SBSIVisual User Manual
Contents
1. 327 e SBSIVisual bug fixes Downloading a job where no results were available does not now block sub sequent downloads 423 Windows users can now download log files from the Dispatcher server 437 When configuring an FFT cost function variables that are not selected are now not verified and do not block the user progressing through the submission wizard 442 Data file names containing spaces are now reported to the user during con figuration 444 10 e Developer interest 1 6 4 SBSIVisual updated to run using Eclipse 3 7 components 432 Plugin extension point created for adding new simulation algorithms New features in 1 3 5 Version 1 3 5 is an incremental update with only one substantial new feature since 1 3 4 the ability to weight the cost function values See Cost function help pages for details and section 6 7 of the SBSINumerics manual 1 6 5 New features in 1 3 4 e SBSINumerics Access to a parallelized Particle Swarm algorithm an alternative approach to the genetic algorithm for parameter optimization See section 6 6 2 of the SBSINumerics user manual for more details SBSINumerics now supports SBML models with species declarations contain ing initial Assignment elements Easier script based installation on Unix based machines Improvements to FFT cost function configuration see section 6 7 2 of SB SINumerics user manual You can now choose whether to factorize the cost2. gt 1 n mu Copy E Paste X Delete Move Rename t Import ey Export 27 Refresh Close Project Close Unrelated Projects Team Compare With Restore from Local History Properties Select Select an import source type filter text Y gt General Archive File F5 gt Ne Now choose the Import existing projects into workspace option Create new projects from an archive file or directory L Existing Projects into Workspace C File System El Preferences da 3 Now browse for the project folder on your filesystem and ensure it is selected You need to select the checkbox to copy resources into your workspace Otherwise the project will continue to exist in its current location and will just appear in the SystemView without actually being in the workspace folder which will break the optimization functionality 39 Import Projects d Some projects cannot be imported because they already exist in the workspace Select root directory Users radams Desktop W52 Browse O Select archive file Browse Projects demoP Users radams Desktop WS2 demoP Select All erb2 Users radams Desktop WS2 erb2 pl Users radams Desktop W52 p1 Deselect All p53 Users radams Desktop WS2 p53 picci p53b Users radams Desktop W52 p53b simile Users radams Desktop WS2 simile Refresh stochastic Users radams Des
3. SBSIVisual User Manual VERSION 1 4 2 Authors Richard ADAMS Neil HANLON Nikos TSORMAN January 11 2012 OOOO BBSRO CENTRE FOR SYSTEMS BIOLOGY AT EDINBURGH Contents 1 Getting started eSee ep ewen ee ee eeaekeee eae ee es A E eee es See oe ae 1 2 1 Multiple workspaces 0 00 00 eee eee 1 3 Working with the example project 2 20 008 1 3 1 Installing the example workspace Lin iii see 1 5 Hooking up to SBSINumerics a o aaa A 1 6 1 New features in 1 4 2 noaa a aa 1 6 2 New features in 14 1 1 6 3 New features in 1 4 0 1 6 4 New features in 1 3 5 ooa a aa a 16 5 New features in 1 3 4 Hob Bisi sapiens ii a 2 1 Run optimization locally oa i See ee ee E eae eee eee eee eee eG 2 2 Choose data and Models on a a a a a a nd li EGR nt LA anni 2 6 Run optimisation remotely 0 0 0 2 00 eee eee 2 6 1 Configuring a remote backend server epee Saeevee ene see eee eee eae es 2 7 Test model compilation remotely 02 00 eee eee 3 1 Run local simulations 2 2 ee 13 14 15 17 18 19 2l vA 23 24 20 26 27 4 Concepts 4 1 Model Configuration History 4 2 The workbench paia ese peewee iii OPE DOPRE EII 5 2 Creating a new SBSI project 2 ee Laden osas a As 5 5 Visualizing cost function history eee eee eee ee AAA ik tad eden ra aos na
4. Experiments Other Data Other Resources lt Back Next gt Cancel Finish Enter a project name which should be alpha numeric By default a folder structure is created If this folder structure is chosen SBSIVisual uses this to help manage rela tionships between files However you are entirely free to arrange your folders as you see fit You can manipulate files and folders using standard methods see the Workbench introduction for more details 1 5 Hooking up to SBSINumerics There are two ways to access SBSINumerics from SBSIVisual in order to run parameter optimizations Firstly you can install SBSINumerics locally or secondly you can run optimizations on our server Or you can do both If you have installed SBSINumerics on your machine you need to tell SBSIVisual where you have installed it To do this click Options gt Preferences and then choose SBSIVisual gt SBSINumerics preferences from the tree of possible preferences Now enter the path to your installation For example if you have installed SBSINumerics in myhomeaccount numerics then that is the path to enter it needs to be a full path from your file system If you now try Optimize gt Local optimization then you should be able to proceed with the configuration To do this first of all please contact us to request a login and passwd Once you have these credentials you can enter them via Options gt Preferences SBSI Web service ADO Preferences
