TIPRoot - NCSU Tree Improvement Program Database
Contents
1. Section 9 02 Multiple Use this page to create mutliple PRS sheets easily The parameters specifying the sheet contents must be provided in a file one PRS sheet specification per line The Last Updated August 27 2014 8 51 AM 4 file can be in Microsoft Excel comma separated value CSV or tab delimited format The first line in the file should be a header containing at least these column names Parent1 Parent2 Cooperator Selection Name Region Deployment Checklot Pollen Cloud If you are signed on as a TIP staff member or administrator you must also include a Cooperator Name column For Cooperator users the cooperator name will be assigned automatically from the user details Extra columns may be present in the file but will be ignored Section 9 03 Prior Multiple Reports This page relates to Section 9 02 Since it may take some time for multiple PRS spec sheets to generate a user may want to leave TIPRoot and return ata later time When the user returns they may visit this page and the previous reports that they have generated will be listed on this page Section 9 04 Seed Mix Report Not Completed To Be Updated Section 10 PRS This section covers the Performance Rating System PRS database If you are looking for information about generating PRS spec sheets see Section 9 Section 10 01 PRS Versions This link connects to a page that will list all the PRS database versions that have been created Each versi2. This page provides additional details for users of the database including the user name and password Once a user has access to the database this is the location where they can change their password Section 9 PRS Reports This section covers how to generate Performance Rating System PRS spec sheets If you are looking for links for the entire PRS database see Section 10 Last Updated August 27 2014 8 51 AM 3 Section 9 01 Single A single PRS spec sheet can be generated using this tool If you have a large batch of spec sheets that you want to produce consider looking at Section 9 02 This tool can produce a PRS spec sheet for open pollinated tested crosses and untested crosses When attempting to generate a PRS spec sheet for an untested cross the only constraint is that the selection ID for both selections must have been tested in the same breeding region This tool presents a web form to the user with the following options e Parent 1 ID This is the selection ID of the first parent in the cross or open pollinated selection Standard NCSUCTIP selection IDs need to be used here e Parent 2 ID This is the selection ID of the second parentin the cross If the user desires an open pollinated selection they may put OP here or just leave the box blank Fora cross a standard NCSUCTIP selection ID is required e Cooperator Name This field cannot be changed by regular users It is wise to ensure that this n
3. TIPRoot User s Manual North Carolina State University Cooperative Tree Improvement Program TIPRoot Administrator Jarrod Morrice jjmorric ncsu edu Table of Contents LIPO CUCU OM BEE E WE AE II Getting SAU CU Deg W ue EE MI TIPROOt NR EN WEEN Section 1 Organizations ACGMIN c liieesecseseteeeeeesssesecseeeesennenetieesdteeseneeeeeeesaeseeeeenesananseeeseeaeaes Section 2 Progeny Tests AC min Wi ee ecssesccesesssaeespepereeeenesenneneneaessnseneneassneaeanenseeoeaes Section 3 Pedigrees Admin ene Temas ecsageeeseneceeeearsensenenenesensenenensaneaearsnseeaeees Section 4 Relatives Admin seveecc ftereeees Sees naeeecenscoeeeeesensenenenesseseneneassneaeanenseeatens Section 5 Data Inventory Admin ss ssssssssnndbnssnsnnunnunnuninnnnnnnnnnnnnnnnnnnnnnnnannannnannnnnnnnnnnnnnnnannnnnannn nnna Section 6 Data Download Admin sssssssssunissnssnunnunnunnunnsnnnnnnnnnnnnnnnnnnnnnnnannnnnnnnnnnnnnnnnnnnannnnnannn nnna Section 7 Soon To Be Measured Admin ssssriiessssussussnssnssnnnnnnnnnnnnnnnnnnnnannnnnnnnnnnnnnnnnnnnnnnnnnnnn annaa Section 8 Account Details ssscrseseescseecergeeceesrseceeeseseseereesesseeeeseeeeeeeseeeeeerseeeneseseseneeeseeeneeneeneees Section 9 PRS RepOTtS dh sssesserunnnenennnnnunsnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnunnnnannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn anann nnn Section 9 01 Sime TE E Kuoa SGE Section 9 03 Prior Multiple Reporter Section 9 04 Seed Mi
4. ame is correct for the user as this cooperator name will be printed on the spec sheet e Cooperator Selection Name This is the namethat is designated by the cooperator for that particular open pollinated or full sibling family Users should not use any type of namesthat would give away the NCSUCTIP selection ID e Region This is the breeding region that the user would like to generate a spec sheet from This is necessary because some selections are present in multiple breeding regions e Deployment checklot This is the checklot that the user would like to compare the performance of their family against The checklot selected should reflect the general region that the family is likely going to be deployed in e Pollen Cloud In the event that the user is generating a spec sheet for an open pollinated family this field provides the option of choosing the pollen to use for the cross The different pollens represent different pollen sources so the pollen cloud that is chosen should be for the region where the orchard is located for that particular seed ADMIN Administrative users are able to change the cooperator member within the Cooperator Name field This is done so that if a Cooperator is having difficulty connecting to TIPRoot NCSUCTIP staff are able to generate the spec sheets on their behalf Upon a successful submission of information to TIPRoot a link will be returned that points to a PDF version of the PRS spec sheet
