TIBCO Spotfire Connector for Pipeline Pilot 1.0
Contents
1. M m LL sc 36 Parameter Single string input x This is an example of a single string parameter Enter value My string value Any string value can be entered Run Computation Single value string with legal values LOS Define Parameter Sle Parameter help Single string legal values example Parameter name Smole string legal values Parameter type StingT ppe se Array Required ta run protocol Parameter Legal Values Validation Script Enable Script Legal Values Script 3 TIBCO Spotfire amp Connector for Pipeline Pilot 1 0 User s Manual r TU Define Parameter gt Enter the list of values e separate line IF you i at protocol design time prion 1 Option z Option 3 Value 4 Example 5 Parameter Legal Valu e 38 Parameter Single string legal values mm Single string legal values example Please select M Only the predefined legal values can be selected from the drop down list Run Computation String array without legal values I7 Define Parameter Parameter help String array input Parameter name tring array input Parameter type StringT ppe ww v Array Required ta run protocol Parameter Legal Values Validation Script Enable Script Legal Values Script 39 TIBCO Spotfire amp Connector for Pipeline Pilot 1 0 User s Manual 1 Parameter String array gt2. 16 As a data transformation From the Tools menu menu and in tools that can add data such as the wizards listed below In the Add Data Table wizard the Replace Data Table wizard the Insert Columns from External Data wizard and the Insert Rows from External Data wizard the TIBCO Spotfire Connector for Pipeline Pilot option will be shown in the Other drop down list once this option has been selected Select this option if you want the Pipeline Pilot computation to be shown among the available transformations in the Add Data Table wizard the Replace Data Table wizard the Insert Columns from External Data wizard and the Insert Rows from External Data wizard See the main TIBCO Spotfire help for more information about transformations and the various wizards Select this option if you want the Pipeline Pilot computation to be available when selecting Tools TIBCO Spotfire Connector for Pipeline Pilot gt Run Computation This option should also be selected if you want to use the computation as a guide tool Details on Add Computation Configure This dialog is used to configure the new computation before it is added to the specified usage point in TIBCO Spottfire Configure Computations Add Computation Pipeline Pilot server http MyPipelinePilotServer 3944 Protocol name AY Scatter Plot Utility Usage made From the Tools menu Name AY Scatter Plot Utility Description This protocol reads a data f
3. Make this computation available to end users Configure Pipeline Pilot Computations dialog and the Pipeline Pilot Computation dialog The description should be written as clearly as possible to help the end users select the correct computation at all situations Lists the specified parameters for the selected protocol You can click to select a specific parameter and then click on the edit parameter button Lu to change the settings of the selected parameter See Editing Parameters for more information Only parameters promoted to the protocol level will be visible in this list Select this check box to make the computation available to end users which do not have the license to configure protocols Keep the check box cleared until you are finished with all configurations and the computation works as it should Details on Edit Computation This dialog is used to edit a previously configured computation gt To reach the Edit Computation dialog 1 Select Tools gt TIBCO Spotfire Connector for Pipeline Pilot gt Configure Computations 2 Click Edit Edit Computation Configure Computations Pipeline Pilot server http MyPipelinePilotServer 3944 Protocol name Spottire Rgroup decomposition DM3 Usage mode As a data source Name Spottire Rgroup decomposition DM3 Description This is the help window for working with components and protocols in Pipeline Pilot To create a protocol drag items from the
4. Below are some examples of what the resulting prompt will look like for a certain Pipeline Pilot configuration In the example below all dialogs with a blue frame come from Pipeline Pilot and all dialogs with a lighter blue grey color come from TIBCO Spotfire Overview EA Edit Parameter demo and promote parameters Single string input H Customize the interface Far the component or protocol Far esisting parameters select the parameter name to change its definition Use the toolbar buttons to add delete String array input Single string legal values Option 1 Destination String array legal values Option 1 amp LlserDir aut txt Help Text Icon Parameters Implementation Results Promote Run Computation Single value string without legal values LS Define Parameter Parameter help This is an example of a single string parameter Parameter name Single string input Parameter type String Type s Array Required ta run protocol Parameter Legal Values Validation Script Enable Script Legal Values Script 35 TIBCO Spotfire amp Connector for Pipeline Pilot 1 0 User s Manual E Define Parameter Enter the list of values that separate line IF you speck at protocol design time 5 Parameter Legal Value
5. Components tab into the workspace Connect them with pipes edit their parameters and then click Run to genera e results As you select components and protocols information about using them is displayed in this help window The param erers are displayed in the adjacent Parameters window For more information go to lt a href javascript Do Link Pilot lt a gt Parameters scihelpdocs user getstart getstart intro _htm gt Getting Started with Pipeline DUC NNNM Ot URL Handed LJ eer em ID Column In URL Handled In String Handled In String Handled Make this computation available to end users Option Pipeline Pilot server Protocol name Usage mode Name Description Description Read only Lists the Pipeline Pilot server that the protocol resides on Read only Lists the name of the protocol on the Pipeline Pilot server Read only Lists where this computation should be available The usage mode is specified in the Add Computation Select Usage Mode dialog prior to this step Add a new computation using the same protocol if you need to change this setting The name of the computation as you want it to be displayed to the end users This can be a different name than the original protocol name Lists the description of the protocol as it was written by the protocol creator You can edit the text by simply writing in the Description field The updated descript
6. The Edit Server dialog is displayed 4 Edit the address to the Pipeline Pilot server 5 Click OK Response The updated server address is shown in the Manage Servers dialog 6 Click OK Response The updated server address can now be selected in the Server Administration Select Server dialog 3 3 Details 3 3 1 Details on Server Administration Select Server You must always connect to a Pipeline Pilot server if you want to use any of the TIBCO Spotfire Connector for Pipeline Pilot tools The Server Administration tool helps you to configure which protocols should be available on each server gt To reach the Server Administration Select Server dialog 1 Select Tools gt TIBCO Spotfire Connector for Pipeline Pilot gt Server Administration Server Administration Select Server Please select Pipeline Pilot server http MyPipelinePilot Server 3944 Manage servers coms Select the Pipeline Pilot server to use from the drop down list If you want to add a server or edit the address to a server click on the Manage servers link 3 3 2 Details on Server Administration Publish Protocols This dialog allows you to specify which of the protocols on the Pipeline Pilot server should be available for configuration of TIBCO Spotfire computations Server Administration gt To reach the Server Administration Publish Protocols dialog 1 Select Tools gt TIBCO Spotfire Connector for Pipeline Pi