5. Ti Navigator I Oz Outline lt e Palette fei Problems a Progress i Project Explorer E Properties A Search E Snippets H LE Tasks p Use F2 to display the description for a selected view CGD EA RA Choose the Problems View which will appear and look something like this 10 errors 1 670 warnings 1 255 others Filter matched 210 of 2935 items Resource Path Location Type YH Errors 10 items E Every metaid attribute value must be unique ac errorclock xml testAPl line 588 SBML Problem E Every metaid attribute value must be unique ac errorclock xml testAPl line 594 SBML Problem E Every metaid attribute value must be unique ac errorclock xml testAPl line 697 SBML Problem mFile unwritable document is missing an sbml ID errorclock xml testAPl line 0 SBML Problem E Outside of a lt functionDefinition gt if a ci eleme CirCl_new xml Goldbeter Diagrams line 130 SBML Problem Clicking on a line will open an editor If the system is configured to open an internal editor then the line causing the problem will be selected In an editor view problems are shown by a warning triangle or exclamation marrk in the left margin If you mouse over this you will get more information on the problem 10 errors 1 670 warnings 1 255 others Filter matched 210 of 2935 items Resource Path Location Type YE Errors 10 items E Every metaid attribute value must be unique ac errorclock xml
6. 24 10 58 10 0 2009 12 11 11 00 05 0 demol FINISHED FINISHED Download Normal finish stopped after maximum Generation demol bluegene 2009 11 23 11 02 54 0 2009 11 23 21 38 42 0 BG1 FINISHED FINISHED Download Normal finish stopped after maximum Generation BG1 bluegene 2009 11 23 00 28 44 0 2009 11 23 10 10 44 0 jz FINISHED FINISHED Download Normal finish stopped after maximum Generation j2 sbsidevl 2009 11 23 00 00 57 0 2009 11 23 00 26 05 0 tl FINISHED FINISHED Download Normal finish stopped after maximum Generation tl sbsidewl 2009 11 18 13 52 25 0 2009 11 20 14 23 15 0 WW FINISHED FINISHED Download Normal finish stopped after maximum Generation sbsidevl 2009 11 18 13 49 13 0 2009 11 18 13 52 42 0 24 Clicking on the column titles sorts the table by that column When some results are available it is possible to download them by clicking on the download button You will then be prompted for a location in your workspace to save the results You can click on Refresh button in the top right corner of the table to refresh the view of the progress Results can be viewed in a similar way to a locally run optimisation The table view shows job status in two ways a coarse grained status one of Running Finished or Error and a finer grained Running status which tracks the progress of running jobs The Running stages are as follows e RECEIVED a new job has been submitted f
7. Alternatively you can just visualize a single time series by selecting the data file and choosing the choice to choose which data sets to display along with axes and titles Another alternative is to Quick Visualize Results which enables you to cycle through plots Visualize data from the context menu Again the dialog gives you 16 of single species against a particular data set You can also inspect the overall progress of the optimization run by viewing a plot of the cost function value over time To do this access the results subfolder of the folder you selected for the output results select a log file starting with PGALog then click on the menu Plot Cost Function 293 Import ey Export Refresh FS F Team b Compare With m Replace With gt Plot Cost Function gt Plot all files _ 2 Plot this file Properties Ve rr You can choose to plot just a single file or all files if there is 1 log file they are listed in temporal order Whichever choice you make you will see a graph appear of the cost function plotted as a function of iteration number Progress O Data view M Cost function 0 8 E 2 20 6 E Cost Function 0 4 0 50 100 150 200 250 300 350 Generations A slope with a negative gradient implies a decrease in the cost function over the search iterations the desired outcome A flatline indicates that the search h
