Pipeline Pilot Interface to LeadIT User Guide
Contents
1. 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 11 Download and Import current LeadIT Package 12 InstallleadlT 22 2 Ho oo oos L3 Create or Update Protocols 35 ee ee een ua 21 About Feadll 2 es 28 28 amp an eh aces da ea ee ek 22 Lead Component in Pipeline Pilot xx au wer ho a oe Re eh 2 2 1 Binding mode prediction 439 39 49 3433 2208 2 34 2 2 2 Virtual high throughput screening o ooo 3 Installation 3 1 BioSolvelT Web Installation 3 2 Using the LeadlT Installation Component o o ooo co 3 3 Using Global Variables a aut 0 ce UE FE 3 4 Using Custom External LeadlT Installations 3 4 1 To Connect to an LeadiT Installation on the Pipeline Pilot Server 3 4 2 To Connect to an Lead Installation on a Remote Linux Server 35 Running LeadlT in Parallel inPipelinePilot 3 5 1 Running in Parallel on the Pipeline PilotServer 352 Running in Parallel on a Remote Linux Cluster 3 5 3 Example Scenarios and Required Settings ARA ub ace ue en Gee Pe E dy a a a a o o N N N 4 CONTENTS 4 Trouble Shooting 21 4 1 Problems using the ssh Method e x ex cias eine Sark ee ee Y x 22 Seve edd obo S de Bow E d 222. Use BioSolvelT Uninstaller component to uninstall all LeadlT versions Note that this kind of deinstallation only removes LeadiT versions installed by LeadlT in staller component or BioSolvelT web installer component Trouble Shooting The most commonly seen problems with LeadlT in Pipeline Pilot is with the connection to the external LeadlT installation For one thing LeadIT 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 LeadlT can locate the licenses Once LeadlT runs fine on your system the remaining key task is to make sure the path to the executable is correct within the Pipeline Pilot component When the error messages pop up they may contain an LeadITError in the error message box as in figure 4 1 Go to the Jobs tab below the Protocol workspace and check under the last run job for a file called LeadITComponent Debug as in figure Clicking on the link brings up HTML report with input and output data in a browser A correctly started LeadIT job outputs the following header if there is a problem you will see some of this header and the point where the problem occurs LeadIT Copyright Prediction of Protein Ligand Interactions BioSolveIT GmbH Version 1 0 0 1 An der Ziegelei 79 Modules CDOCK FLEXE PHARM SCREEN PERMUTE 53757 St Augustin Ge
3. see the help text associated with this parameter 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 possible 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 2 FURTHER HELP AND BIOSOLVEIT PDF REPORTER 23 Last error ex LeadlT Docking Error LeadlT executable run into Error LeadlT Exit Code not 0 See Jobs Window gt LeadlT Docking Debug for more Information OK Help Locate Error Details gt gt Figure 4 1 An error box reporting that the LeadlIT exited with error Protocol Name Status Start New Protocoll Error Wed Oct Errors txt a LeadIT Docking De Jobs Help Error Figure 4 2 The full error report can be found in the Jobs tab 24 CHAPTER 4 TROUBLE SHOOTING Tips and Tricks 5 1 Other Significant Parameters in the LeadlT Component For detailed documentation of all parameters 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 workflow or change the outcome of calculations or those that may help you understand what is
4. 25 5 1 Other Significant Parameters in the Lead Component 25 5 1 1 lt Has Same File System gt u 08 una Eo HP eR Vs 25 5 2 Accessing Other Domains within PipelinePilot 25 Quick Start Steps Download and Import current Lead T Package Download current LeadIT in PipelinePilot package on http www biosolveit de download 2 Extract LeadlT package 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 LeadIT Drag and drop LeadlT installation component from the components collection to an empty protocol Add your license for the executable of LeadlT in the field for the parameter Run Lead IT gt on PP Server gt License Server or License File in the Implementation tab if your license is available from a license server simply type in the name of the server in this format servername 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 new components into a new 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 protoc
5. Hiller Birte Seebeck and Marc Zimmermann Institutions We the developers acknowledge GMD now FhG for supporting the work on LeadiT for nearly a decade and BMBF for funding LeadiT related scientific work We also thank our early cooperation partners BASF AG Ludwigshafen Merck KGaA Darmstadt and Boehringer Ingelheim Biberach an der Riss for enthusiasm support and many fruitful discussions Also we are grateful for support from Tripos during many years of a fruitful developer distributor relationship Finally we would like to thank all other companies and academic institutions who collaborated with us and helped us in a multitude of ways to create this great piece of software This document contains proprietary information of BioSolveIT 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 c 1991 1995 by Stichting Mathematisch Centrum Amsterdam The Netherlands Torsion angle data by GMD SCAI CCDC BASF AG
