
The first row (header) must contain the following:

date	sample_id	well_A01	row	column	source_observation_unit_name	ncbi_taxonomy_id	dna_person	notes	tissue_type	extraction	concentration	volume	is_blank

Required fields:

date (should be YYYY-MM-DD)
sample_id (the unique identifier for the sample in the well)
well_A01 (the position of the sample in the plate)
row (the row position of the sample in the plate e.g. A)
column (the column position of the sample in the plate e.g. 10)
source_observation_unit_name (must exist in the database. the identifier of the origin material. in order of most desirable identifier to least desirable identifier that can be used here: tissue sample name, plant name, plot name, accession name)

Optional fields:

ncbi_taxonomy_id (NCBI taxonomy identifier)
dna_person (the name of the person who prepared the well)
notes (any additional notes on the well)
tissue_type (free-text for what type of tissue is present in the well)
extraction (free-text for the extraction method e.g. CTAB)
concentration (concentration in ng/ul)
volume (volume in ul)
is_blank (indicates if well is blank. write 1 if blank, otherwise leave empty.)

This is for uploading a Coordinate Android Application exported plate layout.
File must be a CSV file (.csv)
(Excel format not supported)

Header:
The first row (header) must contain the following:

date	plate_id	plate_name	sample_id	well_A01	well_01A	tissue_id	dna_person	notes	tissue_type	extraction

Required fields:

date (should be YYYY-MM-DD)
plate_id (an identifier for a grouping of plates. called "Genotyping Project Name" in genotyping trial submission form. e.g. NextGenCassava)
plate_name (the unique name for the individual plate. called "Plate ID" in genotyping trial submission form. e.g. 18DNA00001)
sample_id (the unique identifier for the sample in the well. e.g. 18DNA00001_A01)
well_A01 (the position of the sample in the plate in this format A01)
well_01A (the position of the sample in the plate in this format 01A)
tissue_id (the identifier of the origin material. in order of most desirable identifier to least desirable identifier that can be used here: tissue sample name, plant name, plot name, accession name.)
dna_person (the name of the person who plated the individual sample. can be any name.)

Optional fields:

notes (any additional notes on the well)
tissue_type (free-text for what type of tissue is present in the well)
extraction (free-text for the extraction method e.g. CTAB)

Intro
File format
Upload inventory
Fix missing seedlots problem
Try submitting inventory again

What is a seedlot inventory?
- Seedlots represent physical seed in packets.
- This seed can be from crosses or for named accessions.
- Seedlots can have a specific location, box, weight(g), and count.
- Seedlots can belong to breeding programs and organizations.
- Seedlots can be used in trials (e.g. they were planted in a plot) and they can be harvested from a plot or plant (e.g. a cross was performed and seeds were collected.)
- A seedlot inventory consists of giving a location and current weight(g) to your seedlots. The seedlot name is the unique identifier for each seedlot and so should be encoded in a barcode on each seedlot packet.
- You can use the "Seed Inventory" Android Application to scan seedlot barcodes and record weight. If you prefer you can create your own CSV file and upload that, if you do not want to use the Seed Inventory Application. For info about the format of the file to upload, go to the next tab.
- For more info about the "Seed Inventory" Android Application go to Seed Inventory.
- It is also possible to manually enter a transaction by going to the seedlot detail page and clicking "Add New Transaction".
Make sure you are collecting seedlot inventory in the following format

The "Seed Inventory" Android Application will export this same exact format by default.
Select your file and upload seedlot inventory

Upload File (.csv):
Fixing the missing seedlot(s) problem
- Seedlots must exist in the database prior to updating or adding inventory. The reason for this is that the inventory does not give information about the content (a named accession or a cross name) and this information is required for a seedlot to exist in the database. We also want to be careful about adding new seedlots into the database because we do not want data to be incorrectly linked to duplicates.
- When adding seedlots into the database, you can upload an Excel file or you can add seedlots one at a time.
Seedlot Inventory Upload Error Messages
Submit your inventory again. You should have corrected all errors by now, but if not please take a look at the errors in the red box below. You can continue to modify your file and then click Upload until it works.