5. anted in the specified county given the user s level of minimum winter temperature risk A link is also displayed that allows the user to download the displayed PRS values to a spreadsheet Section 10 06 Deployment Counties This tool is designed to allow the user to find the counties that a family would grow in based on the user s minimum winter temperature risk level This tool is designed for users that have a specific family and are wondering the locations that would be appropriate to plant the family based on minimum winter temperature adaptability The user will be presented with the following options e PRS Version Choose the version of the PRS database to use The breeding region that the PRS TN version is associated with is also displayed with the version name e Parent 1 ID The selection ID for the first parent of the family Last Updated August 27 2014 8 51 AM 7 e Parent 2 ID The selection ID for the second parent of the family If an OP family is desired the user may specify OP or leave this blank e Pollen Cloud If the user specified an OP selection it will be necessary to also select the pollen cloud to use The different pollens represent different pollen sources so the pollen cloud that is chosen should be for the region where the orchard is located for that particular seed e Temperature Decrease This specifies the number of degrees cooler that the resulting list of counties can be when compared to th
6. e family s minimum winter temperature origin The minimum winter temperature origin can be thought of as the temperature that the family is thought to be adapted to After the user has submitted the above information to the database the counties that fit within the temperature requirements are listed along withtheir minimum winter temperature A link is also displayed that allows the user to download the displayed counties to a spreadsheet Section 10 07 PRS data for Selection This tool allows a user to find out all the PRS information that is available for a specific selection ID All the user needs to do is enter the selection ID The result from this displays all the breeding values genetic values and the PRS values for every cross that the selection has been usediin When displaying the PRS values each combination of checklot and pollen cloud where applicable is used to get all combinations Section 11 Database Tasks Admin This page displays some of the recent tasks that have been performed on the database Each task has a Details link that displays more specific information about that task including errors that had occurred Section 12 Users Admin To Be Updated Last Updated August 27 2014 8 51 AM 8
7. ersion to use when generating PRS spec sheets Section 10 02 Breeding Values This tool allows a user to download breeding values The top of the page lists the PRS versions that exist within TIPRoot Once a PRS version has been selected the breeding values for all the selections in that database are then displayed underneath it In addition there is a link below the version selection that allows the user to download a spreadsheet with the breeding values Section 10 03 Genetic Values This tool allows a user to download genetic values i e for specific crosses The top of the page lists the PRS versions that exist within TIPRoot Once aPRS version has been selected the genetic values for all the crosses in that database are then displayed underneath it In addition there is a link below the version selection that allows the user to download a spreadsheet with the genetic values Section 10 04 PRS Values This tool displays the PRS values foraspecific PRS version This is what is normally thought of when thinking about the PRS database Once the user accesses this page they will be presented with the following options e OP or Full sib Crosses Choose if you want the output to contain OP Full sib crosses or both e PRS Version Choose the version of the PRS database to use The breeding region that thePRS version is associated with is also displayed with the version name e Deployment Checklot This is
8. n The list of available counties changes accordingly with the selection of the state This location is used to obtain the minimum winter temperature of where the seedlings are likely to grow up e Deployment Checklot This is the checklot that the user would like to compare the performance of the families against The checklot selected should reflect the general region that the family isdikely going to be deployed in e Pollen Cloud If the user specified an OP selection it will be necessary to also select the pollen cloud to use The different pollens represent different pollen sources so the pollen cloud that is chosen should be for the region where the orchard is located for that particular seed e Temperature Decrease This specifies the user s level of risk that they are willing to take in planting families from warmer regions Each family originates from a location with a specific minimum winter temperature The temperature decrease indicates how many degrees colder than the family s minimum winter temperature origin the user would be willing to plant the family This information along with the specified location will subset the list of families that fit those criteria After the user has submittedthe above information to the database the PRS values for the families meeting the specified minimum winter temperature requirements will display in the page below The families displayed indicate all the selections that can be pl
9. on of the database will contain a link called Details or Manage the name depends on your user type ADMIN At the top ofthe PRS Versions page there is a link Add PRS Version that allows administrators to add anew PR database On the Add PRS Version link administrators can establish a new version of PRS and link it with a specific breeding region Once the version is established it can then be seen on the PRS Versions page The Details page outlines basic information about that PRS database version including the breeding region that it is associated to and the base date i e the date the Big BLUP analysis was performed that the database is associated with Within this page there is also a list of the cutoff values for the grades for rust straightness and forking There are also links to the breeding and genetic values that were used as the basis of the DST database ADMIN Prior to BLUP analysis an administrator can upload a list of test and series that would be associated with that version of the database By doing so the administrator will be able to quickly download data for the BLUP analysis that is associated with that PRS version Once the BLUP analysis has been completed the BLUP values can then be uploaded and Last Updated August 27 2014 8 51 AM 5 associated with the PRS version In addition the administrator also has the option of selecting PRS version as the v
