User Manual

This manual describes how to access data and use the tools on the Pulse Crop Database.  Please see the links below and to the left to navigate to different parts of the manual.

Homepage Overview

The PCD homepage is divided into a few key areas to help facilitate navigation.  The Crops Quick Start (Fig. 1A), has icons for each crop represented in PCD.  Clicking on the crop icon takes you to the Crop Overview page (see Crop Overview Page) which allows for quick access to all the data associated with that crop.  To the right of the Crop Quick Start is the Tools Quick Start (Fig. 1B).  This area has links to common tools and data search interfaces.  The center region of the homepage contains a News and Events section (Fig. 1C) which has news about PCD as well as from the community.  The homepage also has the traditional pull-down menu bar in the header (Fig. 1D) which also provide access to the crop overview pages, data, search pages, tools, and general information.  

Figure 1.  PCD Homepage

The items under the Search and Tools menus are discussed in other tutorials, but we want to highlight the Data and General menus in this section of the tutorial.   Under the Data menu (Fig 2A), you can see a data overview, learn how to submit data, download data, view publication datasets and view information on PCD trait and marker type abbreviations.  A summary overview of all data on PCD, which can be broken down by crop and/or data type, is found on the Overview page. Under Data Submission, there are details about submitting data to PCD.  PCD will accept published data and we highly recommend contacting us before starting to fill in the data templates.  There are two links to the contact form on this page. 

The Data Download page contains links to all the various data types in PCD.  The links redirect you to either a search page, analysis page, or a table where the information about the data and links to download files are located.  For the RefTrans, Unigene, and genome data, the links take you to the analysis page with details about the data and these pages have a link on the left for the download page.  For germplasm, markers, QTLs, transcripts and sequences, the links take you to the search page for that data.  On the search page, choose your parameters and click submit to retrieve data.  The resulting table can then be downloaded.  The Publication Datasets page contains supplementary data for publications.  These authors chose to make the supplementary information available on PCD and the files were posted prior to submission so the reviewers could access the data.

The Trait Abbreviations page contains the QTL traits that are in PCD and the abbreviations that are used for the internal PCD database generated QTL ID.  We have tried to keep our abbreviations consistent with those used in the trait and crop ontologies.  On the Marker Types page, there is a table of the marker types that are in PCD.  The markers have been generally grouped by the same technologies and we have provided a link to a reference that describes the marker technology.  The Field Book link takes you to information about the Android App that is used for data collection and upload to PCD.

Figure 2.  Data and General menu items.

The General menu (Fig. 2B) contains links to a variety of different items.  If you would like to subscribe to the PCD mailing list, please click on Mailing Lists and complete the web form.  The General menu also has links to past presentations about PCD, work that is in progress and completed, and how to reference PCD.  The Help menu (Fig. 2C) has a link to the PCD User Manual and video tutorials.  There is also a Contact link that opens a fillable web form.  We appreciate input on the website as well as reports of website bugs and data errors.  

Crop Overview Page

All the available data for each crop is easily found through the Crop Overview Page.  From the PCD homepage, the crop overview pages are accessed either by clicking on the Crops menu in the toolbar and selecting the crop of interest (Fig. 3A) or clicking on the crop under the Crops Quick Start section (Fig. 3B).

Figure 3.  Accessing the Crop Overview Pages from the homepage.

On the Crop Overview Page, there are two main sections.  The left side toolbar is static and has a Data section and a Tools section (Fig. 4A).  Clicking on the links in these sections either changes the information to the right of the toolbar (Fig. 4B), or opens another tab with the linked information.  The Crop Overview Page defaults to the Overview section for each crop which contains basic information and a summary of the available data in PCD.

Figure 4.  PCD Crop Overview Page

Many of the left toolbar links will dynamically change the content to the right of the toolbar (Fig. 5).   For example, when the Germplasm link is clicked, a list of germplasm in PCD is displayed.  Green text indicates a hyperlink that will display more detailed information.  For Transcripts, a table with summary information for the RefTrans and Unigene assemblies is displayed along with links to more detailed information.  

Figure 5. Dynamic data

The the left toolbar links open new tabs.  As an example, the Genetic Maps link opens a new tab that has a table of all the genetic maps for the crop (Fig. 6).  Green text on the table indicates links to detailed information.  The Markers, Publications, Sequences, and Trait Loci links open search interfaces for the selected data type.  Please see the separate tutorials for more information on how to use the different data searches and tools. 

Figure 6.  Genetic Map page and example of detailed information available under hyperlink indicated by green text

Data Searches

To access the different data searches, click on the Search menu in the header and then select the data type you would like to search (Fig. 7).  To learn more about each search interface, please see the links below the figure.

Figure 7.  Search menu in header provides links to different searches.