8. deobfuscated on your machine to restore the original identifiers Another option is to compress the log files generated during the search By default this is enabled This means that the full search history of all the tested parameter values is discarded and only a record of the cost function values is returned This makes the downloads much smaller especially for large fittings with many parameters 23 Please log in to both SBS Dispatcher Web Server and back end server if selected to proceed Please enter credentials for SBSI Dispatcher Web Server User name dre vare Password SESI Dispatcher Web Server URL https sbsidevl inf ed ac uk 8084 sbsiservices dew Job Name Job Description Fl Obfuscate mi Compress log files Test credentials 2 6 1 Configuring a remote backend server This section of the login page is a generic login for a backend supercomputer There are A fields to complete e The host name of the server e The number of processors to request This will be determined by the size of your model and the characteristics of the backend server e Wallclock time this is a time after which a job will be cancelled Again an ap propriate setting will need to be found by trial and error together with knowledge of the available settings on the backend server Requesting a longer wallclock time may result in a longer wait in the supercomputer queue e Optional command line arguments this is a
9. necessary 1 Click Help gt Install New Software In the resulting dialog click on the Add button and add the following names and urls e Name BioPEPA Location http groups inf ed ac uk pepa update e Name BIRT Location http download eclipse org birt update site 2 5 e Name emf Location http download eclipse org modeling emf updates 39 000 Install Available Software Select a site or enter the location of a site eare Work with type or select a site Find more software by working with the Available Software Sites preferences type filter t e Add Site Details M Show on Co M Group it ra Contact al lt Back Next gt Finish 2 Click Next then in the Work With drop down list choose Eclipse BioPEPA plugin keeping other defaults the same span style font weight bold It is essential that the check box Contact all update sites during install is selected for the installation to succeedj span Available Software Check the items that you wish to install Work with biopepa http groups inf ed ac uk pepa update Find more software by working with the Available Software Sites preferences type filter text il Name esi 41 w000 Uncategorized Ei E The Eclipse Bio PEPA Plug in 0 1 9 lO Ll The Eclipse PEPA Plug in 0 0 23 Details M Show only the latest versions of available software C Hide ite
10. testAPl line 588 SBML Problem E Every metaid attribute value must be unique ac errorclock xml testAPl line 594 SBML Problem E Every metaid attribute value must be unique ac errorclock xml testAPl line 697 SBML Problem mFile unwritable document is missing an sbml ID errorclock xml testAPl line 0 SBML Problem Outside of a lt functionDefinition if a ci eleme CirCl_new xml Goldbeter Diagrams line 130 SBML Problem 6 3 Progress View The Progress view gives information about long running processes that are running in the background The Progress view is enabled at start up or can be opened via Window gt Other which opens the following dialog 50 AOO Show View 5 type filter text El Console ati Markers fi Navigator Da Outline Palette rat Problems Progress Ef Project Explorer E Properties 4 Search E Snippets y 2 Tasks Use F2 to display the description for a selected view Cancel and choose Progress If i ___ you run a simulation you will see the following output ess E Console Ei Problems Data view Running simulation of Users radams Desktop NeilBugWorks pace Goldbeter Models repressilator ml us OR Clicking on OK will give further information on the outcome of the job Very long running jobs will display a progress bar and provide the option to cancel a long running job 6 4 System view The system view provides a tree view on the under
11. the original s configuration 1 To re run the last optimization job of a model just launch the wizard with that model All configuration parameters are the same including cost function if none of the data sets have been moved see below 2 To re run a given optimization job run the wizard choosing the model inside the config_data folder of that job s output Also choose the data sets inside the config data folder choose all of them as they were all used in the original run However there is a caveat to the use of the configuration history 1 Please note that cost function configuration is linked to the data sets being used and not to the model A history is kept of which data sets were used for an optimization job but if they are moved then this is lost 4 2 The workbench The workbench is a folder on your filesystem that the application uses to manage files The application can respond to changes to files in this directory and run processes such as format validation in the background It is best if the user does not modify this filesystem outside of the application By default the workspace is set up in the installation directory of the application The System view provides a tree view onto the filesystem and allows typical operations such as opening files deleting renaming etc available from the context menu 32 New Open Open With Copy Paste XK Delete Move Rename ta Import ey Expor
