Pipeline Pilot Interface to FTrees Fragment Spaces User Guide
Contents
1. FTrees Pipeline Pilot Interface to Flrees Fragment Spaces Version 2 4 5 1 User Guide for FTrees version 2 4 5 and above and Pipeline Pilot version 8 0 and above Edgar Derksen Sally Hindle T HA i y CH 1 amp Fraunhofer Institut A Algorithmen und Wissen IL schaftliches Rechnen The idea of Feature Trees was born in 1997 during Matthias Rarey s six month research stay at SmithKline Beecham Pharmaceuticals R amp D King of Prussia PA USA and then further developed at Institute for Algo rithms and Scientific Computing SCAI then part of the German National Research Center for Information Technology GMD and now the Fraunhofer Gesellschaft FhG Since 2002 BioSolveIT GmbH has been respon sible for the licensing and continuing development of the FTrees software At this point we would like to thank Scott Dixon SmithKline Beecham now Metaphorics LCC Markus Wa gener SmithKline Beecham now N V Organon and Jens L sel for a lot of helpful and constructive discussions during Matthias Rarey s stay at Smithkline Beecham and afterwards Without them the idea of Feature Trees would not have been evolved in the way it has Also Matthias Rarey thanks the GMD and Smithkline Beecham for funding his research stay in King of Prussia In summer 2000 the Feature Tree comparison algorithms were extended to search directly in large combinatorial chemistry spaces A two stage dynamic programming algorithm enables searching d2. loaded gt gt CONTACT software BioSolveIT ftrees2 0 1 static_data contact_ft dat loaded gt gt TRANSFORM software BioSolveIT ftrees2 0 1 static_data transform dat loaded gt gt GRAPHIC software BioSolvelT ftrees2 0 1 static_data graphic_ft dat loaded 4 2 Problems using the ssh Method You may also experience problems using the ssh login for example the user name is un known or the host is not found 4 3 Further help and BioSolvelT PDF Reporter More complicated errors may arise during the running of Flrees Again though the errors will be collected and as much information shown as possible If you are familiar with FTrees you may want to take a look at all the output of the job yourself to see if you can recognize the problem In this case you can look in the temporary folders Pipeline Pilot sets up inter nally to find the output or if you are working with the ssh method set the parameter lt Run FTrees gt via SSH gt Options gt Delete Results gt to False so that you may then find the files retained on the ssh host these will be in the directory set under the ssh parameter lt Run FTrees gt via SSH gt Options gt Temp Path gt see the help text associated with this param eter to find its default value essentially a cryptically named folder whose name begins with the date and time of the job If you still do not know what is causing the errors write down as much information as p
3. 1 config_ft dat 3 5 UNINSTALLATION 15 4 For the parameter lt Run FTrees gt via SSH gt Host gt enter the Linux machine host name e User specific steps 1 For the parameter lt Run FTrees gt via SSH gt User gt enter the user login name for ssh on the Linux machine 2 For the parameter lt Run FTrees gt via SSH gt Password gt enter the user pass word for ssh on the Linux machine 3 There are more advanced options to be found under lt Run FTrees gt via SSH gt Options gt for more specific ssh parameters Note the option lt Run FTrees gt via SSH gt Options gt Delete Results gt may be useful for trouble shooting later You can save these settings in the components be sure not to save your own user specific login details in components available to others All files necessary for the Flrees calculation will be transferred via scp between the Pipeline Pilot server and ssh Linux machine Files copied and files created the remote server are automatically deleted at the end of the job leaving no trace However in case the user would like to leave a copy of the calculation and result files on the Linux machine or for trouble shooting as mentioned above it is possible to set a parameter to tell Pipeline Pilot not to delete these files lt Optionally gt lt sshDeleteResults gt False 3 5 Uninstallation Use the Flrees installer component to uninstall previous Flrees versions by swit