Genes and Transcripts

The Genes and Transcripts Search is located under the Search menu in the header.  The Genes and Transcripts Search allows you to search sequences that are available in PCD with several different parameters.  A few parameters can be used to return a broad range of results, or numerous parameters can be used to find very specific data.  Searches can be limited to a certain genus and species. Once a genus has been selected, the species list will be populated and then a species selection can be made (Fig. 8A).  Searches can also be limited to datasets, such as genome and RefTrans assemblies or NCBI genes.  For a genome assembly dataset, the search can be restricted to a chromosome or scaffold and further restricted to a region on that chromosome or scaffold (Fig. 8B).  Searches for a specific gene or transcript name, or a list of names that are uploaded as a text file, are also possible with this search interface.

Figure 8.  PCD Genes and Transcript Search interface.

Right about the the "Search" button is an option to customize the output (Fig. 9A).  Users can choose which columns are displayed before retrieving the search results.  All search results are returned as a table with hyperlinks to more info (Fig. 9).  The table can be downloaded and a Fasta file of the returned sequences can also be downloaded (Fig. 9B).  To do another search, click reset.

Figure 9. Gene and Transcript Search results table.

Germplasm

The Germplasm Search can be accessed through the Search menu in the header.  Information about germplasm linked to data in PCD can be searched by species (Fig. 10A) and/or name (Fig. 10B).  A list of germplasm names, in a text file, can also be uploaded to search for multiple germplasm at once.

Figure 10.  PCD Germplasm Search interface.

Results are returned in a table format that can be downloaded (Fig. 11A).  Green text indicates hyperlinks to more detailed information (Fig. 11B).  Searches can be refined by editing the parameters or a new search can be initiated by clicking the reset button.

Figure 11.  PCD Germplasm Search results.

Markers

To search the markers in PCD, click on the Search menu in the header and select Marker Search.  The Marker Search is useful for retreiving information about markers and can be a broad search or a very specific search depending on the number of parameters used.  Markers can be searched by typing in a marker name, or a text file of multiple marker names can be uploaded to search for multiple markers at once (Fig. 12).  The search can also be restricted by the marker type (Fig. 12A), the species the marker was developed in, or the species the marker was mapped in.  To find out more information about the marker types, click the question mark logo next to Marker Type.  For markers that have been mapped to a genetic map, the search can be restricted to a certain linkage group (Fig. 12B).  And the search can be even further restricted to a certain locations on the linkage group.

Figure 12.  PCD Marker Search interface

The search results are returned in a table format (Fig. 13).  There are hyperlinks within the table that take you to more details about the marker or where the marker is mapped.  This data table can be downloaded in a format that can be easily opened in applications such as Excel (Fig. 13A).  Clicking on the marker name (Fig. 13B), displays the marker page which has information such as alignments and map positions.  If you would like to change the search, either edit the parameters or click the reset button to start all over.

Figure 13.  Marker Search results

Publications

To search publications on PCD, click on the Search menu and select Publication Search.  The Publication Search is like many common literature searches, but is limited to publications that have been added to PCD.  The publications can be searched by using keywords within different fields (Fig. 14A).  Multiple fields and keywords can be entered and more fields can be added by clicking the Add/Remove buttons (Fig. 14B).  A range of years can also be entered (Fig. 14C). 

Figure 14.  PCD Publication Search interface

The search results table has information about each publication (Fig. 11A).  By clicking the publication title, more detailed information is displayed.  Most publications also have a link to the publisher website or PubMed record in their titles (Fig. 11B).

Figure 15.  Publication search results and detailed publication information

QTLs and MTLs

Quantitative trait loci (QTLs) and Mendelian trait loci (MTLs) that are entered in PCD are searchable from the QTL Search option under the Search menu in the header.  The search can be restricted by QTL or MTL as well as by species (Fig. 16A).  A certain trait ontology category can be selected to limit the returned results to only that trait type.  If you are looking for a specific trait, you can do a keyword search of the trait names or search by the published name or the PCD assigned name (Fig. 16B).  Please see the PCD Trait Abbreviation Table hyperlinked in the directions for the search for more information about the trait abbreviations used in PCD.  

Figure 16.  PCD QTL Search interface

The results are returned in a table that has green hyperlinks to more information about the QTL or MTL, the map it is located on, and the species it is from (Fig. 17).  The table can also be downloaded (Fig. 17A).  Clicking on the QTL label, opens the QTL information page which has a link to map positions (Fig. 17B).  From the map position table, the QTL can be viewed in MapViewer.

Figure 17.  PCD QTL Search results

Sequences

To search sequences, click on the Search menu on the homepage header and select Sequence Search.  This search is useful for retrieving information about certain sequences from a larger dataset, or all the sequences from one or more datasets.  The Gene and Transcript Search page is for searching genes and transcripts only, whereas the Sequence Search page also includes other sequence types.  A few search parameters can be used to return a broad range of results, or more parameters can be selected to find very specific data.  This is not a BLAST search, BLAST is available under the Tools menu. 