12. 0000 9 8968064 b Best_Tseries Mew F aaas g 2034525 EN best Tsere Open 10000 0 203098 p 10008 a 7067536 i Best_Tseries Open With loan a 203432 E Best Terit c 38C ID Ben Tiaris apy E bs Gata view C EI best Tseries Best_Tserles E Delete Bescon A6 Move laad21100 BestCost AB Rename F2 i BestCost_AB iy Import _ gt eCopt AB A T BesrGogtexn Export Martian BestCosttut Refresh FS ao blocco i BestCosttxt ch 2 Bestcosto MC E E gt PGA Stopint Compare to experimental data PGAStopinfe Visualize data aiw A Paty aca PGAStopinfe Team p PGAStopink Compare With r E L PGALog run Replace With Fi l B PGA L63 run Data scaling b 0 parancid_ardrai D PGALeg run PGALeg run Properties xp int _ abt_1__1 1_2_ A arms ral E gt ARCI wih log 1265055030523 Zaphod b Es Rewizitin_abr_ 1267706103335 abc_fram le verbosity 1208237 167863 assarsassanzanina_ 1268237419744 2 p Abert rain XES AL E Downs fjobFolder fazzzazanizazazzaza 1682374 lore RESULTS results Best Tseri ABCO LOD dar After selecting the menu option for Quick visualize results the following dialog appears This dialog presents all the files that exist under the exp_data folder The user has the option to select one or more of them By pressing OK the results data will be plotted against the experimental data in individual tabs for any of the experimental data files BOO Please cho
13. MinMitOscil_1j1_2 src DeCodeSBML cpp printModelCPPFilelnciudes Writing Species Writing Rules Assignment Ruled formula Assignment Rulel formula NUM Const 0 Reaction reactionl 1C EA If successful it is likely your model is suitable for optimising with SBSI If not then please send your error report to the SBSI development team for advice 26 Chapter 3 Running simulations 3 1 Run local simulations Running local simulations can be activated by Ctrl R by clicking on the Simulation main menu or by selecting an SBML file in the System View and accessing the Simulation command from the context menu To configure a simulation you need to e Provide a model from the workspace e Optionally specify a location to save the results to e Choose a simulation algorithm e Optionally configure the simulation parameters e Optionally configure how you want the results to be presented The simulation algorithms are provided by third party libraries and SBSI does not itself check that the chosen algorithm is appropriate for the model In general the deterministic LSODA algorithm from COPASI works reliably for curated models from the Biomodels DB The following algorithms are bundled with SBSI e Copasi LSODA Stochastic hybrid e Dizzy Runge Kutte level 1 SBML models only If you have SBSI Numerics then you can access its inbuilt CVODE solver by setting the location of your install in Options gt Preferenc
14. Tha nal Lar PA E Ei ofwconfig xml New b j report html I i Open hi report Open With results El demo E Copy C demo4 Paste HV M demo55howThisOne MH Delete bo gt Exercise5a c Move E gt Exercise5d 1 Rename F2 gt Exercise5d 3 Limba E 7 ExerciseSd 4a Es Import te gt Exercise5d 4b La Export F eld p iB 2 Refresh FS oe Validate rtodelete Run As b adels Debug As gt yjective Functions Profile As gt her Resources Team p wconfig html Compare With b wronfig xm Replace With be edatorPreySedml sedx Simulate R ndra 5 pa ES Source be l Properties Hel Jeter iii and an HTML view will open If the optimization run produced results you will be able to see thumbnail graphs of simulation results the parameter values found and links to the configuration files 15 To explore the results in more detail open up the job folder and open results results folder In this folder you will see something like the following Y gt RESULTS P 2 ckpoint Pp exp_data Y 2 results Best_Tseries_ model_1259105161279 250 dat EB E IST E E COC TT I y Dt Po fo TT o a Best_Tseries_model_1259105161279 250 sbsihead Best_Tseries_ model_1259105161279 500 dat Best_Tseries_model_1259105161279_ 500 sbsihead Best_Tseries_model_1259105161279_750 dat Best_Tseries_model_ 1259105161279 750 sbsihead Best _Tseries_model_1259105161279 918 dat BestCost_model_1259105161279 txt 250 BestCost_model