10. that can only be accessed and used by administrators of the database Special formatting and headers will be used todifferentiate these user specific tools and capabilities The section header will be appended with Admin for tools that can only be used by administrators of the database When there is restricted access within a tool a new paragraph will be usedjto describe the administrator s abilities The paragraph will be formatted as ADMIN This is asample paragraph Tools that have additional capabilities for administrators will be formatted this way to show that the capability is restricted to certain users Il Getting Started To use TIPRoot you must first be given login credentials from the administrator see cover page for user manual forcontact information Once provided login credentials point your web browser to the following URL https tracker cnr ncsu edu tipdb On the left hand side of the webpage you will see a list of links that are currently available Since you have not logged in the number of links will be greatly limited However there should be two links available Login and WRAP Login NCSU If you are not affiliated with NCSU i e do not have an NCSU e mail address then you will use the Login link If you are affiliated with NCSU use the WRAP Login NCSU link and follow the standard protocol for logging into NCSU Once you login the left hand list of links will expand to provide
11. the checklot that the user would like to compare the performance of the families against The checklot selected should reflect the general region that the family is likely going to be deployed in e Pollen Cloud If the user specified an OP selection it will be necessary to also select the pollen cloud to use The different pollens represent different pollen sources so the pollen cloud that is chosen should be for the region where the orchard is located for that particular seed After the user has submitted the above information and submitted it to the database the PRS values will display in the page below A link is also displayed that allows the user to download the displayed PRS values to a spreadsheet Section 10 05 Progeny Performance This tool obtains the DIS TH values from a specific version of the PRS database and subsets the output based on the users desired location for planting anda specified temperature risk Users are presented with the following options Last Updated August 27 2014 8 51 AM 6 e OP or Full sib Crosses Choose if you want the output to contain OP Full sib crosses or both e PRS Version Choose the version of the PRS database to use The breeding region that the PRS TN version is associated with is also displayed with the version name e Deployment State The state that the seedlings are intended to be planted in e Deployment County The county that the seedlings are intended to be planted i
12. x Report EEN Section LO PRS AW Sanici SRED Ale Section 10A SO7 EE Section 10 03 Genetic Values EEN Section 10 04 AE Section 10 05 Progeny Performance EEN Section 10 06 Deployment Counties EEN Section 10 07 PRS data for Selection ENEE Section 11 Database Tasks Admin c cssssssssesesseeseseseeecenseseesseseeeeseseeneaseesaneeesenesanenseeeneeeeaes Section 12 Users Aq eege eege ere Last Updated August 27 2014 8 51 AM I Introduction TIPRoot is a database for the North Carolina State University Cooperative Tree Improvement Program NCSUCTIP TIPRoot was developed as a means to help the staff at NCSUCTIP organize data for breeding testing and selection as well as allow access to certain portions of the data for Cooperators associated with the Cooperative This document was written to outline the different tools that are available to Cooperators and the NCSUCTIP staff that administer the database This document is meant to be an overview of what can be done with TIPRoot and how to perform those tasks It is not meant to be a technical document that covers the database schema or code To avoid confusion of creating and managing multiple documents this User Manual contains all the tools that are available on TIPRoot Thatmeans thatsome tools that are listed in this document will not be available to all users of the database In addition there may be tools that can be accessed by all users but there may be parts of the tool
13. you with all the tools that are available for your account The number of links that show will be dependent on your account settings Last Updated August 27 2014 8 51 AM 2 If you are not NCSU affiliated the first thing you need to do when you log in should be to verify your information and to change your password On the left hand list of links there should be a link called Account Details The Account Details shows your account information and provides an option for changing your password Verify that the information provided is correct and change accordingly The e mail address provided is the one that will be used if for some reason you forget your user name or password lit TIPRoot Tools Section 1 Organizations Admin This link provides displays a table of the cooperators that are a part of NCSUCTIP The table indicates the associated information with that Cooperator including type of membership organization ID and abbreviation and whether or not the cooperator sells seedlings important for wording on PR Spec Sheets Section 2 Progeny Tests Admin To Be Updated Section 3 Pedigrees Admin To Be Updated Section 4 Relatives Admin To Be Updated Section 5 Data Inventory Admin To Be Updated Section 6 Data Download Admin To Be Updated Section 7 Soon To Be Measured Admin To Be Updated Section 8 Account Details This link is only available to users that are not affiliated with NCSU
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