Figure 18. PCD Sequence Search interface

Sequence searches can be limited by genus and species, or sequence type (Fig. 18A).   The search can also be restricted to a certain genome dataset and further restricted to a certain chromosome or scaffold location for within that assembly (Fig. 18B).  The sequences in PCD can also be searched by sequence name, and there is an option to upload a text file of sequence names (Fig. 18C).      

Figure 19.  Search results table

All search results are returned in a table with hyperlinks to more information (Fig. 19A).  The results table can be downloaded and a Fasta file of the sequences on the table can also be downloaded (Fig. 19B).  To do a different search, either edit the parameters and search again, or click the Reset button.

MegaSearch

PCD also has a more powerful search interface called MegaSearch.  MegaSearch allows for additional customization of downloaded results and also allows users to preview the results before downloading.  Access the MegaSearch interface via the link in the Search menu.  To begin a search, first select the Data Type (Fig. 20A).

Figure 20.  The MegaSearch interface.

Once a Data Type is selected, the Query section appears (Fig. 20B) where further filters can be selected.  Note the number of data rows that appears right above the Query box.  This number can be refreshed to reflect the number of data rows yielded by the search parameters by clicking the "Refresh Count" button (Fig. 20B).  This helps the user determine how much data is being returned by the search.  Once the search parameters are set, there are options for which data fields are downloaded (Fig. 20C).  Users can also view the data prior to download or download a FASTA file (dependent on Data Type).

Trait Descriptors

Users can also search the Trait Descriptors used for phenotypic data stored on PCD.  Currently, the only phenotype data is from the USDA-GRIN data that is searchable in BIMS.  Access the Trait Descriptor search interface via the Search menu.  The Trait Descriptor search has options to filter by group, trait category, and/or keyword (Fig. 21A).

Figure 21.  Trait Descriptor Search interface.

The search results are displayed in a table with hyperlinks to more information about the descriptor and trait (Fig. 21B).  The results table can also be downloaded (Fig. 21C).

Traits

Users can view the list of traits in PCD two different ways.  The list of trait abbreviations can be viewed using the link under the Data menu, and the traits can be searched using the link under the Search menu.  The Trait search interface allows users to search by category and/or keyword (Fig. 22A).

Figure 22.  Trait Search interface.

The search results are returned in a table format (Fig. 22B) with hyperlinks to more details about the trait.  The results can also be downloaded (Fig. 22C).

Tools

To access the different Tools available on PCD, click on the Tools menu in the header and then select the tool you want to use (Fig. 23A).  Many of the tools are also quickly accessed through links in the Tools Quick Start (Fig. 23B). To learn more about each search tool, please see the links below the figure.

Figure 23.  Tools menu in header and Tools Quick Start on homepage

BLAST

PCD offers BLAST with sequence databases from the crops featured on the database (Fig. 24).  Genome, unigene, and reference transcriptome assemblies are available along with model genome sequences from Medicago truncatula, Lotus japonicus, and Glycine max.  

Figure 24.  Blast Tool homepage.

The Tripal BLAST interface (Fig. 25) looks and functions like the interface available on NCBI and information on the different settings and how to use BLAST can be found in the BLAST Help manual.  Please note that one you initiate a job, you are taken to an unique results page that you can book mark and return to later.  

Figure 25.  Tripal BLAST interface

The BLAST module displays the results in a interactive interface.  At the very top are links to download the results in the standard output formats (Fig. 26A).  Below is a table with graphical results that can be viewed by clicking the arrows to expand the section (Fig. 26B).

Figure 26.  Results from BLAST module.

Users can also view the alignments to the genome scaffolds in JBrowse using the hyperlink to the scaffold (Fig. 27A).  To see the BLAST result in JBrowse, click the box in the JBrowse left-side menu (Fig. 27B).  Features that are in the PCDdatabase (CDS, peptides, unigenes, RefTrans), will have links to more information in PCD.

Figure 27.  BLAST link to JBrowse.

JBrowse

PCD has an instance of the JBrowse genome browser for viewing genome data.  A list of the genomes available in PCD can be accessed by clicking the JBrowse link in the Tools menu (Fig. 28).  There is a list of genomes with links to open JBrowse under the 'Version' column (Fig. 28A), and links to more information about the genome under 'More Information' (Fig. 28B).  

Figure 28.  The JBrowse homepage on PCD.

Within the JBrowse window for each genome, there is a left side bar where tracks can be turned on and off (Fig. 29A).  There is also a toolbar above the genome region being displayed where the user can zoom in and out, scroll, and select sequences (Fig. 29B).  Users can also type a scaffold name and location or a gene or mRNA name in to view that specific feature.  Clicking on a gene or mRNA feature also opens a window with more details and a link to information about that feature on the PCD database.  Please watch the JBrowse tutorial for more details about how to navigate and use JBrowse.