7. all protocols that have been selected to be available for available in configuration into computations in TIBCO Spottfire TIBCO Spotfire 3 3 3 Details on Manage Servers gt To reach the Manage Servers dialog 1 Click on the Manage servers link in the Server Administration Select Server dialog TIBCO Spotfire amp Connector for Pipeline Pilot 1 0 User s Manual Manage Servers Available Pipeline Pilot servers My Pipeline Pilot Server1 9944 http MyPipelinePilotServer2 9944 Hep OK Cancel Option Description Available Pipeline Lists all available Pipeline Pilot servers You must always connect to a Pilot servers Pipeline Pilot server if you want to use any of the TIBCO Spotfire Connector for Pipeline Pilot tools Add Opens a dialog where you can add a new server to the list Edit Opens a dialog where you can edit the path to the server selected in the list Delete Removes the selected server from the Available Pipeline Pilot servers list 3 3 4 Details on Add Edit Server gt To reach the Add Server dialog 1 Inthe Server Administration Select Server dialog click on the Manage Servers link 2 Inthe Manage Servers dialog click Add gt To reach the Edit Server dialog 1 Inthe Server Administration Select Server dialog click on the Manage Servers link 2 Inthe Manage Servers dialog click to select a server then click Edit Edit Server Pipeline Pilot s
8. computation that is available in the Add Data Table or Replace Data Table tools is unavailable when you select to run a Pipeline Pilot computation from the Tools menu If you have the license for configuring computations you may see computations that have not yet been made available to end users with the check box in the Edit Computation dialog These computations have No in the Published field as indicated in the image Run Computation Description Shows the description of the selected computation as it was set up during the configuration Parameters Lists the parameters that have been defined for the selected protocol 5 3 Details on Parameter Prompt Dialogs The Parameter prompt dialogs may look very different depending on the type of parameter and the text that the person configuring the computation has entered in the Edit Parameter dialog Below are some examples of the various prompt types Note that the look of each prompt dialog type also varies depending on whether the parameter is a single value or an array and whether or not it has some legal values defined See also More About Parameters and Prompt Dialogs Data from Spotfire Use this dialog to define what data from your currently open analysis in TIBCO Spotfire should be used as input to this parameter Parameter Source The SD file to cluster Data table Molecular structures from 3kdb Available columns Selected columns Structure lt MOLFILE gt Ad M
9. e b diro O ERRORS Exo PR OH Late 43 E Edit Output Handler dialog eeeeseeeeeess 24 Edit Parameter dialog oon uc trece reds 20 Edit Server didlOB user e dde tei reed xd id ass 6 Editing computations aeee a vane boxe B ERAN A GIPUR E USUDU NIE 13 par dimetel sms cac reae RE E E AE uu arat ME 20 G Guide tools CODFIB UID B asda ivesvn det bero xe pd Fonts rt Bethel VE M rus 43 What are CHEV as iiec o ety T dei dre enda 43 I IntroductiOD 2 siceo e eo reo eere Fo eeepc E pede eei o ved o 1 L VOB SISA i icciccins evoanie in epe tree pa Ete boit tata essen a 2 Guide Tools M Manage Servers dialog usada rb veru vto e e atr e be Rr cds 5 P Parameter prompt dialogs descrpElobisscotosv sdexie rt Eel pb eara edle Ee vere xtel vba 31 more ADO UT sod ve a De ade es 34 Parameters details on handlers ec re eh Ep tnn 20 CCTV cocente E 8 Homne TOR Pep TT m 31 34 Pipeline Pilot Computation dialog 30 Pipeline Pilot protocols converting into COMPUTATIONS ceccceecccsecceeeeeseeeenes 7 publishing to Spotfire eeesseeeeeeeeeennene 3 Pipeline Pilot server administration of available protocols 3 4 LORIE PETRA TTD RTT 2 R Running computations R n ComputeltlQEbs tu dopo ts EM Vr totu ue REI HP HT ESSERI 30 using COMPUTATIONS ce c on a m UU ODER 29 S Select Serve ied uir crier
10. is displayed when you click the Prompt Settings button in the Details on Configure Pipeline Pilot Guide Tools dialog or after you ve entered all parameters when setting up a guide tool Select Prompted Parameters The following parameters are prompted for at runtime Source Ei MyOupput E TestOutput Destination E Delimited The list displays all parameters for the selected guide tool Select the parameters that should prompt the user for values when running the selected guide tool 45 TIBCO Spotfire amp Connector for Pipeline Pilot 1 0 User s Manual 7 Appendix 7 1 Third Party Software Notices gt Pipeline Pilot nalpp dll 7 5 2 300 Copyright 2009 Accelrys Software Inc All rights reserved 46 8 Index A Add Computation dialogs COATS a ace bo sns ou ise der ob ERi UR ERR b Ue dade UT 16 Select Pipeline Pilot Protocol e 14 Select Usage Mode roo o ath obi Dex A 15 Add Output Handler dialog eeeeessssee 24 Add Server dialogues ceva Pici lr e rn a cn 6 Adding a new computation eeeesseeeeenneeneennnnns 7 C Computations Siebel TRI aA ERE 7 dN T E A 8 Belles estu dM etam M IE 29 Configure Pipeline Pilot Computations dialog 13 Configure Pipeline Pilot Guide Tools dialog 44 Configuring COITIDUEatIOTiS ducto odo es Vet Edu e rmt fue ete uhi 13 Pulde TOONS aiias
11. places in the Spotfire user interface gt Torun a computation from the Tools menu When the usage mode is set to From the Tools menu the computation is displayed as a standalone tool in the Pipeline Pilot Computation dialog 1 Select Tools gt TIBCO Spotfire Connector for Pipeline Pilot gt Run Computation 2 If you have not previously logged into a server then you will be prompted to do so now 3 Depending on the type of computation you may be presented with one or more prompt dialogs where you need to provide some input See the Details on Parameter prompt dialogs for more information gt To use a computation as a data source in the wizards When the As a data source option has been selected the computation is added to all places where you can select a new data source It can be used in the Add Data Table wizard the Replace Data Table wizard the Insert Columns from External Data wizard and the Insert Rows from External Data wizard See an example below It is also available if you select File gt Open From gt TIBCO Spotfire Connector for Pipeline Pilot 1 Select File gt Add Data Table Comment Follow the same steps for either of the wizards listed above if you want to add Pipeline Pilot data somewhere else Click Other Select TIBCO Spotfire Connector for Pipeline Pilot from the drop down list Click Browse In the Pipeline Pilot Computation dialog select the computation of interest and click OK 6 Cont
12. ren pA Coan seed Tu EN Ros ATi cx Us 14 Server TOR CGI case b e EDO E E COH CHR D aan EIE CUD SENE DI 2 IVAN AS VIN earren ueste qund droits deus di 3 Server Administration dialogs Publish Protocols ccccccecsccseccesscececeseseeueseeuseeeeseuness 4 Select SEVER oosotomtv Ned i e be PER 4 U Usine computations csse od pottea pi a 29 47
13. the selected visualization of your TIBCO Spotfire analysis specify custom expressions to use when defining straight lines using the defined properties TIBCO Spotfire amp Connector for Pipeline Pilot 1 0 User s Manual Horizontal Line Line position Fixed value Aggregated value amp Custom expression DocumentProperty Lower Limit Line name Automatic J Custom Hep ok Cancel You reach the dialog shown above by selecting Edit Visualization Properties going to the Lines amp Curves page and Add Horizontal Line Y axis Straight Line 4 If desired add more lines 5 Look at the results a0 TO 60 14 7 10 13 16 19 22 25 28 31 34 37 4 In the image above both the higher limit and the lower limit have been shown in the scatter plot Set link template This output handler specifies the LinkTemplate property on a column so that the content of that column is shown as hyperlinks leading to the URL defined in the protocol Search for LinkTemplate in the main TIBCO Spotfire help for more information about this property 10 Configure Computations A simple example if we have a table visualization containing a column with different animals we can use the set link table output handler to connect each animal type to its corresponding Wikipedia page by doing the following 1 In the Pipeline Pilot protocol specify an output string parameter with the default value http en wi
14. x String array input EA Define Parameter Enter the list of values that separate line IF you speck Enter values one value per row at protocol design time One string Two strings Three strings Any string values can be entered Parameter Legal values oom ail 40 Run Computation String array with legal values LOS Define Parameter PEE Parameter help String array legal values Parameter name String array legal values Parameter type StringT ppe ww v Array Required ta run protocol Parameter Legal Values Validation Script Enable Script Legal Values Script 41 TIBCO Spotfire amp Connector for Pipeline Pilot 1 0 User s Manual E Define Parameter Parameter String array legal values nm This is a string aray with legal values Enter the list af values that ar separate line If you specity 1 Enter values one value per row at protocol design time E e ESSI Option 1 Option 2 prion 1 Option 3 Option z Option 3 Value 4 Value 5 Example 6 4 t Only the predefined values can be selected by entering them in the textbox Parameter Legal Values Jade t 42 Guide Tools 6 Guide Tools 6 1 What are Guide Tools The Pipeline Pilot guide tools are five slots in the Tools menu where you can place any five Pipeline Pilot computations and use them directly fr