4. but are looking to generate new ideas Change the parameter lt FIrees Options gt Target Similarity gt an Flrees similarity value to do this If you find that the resulting molecules are too similar amongst each other you can also set the diversity that must be seen between the resulting molecules Change the parameter lt FTrees Options gt Target Diversity gt 2 3 THE EXAMPLE FRAGMENT SPACE TFS 9 The resulting molecules exit the Pass port of the component If you see any molecules exiting from the Fail port then these are queries that could not be interpreted correctly 2 3 The Example Fragment Space tfs A ready to use Fragment Space the knowledgespace can be downloaded from http www biosolveit de download The Fragment Space package knowledgespace x x x indep zip must not be unpacked as the component will read the zip file directly Out of interest you may be curious about what is in the Fragment Space bundle The follow ing files are included knowledgespace fsf This is the main Fragment Space file It includes pointers to the molecule fragment file Feature Tree fragment file joining rule file and the joining rules themselves linking rules knowledgespace mol2 The actual molecule fragments themselves The fragments were generated using publically available data knowledgespace fdf The Feature Tree descriptors for the molecule fragments knowledgespace ldf The linkage rules for the fragments 10 CHA
5. in the error message box as in figure Go to the Jobs tab below the Protocol workspace and check under the last run job for a file called FTreesComponent Debug as in figure Clicking on the link brings up HTML report with input and output data in a browser A correctly started Flrees job outputs the following header if there is a problem you will see some of this header and the point where the problem occurs FIREES Feature based molecular similarity finder Version 2 0 2 11 08 08 Modules PVM FFS A written by Matthias Rarey Marc Zimmermann Sally Hindle Robert Fischer 17 18 CHAPTER 4 TROUBLE SHOOTING copyright by BioSolve IT GmbH FhG SCAI Sankt Augustin Germany for further information mail ftrees info biosolveit de Additional copyright notes getline library C 1993 by Chris Thewalt PVM library C 1997 by University of Tennessee Knoxville TN gt gt FTrees configuration file software BioSolveIT FTrees ftrees2 0 1 config_ft dat loaded gt gt Licensed modules FTrees PVM FFS gt gt PVM status no pvm daemon running sequential gt gt Scripts ar xecuted in sequential mode start PVM for parallel mode gt gt SETTINGS software BioSolveIT ftrees2 0 1 static_data ftrees_settings dat loaded gt gt CHEMPAR software BioSolveIT ftrees2 0 1 static_data chempar dat
6. PTER 2 INTRODUCTION Installation 3 1 BioSolvelT Web Installation The easiest way to download and install BioSolveIT packages and tools is to download and run BioSolveIT Web Installer component Download BioSolvelT in PipelinePilot package from http www biosolveit de download Read UserGuide within that package for fur ther details Note that both PP Client and PP Server need web access to run BioSolveIT Web Installer Without web access you need to follow one of the following sections in this chapter 3 2 Using the FTrees FS Installation Component The Flrees components are set by default to use a so called auto installation of Flrees This works as follows When you run either of the Flrees Calculator or Similarity components and the parameter lt Run FTrees gt is set to on PP Server and the parameter lt Run FTrees gt on PP Server gt Use gt is set to FTrees Auto Installation they search for a Flrees installation in the directory lt scitegic install directory gt public bin BioSolvelT and use this installation to run the calculation A html report pupup shows if a Flrees installation is not found in this directory Use FTrees installer component to install Flrees prior to run calculations In case of a de fault setup you don t need administrator rights to do this as it is actually Pipeline Pilot that carries out the installation and not you as a user In special cases your system administrator prevents installat
7. ching Pa rameter Uninstall Previous Versions to True Use BioSolvelT Uninstaller component to uninstall all FTrees versions Note that this kind of deinstallation only removes Flrees versions installed by Flrees in staller component or BioSolvelT web installer component 16 CHAPTER 3 INSTALLATION Trouble Shooting 4 1 Problems connecting to the external installation Other most commonly seen problems with Flrees in Pipeline Pilot is with the connection to the external Flrees installation For one thing Flrees itself must be correctly installed on the system independently of Pipeline Pilot it is essential first to make sure this is the case especially to make sure that Flrees can locate the licenses Once FIrees runs fine on your system the remaining key task is to make sure the paths to the executable and configuration file are correct within the Pipeline Pilot components If something is amiss with the connection to the external installation you will see an error message box pop up Check the paths to the executable or to the configuration file If it seems Flrees could be started but not run the problem almost always lies either with the path to the configuration file or with licenses not being found Also make sure that you have a FTrees license FFS If Flrees runs OK independently from Pipeline Pilot then it is likely to be the path to the configuration When the error messages pop up they may contain an FTreesError