Figure 29.  JBrowse interface for a genome.

PathwayCyc

PathwayCyc pathways were generated using Pathway Tools and are available under the PathwayCyc link in the Tools menu.  Pathway Tools allows users to view metabolic pathways that are in genomes.  Please see the manual for Pathway Tools for more information on use.  To access the different genomes, click on the hyperlink in the genome name (Fig. 30).

Figure 30.  PathwayCyc page with genome list.

Once the genome is selected, the PathwayCyc interface opens and an overview of the genome statitstics is shown.  Using the 'Metabolism' menu, the Cellular Overview can be opened as in Fig. 31.  Individual pathways can be selected and explored.

Figure 31.  CDC Frontier cellular overview

MapViewer

MapViewer is a new tool for viewing genetic maps on PCD.  There are multiple ways to access MapViewer and the first way is from the Tools menu in the header.  The link under Tools opens a MapViewer interface (Fig. 32).  On this interface, select the species, map, and linkage group to be viewed and click submit (Fig. 32A).  The selected linkage group then opens in a new window (Fig. 32C).  There are also links to tutorials and examples (Fig. 32B).

Figure 32.  MapViewer interface found under Tools menu.

Another way to access the maps is via the Map Overview page (Fig. 33).  The Map Overview page displays a summary graphic of all linkage groups (Fig. 33A) and clicking a linkage group opens a more detailed view in MapViewer.  The Map Overview page also has informaiton about the population that the map was generated from (Fig. 33B) and also links to lists of the markers and QTLs on the map (Fig. 33C).

Figure 33.  Map Overview page.

MapViewer displays the complete linkage group, and QTLs, on the left, and the selected region on the right (Fig. 24A).  The selected region can be changed by dragging and resizing a window on the complete linkage group on the left side. There is a legend of the marker colors below the linkage group figure.  Information about the markers is displayed when the pointer is over a marker name on the right side graph (Fig. 34B).  Clicking on the marker name, opens the marker details page.

Figure 34.  MapViewer displays a static linkage group graph on the left and a dynamic graph on the right.

A different map or linkage group can be displayed using the controls at the bottom of the MapViewer page (Fig. 35A). A comparison map can also be turned on by clicking on the "Show comparison map" box (Fig. 35B).  The color of the markers and which markers are displayed can be changed with the controls and the ruler and marker positions can also be toggled on or off (Fig. 35C).  After changing any of the four parameter sections, the Submit button must be pressed to display the changes.  There are also places to click to view the Dot Plot and Correspondence Matrix for the compared maps.

Figure 35.  MapViewer control panel.

When comparison maps are displayed (Fig. 36), the common loci are connected with a line and the zoomed in area for each map can be adjusted independently.  See the next section of the manual to learn about exporting figures from MapViewer.

Figure 36.  Comparison map view.

 

Pictures from MapViewer

MapViewer allows users to export figures as a high-resolution PNG file that is suitable for publication.  Items that can exported have a clickable camera icon that will trigger a file download.  Users can export the map overview which has all the linkage groups (Fig. 37), a single linkage group (Fig. 38), a linkage group comparison (Fig. 39), a dot plot (Fig. 40) or a correspondence matrix (Fig. 41).

Figure 37.  How to download a map overview.

 

Figure 38.  How to download a linkage group figure.

 

Figure 39.  How to download a linkage group comparison figure.

 

Figure 40.  How to download a linkage group comparison dot plot.

 

Figure 41.  How to download a linkage group comparison correspondence matrix.

Synteny Viewer

PCD uses the Tripal Synteny Viewer, developed by the Fei Bioinformatics Lab, to display the analysis results of genomes that were compared using the program MCScanX.  Synteny Viewer is accessed under the "Tools" menu.  To get started with Synteny Viewer, first select a genome (Fig. 42A).  The "Chromosome/Scaffold" menu will then populate with the names of the appropriate scaffolds or chromosomes and one of these sequences can be selected (Fig. 42B).  The final option is to select one or more genomes for comparison (Fig. 42C), and then the "Search button" is clicked to start the search.  Alternatively, if the block ID number is already known, the block ID value can be input directly to return just those results.

Figure 42.  Options for Synteny Viewer search.

When the search is complete, a new page opens with the results.  There is a summary of the input settings at the top of the page.  When multiple genomes are queried, there are tabs to switch between the results and the circular graph will change when a different genome is selected.  The syntenic regions are indicated on the circular graph by gray lines.  When the mouse hovers over the gray line, a summary is displayed (Fig. 43).  Clicking on the gray lines, opens a page with more details (see below, Fig. 45).

Figure 43.  Synteny results in circular graph.