6. LeadIT US Pipeline Pilot Interface to LeadlT Version 2 1 8 1 User Guide for LeadlT version 2 1 8 and above and Pipeline Pilot version 8 0 and above Edgar Derksen Sally Hindle LT ES T H1 Fraunhofer Institut Algorithmen und Wissen schaftliches Rechnen 110 The development of LeadlT began back in 1993 in the context of the project RELIWE funded by the German Federal Ministry of Education and Research BMBF In the following three years Matthias Rarey and Stephan Wefing under the leadership of Thomas Lengauer laid the foundation of LeadlT For his PhD thesis Matthias developed the first prototype of LeadlT Subsequently as the head of the Computational Chemistry group at GMD he guided the further development of LeadlT and its various extension modules Today he is the Director of the Zentrum f r Bioinformatik at the University of Hamburg and as such initiates a multitude of docking related projects and provides guidance to the developers also in his role as a member of the board of BioSolvelT Since 1996 many people have contributed to this code and the related research This list is an attempt to ac knowledge all co workers in this ongoing project Developers in alphabetical order e Holger Claussen now BioSolveIT developed FlexE to enable docking into ensembles of protein struc tures and provided a multitude of general enhancements in LeaalT e Ingo Dramburg now self employed developed a SMARIS M based mechan
7. Pipeline Pilot server via ssh e General Steps 1 Set Run LeadIT gt to via SSH 2 For the parameter Run LeadIT gt via SSH gt Executable gt enter the path to the LeadlT installation on the Linux machine For example software BioSolveIT leadit bin leadit 3 For the parameter lt sshHost gt enter the Linux machine host name e User specific steps 1 For the parameter Run LeadIT gt via SSH gt User enter the user login name for ssh on the Linux machine 2 For the parameter Run LeadIT gt via SSH gt Password enter the user pass word for ssh on the Linux machine 3 There are more advanced options to be found under Run LeadIT gt via SSH gt Options for more specific ssh parameters Note the option Run LeadIT gt via SSH gt Options gt Delete Results gt this may be useful for trouble shooting later You can save these settings in the component be sure not to save your own user specific login details in components available to others All files necessary for the LeadlT calculation will be transferred via scp between the Pipeline Pilot server and ssh Linux machine Files copied and files created the remote server 3 5 RUNNING LEADIT IN PARALLEL IN PIPELINE PILOT 15 Implementation User Mode Default v E Run LeadIT via SSH E via SSH E Executable leadit exe software BioSolvelT LeadIT leadit Host hosti User userl Ane Password Implementation Parame
8. bed in sec tion 3 2 Note that global variables will only be used if components are set to run auto in stallation see section B 2 but no installation is done by an LeadiT installation component yet Goto Administratin Portal accessible through the Server Home Page at http localhost9944 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 installation for that protocol The first variable file server Lead T executable must be set to the full path of LeadlT exe cutable available by the PP Server Example C Program Files x86 BioSolveIT FTrees ftrees exe The second variable file server LeadlT config must be set to the full path of LeadlT con figuration Example C Program Files x86 BioSolveIT FTrees config_ft dat In comparison to LeadlT auto installation see section B 2 you need to check the compati bility between your defined installation and the components 3 4 Using Custom External LeadlT Installations You can also use an existing external instal
9. ct Filename in the parameter tab By default 10 different docking poses will be calculated You can change this value at the paramter Number of Solutions be aware that LeaalT can create hundreds of poses To see a simple visual result of the poses with their scores drag and drop the compo nent HTML Table Viewer to your pipeline Connect the output pass port of LeaalT component to the input port of HTML Table Viewer Your workflow should look like the example in figureP 1 and is ready to run 2 2 2 Virtual high throughput screening 1 2 Start with a molecule reader as described in In this example the reader de fines the library you want to screen You can also replace the MOL2 reader with any molecule reader available in the Pipeline Pilot collection Remember to change the Maximum parameter to read all molecule records from the file 2 2 LEADIT COMPONENT IN PIPELINE PILOT 9 Mol Reader EiosolvelT Sort Data Range Filter HTML Table Tool Viewer Figure 2 2 Starting example for virtual high throughput screening 3 Set up LeadlT component as described inf2 2 1 4 Change the lt Number of Solutions gt parameter to 1 If you want to take more poses into account you have to do some extended analysis of the results after the docking calculation using the components available to you in Pipeline Pilot check the Pipeline Pilotdocumentation for more information The result will now be one pose per inpu