There exist these problems in your file:

Finished! Your seedlot inventory is in the database

The seedlot inventory file was uploaded successfully

You may want to proceed to the seedlot detail page(s) for the seedlot(s) you just updated.
You can print barcodes for the seedlots.

Finished! Your seedlot inventory is in the database

The seedlot inventory file was uploaded successfully

You may want to proceed to the seedlot detail page(s) for the seedlot(s) you just updated.
You can print barcodes for the seedlots.

Seedlots may be uploaded in a CSV file (.csv)
(Excel .xls and .xlsx format not supported)

Header:
The first row (header) should contain the following:

box_id	seed_id	inventory_date	inventory_person	weight_gram

Required fields:

box_id (the name of the box that the seedlot is in. also called box_name.)
seed_id (unique identifier for the seedlot. must exist in the database. also called seedlot_name)
inventory_date (a timestamp for when the seedlot was inventoried)
inventory_person (the name of the person doing the inventory. can be any name. also called operator_name)
weight_gram (the weight in grams of the seedlot)

Intro
What seedlots do you have?
File format
Upload seedlots
Fix errors in file
Try submitting seedlots again

What are seedlots?
- Seedlots represent physical seed in packets.
- This seed can be from crosses or for named accessions.
- Seedlots can have a specific location, box, weight(g), and count.
- Seedlots can belong to breeding programs and organizations.
- Seedlots can be used in trials (e.g. they were planted in a plot) and they can be harvested from a plot or plant (e.g. a cross was performed and seeds were collected.)
Seedlots fall into two categories

Select One:
Make sure your file matches the correct file format
Provide basic information about the seedlots and upload your file

Breeding Program:

Location of seedlot storage:

Organization Name:

Upload File (.xls):

Upload File (.xls):
Fix all errors in your file
- Accessions must exist in the database prior to adding seedlots of them. The reason for this is that an accession can be exist in many seedlots and therefore exists as a separate entity in the database. We also want to be careful about adding new accessions into the database because we do not want incorrectly duplicated data.
- When adding accessions into the database, you can use either a list of accessions or an Excel file.
- Crosses must exist in the database before adding your seed lots. The reason for this is that a cross can produce many seed lots and so the cross must exists as a separate entity in the database. We also want to be careful about adding new crosses into the database because we do not want data to be incorrectly linked to duplicates.
- When adding crosses into the database, you can upload an Excel file or you can add seedlots one at a time.
Seedlot Upload Error Messages
Submit your seedlots again. You should have corrected all errors by now, but if not please take a look at the errors in the red box below. You can continue to modify your file and then click Upload until it works.

There exist these problems in your file:

Finished! Your seedlots are now in the database

The seedlot file was uploaded successfully

You may want to proceed to the seedlot detail page(s) for the seedlot(s) you just created.
You can print barcodes for the seedlots.

Finished! Your seedlots are now in the database

The seedlot file was uploaded successfully

You may want to proceed to the seedlot detail page(s) for the seedlot(s) you just created.
You can print barcodes for the seedlots.

Seedlots may be uploaded in an Excel file (.xls)
(.xlsx format not supported)

Header:
The first row (header) must contain the following:

seedlot_name	accession_name	operator_name	amount	weight(g)	description	box_name

Required fields:

seedlot_name (must be unique)
accession_name (must exist in the database. the accession_name is the unique identifier for the named genotype)
operator_name (the name of the person who oversaw the inventory process. can be any name.)
amount (number of seeds in seedlot. can be provided in conjunction with weight(g). must provide a value for amount or weight(g) or both.)
AND/OR
weight(g) (weight in grams of seedlot. can be provided in conjunction with amount. must provide a value for amount or weight(g) or both.)

Optional fields:

description (information about why this seedlot is being added)
box_name (the box name that the seed is located in. can be any name.)