Under the circular graph is a table listing the syntenic blocks (Fig. 44) that are displayed as gray lines in the circular graph.  Clicking on the block name opens the same details page as clicking on the gray lines on the circular graph.

Figure 44. Synteny block table.

The syntenic block details page has an overview section at the top listing the details for each genome in the comparison, a side-by-side graphic of the syntenic block from each genome, and a table showing the genes in the syntenic block from each genome (Fig. 45).  The side-by-side graph can be zoomed-in by using the scroll wheel on the mouse and the view can be shifted up or down by click and dragging.  Clicking on the gene name in either the table or on the graphic will open the feature details page from the PCD database.

Figure 45.  Syntenic Block details page.

 

PCD Video Tutorials

Please click on the below links to view the video tutorials.  The videos were recorded when the database was called CSFL, but the functionality is still the same.

Homepage Overview

Crop Overview Page

Data Searches

Tools

BIMS (Breeding Information Management System)

PCD BIMS (Breeding Information Management System) is a Tripal module being developed by Mainlab Bioinformatics which allows users to explore the publically available breeding data in PCD while also providing a data management solution for private breeding programs.  BIMS is now open for breeders to create an account and start using it with current functionality. It is being continuously developed and once complete it will provide individual breeders with a secure and comprehensive online breeding management system that allows them to store, manage and analyze their private data, fully integrated with publicly available genomic, genetic and breeding data within Tripal databases such as PCD.

The BIMS tool now supports the use of Field Book, an Android app developed by the Poland Lab at Kansas State University for collecting phenotype data in the field.  Field Book is a free app that is available through the Google Play Store.  It provides easy and customizable interfaces for entering all types of biological data.  For more details about Field Book, please visit the developer's website to view the current manual and for more information. In the following sections we provide information on how to use the current version of BIMS, which will be updated as more functionality becomes available. If you would like to be kept informed on progress please sign up for the PCD BIMS mailing list. The links below provide information on how to access PCD BIMS, View Data, Search Data, Create a Breeding Program, Import Data, Manage Data using Field Book and Archive Data. If you have any questions please contact us via the contact form on PCD. We will be holding monthly "how-to webinars" and are happy to provide individual program training and guidance and solicit input on further development.

BIMS: Accessing BIMS

BIMS can be accessed via the "Tools" menu (Fig. 1A) and then selecting "BIMS", or from the Manage Breeding link in the Tools Quick Start area (Fig. 1B) of the home page.  The BIMS interface will then open.  Public data is available for all users of CSFL without requiring an account.  Users can download public data from BIMS without an account, but will need a CSFL user account to save search results within the website. Access to private breeding data also requires users to log in with their CSFL user account.  To create a breeding program, users must first create a CSFL account and contact using the contact form for breeder privilege.

Figure 1.  How to access BIMS on CSFL

 

BIMS: Viewing Data

There are three main areas of the BIMS interface.  The first part is the header region (Fig. 2A) which displays the current crop and program, allows users to change their selected crop and program, has a link to the CSFL homepage (Site Home), and displays the user name.  The second part of the interface is the accordion menu on the left side (Fig. 2B).  This menu allows users to switch between different sections of the BIMS program.  The last region is the tab region (Fig. 2C) and this is where users primarily interact with BIMS.  Each tab in BIMS has an "Instructions" section that can be expanded by clicking on it.  The "Instructions" have information on how to use that tab.

Figure 2.  The main sections of the BIMS interface

 

To view data that has already been loaded into BIMS, you first need to select a crop and breeding program (Fig. 3A).  Once selected, the crop and program names will appear in the header of the BIMS window  (Fig. 3A).  You can change these by clicking on "Crop" or "Program" in the header, then selecting the desired crop/program (Fig. 3B).  Details of the selected program will be displayed once a new selection is made (Fig. 3C).

Figure 3.  Selecting a Crop/Program in BIMS

 

Once the program has been loaded, you can explore data that has been loaded into BIMS by clicking on the "Manage Breeding" section of the accordion menu.  Under "Manage Breeding" there are links to view information about the Program, Trait, Location, Cross, Accession, and Trial.  To view information about a certain trait, click on "Trait" (Fig. 4A) and the "Manage Trait" tab will appear.  In that tab, click on the trait of interest (Fig. 4B).  Once a trait is selected, the "Trait Details" will be displayed (Fig. 4C).  If you are viewing data from a private breeding program, you can also edit the information for all the items under Manage Breeding.  Breeders with private breeding programs will also see an "Actions" section under the details window.  The "Actions" section allows breeders to edit the properties or delete the item.