10. e job on the Pipeline Pilot server ssh PPServer ssh Parallel Processing Options False Number of PP servers in list Number of ssh Hosts in list 1 Number of Processes Behavior The calculation will run as one complete job on the ssh host ssh PPServer PPServer Parallel Processing Options True Number of PP servers in list 1 Number of ssh Hosts in list Number of Processes 1 Behavior Default Induces the pipeline effect the job will run in chunks on the server processor s ssh PPServer PPServer Parallel Processing Options True Number of PP servers in list 1 Number of ssh Hosts in list Number of Processes 1 Behavior A true parallel effect the job will be run in chunks on the server processors ssh PPServer PPServer Parallel Processing Options True Number of PP servers in list Number of ssh Hosts in list 4 each with two processors 2 2 2 2 Number of Processes Behavior A true parallel effect the job will run in chunks in par allel split across 8 processors ssh PPServer ssh Parallel Processing Options True Number of PP servers in list 1 Number of ssh Hosts in list 5 each with 2 processors Number of Processes 10 Behavior A true parallel effect the job will run in chunks in par allel split across 10 processors 20 CHAPTER 3 INSTALLATION 3 6 Uninstallation Use the LeadlT installer component to uninstall previous Lead T versions by switching Parameter Uninstall Previous Versions to Irue
11. enter a list of the server names at the parameter lt Server gt Below that for the parameter Processes enter a list of the number of processes each server should receive The lists are both comma separated and must be in corresponding order Remember to adjust also the Batch Size accordingly Note the path to the external installation of Lead T must be same on all servers 3 5 2 Running in Parallel on a Remote Linux Cluster We have developed an implementation in the component whereby a large cluster can be incorporated to run Lead jobs without them having to be Pipeline Pilot servers However it must be a Linux cluster and the component must use the ssh method You must also have enough LeadIT licenses available to the cluster The settings in the Implementation tab must be made as for running the ssh method with two important changes Instead of one Run FTrees gt via SSH gt Host enter a comma separated list of the host names in the Linux cluster Then you must choose how many batchs in total you want the job to be split into and enter this total in the lt Processes gt parameter Remember to change the Batch Size to fit with the number of processes Figure B 5 may help clarify how the method works The Pipeline Pilot server will run with the number of processes given in lt Processes gt How ever in this case the processes the server receives are not the Lead T calculations them selves but instructions for start
12. er the path to the executable and configuration file as parameters in the Implementation tab Pipeline Pilot will then just start LeadlT 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 2 e Requirement LeadlT is installed on the Pipeline Pilot server You can see 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 1 You must find where the LeadiT installation is on that machine El Pipeline Pilot Professional Client File Edit View Tools Window Help DE amp e x sBerl22o tz zl Am Favorites J Generic Chemistry eder Prot comp Help Help es Parameters Implementation Information Error Ready Server localhost 6 0 2 Figure 3 1 See where your Pipeline Pilot Server is installed e General Steps 1 Set Run LeadIT gt to on PP Server 2 Set Run LeadIT Use to Preinstalled LeadIT 3 For the parameter Run LeadIT gt on PP Server gt Executable gt enter the path to the LeadIT installation on the Pipeline Pilot server For example C Program Files BioSolveIT leadit3 leadit exe 4 Add your license for the executable of LeadlT in the field for the parame
13. happening in the component 5 1 1 Has Same File System gt Implementation lt Run LeadIT gt via SSH gt Options gt Has Same File System gt Normally for an ssh job Pipeline Pilot must first copy all the data required by LeadlT to the Run FTrees gt via SSH Host gt using scp This is time consuming It is possible that the Pipeline Pilot Server and 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 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 Run FTrees gt via SSH gt Host 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 computer 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 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 t