15. Configuring Pipeline Pilot Guide TOols cccccceccccceseeecceeseeceesseeceeuseeeseageeeceeaseeessgeeessageeessaaes 43 Details on Configure Pipeline Pilot Guide Tools seeesseeeseeeeeenreeeennnmn 44 Details on Select Prompted Parameters ccccccccccceececeeseeceeeeeceeceeseaceeseeeeseeeesseeesseeeseaeessagees 45 APPENDUX uciasskuisiaksknER UEEFEEN FEES FELENUEE FREKFEZEFE2VAE CA cux FOU GE OD OOV ERO E XI E XR EXE SE CR OK 46 Third Party Software NGUCCS uiu parker aa urea rex Un Mes dier Unten aes e Eure eile 46 INDEX e 47 Introduction 1 Introduction These additional help topics provide a description of the functionality available in the TIBCO Spotfire Connector for Pipeline Pilot It is important to note that these topics do not cover protocol generation in detail nor any work done within Pipeline Pilot See Accelrys for training in these areas Neither does these help topics cover any further analysis done in TIBCO Spotfire See the main TIBCO Spotfire help topics for more information about the available functionality The TIBCO Spotfire Connector for Pipeline Pilot allows you to combine the visual interactive analytics of Spotfire with the high throughput data pipelining capabilities of Accelrys SciTegic Pipeline Pilot The connector allows you to deploy Pipeline Pilot protocols to other TIBCO Spotfire users so that they can take a
16. Input parameters Edit Parameter Source TIBCO Spotfire configuration Pipeline Pilot parameter information Description Description The file s or URL source ta read The file s or URL source ta read Direction Type Ur Input Attributes Required single value Output Handler Legal values Value amp Prompt at runtime in Default values Pipeline Pilotparametersben zos id smi bd Option Description Parameter Displays the description of the parameter for the TIBCO Spottfire users description The general description that was written upon creation of the protocol can be edited for further detail The description written here is displayed in the prompt dialog if a prompt step is defined This allows you to write specific instructions on the type of input that 1s required for this parameter Direction Handler Value Prompt at runtime Pre defined value Set Configure Computations Note If the protocol requires certain columns to be included it is important to add that information here to help users select the correct columns in the prompt dialog Specifies whether this should be an Input or Output parameter Specifies how the parameter should be handled Empty unhandled No input handler has been selected This option can be used if the parameter not is required by the protocol String Specifies that the input parameter should be treated as a string It can either be a single value or an arr
17. OLFORMULA CDBREGNO LC MS Al rows 273 rows Filtered rows 273 rows Marked rows defined by BI Marking 0 rows ok Cae Option Description Description In most cases the text at the top of the dialog should give you instructions regarding what type of input is required If you do not understand what data to choose please contact the person who 31 TIBCO Spotfire amp Connector for Pipeline Pilot 1 0 User s Manual 32 Data table Available columns Add gt lt Remove All rows Filtered rows Marked rows String configured the computation Select the data table in your current analysis from which the data should be picked Lists the columns in the selected data table that are available for selection Moves the selected column to the Selected columns list Removes the selected column from the Selected columns list Specifies that all rows from the selected columns should be retrieved Specifies that only the rows remaining after filtering should be retrieved Specifies that only the marked rows should be retrieved If multiple markings are available in the analysis select the one to define your input data from the drop down list Parameter SMILESColName The name of the property in the data which holds the SMILES information Enter value SMILES Option Enter value med Description Type a string value matching the parameter you are prompted for In mo
18. Sting Tue ALogP Y Property String True Molecular Weight Hle Type String False Html Tooltip Sting False S X Property S X Property Y Property Destination Un True S RunDirectory Chart htm 4 n Option Description Available Lists the protocols that have been specified to be available in TIBCO protocols Spotfire using the Server Administration Publish Protocols dialog Description Shows the description of the selected protocol as the creator of the protocol wrote it in Pipeline Pilot Parameters Lists the parameters that have been defined for the selected protocol 4 4 4 Details on Add Computation Select Usage Mode This dialog is used to specify where you want the new computation to appear It is automatically shown when you have selected to add a Pipeline Pilot protocol You cannot go back to change the selection once you have clicked OK add another computation instead Add Computation Select Usage Mode Select how the computation should be invoked As a data source As a data transformation From the Tools menu The selection made in this dialog affects the choices available for further configuration of the computation at a later stage Option Description As a data source Select this option if you want the Pipeline Pilot computation to be shown among the available data sources from the File gt Open From 15 TIBCO Spotfire amp Connector for Pipeline Pilot 1 0 User s Manual 4 4 5
19. TIBCO Spotfire Connector for Pipeline Pilot 1 0 User s Manual V TIBCO The Power of Now Important Information SOME TIBCO SOFTWARE EMBEDS OR BUNDLES OTHER TIBCO SOFTWARE USE OF SUCH EMBEDDED OR BUNDLED TIBCO SOFTWARE IS SOLELY TO ENABLE THE FUNCTIONALITY OR PROVIDE LIMITED ADD ON FUNCTIONALITY OF THE LICENSED TIBCO SOFTWARE THE EMBEDDED OR BUNDLED SOFTWARE IS NOT LICENSED TO BE USED OR ACCESSED BY ANY OTHER TIBCO SOFTWARE OR FOR ANY OTHER PURPOSE USE OF TIBCO SOFTWARE AND THIS DOCUMENT IS SUBJECT TO THE TERMS AND CONDITIONS OF A LICENSE AGREEMENT FOUND IN EITHER A SEPARATELY EXECUTED SOFTWARE LICENSE AGREEMENT OR IF THERE IS NO SUCH SEPARATE AGREEMENT THE CLICKWRAP END USER LICENSE AGREEMENT WHICH IS DISPLAYED DURING DOWNLOAD OR INSTALLATION OF THE SOFTWARE OR IF THERE IS NO SUCH SOFTWARE LICENSE AGREEMENT OR CLICKWRAP END USER LICENSE AGREEMENT THE LICENSE S LOCATED IN THE LICENSE FILE S OF THE SOFTWARE USE OF THIS DOCUMENT IS SUBJECT TO THOSE TERMS AND CONDITIONS AND YOUR USE HEREOF SHALL CONSTITUTE ACCEPTANCE OF AND AN AGREEMENT TO BE BOUND BY THE SAME This document contains confidential information that is subject to U S and international copyright laws and treaties No part of this document may be reproduced in any form without the written authorization of TIBCO Software Inc TIBCO and Spotfire are either registered trademarks or trademarks of TIBCO Software Inc and or subsidiaries of TIBCO Software Inc i
20. ameters However this execution will not affect your current document Once the execution is finished the Configure Pipeline Pilot Guide Tools dialog is updated so the name of the specified computation is shown after the selected slot name If desired repeat steps 2 to 5 for the other slots Click OK Response The Configure Pipeline Pilot Guide Tools dialog is closed and the guide tool is ready to be used Details on Configure Pipeline Pilot Guide Tools This dialog allows you to configure five different computations that can be run directly from the pre configured slots under the Tools gt TIBCO Spotfire Connector for Pipeline Pilot menu They can also be incorporated in a guided analysis via a link in a text area Configure Pipeline Pilot Guide Tools Pipeline Pilot Guide Tool 2 Pipeline Pilot Guide Tool 3 Pipeline Pilot Guide Tool 4 buts HTML Select Computation Prompt Settings Pipeline Pilot Guide Tool 5 Clear Computation Option Description Select Opens the Pipeline Pilot Computation dialog where you can select a Computation computation that should be placed in the selected guide tool slot Prompt Settings Opens the Select Prompted Parameters dialog where you can select which values the user should be prompted for when running the Guide Tools selected guide tool Clear Computation Removes the computation from the selected guide tool slot 6 4 Details on Select Prompted Parameters This dialog