Figure 4.  Selecting and viewing Trait Details

 

You can also view information specific to multiple data types, such as Trait data from a particular trial within a program.  For example, in Figure 5 we are viewing DAYS_TO_FLOWER trait data that is only from the LENTIL.2018PULLMAN.LSP dataset.  To do this, you would select Trial from the accordion menu (Fig. 5A) and then "LENTIL.2018PULLMAN.LSP" and click "View" in the tab area (shown below in Fig. 6), then select a trait from the tab area (Fig. 5B).  Details will be displayed to the right (Fig. 5C).

Figure 5.  Viewing data specific to multiple data types

 

For the other data types, their details are accessed the same way.  First select the data type under "Manage Breeding" (Fig. 6A), then select one of the names (Fig. 6B), and then the details will appear (Fig. 6C).  For these data types, in the "Details" section there is also a "View" button that opens another tab that displays further statistics/data.

Figure 6.  Details for other categories

 

BIMS: Searching Data

You can search the data in a breeding program using BIMS.  Click on the "Search" section of the accordion menu and then click on "Accession" (Fig. 7A).  This will open the "Search Accession" tab (Fig. 7B). 

Figure 7.  Opening the Search tab

 

The first step to start a search is to select a property or trait under the "Choose property" section (Fig. 8A).  In this example, we first chose a "Trial" (LENTIL.2018.PULLMAN.LSP) under "Properties" and then "Days: planting to flowering" under "Traits".  After the property is selected, the "Set filter" section will populate with options for that data type (Fig. 8B, currently showing trait data for "Days: planting to flowering").  After selecting the options you want, click "Add."  The selected filter will then appear in the "Search results" section.  If you want to reset the search, click the "Reset" button (Fig. 8C).

Figure 8.  Selecting a Property and setting a Filter in the Search Tab

 

You can further filter the search results by adding another property or trait under the "Choose property" section.  In this example, we have further refined the search by adding the "Days: planting to flowering" trait (Fig. 9A).  The "Set filter" section will show available data for the previous filter you chose. For example, the statistics shown here for the "Days: planting to flowering" trait are only for those accessions included in the previously selected trial. You can choose which values to filter by, or for data that is numerical you can set the minimum and maximum value you wish to see for that trait, and then click "Add" (Fig. 9B).  The new filter is added to the "Search results" section and the selected filters can be removed with the "Remove" button under "Search results" (Fig. 9C).  To view the search results, and to generate a file to export, click on "View" under "Search results" (Fig. 9C).

Figure 9.  Adding more filters to the search and viewing results

 

When the "View" button is clicked (Fig. 9C), a new tab opens called "Search Results" (Fig. 10).  On this tab there is a "Column options" section (see Fig. 11), followed by options to save or download your search results (Fig. 10A) and a preview of the data table (Fig. 10B).

Figure 10.  Search Results tab

 

Users can add more information to the table before exporting data.  To do this, click on the "Column options" section to expand it (Fig. 11).  There are three sections, "Accession Properties", "Sample Properties" and "Traits" (Fig. 11A).  You can select additional items to display by clicking on the check boxes in these sections.  Once all desired selections have been made, click "Update" (Fig. 11B).

Figure 11. Adding more columns to search results table with Column Options section

 

After selecting additional data to display on the table, you can preview the table on the "Search Results" tab (Fig. 12A) and see which filters were used to generate the table by clicking on "Descriptions" in the "Results" section (Fig. 12B).  To download the data table, click on the "Download" button in the "Save Results / Download Data" section (Fig. 12C).  If you do not see your browser start to download the file after clicking "Download," please make sure the pop-up was not blocked.

Figure 12.  Downloading data from the Search Results tab

 

BIMS generates a CSV file of the search results table (Fig. 13).   This table is easily opened by Microsoft Excel and other programs.

Figure 13.  Example CSV file exported from BIMS

 

If you have a CSFL account, you can also save the search results to a list.  You will see a "Save" button with boxes for a list name and description (Fig. 14A).

Figure 14.  Saving lists of search results

 

Saved search results are accessed by clicking on "Search Results" in the "Search" section of the accordion menu (Fig. 15A).  Any search results you have saved will appear under "Saved Results" (Fig. 15B) and you can also see details about the saved lists and delete, view, or edit them (Fig. 15C).

Figure 15.  Accessing saved search results

 

BIMS: Creating a New Breeding Program

To start a new breeding program in BIMS, you must have a CSFL account with the appropriate access level.  Once you have that, select "Program" under Manage Breeding from the accordion menu (Fig. 16A).  This will open the "Manage Program" tab and then you can open the "Program Admin Menu" section (Fig.16B).  Click "Create" to make a new program.

Figure 16.  Opening the Manage Program tab and creating a new program

 

After clicking the "Create" button, the "Add Program" tab opens.  Enter a new Program Name (Fig. 17A) and make sure that the required column names are set to match your dataset (Fig. 17B).  These four columns are required in the phenotype sheet of the data template and if you change the column names here the column names in the phenotype sheet of the template for download will automatically change. If you use Field Book App for phenotype collection, use these column names in the input files. After you have created the program, you will have the option to add other CSFL users as members of the breeding program from the Program Admin menu (Fig. 17C).  Once the program is created, data can be loaded to the program.