8. e which machine is the Pipeline Pilot server by starting your copy of Pipeline Pilot Client on your own workstation and find the name or IP of the server shown at the bottom right of the status bar see figure B 2 You must find where the FTrees installation is on that machine El Pipeline Pilot Professional Client File Edit View Tools Window Help D H amp R aB eao 5 Components Generic E Chemistry eder Prot Comp Help Elf parameters 5 5TT_ Help Parameters Implementation Information Error Ready Server bcalhost 6 0 2 PDA Figure 3 2 See where your Pipeline Pilot Server is installed e General Steps 1 Set lt Run FTrees gt to on PP Server 2 Set lt Run FTrees gt Use gt to Preinstalled FTrees 3 Expand lt opsFTreesExe gt 14 CHAPTER 3 INSTALLATION 4 For the parameter lt Run FTrees gt on PP Server gt Executable gt enter the path to the Flrees installation on Pipeline Pilot server For example C Programs BioSolveIT FTrees2 bin ftrees exe 5 For the parameter lt Run FTrees gt on PP Server gt Configuration gt enter the path to the Flrees configuration file config_ft datassociated with the FTrees installa tion For example C Programs BioSolveIT FTrees2 config_ft dat You can save these settings in the components 3 4 2 To Connect to an FTrees Installation on a Remote Linux Server Your exist
9. er gt Use gt in the Implementation tab to preinstalled FTrees There are actually two ways to use Flrees with an external installation These are by us ing Flrees installed directly on the Pipeline Pilot server you are or by accessing a remote machine where FTrees is installed using ssh method The method is selected using the pa rameter lt Run FIrees gt Both methods are covered in more detail below 3 4 USING CUSTOM EXTERNAL FTREES INSTALLATIONS 13 3 4 1 To Connect to an FTrees Installation on the Pipeline Pilot Server The most common scenario is that you will have an installation of Flrees on the Pipeline Pilot server If you choose this option you just have to enter the path to the executable and configuration file as parameters in the Implementation tab Pipeline Pilot will then just start FTrees whenever it is required by making a call to the executable that you entered This method is given the name on PP Server On Pipelinepilot Server You can see an exam ple in figure 3 1 User Mode Default El Run FTrees on PP Server E on PP Server Use PreinstalledFTrees Executable ft C Program Files 86 BioSolvelT FTrees2 1 3 bin ftrees exe Pal Configuratior C Users Edgar Documents config_ft dat Implementation Parameters Figure 3 1 ops Connect to an Firees Installation on the Pipeline Pilot Server e Requirement Flreesis installed on the Pipeline Pilot server You can se
10. ge to a custom directory 3 From the custom directory import all components xml using PP Client via drag and drop to your components collection Install FTrees Drag and drop Flrees installation component from the components collection to an empty protocol Add your license for the executable of Flrees in the field for the parameter lt Run FTrees gt on PP Server gt License Server or License File gt in the Implementation tab if your license is available from a license server simply type in the name of the server in this format Oservername or if you have a license file then you may browse for it using the facility 3 Run protocol once it will result into a html report showing installation success For alternative installations and more details see chapter 3 Create or Update Protocols Drag and drop Flrees Fragment Space component into a protocol Update via a right click drag and drop of new component onto component reference in a protocol Now you are ready to setup the new components and run your protocol CHAPTER 1 QUICK START STEPS Introduction 2 1 About Flrees FTrees is a piece of software for calculating the Feature Tree descriptor and comparing two or more of these descriptors to each other The theory behind Feature Trees can be found in 1 Rather than being based on a linear description such as bit strings or vectors the Feature Tree descriptor represents the molecu