21. ay Integer Specifies that the input parameter should be treated as an integer It can either be a single value or an array Real Specifies that the input parameter should be treated as a real This parameter type corresponds to the DoubleType in Pipeline Pilot It can either be a single value or an array Note that if there are legal values set for a Real parameter no validation will be done Data from Spotfire Specifies that the input parameter should be data from a data table currently available in TIBCO Spotfire A prompt allows you to specify what data to use at runtime The Data from Spotfire input handler can be used for the parameter type URL or DestinationURL in Pipeline Pilot PP The PP protocol then needs to have one of two file reader components e g a tab delimited text reader or an SD file reader The second reader must be used when the data contains Molfiles and the first reader is used in any other case Note If the protocol requires certain columns to be included it is important to add that information in the Parameter description to help users select the correct columns in the prompt dialog Select this option to prompt the end user of the computation for input Not available for the Data from Spotfire option Select this option to specify a value or an array of values to use as input manually Opens a dialog where you can specify the input parameter 21 TIBCO Spotfire amp Connector for Pipeline P
22. be used as document properties in the analysis You can either predefine the document properties or prompt for them at runtime The properties must be defined on the form prefix suffix Search for Document Properties in the main TIBCO Spotfire help for information about where document properties can be used Add rows Specifies that the output parameter should be sent to the Add rows tool so that it can be used to add new rows to the currently available data tables Replace data table Specifies that the output parameter should be sent to the Replace data table tool where it can replace any of the currently open data tables Data This output parameter returns some form of data to Spotfire and is always used when the usage mode for a computation is a data source or a data transformation Set link template This output handler specifies the LinkTemplate property on a column so that the content of that column is shown as hyperlinks leading to the URL as it has been defined in the protocol Search for LinkTemplate in the main TIBCO Spotfire help for more information about this property The title of the table visualization and the column name for the column Add Edit Remove Configure Computations which should contain the hyperlinks is specified in a prompt dialog Show in text area This output handler populates a text area in Spotfire with the values of the output parameter It is possible to show the values in an exis
23. d as a new data table This gives the end users of the computation the opportunity to decide how to use the results for themselves The Add columns Add data table Add rows Replace data table and Data output handlers all require a file to be produced by the Pipeline Pilot protocol The file type can be either a tab delimited text file or an SD file The path to the file must be given to a parameter of the type URL or DestinationURL in Pipeline Pilot which is then configured in TIBCO Spotfire with one of the handlers listed above Configure Computations Some output handlers require a little more configuration than others See the examples below Add properties This output handler allows you to use the output parameter results as document properties in the analysis Example You can use the resulting document properties to define lines in a visualization representing the approved higher and lower limits of the displayed values 1 In the Pipeline Pilot computation specify the property names to use Add Output Handler Add Properties c ese Wy 3 Enter property names one name per row Higher Limit 4 Lower Limit m The number of entered property names must match the number of values returned by the parameter If you have not created the protocol yourself this information should be available from the creator of the protocol 2 Run the computation to apply the properties to the current analysis 3 In
24. data source cannot have an input parameter that operates on existing data e g a parameter that is configured with a Data from Spotfire input handler TIBCO Spotfire amp Connector for Pipeline Pilot 1 0 User s Manual 4 2 Editing a Computation Once some Pipeline Pilot protocols have been made available in TIBCO Spotfire you can start to configure computations A computation is what determines how the result from the Pipeline Pilot protocol should be used in TIBCO Spotfire gt To edit a computation 1 Select Tools gt TIBCO Spotfire Connector for Pipeline Pilot gt Configure Computations Response The Configure Pipeline Pilot Computations dialog is displayed 2 Click Edit Response The Edit Computation dialog is displayed 3 If desired edit the Name or Description of the computation or edit the parameters by clicking on the button to the right of each parameter Comment See Editing Parameters for more information 4 To publish a computation so that end users can see it select the Make this computation available to end users check box 5 Click OK Response The computation is updated 4 3 Editing Parameters You can edit some settings for the parameters which have been defined at the creation of the Pipeline Pilot protocol This is done by clicking on the a button to the right of the parameter in the Add Computation Configuration dialog or in the Edit Configuration dialog It is normally a good idea
25. dvantage of powerful computations without having to learn any details of creating protocols themselves The TIBCO Spotfire Connector for Pipeline Pilot gives you the opportunity to define input prompts and appropriate output parameters The Pipeline Pilot computation can then be run from within TIBCO Spottfire TIBCO Spotfire amp Connector for Pipeline Pilot 1 0 User s Manual 2 Logging In 2 1 Logging In When you run any of the TIBCO Spotfire Connector for Pipeline Pilot tools and you have selected which server to run against a login dialog appears Pipeline Pilot Server Login Please login to Pipeline Pilot Server Lsemame Password 89m r Qm ever Rir Kile IPTE TEM mr LEE 2 a TIN LIC LIL E II cd Wt m E Cr i myuseramze Remember my usemame password for this session m Enter your Username and Password and click on the OK button to connect to the Pipeline Pilot SCIVCT If you are working on a large company with multiple Pipeline Pilot servers you may occasionally also need to change the server you are connecting to This is done in the Select Server step before reaching the login dialog New servers can be added to the list by clicking on the Manage Servers link in the Server Administration Select Server dialog Server Administration 3 Server Administration 3 1 Determining which Pipeline Pilot Protocols Should be Available in Spotfire When you have created a set of prot
26. er s Manual Add properties Add Output Handler Add Properties Prompt Set predefined value Enter property names one name per row My Property No MyProperty Mo2 MyProperty No3 L ok Cw Option Description Prompt Click this radio button to prompt the end user of the computation for property names Set predefined Click this radio button to predefine the property names to use for this value output parameter Enter property Type the names of the document properties that should use the results names one name from the output parameter per row 26 Configure Computations Set link template Add Output Handler Set Link Templ Prompt Set predefined value Enter table plot title Table Enter column name Animal es Option Description Prompt Click this radio button to prompt the end user of the computation for the table visualization title and the column name of the column to edit Set predefined Click this radio button to predefine the table visualization title and the value column name Enter table Type the title of the table visualization you wish to edit visualization title Enter column Type the column name of the column containing the data that is going name to be converted to hyperlinks Show in text area Add Output Handler Show in Text A 3 Prompt Set predefined value Enter text area title Results e_ Option Description Prompt Click this radio bu