Figure 17.  Creating a new program and adding members

BIMS: Importing Data

Importing data to BIMS requires the use of templates. Phenotype data either needs to be files exported from Field Book or data entered into the BIMS templates.  To download the BIMS templates, choose "Data Import" in the accordion menu and then click "Template List" (Fig. 18A).  This will bring up the "Data Templates" tab with information about each template and links to download them (Fig. 18B).  You can also download all templates as a single Excel file by clicking below (Fig. 18C).

Figure 18.  Downloading BIMS data templates

 

To upload data files, click on the "Upload data" link (Fig. 19A) under the "Data Import" section and the "Upload Data" tab will open.  Then, under the "Upload data by Excel template" section on the right side, select your data file and click "Upload" (Fig. 19B).  Enter a file description if desired, and once the file has uploaded, click "Submit".  The file name will then appear in the "Uploaded Files" section (Fig. 19C).

Figure 19.  Upload Data tab in BIMS

 

To view the progress of an upload job, click on the file name under "Uploaded files" (Fig. 20A).  Summary information about the file will appear below and then click the "View" button (Fig. 20B).  The "Uploading Job" tab appears and will show the "Job Details" table (Fig. 20C).  On the table you can see the job progress.  If the job is still running, you can click the "Refresh" button to update the job progress.

Figure 20.  How to view upload job progress

 

BIMS also provides links to log files on the "Upload Job" tab.  When a job successfully loads, there may be up to three types of logs: New Data Logs, Warning Logs, and Duplicate Logs.  To view the logs, first expand the log type section you want to view (Fig. 21A) and then click on "view" to see the log messages (Fig. 21B).  New Data Logs describe the new data that was loaded.  Warning Logs indicate if any data was skipped due to incorrect column headers or typos, but this data was not critical for BIMS to load data so the job still completed.  It is recommended that you look at the Warning Logs to make sure data was not omitted accidently.  The Duplicate Logs display what data was a duplication of data already present in BIMS.

Figure 21.  BIMS upload job logs

 

If there is an error in the data that causes the upload job to fail, you will see "FAILED" under the job progress (Fig. 22A).   An Error Log section will also be available on the "Uploading Job" tab.  Expand the Error Log section (Fig. 22B) and click on "view" (Fig. 22C) to see the error messages.  Use the Error Log information to correct the original file.

Figure 22.  Failed jobs and the Error Logs

 

To re-run a failed job, use the "Re-Run Job" section on the "Uploading Job" tab.  Select and upload the revised file (Fig. 23A) and then click the "Re-Run the Job" button (Fig. 23B).  To monitor the re-run progress, click on the "Refresh" button (Fig. 23C). If the error was something that you did online, not in the template, for example you had a typo in the configuration setting, it is best not to use Re-Run Job, but go back and start the loading process again.

Figure 23.  Re-running a job

 

BIMS: Field Book Management

For breeders using the Field Book App, BIMS can help generate the trait and field input files to configure Field Book for data entry and BIMS can also import data in the trait and field files from Field Book.  For ongoing trials, BIMS can also help breeders sync data between different devices by loading the exported data from multiple devices into BIMS and generating an input file with combined information.  When breeders first create their programs, they have chosen the names for the four required columns. These columns must match the column names in the Field Book Input file. The configuration settings are accessed either by clicking on "Configuration" under the "Field Book Management" section on the left-hand accordion menu (Fig. 24A) or by clicking on the icon in the header (Fig. 24B).  On the "Configuration" tab (Fig. 24C) there are two sections; "Field Book required columns" and "Field Book custom columns".  The first section is to set names for Accession and the three required columns in Field Book Input file, the second section is for users to choose the optional columns they want to add to the Field Book Input file. When Field Book Input files are generated, these optional columns will be available for inclusion.

Figure 24. Field Book configuration options

 

Two different file types for input into Field Book can be generated using BIMS.  The first file type is the Trait (.trt) file when breeders want to add traits to Field Book using a file instead of creating them one by one in the Field Book App.  This file contains the details of the phenotypic traits being recorded.  To generate this file, click on "Trait" (Fig. 25A) and the "Trait" tab will open.  On the "Trait" tab, there will be a list of traits that have already been loaded into the program on BIMS (Fig. 25B).  Select the traits you want to export and then click the "Generate" button (Fig. 25C).  A .trt file will then download.