14. ing the ssh jobs The server iterates through its 10 jobs each time spawning an ssh job on a Linux host Beware that the Pipeline Pilot server does not know how many processors the Linux hosts have so make sure you choose the number of lt Processes gt to fit the number of Linux hosts and their number of processors respectively be careful not to overload the Linux hosts FigureB 6 shows the detailed settings required to set up the calculation as in figure B 5 3 5 RUNNING LEADIT IN PARALLEL IN PIPELINE PILOT 17 10 Processes 1 Server 10 ssh logins 5 ssh hosts Host 1 Host 2 Ce Host 4 Host 5 Figure 3 5 The method of parallel processing on Linux clusters in the Lead T component The Pipeline Pilot server is given 10 processes The 10 processes start an ssh job respectively distributed amongst the ssh hosts As you may already have realised you could enter more than one Pipeline Pilot server at the Server parameter along with another entry for number of Processes as a comma separated list to execute a doubly parallel calculation Note to get this method to work you will need to change the maximum number of processes per Pipeline Pilot server The Pipeline Pilot Client will let you enter any number for the Processes parameter and does not warn you if this number is above the maximum Changing the maximum number requires Administrator rights The number of processes per Pipeline Pilot server is usually restricted to
15. ions True Mi Batch Size 1 El Server localhost Processes 1 Preserve Order True v r Implementation Parameters Figure 3 4 The options for tuning parallel processing are found in the Implementation tab It is important to note that a balance must be achieved between the overhead caused by running several calculations instead of one and the size of the calculation there is a lot 16 CHAPTER 3 INSTALLATION of overhead involved in sending all the essential data to different computers and collecting the results For the Lead T component however we still think parallel computing will work also for parallel jobs with batch size 1 Of course these figures depend on the speed of your machines and network experiment with your set up if you intend to carry out large calculations often Also we advise you to read the Pipeline Pilot documentation about parallel processing to understand more fully how it works Note to set up large parallel processing jobs you will need Administrator rights to change one setting 3 5 Running in Parallel on the Pipeline Pilot Server You may have a multi processor machine as your Pipeline Pilot server If you also have the appropriate number of Pipeline Pilot and LeadiT licenses the simplest way to start a parallel calculation is to raise the number of processes to the number of processors of the machine You could also have more than one Pipeline Pilot server available in your network If so you can
16. ism and chemical rules for systematic testing and manipulation of compounds e Marcus Gastreich now BioSolvelT contributed significantly to an improved chemical model in LeadiT s static data e Sally Hindle now BioSolvelT developed FLEXSIS PHARM which allows docking to take place under constraints placed in the protein active site e Andreas K mper now MPI implemented various enhancements and extensions in Lead T e g the Tripos force field e Bernd Kramer now 4SC developed parts of the scoring function and interaction model in LeadlT e Markus Lilienthal now BioSolveIT implemented various post optimization procedures and grid enabling technology e Gordon M ller now BioSolvelT is steadily improving the robustness of the software underneath the surface e Matthias Rarey now ZBH developed the combinatorial extension module FLEXSISC adjunct for LeadlT c f above e Frank Sonnenburg now BioSolvelT developed the Python wrapper pyflexsis e Stephan Wefing now BioSolveIT developed major parts of the physico chemical models behind LeaalT Other contributors in alphabetical order Gerhard Barnickel Merck KGaA Joachim B hm Roche Hans Briem Schering Christian Buning Sanofi Aventis Gerhard Klebe Univ of Marburg G nther Metz Santhera Thomas Mietzner BASF Martin Stahl Roche Gert Vriend Univ of Nijmegen Students involved in development and documentation in alphabetical order were Christoph Bernd Claus
17. king project for the calculation The project is a file with xx extension You can find examples within this package or you can use the Lead T GUI to create a new project Number of Solutions For each incoming molecule the Lead T component runs a docking calculation using the defined project which results in a set of poses These are ranked by docking score Only the best Number of Solutions poses are output from the component CHAPTER 2 INTRODUCTION Error port If the calculation for the input molecule fails the input molecule will be passed to error port The following two examples form a first simple tutorial to see how the Lead T component works 2 2 1 Binding mode prediction Mol Reader BiosolwelT HTML Table Tool Viewer Figure 2 1 Starting example for binding mode prediction First you need a source for the input molecules Drag and drop a molecule reader component like Mol2 Reader to your empty pipeline area Select a MOL2 file in the parameter tab with the parameter lt Source gt You can try out a MOL2 file in the examples folder of this package Set the Maximum parameter to 1 to ensure you start with only one molecule This will form a quick example as a first test Drag and drop the LeadlT component to your pipeline area and connect the output port of the molecule reader to the input port of the LeadlIT component Go to the LeadlT component and define a project with the parameter Proje