27. erver address hitp MyPipelinePilot Server 9944 Help Type the address to the Pipeline Pilot server in the field Configure Computations 4 Configure Computations 4 1 Adding a New Computation Once some Pipeline Pilot protocols have been made available in TIBCO Spotfire you can start to configure computations A computation is what determines how the result from the Pipeline Pilot protocol should be used in TIBCO Spotfire It could be a new data source a transformation step used when retrieving data from other sources or a stand alone tool used from a link in a text area of a guided analysis Each protocol can result in several different computations gt To add a new computation 1 Select Tools gt TIBCO Spotfire Connector for Pipeline Pilot gt Configure Computations Response The Configure Pipeline Pilot Computations dialog is displayed 2 Click Add Response The Add Computation Select Server dialog is displayed 3 Select the Pipeline Pilot server of interest from the drop down list Comment See Managing Pipeline Pilot Servers for more information about how to add Pipeline Pilot servers to the list of available servers 4 Click OK Response The Add Computation Select Pipeline Pilot Protocol dialog is displayed 5 Select the protocol of interest from the list of Available protocols Comment Only the protocols that have been published in the Server Administration Publish Protocols dialog will be avai
28. h join method to use Click this radio button to predefine which join method to use Data will be kept and columns added only for rows that are available Configure Computations in the current data table If additional rows exist in the new data they will not be added to the current data table Full outer Data will be kept and columns added for all rows available in any of the data tables If additional rows exist in the new data they will be added to the current data table Inner Data will be kept and columns added only for rows that are available in the new data If the new data contains fewer rows than the current data table rows will be removed from the current data table after this operation Right outer Data will be kept and columns added only for rows that are available in the new data If the new data contains fewer rows than the current data table rows will be removed from the current data table after this operation Add data table Add Output Handler Add Data Table 3 Prompt Q Set predefined value Enter data table name Pipeline Pilot Results Option Description Prompt Click this radio button to prompt the end user of the computation for the name of the new data table Set predefined Click this radio button to predefine the name of the resulting data table value Enter data table Type the name of the new data table name 25 TIBCO Spotfire amp Connector for Pipeline Pilot 1 0 Us
29. ile and generates a report with an xy scatter plot that shows the relationship between two properties lt p gt lt b gt See No z bz p eul li a href javascrpt DoLink DDD69C6F 43BC 4 1c0 86BE1D88E458j XY Chart a lis ul Parameters EE n URL Unhandled LJ H X Property Y Property File Type Tooltip Destination String Unhandled In String Unhandled In arr rum In URL Unhandled Make this computation available to end users Option Pipeline Pilot server Protocol name Usage mode Name Description Description Read only Lists the Pipeline Pilot server that the protocol resides on Read only Lists the name of the protocol on the Pipeline Pilot server Read only Lists where this computation should be available The usage mode is specified in the Add Computation Select Usage Mode dialog prior to this step Add a new computation using the same protocol if you need to change this setting The name of the computation as you want it to be displayed to the end users This can be a different name than the original protocol name Lists the description of the protocol as it was written by the protocol creator You can edit the text by simply writing in the Description field The updated description will be shown in the Description field of the 17 TIBCO Spotfire amp Connector for Pipeline Pilot 1 0 User s Manual 4 4 6 18 Parameters
30. ilot 1 0 User s Manual 22 Output parameters Edit Parameter Destination TIBCO Spotfire configuration Pipeline Pilot parameter information Description Description The filename for the destination data Be sure to specify an The filename for the destination data Be sure to specify extension such as txt or xls To save in compressed zipped an extension such as txt or xls To save in compressed format add the extension gz to the filename zipped format add the extension gz to the filename Direction Type Ur Input Attributes Required single value Output Handlers Legal values Add Columns Option Description Direction Handlers Default values S Run Directory ngroups txt Description Displays the description of the parameter for the TIBCO Spotfire users The general description that was written upon creation of the protocol can be edited for further detail Specifies whether this should be an Input or Output parameter Specifies how the parameter should be handled Add columns Specifies that the output parameter should add new columns to the currently available data table If the computation is run as a tool you will be prompted to specify which join type to use Add data table Specifies that the output parameter should be sent to the Add data table tool so that it can be used as a new data table in the open analysis Add properties Specifies that the output parameter values should
31. inue with the wizard according to the instructions in the main TIBCO Spotfire help os o p gt To use a computation as a transformation in the wizards When the As a data transformation option has been selected the computation is added to all places where you can perform a transformation It can be used in the Add Data Table wizard the Replace Data Table wizard the Insert Columns from External Data wizard and the Insert Rows from External Data wizard Example 1 Select File gt Add Data Table Comment Follow the same steps for either of the wizards listed above if you want to add a Pipeline Pilot transformation somewhere else 2 Select the source type for the data you wish to transform Click Browse 4 If the transformation section of the dialog is hidden click on the show transformation 9 arrow to display it 29 TIBCO Spotfire amp Connector for Pipeline Pilot 1 0 User s Manual 5 2 30 In the Transformations drop down list select TIBCO Spotfire Connector for Pipeline Pilot Click on Add In the Pipeline Pilot Computation dialog select the computation of interest and click OK Continue with the wizard according to the instructions in the main TIBCO Spotfire help Details on Pipeline Pilot Computation gt To reach the Pipeline Pilot Computation dialog In Select Tools TIBCO Spotfire Connector for Pipeline Pilot Run Computation If you have not previously logged into a ser
32. ion will be shown in the Description field of the 19 TIBCO Spotfire amp Connector for Pipeline Pilot 1 0 User s Manual 4 4 7 20 Configure Pipeline Pilot Computation dialog and the Pipeline Pilot Computation dialog The description should be written as clearly as possible to help the end users select the correct computation at all situations Parameters Lists the specified parameters for the selected protocol You can click to select a specific parameter and then click on the edit parameter button Lu to change the settings of the selected parameter See Editing Parameters for more information Only parameters promoted to the protocol level will be visible in this list Make this Select this check box to make the computation available to end users computation which do not have the license to configure protocols Keep the check available to end box cleared until you are finished with all configurations and the users computation works as it should Details on Edit Parameter The parameters of a computation can be edited by clicking on the edit parameter button in the Add Configuration Configure or the Edit Configuration dialog However the available handlers for a certain parameter will depend on the type of parameter You cannot select a handler that does not agree with the character of the selected parameter The usage mode of the computation also limits the available handlers TIBCO Spotfire configuration