Figure 25.  Generating Trait file for Field Book

 

The Field file (.csv) can also be generated for import into Field Book.  This file has the list of accessions and columns for the required columns (unique identifier, primary order, secondary order).  The Field file is generated by clicking on "Field" (Fig. 26A) to open the "Field" tab.  On the "Field" tab there are three options for generating the file (Fig. 26B).  The first option is to generate a "New Trial".  This can be used when breeders want to do another trail with accessions that are already in the database. If you have saved an accession list from a previous search (see Searching Data section), the option to use that list is available (Fig. 26C).  You can also select other accession properties to add to the file.  To generate the file, click the "Generate" button (Fig. 26D) and the file will download. In the generated file from this "New Trial" option, only the accession is provided and the three required colums (the unique identifier, primary order, and secondary order) will be empty since they depend on the planting design. The breeders should fill in those columns before importing into Field Book App.

Figure 26.  Generating a Field file for a New Trial

 

Field files can also be generated from an Existing Trial.  Files from Existing Trials (Fig. 27A) contain the accessions from the existing trial that is selected as well as the custom columns the user chooses. This functionality is to provide a way to sync data from multiple devices that have Field Book App to check which individual has been phenotyped already. Breeders can first upload the data from multiple devices, then generate an updated input file from the existing trial with a trait value.

Figure 27.  Generating a Field file from an Existing Trial or Cross

 

The Cross option (Fig. 28) allows you to generate an input file for a new cross. When users upload a file with information on the cross and the planting (Fig. 28A, eg. cross name, primary order, and progeny in each primary order) and type in a prefix for the unique id (Fig. 28B), then BIMS generates a Field Book input file with new progeny names and three required columns automatically filled in (Fig. 28C). In the uploaded file (Fig. 28A), the order of the columns is important, not the column head.

Figure 28.  Example input file and output file for Generating a Field file for a new Cross

 

If you have already configured Field Book and would like to transfer the Trait and Field information to BIMS, that can be done by importing the Trait and Field files from Field Book.  To import a Trait file, use the "Upload trait file" option (Fig. 29A).  Select your file (Fig. 29B) and click "Upload."  Once the file has uploaded, click "Submit" (Fig. 29C) to start the import job.  The file then appears in the "Uploaded files" section (Fig. 29D).

Figure 29.  Importing Trait files from Field Book into BIMS

 

Field files can also be imported into BIMS from Field Book.  Click on "Upload field file" (Fig. 30A) and then upload the field file and click "Inspect" (Fig. 30B).  After BIMS checks to see if the required columns are present in the Field file, the "Upload an exported field file" section appears (Fig. 30C) and the location and trial can be selected.  The file upload job is then initiated by clicking "Submit".  Successfully uploaded files will appear under "Uploaded files" (Fig. 30D).

Figure 30.  Importing Field files from Field Book into BIMS

 

BIMS: Archiving Data

Creating an archive file of all the data in a breeding program is easily done using the "Archive" function in BIMS.  Select "Archive" in the accordion menu and then "Manage Archive" (Fig. 31A).  On the "Manage Archive" tab, there is an "Archive Data" button (Fig. 31B) which will generate an Excel file that contains all the data in the current breeding program (Fig. 31C).

Figure 31.  Generating an archive file

 

BIMS: FAQ and Troubleshooting

FAQ

How do I search data?

How do I view/edit data in a program?

How do I import data?

How do I manage Field Book trait and field files with BIMS?

How do I create a new breeding program?

 

Troubleshooting

Section Problem Solution
General I have selected a crop and program, but do not see any options under Manage Breeding and other BIMS sections. Please refresh the page in your internet browser.
  I still have problems with viewing BIMS information, even after refreshing the page. Please clear the cached images/files, cookies, and hosted app data from your internet browser's history.  You will have to log back into BIMS and reopen your program.
Data Import/Field Book Management My data upload failed. Please make sure that the upload didn't fail due to data errors or typos first by looking at the error logs (see Importing Data section for more details).  If you need help, contact us.
  Even after I changed the max/min value of the trait descriptor in the template, BIMS still gives an error saying that I have data outside the acceptable range. Once your descriptor has been loaded, you have to edit the the descriptor data in BIMS, not the template (go to Manage Breeding, Trait, choose the trait and click 'Edit' .)
 

What do the errors below mean?

The required column (unique_id) is missing



The required column (primary_order) is missing



The required column (secondary_order) is missing

BIMS allows you to change the column names in the template for 'accession_id', 'unique_id', 'primary_order', and 'secondary_order'. You get this type of error when the column names in your template do not match those in BIMS. Once you change it in BIMS, the templates downloaded from BIMS also change. Please refer to Figure 24 in the manual.
  The output from Field Book Management - Generate input file (Field) - Cross option doesn't seem correct. Please check that your file columns are in the order of cross name, row and the number of progeny for each row that you will plant. In this file, the order of the columns is important, not the column head. Please refer to Figure 28 in the manual.
Search I can't download my file. Please make sure that you allow pop-ups on your browser. Please refer to how to allow pop-ups on chromefirefox or internet explorer.