11. ing Flrees installation could be on a Linux computer remote from the Pipeline Pilot server in this case we offer an alternative so you can use the remote installation instead Here the calculations carried out by Flrees will be done on the remote Linux machine Pipeline Pilot logs into the Linux machine using ssh having copied all relevant files to the machine and will run the calculation there finally copying back all data it needs to the Pipeline Pilot server to continue with the pipeline This method is given the name v a SSH You can see an example in figure 3 Implementation User Mode Default v E Run FTrees via SSH v E via SSH Executable ft software BioSolvelT ftrees ftrees Configuratior home ederk22s config_ft dat Host rho User ederk22s oe Password Figure 3 3 via SSH Connect to an Flrees Installation on a Remote Linux Server via ssh e Requirement Flrees is installed on a Linux machine available to the Pipeline Pilot server via ssh e General Steps 1 Set lt Run FTrees gt to via SSH 2 For the parameter lt Run FTrees gt via SSH gt Executable gt enter the path to the Flrees installation on the Linux machine For example software BioSolveIT ftrees 2 0 1 bin ftrees 2 0 1 3 For the parameter lt Run FTrees gt via SSH gt Configuration gt enter the path to the FTrees configuration file config_ft datassociated with the FTrees installation For example software BioSolveIT ftrees 2 0
12. ions by PP and you need to ask him to install Flrees As this installation knows nothing about the licenses you may have for Flrees you have to supply the license information separately This is supplied using the parameter lt Run FTrees gt on PP Server gt License Server or License File gt as described above in the section The installation is carried out once only for that Flrees version and only once per server not per user The software is available to all users once it is installed 11 12 CHAPTER 3 INSTALLATION 3 3 Using Global Variables Use global variables as an alternative to the FTrees installation component decribed in sec tion Note that global variables will only be used if components are set to run auto installation see section 3 2 but no installation is done by an FTrees installation component yet Goto Administratin Portal accessible through the Server Home Page at http localhost 9944 if PP Server is installed on your local machine The Server Home Page is also available through your PP Client in menu lt Help gt Server Home Page gt Use default name scitegicadmin and password scitegic if you have not changed it yet Browse to lt Setup gt Globals gt Add Custom Global Protocol Properties Note that defining parameters within your protocol will override global variables if they are named the same Use parameters within your protocol instead of global variables only if you want to use a custom in
13. irectly in chemistry spaces without an explicit enumeration of molecules 2 This work was also done during a research stay in the US this time at Roche Bioscience in Palo Alto The chemistry space search algorithm was developed in cooperation with Martin Stahl Hoffmann La Roche Basel and we would like to thank him for this excellent cooperation We also wish to thank Hans Joachim B hm Hans Maag both Roche and Thomas Lengauer GMD for making this research stay possible Since then the Feature Trees software has been further developed and extended by several contributors in cluding Marc Zimmermann FhG MTrees and the new Dynamic Matchsearch algorithm Robert Fischer Sally Hindle and other developers at BioSolveIT GmbH and the Center for Bioinformatics ZBH University of Ham burg This document contains proprietary information of BioSolvelT GmbH and is protected by copyright It is provided together with Software of BioSolvelT under a license agreement and may be used only in accordance with the terms and conditions of this agreement The document serves solely for the purpose of using the Software No part of the document may be transferred to any third party or reproduced as a whole or in parts without written permission from BioSolvelT Base software 2001 by Fraunhofer Gesellschaft FhI SCAD Getline library 1993 by Chris Thewalt PVM library 1997 by University of Tennessee Knoxville TN Python library 1991 1995 by S