Seedlots may be uploaded in an Excel file (.xls)
(.xlsx format not supported)

Header:
The first row (header) must contain the following:

seedlot_name	cross_name	operator_name	amount	weight(g)	description	box_name

Required fields:

seedlot_name (must be unique)
cross_name (must exist in the database. a cross_name can represent a cross between accessions e.g. AxB, but a cross can also represent a cross between specific plots in the field if you have this information)
operator_name (the name of the person who oversaw the inventory process. can be any name.)
amount (number of seeds in seedlot. can be provided in conjunction with weight(g). must provide a value for amount or weight(g) or both.)
AND/OR
weight(g) (weight in grams of seedlot. can be provided in conjunction with amount. must provide a value for amount or weight(g) or both.)

Optional fields:

description (information about why this seedlot is being added)
box_name (the box name that the seed is located in. can be any name.)

Accessions may be uploaded in an Excel file (.xls)
(.xlsx format not supported)

Header:
The first row (header) should contain the following:

accession_name	species_name	population_name	organization_name(s)	synonym(s)	location_code(s)	ploidy_level(s)	genome_structure(s)	variety(s)	donor(s)	donor_institute(s)	donor_PUI(s)	country_of_origin(s)	state(s)	institute_code(s)	institute_name(s)	biological_status_of_accession_code(s)	notes(s)	accession_number(s)	PUI(s)	seed_source(s)	type_of_germplasm_storage_code(s)	acquisition_date(s)	transgenic	introgression_parent	introgression_backcross_parent	introgression_map_version	introgression_chromosome	introgression_start_position_bp	introgression_end_position_bp

Required fields:

accession_name (must be unique)
species_name (must exist in the database)

Optional fields:

population_name (a population is a grouping of accessions. if the population already exists in the database, the accession will be added into it, otherwise, the new population will be created.)
organization_names (the name(s) of the organization(s) which use this accession. multiple organizations can be given with comma separation (e.g. NARO,IITA))
synonyms (an accession can be known by many names including local popular names. a synonym name can be used instead of the accession_name throughout the database; because of this, synonyms must themselves be unique. multiple synonyms can be given with comma separation (e.g. accession_synonym1,accession_synonym001))
location_code(s) (location code(s) for the accession. many can be uploaded at once in comma separated list)
ploidy_level(s) (a number indicating the ploidy (e.g. 2 for diploid, 3 for triploid), numeric. many values can be uploaded as comma separated list.)
genome_structure(s) (genome structure(s) for accession which take into account ploidy and ancestral genome info e.g. AAA, AB. many can be uploaded as comma separated list.)
variety(s) (variety can be defined as a group of individuals or plants having similar traits that can be reproduced "true to type" from generation to generation. may be uploaded as comma separated list.)
donor(s) (the accession_name of the donor accession. may be uploaded as comma separated list.)
donor_institute(s) (the institute of the donor accession. may be uploaded as comma separated list.)
donor_PUI(s) (the permanent unique identifier of the donor accession. may be uploaded as comma separated list.)
country_of_origin(s) (the country of origin. may be uploaded as comma separated list.)
state(s) (the state of origin. may be uploaded as comma separated list.)
institute_code(s) (the institute code of origin. may be uploaded as comma separated list.)
institute_name(s) (the institute name of origin. may be uploaded as comma separated list.)
biological_status_of_accession_code(s) (code indicating the state of accession. may be uploaded as comma separated list.)
notes(s) (free text for notes. may be uploaded as comma separated list.)
accession_number(s) (accession number for accession from germplasm bank. may be uploaded as comma separated list.)
PUI(s) (permanent unique identifier of the accession. may be uploaded as comma separated list.)
seed_source(s) (origin of seed source. may be uploaded as comma separated list.)
type_of_germplasm_storage_code(s) (code indicating the type of germplasm storage. may be uploaded as comma separated list.)
acquisition_date(s) (date(s) of acquisition YYYYMMDD for accession. may be uploaded as comma separated list.)
transgenic (indicates if accession is transgenic. Please indicate 1 if transgenic and empty if otherwise.)
introgression_parent (if the accession you are adding has an introgression that originated from one of the parents, you can specify the parent here)
introgression_backcross_parent (the backcross parent for introducing an introgression into the accession being added)
introgression_map_version (the map version for identifying the start and stop position of the introgression. e.g. AGPv2)
introgression_chromosome (the chromosome number that the introgression is on.)
introgression_start_position_bp (the start position of the introgression in base pairs)
introgression_start_position_bp (the end position of the introgression in base pairs)