18. lation of the LeadlT software This means you also have the opportunity to use settings different to those set by default To do this you must already have LeadiT installed somewhere on your system outside of Pipeline Pilot To install LeadlT yourself visit the download page at BioSolvelT http www biosolveit de download and fetch the download package for your system for the latest LeadlT package Follow the instructions in the package to install Lead T and receive your licenses Enter the license information for LeadlT as described in the package and not using the parameter Run LeadIT gt on PP Server gt License Server or License File gt as for the internal installation To use an external installation of LeadlT you must change the value of the parameter Run LeadIT gt on PP Server gt Use in the Implementation tab to preinstalled LeadIT There are actually two ways to use LeadlT with an external installation These are by using LeadlT installed directly on the Pipeline Pilot server or by accessing a remote machine where LeadiT is installed using ssh method The method is selected using the parameter Run LeadIT Both methods are covered in more detail below 3 4 USING CUSTOM EXTERNAL LEADIT INSTALLATIONS 13 3 4 1 To Connect to an LeadlT Installation on the Pipeline Pilot Server The most common scenario is that you will have an installation of Lead T on the Pipeline Pilot server If you choose this option you just have to ent
19. llation of LeadlT This works as follows When you run either of the Lead T Calculator or Similarity components and the parameter Run LeadIT gt is set to on PP Server and the parameter Run LeadIT gt on PP Server gt Use gt is set to FTrees Auto Installation they search for a LeadIT installation in the directory scitegic install directory public bin BioSolveIT and use this installation to run the calculation A html report pupup shows if a LeadlT installation is not found in this directory Use LeadlT installer component to install LeadlT 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 installations by PP and you need to ask him to install Lead As this installation knows nothing about the licenses you may have for LeadlT you have to supply the license information separately This is supplied using the parameter Run Lead IT 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 LeadlT 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 LeadIT installation component decri
20. o do this Also check first 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 pass word e Inthe Security tab go to Authentification e For the Authentification Method choose DOMAIN and a set of parameters will appear 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 25 26 CHAPTER 5 TIPS AND TRICKS 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
21. ol CHAPTER 1 QUICK START STEPS Introduction 2 1 About LeadIT LeadlT is one of the most established protein ligand docking tools in the literature Cited hundreds of times it has proved to be highly successful in numerous drug discovery appli cations for references please visit http www biosolveit de references The main applications of LeadlT are binding mode prediction and virtual high throughput screening vHTS 1 Binding mode prediction For a protein with known three dimensional structure and a small ligand molecule Lead T accurately predicts the geometry of the protein ligand complex within a few seconds To use LeadIT for binding mode prediction within Pipeline Pilot see the example in section 2 2 1 2 Virtual high throughput screening vHTS LeadlT sets new records for vHTS You can screen a library of approximately 1 000 000 compounds in about 8 hours on a 30 node cluster For further references and information visit http www biosolveit de To use LeadlT for vHTS within Pipeline Pilot see the example in sectionp 22 and setup for parallel processing in section 3 5 2 2 LeadlT Component in Pipeline Pilot You can see the general steps required in order to use the LeadlT Pipeline Pilot component in section 1 here we will cover the component parameter settings in more detail to help you fine tune your calculation The component parameters and the error port are used as follows Project Filename Set the doc