14. irst that you should change these settings as they may have already been set to fit the current environment e Go to the Scitegic Server Home Page for example via the Help menu in your Pipeline Pilot client e Click on Pipeline Pilot Administration Portal and log in with the Administrator user name and password e In the Security tab go to Authentification e For the Authentification Method choose DOMAIN and a set of parameters will ap pear e Enter the domain name in the field Domain and choose Full for Impersonation e Choose DOMAIN for Retrieve Groups and leave Limit access to listed domains set to No e click Save and log out again After you have done this you will need to enter your domain login details when you start the Pipeline Pilot Client Bibliography 1 M Rarey and J S Dixon Feature trees A new molecular similarity measure based on tree matching Journal of Computer Aided Molecular Design 12 471 490 1998 2 M Rarey and M Stahl Similarity searching in large combinatorial chemistry spaces Journal of Computer Aided Molecular Design 15 497 520 2001 23
15. le as an unrooted tree where the nodes of the tree de scribe the major building blocks of the molecule The comparison of two Feature Trees then proceeds using a recursive matching algorithm splitting the trees into smaller and smaller subtrees The Feature Tree approach has several advantages the most important being the fact that the alignment of two Feature Trees can be translated into a comprehensible map ping of the two underlying molecules For more details on the algorithms and achieved results see 1 The very nature of the Feature Tree means it is also perfectly suited to working with frag ments of molecules Molecular fragments can be described by a Feature Tree just like a com plete molecule and therefore can also be compared to each other Together with the rules describing how fragments are allowed to be joined the molecule fragments form a Flrees Fragment Space Complete molecules can be used to search in the Fragment Space using the joining rules to guide the construction of fragments see Figure 2 1 for an illustration This technique is especially advantageous for searching in combinatorial sets of molecules like combinatorial libraries or combinatorial chemistry spaces 2 contains more complete details about how the search algorithm works 2 2 Flrees FS Component in Pipeline Pilot The Flrees FS component can be thought of as a molecule generator for Pipeline Pilot The component has no input port but takes a query file a
16. m gt The name of this parameter stands for ssh Has Same File System Normally for an ssh job Pipeline Pilot must first copy all the data required by FTrees to the lt Run FTrees gt via SSH gt Host gt using scp This is time consuming It is possible that the Pipeline Pilot Server and lt Run FTrees gt via SSH gt Host gt actually share the same file system rendering the scp process unnecessary Select True if the Pipeline Pilot Server and lt Run FTrees gt via SSH gt Host gt share the same File System no copying of data is necessary Selecting False means Pipeline Pilot copies all the data to and back from the lt Run FTrees gt via SSH gt Host gt this is just a little slower but will always still work Leave the parameter set to False if you are uncertain 5 2 Accessing Other Domains within Pipeline Pilot Often in house data or even your own working data are accessible from a windows com puter via a domain a path starting for example z or which you cannot find from within Pipeline Pilot That means you must first literally transfer the data to the Pipeline Pilot Server itself If you are using a Linux Pipeline Pilot server this hint does not apply 21 22 CHAPTER 5 TIPS AND TRICKS To get around this problem and make the Pipeline Pilot working environment much more flexible you can allow users access to domains you need Administrator rights to be able to do this Also check f
17. ossi ble relating to your installation scheme You can also create a PDF Report unsing BioSolveIT PDF Reporter component which summarizes installation data into one pdf file Send all the information to support biosolveit de 4 3 FURTHER HELP AND BIOSOLVEIT PDF REPORTER Last error FTrees Calculator Error FTrees executable run into Error FTrees Exit Code not 0 See Jobs Window gt FTrees_Calculator_Debug for more Information DK Help Locate Error Details gt gt Figure 4 1 An error box reporting that the Flrees exe could not be found Jobs Protocol Name Status New Protocoll Finished Errors txt FTrees Calculator Debug New Protocolil Running New Protocoli2 Finished Jobs Help Error Figure 4 2 The full error report can be found in the Jobs tab 19 20 CHAPTER 4 TROUBLE SHOOTING Tips and Tricks 5 1 Other Significant Parameters in the FTrees Components For detailed documentation of all parameters for allcomponents refer to the documentation you find in the Help area of the Pipeline Pilot window We list here particularly interesting parameters those that greatly influence the protocol or change the outcome of calculations or those that may help you understand what is happen ing in the components 5 1 1 lt Has Same File System gt FTreesCalculator Similarity Implementation lt Run FTrees gt via SSH gt Options gt Has Same File Syste