33. ition are output via the Fail part In this case we use an MOL RXN file ta convert all carboxylic acids in a data source to acid chlorides and view them using the HTML Molecular Table Viewer The rules for drawing a reaction are simple The atom Mame Direction Type Handled a fon Ex He Option Available computations Add Edit Delete Description Parameters Description Lists the currently available computations The usage mode the server name and whether or not the computation has been made available to end users published are also shown If you have not previously logged in to a Pipeline Pilot server you need to do so now Opens the Add Computation wizard where you can choose which protocol from the server you wish to add as an available computation You also get a chance to configure the computation according to your own choice Opens the selected computation for editing Deletes the selected computation Displays the description added by the creator of the protocol This description can also be changed by clicking Edit Displays the available parameters 13 TIBCO Spotfire amp Connector for Pipeline Pilot 1 0 User s Manual 4 4 2 Details on Add Computation Select Server This dialog allows you to select from which Pipeline Pilot server you wish to add a computation gt To reach the Add Computation Select Server dialog 1 Select Tools gt TIBCO Spotfire Connector for Pipeli
34. kipedia org wiki 2 Configure a computation in TIBCO Spotfire using the Pipeline Pilot protocol and edit the output parameter to use the Set link template output handler Edit Parameter LinkTemplate TIBCO Spotfire configuration Description This parameter determines the link template for the hyperlinks that will be formed from the specified column Direction 3 Input Output Handlers Set Link Template Pipeline Pilot parameter information Description Type String Attributes Optional single value Legal values Default values http en wikipedia org wiki iS 3 Determine whether to prompt the end user for input or predefine the table and column to use Add Output Handler Set Link Templ 5 Prompt Set predefined value Enter table plot title Table Enter column name Animal 4 Run the computation Table M F X Animal Type Life expectancy Cat Carnivore 15 Dag Carnivore 12 Rabbit Herbivore a Show in text area This output handler populates a text area in Spotfire with the values of the output parameter 11 TIBCO Spotfire amp Connector for Pipeline Pilot 1 0 User s Manual 12 In this example we have a text area entitled Results available in the analysis and we want the output results from a computation to be shown on a specific location in that text area 1 In the text area type PipelinePilotResult where you want the results from the output parame
35. lable See Determining which Pipeline Pilot Protocols Should be Available in Spotfire for more information 6 Click OK Response The Add Computation Select Usage Mode dialog is displayed 7 Click on a radio button to determine how the computation should be used Comment It could be used as a new data source as a transformation step used when retrieving data or as a stand alone tool See the note below for more information 8 Click OK Response The Add Computation Configure dialog is displayed 9 If desired edit the description of the computation or edit the parameters by clicking on the button to the right for each parameter Comment See Editing Parameters for more information 10 Determine whether or not the computation should be available to end users by selecting or clearing the check box at the bottom of the dialog 11 Click OK Response The new computation is added to the list of Available computations in the Configure Pipeline Pilot Computations dialog and it can also be used from the specified location as defined in the Add Computation Select Usage Mode dialog Note Protocols that are intended to be used as a data source or as a data transformation in TIBCO Spotfire must have one and only one output parameter of the type URL or DestinationURL in Pipeline Pilot This parameter is then automatically populated with the Data output handler in the configuration of the protocol in TIBCO Spottfire A protocol that should be used as a
36. lot gt Server Administration 2 If you have not previously logged into a server then you will be prompted to do so now Server Administration Publish Protocols lo fon ex Pipeline Pilot protocols available for selection Selected protocols available in TIBCO Spotfire B Protocols rem Protocols j Portlets Spotfire SciTegic Examples lt Remove SciTegic Examples Sy Chemistry Sy Chemistry Cheminformatics y Cheminformatics Bioisosters Chemical Reactions Chemical Reactions a2 01 Performing Simple Transformation F ul aF 02 Standardizing Nitro Groups Compound Library Analysis 5 03 Clipping Alcohols off of Esters Compound Library Cleanup 5 9 04 Using RGroup Atoms in Reactions J Compound Library Enumeration 5 9 05 Using Protecting Groups J Compound Library Searching z Maximal Common Substructure Search Non Specific Structures NONS pKa Calculations mg SAR Tables j Leaming and Clustering Merging and Manipulating Data H Molecular Toolkit Data Modeling Generic Integration LJ R Statistics Reporting Sequence Analysis lt T a CaTa nie uta 4 m p i m p Heb Lok canca Option Description Pipeline Pilot Lists all protocols that are available on the selected Pipeline Pilot server protocols available and have not yet been published to TIBCO Spotfire for selection Selected protocols Lists
37. n the United States and or other countries All other product and company names and marks mentioned in this document are the property of their respective owners and are mentioned for identification purposes only This software may be available on multiple operating systems However not all operating system platforms for a specific software version are released at the same time Please see the readme txt file for the availability of this software version on a specific operating system platform THIS DOCUMENT IS PROVIDED AS IS WITHOUT WARRANTY OF ANY KIND EITHER EXPRESS OR IMPLIED INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY FITNESS FOR A PARTICULAR PURPOSE OR NON INFRINGEMENT THIS DOCUMENT COULD INCLUDE TECHNICAL INACCURACIES OR TYPOGRAPHICAL ERRORS CHANGES ARE PERIODICALLY ADDED TO THE INFORMATION HEREIN THESE CHANGES WILL BE INCORPORATED IN NEW EDITIONS OF THIS DOCUMENT TIBCO SOFTWARE INC MAY MAKE IMPROVEMENTS AND OR CHANGES IN THE PRODUCT S AND OR THE PROGRAM S DESCRIBED IN THIS DOCUMENT AT ANY TIME Copyright O 1996 2009 TIBCO Software Inc ALL RIGHTS RESERVED THE CONTENTS OF THIS DOCUMENT MAY BE MODIFIED AND OR QUALIFIED DIRECTLY OR INDIRECTLY BY OTHER DOCUMENTATION WHICH ACCOMPANIES THIS SOFTWARE INCLUDING BUT NOT LIMITED TO ANY RELEASE NOTES AND READ ME FILES TIBCO Spotfire is covered by U S Patent No 6 014 661 and U S Patent No 7 216 116 Other patent s pending TIBCO Software Inc C
38. ne Pilot gt Configure Computation Response The Configure Pipeline Pilot Computation dialog is displayed 2 Click Add Add Computation Select Server Please select Pipeline Pilot server http MyFipelinePilotServer 8944 Help OK Cancel Select the Pipeline Pilot server to use from the drop down list 4 4 3 Details on Add Computation Select Pipeline Pilot Protocol In this dialog you select which Pipeline Pilot protocol to add as a new computation available in TIBCO Spottfire gt To reach the Add Computation Select Pipeline Pilot Protocol dialog 1 Select Tools gt TIBCO Spotfire Connector for Pipeline Pilot gt Configure Computations 2 If you have not previously logged into a server then you will be prompted to do so now 3 Inthe Configure Pipeline Pilot Computation dialog click Add 14 Configure Computations Add Computation Select Pipeline Pilot Protocol Le edes Available protocols Description E E Protocols 5 23 Spatfire Creates an xy scatter plot of the data iw Spotfire Compute Properties L5 Spotfine Rgroup decomposit This protocol reads a data file and generates a report with an xy Ll Rerationd Test 2 scatter plot that shows the relationship between two properties E I pm Start Up See Also E Ex Web Services Eg SciTegic Web Port Example XY Chart Parameters Mame Type Required Default Source Un True data Examples Sample Drugs sd X Property
39. nput value this could be HTML or PDF The legal values are shown as selectable values in the prompt dialog if the parameter requires input from the end user at runtime Lists the default value of the parameter Note If you are using a Pipeline Pilot protocol with an output parameter intended as a URL to a file then this parameter must have the directory set to one of the following runDirectory jobDir or userDir If the parameter is set to any other path you must configure this in Pipeline Pilot or the file will not be found from TIBCO Spottfire Details on Add Edit Output Handler The Output Handler dialog looks different depending on the type of output handler you have selected Below are examples of the various output handler dialogs Add columns Add Output Handler Add Columns I JE c feel Set predefined value Join method Q Left outer rows from current data only Full outer all rows from both curent and new data Inner rows matching in both current and new data only Right outer rows from new data only Target table Mame Pipeline Pilot Results 9k Canes Note To use this output handler the computation must supply a data table where one of the columns can be used to match an ID column in the existing data table Option Prompt Set predefined value Join method Left outer Description Click this radio button to prompt the end user of the computation to determine whic