22. rmany Original Author Matthias Rarey www biosolveit de Contact leadit biosolveit de For information about additional contributors and copyright notes please consult the user guide or type help about gt gt Running on DELTA Windows 5 1 with 2 processors gt gt Loaded settings v 1 1 0 from C userdir leadit settings pxx gt gt LeadIT base license check BioSolveIT keys succeeded gt gt Licensed modules LeadIT CDOCK FlexE PHARM PERMUTE SCREEN DEVELOP 21 22 CHAPTER 4 TROUBLE SHOOTING 4 1 Problems using the ssh Method You may also experience problems using the ssh login for example the user name is unknown or the host is not found 4 2 Further help and BioSolvelT PDF Reporter More complicated errors may arise during the running of LeadlT Again though the errors will be collected and as much information shown as possible If you are familiar with Lead T 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 internally to find the output or if you are working with the ssh method set the parameter Run Flrees gt via SSH gt Options gt Delete Results 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 Run FTrees gt via SSH gt Options gt Temp Path
23. t molecule 5 The resulting poses need to be sorted to create a ranked list of your library Drag and drop a Sort Data component and connect it to Lead T component Set the parameter lt SortProperty1 gt to value BSIT LeadlT Total Score The lowest scores are the best in LeadlT so set the parameter lt SortDirection1 gt to Increasing 6 To select a subset of the resulting ranked list you can add a filter In this example we want to filter the 100 best results Drag and drop the component Range filter and connect it to the Sort Data component Set the parameter List to 1 100 7 Finally add a viewer or a writer component to view and or save your results Your pipeline may look like the example in figureD 2 Change the workflow to your needs and for example try out some more detailed analysis 10 CHAPTER 2 INTRODUCTION Installation 3 1 BioSolvelT Web Installation The easiest way to download and install BioSolvelT 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 LeadlT Installation Component The LeadlT components are set by default to use a so called auto insta
24. ter Run LeadIT gt on PP Server gt License Server or 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 servername or if you have a license file then you may browse for it using the facility You can save these settings in the component 14 CHAPTER 3 INSTALLATION Implementation User Mode Default El Run LeadIT on PP Server E on PP Server 3 Use Preinstalled LeadIT 1 License Server or License File server El Executable leadit exe C Program Files BioSolvelT LeadIT leadit exe zi Implementation Parameters Figure 3 2 PPServer Connect to an LeadlT Installation on the Pipeline Pilot Server 3 4 2 To Connect to an LeadlT Installation on a Remote Linux Server Your existing LeadlT 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 LeadlT 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 label ssh You can see an example in figure 3 e Requirement LeadlT is installed on a Linux machine available to the
25. ters Figure 3 3 ssh Connect to an LeadlT Installation on a Remote Linux Server via ssh 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 Run LeadIT gt via SSH gt Options gt Delete Results False 3 5 Running LeadlT in Parallel in Pipeline Pilot LeadlT in Pipeline Pilot takes advantage of the parallel computing options available in Pipeline Pilot to speed up longer calculations This section tells you how to adjust the op tions to your system and needs You will find the options in the Implementation tab as in figure The most important limitation to a parallel processing calculation is the number of LeaalT licenses that you have If you only have a single license then parallel calculations will not be possible Further choices in the set up of the parallel computing computing calculation depend on the number of Pipeline Pilot licenses you have plus your choice of connection to the external LeadlT installation on PP Server or via SSH Implementation User Mode Expert v E Run LeadIT on PP Server v El on PP Server Use Preinstalled LeadIT X License Server or License File riz A Executable leadit exe software BioSolvelT LeadIT leadit m E Parallel Processing Opt
26. the number of processors of the server You must override this maximum to be able to set the number of processes you want for your parallel calculation In the above example the maximum must be set to 10 or more Take the following steps e Goto 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 last field of the table Maximum number of simultaneous parallel processing subprotocols allowed change the value click Save and log out again 18 CHAPTER 3 INSTALLATION Implementation User Mode Expert gt E Run LeadIT via SSH on PP Server E via SSH Executable leadit exe software BioSolvelT LeadIT leadit Host hostl host2 host3 host4 host5 E User userl Password Options E Parallel Processing Options True Batch Size 1 TE Server Processes 10 Preserve Order True vir Implementation Figure 3 6 The options for parallel processing for the example shown in figure 8 5 would look similar to these 3 5 RUNNING LEADIT IN PARALLEL IN PIPELINE PILOT 19 3 5 3 Example Scenarios and Required Settings ssh PPServer Parallel Processing Options Number of PP servers in list Number of ssh Hosts in list Number of Processes PPServer False 1 Behavior The calculation will run as one complet
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