18. s a parameter The results of searching with your queries is a set of resulting molecules output into the pipeline The component requires two files 8 CHAPTER 2 INTRODUCTION Figure 2 1 The Flrees FS component takes a query molecule as input and uses it to generate new molecules from a Fragment Space based on a set of joining rules the new molecules are sent via the Pass port into the pipeline Fragment Space File A Fragment Space must be provided for the component as a zip package This is because a Fragment Space consists of several files and these must be kept together during any file transfer process Inside the zip package are the four files that form the Fragment Space in the format required by Flrees FS If you already have your own Fragment Spaces be sure to have all four files ready and pack them together using a zip program The four files that form a Fragment Space in Flrees FS format can be seen as an example in section 2 3 Query The query file can be in any molecule input format readable by Pipeline Pilot a Feature Tree file faf or the special Feature Tree database format used by the Flrees Writer and Reader components ft db You can use a multiple query file make sure you adjust the maximum number of queries parameter The results of the search can be tuned according to how similar the resulting molecules are to the queries Often you do not want to see molecules almost exactly identical to your queries
19. stallation for that protocol The first variable file_server_FTrees_executable must be set to the full path of Flrees exe cutable available by the PP Server Example C Program Files x86 BioSolveIT FTrees ftrees exe The second variable file_server_FTrees_config must be set to the full path of Flrees config uration Example C Program Files x86 BioSolveIT FTrees config_ft dat In comparison to FIrees auto installation see section 2 you need to check the compatibil ity between your defined installation and the components 3 4 Using Custom External FTrees Installations You can also use an existing external installation of the Flrees software at each component This means you also have the opportunity to use settings different to those set by default To do this you must already have Flrees installed somewhere on your system outside of Pipeline Pilot To install Flrees yourself visit the download page at BioSolvelT http www biosolveit de download and fetch the download package for your system for the latest FTrees package Follow the instructions in the package to install Flrees and receive your licenses Enter the license information for Flrees as described in the package and not using the parameter lt Run FTrees gt on PP Server gt License Server or License File gt as for the internal installation To use an external installation of FTrees you must change the value of the parameter lt Run FTrees gt on PP Serv
20. tichting Mathematisch Centrum Amsterdam The Netherlands 2015 BioSolveIT GmbH An der Ziegelei 79 53757 St Augustin Germany Phone 49 2241 2525 0 support biosolveit de Contents Contents 1 Quick Start Steps 1 1 Download and Import current Flrees FS Package PATA A fee 1 3 Create or Update Protocols 2 Introduction 2 1 About Firees 2 2 Flrees FS Component in Pipeline Pilot 2 3 The Example Fragment Space tfs 3 Installation 4 pre 3 2 Using the Flrees FS Installation Component ee a 3 4 1 Io Connect to an Flrees Installation on the Pipeline Pilot Server 3 4 2 To Connect to an Firees Installation on a Remote Linux Server 3 5 Uninstallation Trouble Shooting 4 1 Problems connecting to the external installation 4 2 Problems using the ssh Method 4 3 Further help and BioSolveIT PDF Reporter 3 N ao a A o N N 11 11 11 12 12 13 14 15 17 5 Tips and Tricks 5 1 Other Significant Parameters in the Flrees Components 5 1 1 lt Has Same File System gt dira abre CEES 5 2 Accessing Other Domains within Pipeline Pilot References Bibliography CONTENTS Quick Start Steps Download and Import current FTrees FS Package Download current FTrees FS in PipelinePilot package on http www biosolveit de download 2 Extract Flrees FS packa
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