40. ocols on the Pipeline Pilot server you need to specify which ones should be available in TIBCO Spotfire This is done with the Server Administration tool Only those protocols that have been published here will be available for configuration in the Configure Pipeline Pilot Computation dialog Protocols that are intended to be used as a data source or a data transformation in TIBCO Spotfire must have one and only one output parameter of the type URL or DestinationURL in Pipeline Pilot This parameter is then automatically populated with the Data output handler in the configuration of the protocol in TIBCO Spotfire See Adding a New Computation and Editing Parameters for more information about configuration gt To make a protocol available in TIBCO Spotfire l Select Tools TIBCO Spotfire Connector for Pipeline Pilot Server Administration Response The Server Administration Select Server dialog is displayed Select the Pipeline Pilot server of interest from the drop down list Comment If you need to add another server to the list click on the Manage server link and follow the instructions under Managing Pipeline Pilot Servers Click OK Response The Pipeline Pilot Server Login dialog is displayed Enter the Username and Password for the selected server Click OK Response The Server Administration Publish Protocols dialog is displayed Click on the protocol you want to make available in the Pipeline Pilot pro
41. om the Tools TIBCO Spotfire Connector for Pipeline Pilot menu The guide tools can also be incorporated in a guided analysis via a link in a text area Example Text Area Welcome to this analysis A 4 amt Below are shortcuts that will help you analyze your data Perform a K means Clustering Run Pipeline Pilot Ei Export ta HTML mts aibi ah M s This functionality allows the person configuring the Pipeline Pilot computations to make the most commonly used computations more available to the end users Note The configuration of guide tools only applies to the current document so you can have different sets of guide tools in different analyses 6 2 Configuring Pipeline Pilot Guide Tools If you want to be able to use a Pipeline Pilot computation as a stand alone tool from the Tools menu or if you want to be able to incorporate the computation in a text area of an analysis you first need to configure the computation as a Pipeline Pilot Guide Tool Always follow the steps in the Configuration workflow overview below when setting up guide tools gt Configuration workflow 1 Configure the protocol to run as a tool Comment This is done in the Add Computation Select Usage Mode dialog See Adding a New Computation for more details 2 Testthe computation by selecting Run Computation Comment Make sure that the computation works as expected 3 When satisfied with the result configure the computation to
42. onfidential Information Table of Contents INTRODUCTION icsetesctcsets acia eects Ora Uus oiiaii 1 LOGGING IN anusa a a a aa 2 LOGOO Ics at 2 SERVER ADMINISTRATION ccceseceeeceeecnseenseensecnscenecsecnsecnseonssensseneseneseeees 3 Determining which Pipeline Pilot Protocols Should be Available in Spotfire 3 Managing Pipeline Pilot Servers seessesssseessssessseseeeeennn nennen nennen nnns nan n nna nnns 3 Bac cmo e c s E 4 CONFIGURE COMPUTATIONS 1 occorre eren nennen nnn nnn nnn 7 Adding a New ConmplltallOLi a u tSt tuu AE diu uua d eti areae dut qure tu un att used ba Um dele natus 7 Eris a CONDUIT e see tmu dte tbt Sit ft Ors ere Sea mane ne men cu EL Oat doped 8 EIA r OUC E EE OT LEE E E aan cea eee Seaccene 8 BIETET 13 RUN COMPU TATION aee E 29 USNO COMMONS ied ican E 29 Details on Pipeline Pilot Compl tallODr 5t osi ero De aa odis ien ho neha Veces ues des 30 Detaiis on Parameter Prompt Dialogs neasi ino nie Y ra gutta ics Dove Dee Qd vus edu dau vada a a aD eg anda 31 More About Parameters and Prompt Dialogs ccccccceeeeeeeeeeeeeeeeseeeeeaeeeesseeeeseeeeseueessneeesaees 34 GUIDE TOOLS S e sd MM eRe re ene ne ene er ere Ee eee eer errr 43 What are Guide TOONS usi dade ton a eens fade aia aaa ca desse a eaaa A 43
43. run as a guide tool Comment See the step instruction below for more details 4 Create a link to the tool in a Text Area Comment Go to the Function page in the Insert Link dialog and select the tool from its predefined slot under Tools gt TIBCO Spotfire Pipeline Pilot Connector See How to Use the Text Area in the main TIBCO Spotfire help for more information about how to add links 5 Save the analysis Note If the configuration of the protocol needs to be changed all steps above must be repeated Hence you must configure the computation as a guide tool once more 43 TIBCO Spotfire amp Connector for Pipeline Pilot 1 0 User s Manual 6 3 44 gt To specify a computation as a guide tool l Select Tools TIBCO Spotfire Connector for Pipeline Pilot Configure Pipeline Pilot Guide Tool Response The Configure Pipeline Pilot Guide Tool dialog is displayed Click to select the slot you wish to define Comment Use Pipeline Pilot Guide Tool amp 1 if this is your first configuration Otherwise use the first empty slot or the one you wish to change or update Click Select Computation Response The Pipeline Pilot Computation dialog is displayed Select the computation you wish to use as a guide tool Comment Only computations that have been defined with the usage mode From the Tools menu will be available for selection Click OK Response The computation is run so that you can provide any necessary par
44. st cases the text at the top of the dialog should give you instructions regarding what type of input is required If you do not understand what you should write please contact the person who configured the computation Run Computation Integer Parameter Maximum The maximum number of molecules to cluster Enter value m Option Description Enter value Type an integer value matching the parameter you are prompted for In most cases the text at the top of the dialog should give you instructions regarding what type of input is required If you do not understand what you should write please contact the person who configured the computation Real Parameter Data Array of numerical data whose statistics are to be calculated Enter values one value per row 1 14 4 75 92 65 80 46 15 23 Option Description Enter value Type a real value matching the parameter you are prompted for In most cases the text at the top of the dialog should give you instructions regarding what type of input is required If you do not understand what you should write please contact the person who configured the computation 33 TIBCO Spotfire amp Connector for Pipeline Pilot 1 0 User s Manual 9 4 34 More About Parameters and Prompt Dialogs The Parameter prompt dialogs that are displayed for the end users of a computation will also vary depending on the choices made when creating the protocol in Pipeline Pilot
45. ter to appear Results xt This is a text area with lots of interesting information The results from the output parameter S PipelinePilotResult 2 Edit the configuration for the output parameter so that it uses the Show in text area handler and specify the predefined value to the name of the desired text area in this example Results Edit Output Handler Show in Text Ar ca Prompt Set predefined value Enter text area title Results 3 Run the computation Results X This is a text area with lots of interesting information The results from the output parameter These are the result values The results are shown in the specified text area instead of the placeholder 4 4 Details 4 4 1 Configure Computations Details on Configure Pipeline Pilot Computations gt To reach the Configure Pipeline Pilot dialog 1 Select Tools gt TIBCO Spotfire Connector for Pipeline Pilot gt Configure Computations Configure Pipeline Pilot Computations Available computations Usage mode 01 Performing Simple Transformation Reactions From the Tools menu 02 Standardizing Nitro Groups 03 Clipping Alcohols off of Esters From the Tools menu From the Tools menu Description Parameters Molecular transformations and cleanup can be performed using either MDL reaction files RAN or Daylight Smirks files SME Compounds which are not mapped by the reactants in the reaction defin