Intro
File Formatting
Crossing trial
Upload your crosses

What are crosses?
- Crosses represent any pollination that occurs.
- Crosses can be of different types (biparental, self, open, bulk, bulk_self, bulk_open, or doubled_haploid)
- Depending on the cross type, an individual cross can be defined as between two accessions (e.g. accession A is the female and accession B is the male in a biparental cross)
- For an open pollinated cross, the cross can be defined as between female accession A and male population P1 (populations in the database are only defined as groups of accessions)
- An individual cross can be linked to the specific female plot or plant, as well as the specific male plot or plant.
- A cross can have a number of properties associated to it, such as number of flowers, pollination date, etc.
- A cross can produce seed, which goes into a seedlot.
- A cross can ultimately produce progeny, which then become named accessions in the database.
Make sure your crosses are formatted in the right format
Select a crossing trial

Crossing trials are for grouping crosses together. The grouping is most often done for geographic reasons, such as a group of crosses done in the same field trial. This grouping can be used to encapsulate a crossing block field trial that you have saved in the database (e.g. in Manage Trials your crossing block will appear as a field trial with plots)

Crossing Trial:
Enter basic information about the crosses and upload your file

Crossing Trial:

Location of crosses:

Upload File:

Finished! Your crosses are now in the database

The crosses file was uploaded successfully

You may want to proceed to the cross detail page(s) for the cross(es) you just created.
You can print barcodes for the crosses.
You can add crossing information as it becomes available (e.g. number of seeds, progeny, etc).

Finished! Your crosses are now in the database

The crosses file was uploaded successfully

You may want to proceed to the cross detail page(s) for the cross(es) you just created.
You can print barcodes for the crosses.
You can add crossing information as it becomes available (e.g. number of seeds, progeny, etc).

Intro
Add a crossing trial

What are crossing trials?

Crossing trials group crosses. The grouping can reflect crosses done in the same field trial or crosses in a breeding program in a given year. This grouping can be used to encapsulate all the crosses done in a crossing block field trial that you have saved in the database (e.g. in Manage Trials your crossing block will appear as a field trial with plots)
Enter basic information about the crossing trial

Crossing Trial Name:

Breeding Program:

Location of crossing trial:

Year:

Description:

Finished! Your crossing trial is now in the database

Crossing trial was added successfully

You may want to proceed to the crossing trial detail page you just created.
You can add or upload crosses into your crossing trial as they become available.
You can add crossing information as it becomes available (e.g. number of seeds, progeny, etc).

Finished! Your crossing trial is now in the database

Crossing trial was added successfully

You may want to proceed to the crossing trial detail page you just created.
You can add or upload crosses into your crossing trial as they become available.
You can add crossing information as it becomes available (e.g. number of seeds, progeny, etc).

Specify Pollination Date:	Pollination Date (YYYY/MM/DD):
Specify Number of Flowers: Specify Number of Fruits:	Number of Flowers: Number of Fruits:
Specify Number of Seeds:	Number of Seeds:
Add New Accessions for Progeny:	Number of progeny:
Use Prefix and/or Suffix:	Prefix: Suffix:

Attribute	Value
Project Name:
Start Date:
End Date:
Event Type:
Event Description:
Event Web URL:

Cassava Genomes

Breeding programs

NextGenCassava Community

& Partners

SGN SlideShare

New to the database?

Which accessions will be in the field?

Number of Plants:

Number of Columns (required):

Number of columns between two check columns (Optional):

Which seedlots will you grow in the field? This is optional and can be decided later. If you do not know exactly which seedlot packets you will be planting at this time, you can add this information on the Trial Detail Page after the trial has been saved in the database.

Featured Publication

NextGen Cassava

Project Partners

Which seedlots will you grow in the field?
This is optional and can be decided later. If you do not know exactly which seedlot packets you will be planting at this time, you can add this information on the Trial Detail Page after the trial has been saved in the database.