46. th to the file must be given to a parameter of the type URL or DestinationURL in PP which is then configured in TIBCO Spotfire with one of the handlers listed above Adds the handler selected in the drop down list to the list of chosen handlers You can add more than one handler for all parameters See Details on Add Edit Output Handler for more information about available settings for different handlers Opens a dialog where the settings for the selected output handler can be changed Only a few of the output handlers have any settings See Details on Add Edit Output Handler for more information about available settings for different handlers Removes the selected handler from the list of chosen handlers Pipeline Pilot parameter information All the information in this group box is read only It shows the settings specified at the creation of the protocol in Pipeline Pilot and it can be of help if you are going to configure parameters for a protocol that someone else has created Option Description Type Attributes Description Displays the original description of the parameter from the protocol Displays the parameter type Displays whether the parameter is required or optional and whether it 23 TIBCO Spotfire amp Connector for Pipeline Pilot 1 0 User s Manual 4 4 8 24 Legal values Default value should use a single value or multiple values Lists the allowed values for this parameter For example for a file i
47. ting text area or to create a new text area When this output handler is selected you will be prompted to specify the name of the text area where you want the values to appear If a text area with the given title is found in any page of the current analysis that text area will be used If no text area 1s found that matches the given title a new one will be added It is also possible to specify a position in an existing text area where the output parameter values will be added Simply type PipelinePilotResult in the text area of interest and that placeholder will be replaced with the result from the Show in text area output handler The first occurrence of the placeholder will be replaced with the first value Note If no placeholder is found in the specified text area the entire content of the text area will be replaced If more than one placeholder is added each following instance of the output handler will replace the first available occurrence of the placeholder It is therefore possible to display the results from multiple parameters or from multiple computations in the same text area Show in browser This output handler is used to display the output URLs from the computation in your web browser The Add columns Add data table Add rows Replace data table and Data output handlers all require a file to be produced by the Pipeline Pilot PP protocol The file type can be either a tab delimited text file or an SD file The pa
48. to find out as much as possible about a parameter before you edit any of the settings Depending on the type of parameter you can change whether it should be an Input or an Output parameter However changing something that has been created to be of one type to another might lead to strange results The most common case of editing parameters is probably that you need to change the handlers that determine what to do with each parameter However the available handlers for a certain parameter will depend on the type of parameter You cannot select a handler that does not agree with the character of the selected parameter See Details on Edit Parameter for descriptions of all handlers Input handlers Input handlers will determine whether the input will be treated as a string integer or real or as data from a data table currently available in TIBCO Spotfire You can only use one input handler per parameter Input parameters can often be filled with content by prompting the end user for information A protocol that should be used as a data source cannot have an input parameter that operates on existing data e g a parameter that 1s configured with a Data from Spotfire input handler Output handlers If the computation is run as a tool you can use more than one output handler for a parameter For example this means that the result from the computation may be added both as new columns to be incorporated with the current data table in the analysis an
49. tocols available for selection list Click on Add Response The selected protocol is moved to the Selected protocols available in TIBCO Spottfire list Repeat steps 6 and 7 for all protocols you want to make available When you are done click OK 3 2 Managing Pipeline Pilot Servers Use the instructions below to add or edit the list of available Pipeline Pilot servers gt To add a new Pipeline Pilot server to the list of available servers L Select Tools gt TIBCO Spotfire Connector for Pipeline Pilot gt Server Administration Response The Server Administration Select Server dialog is displayed Click on the Manage servers link Response The Manage Servers dialog is displayed Click on Add Response The Add Server dialog is displayed TIBCO Spotfire amp Connector for Pipeline Pilot 1 0 User s Manual 4 Enter the address to the new Pipeline Pilot server 5 Click OK Response The new server address is shown in the Manage Servers dialog 6 Click OK Response The new server can now be selected in the Server Administration Select Server dialog gt To edit the address to a Pipeline Pilot server 1 Select Tools gt TIBCO Spotfire Connector for Pipeline Pilot gt Server Administration Response The Server Administration Select Server dialog is displayed 2 Click on the Manage servers link Response The Manage Servers dialog is displayed 3 Click on Edit Response
50. tton to prompt the end user of the computation for the title of the text area to update with the parameter results Set predefined Click this radio button to predefine the title of the text area to update value with the parameter results 2f TIBCO Spotfire amp Connector for Pipeline Pilot 1 0 User s Manual 28 Enter text area Type the title of the text area that should be updated with the results title from the output parameter in the field Leave the field blank to present the results in a new text area Show in Browser For the Show in Browser handler to work you must design the output parameter of the PP protocol in one of the following ways A PP protocol can be designed in two ways for use with the Show in Browser handler 1 For each output file from PP an output parameter of type URL need to be created A Show in Browser output handler must then be configured for each such parameter 2 Instead of a file output parameters of type String or StringArray can be created in PP and be returned as result properties A Show in Browser output handler must then be configured for each such parameter Run Computation 5 Run Computation 5 1 Using Computations Once the Pipeline Pilot protocols have been configured into computations in TIBCO Spotfire they are ready to be used for various types of calculations Depending on how the computation was set up in the Add Computation Select Usage Mode dialog it will show up on different
51. ver then you will be prompted to do so now In this dialog you select which Pipeline Pilot computation to use in the current situation You can reach this dialog from other places in the user interface too For example it will be available if you have selected to add a data table or a transformation from a Pipeline Pilot computation Pipeline Pilot Computation Select the computation to use Description Name Bineine Published After selecting the SD file with the molecules to cluster and oo es optionally the maximum number of molecules to read from the file Compute Statistics http s No you can choose a specific number of clusters to generate or you can Clustering Molecules ee A leave the number of clusters unspecified and select the average Spotfire Rgroup decomposition htip s s number of molecules per cluster Finally you can select one or more ge ME molecular properties to use in the clustering Parameters Name Direction Type Handled Source l URL Handled Maximum Integer Handled Number Of Clusters In Integer Handled Average Cluster Size In Integer Handled Properties To Use In Sting Handled Destination In URL Handled Destination In URL Handled Option Description Available Lists all Pipeline Pilot computations that have been defined to be computations available at this specific place of usage The usage mode is configured during the set up of a new computation It may often be so that a
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