15. _1259105161279 txt 500 BestCost_model_1259105161279 txt 750 BestCost_model_1259105161279 txt 918 BestCost txt 250 BestCost txt 500 BestCost txt 750 BestCost txt 918 PGA Stopinfo 250 PGA Stopinfo 500 PGA Stopinfo 750 PGA Stopinfo 918 PGALog run1259105956 txt PGALog run1259106006 txt PGALog run1259106053 txt PGALog run1259106105 txt Files ending in dat suffix are the time series generated with the best parameters at checkpoint intervals To compare this with experimental data select a data file and from the context menu choose Compare to Experimental Data Best_Tseries_model_1259105161279 250 dat Il 3 4 r1 b4r4 A A 512345 E Best_Tseries_model_1259105 New bP i2 Best_Tseries_model_1259105 Open 2 Best_Tseries_model_1259105 Open With gt 5 Best_Tseries_model_ 1259105 3 E Best_Tseries_model_1259105 Copy C jg Best_Tseries_model_1259105 Paste sv 2 E Best_Tseries_model_1259105 Delete E gt BestCost_model_125910516 wage le BestCost_model_125910516 a Fo E BestCost_model_125910516 b Benian t3 Import E BestCost_model_ 125910516 E gi E BestCost txt 250 py Export E I BestCost txt 500 l E na 2 Refresh FS E BestCost txt 750 e Compare to experimental data y Visualize data PGA Stopinfo 500 El TT PGA Stopinfo 750 MUNAS d Bona aes Debug As b Then from the ensuing dialog you can choose the data points and time series you want to compare
16. as become stuck in a local minima or that the cost function landscape is flat and there are many solutions with similar cost In this case you need to re run the optimisation with larger mutation probabilites or a larger population size to explore more of the parameter space Help pages for these tasks are available e g Quick visualize Visualize data 2 1 2 Common problems There are several common problems e A model must have an JD Le in the top level model element there needs to be an id attribute This is crucial for many aspects of the optimization process 17 e For a parallel genetic algorithm at least 3 parameters need to be chosen for op timization This is necessary to allow the recombination of parameter values at each generation e Some problems can be caused by choice of wrong scaling type for Chi squared cost function For example if optimization hangs with no sign of progress this can often be overcome by reconfiguring scale type to Direct e A job hangs and attempted cancellation has no effect This occurs sometimes if the job hangs during an initial set up phase In this case open a terminal window and type top This lists active applications one of which will be modelID exe where modellD is the SBML ID of your model Note the process ID of the application then quit top Ctrl C on Unix and type kill 9 ProcessID where ProcessID is the number noted from top Ty
17. aved values in the history for these fields don t match the currently calculated values an error message is displayed and the wizard is blocked until these values are confirmed by clicking on the saved calc choice buttons that appear You may choose either to use the saved value or the newly calculated value This will not need to be confirmed again unless you revisit the page which originated the calculated value the parameter page for popsize or the file browsing page for tFinal 2 5 Configure Cost Functions The Cost Function page is split into two sections The top section is for FFT configura tion the bottom is for chi squared X2 FFT also contains an adjacent table displaying states species present in the model It is important to note that when cost function configuration dialog history is saved it is written to the SBSI header files This is in contrast to the rest of the configuration for an optimization job which is linked to the model Therefore if you copy move a model its configuration history is copied or moved with it but the cost function configuration history does not it is associated with the SBSI data files 21 You can get the current cost of your model prior to optimization via the Get Current Cost button You can therefore tell if fitting produces a better result than what you have already with your existing model values The Cost Function Page validates user input so that obviously incorrect data canno
18. by a function of the amplitude or not e SBSIVisual Access to SBSINumerics through a RESTful web services interface Simplified more secure access to the SBSI server for running remote param eter optimizations You can now access the progress of your parameter fitting jobs on the web at https mook inf ed ac uk 8083 sbsiservices A new graphing and charting feature which is more performant for plotting large data sets and has improved zooming and scrolling features SED ML support is now fully compliant with the Level 1 version 1 specifica tion Best parameters are now inserted into the model after optimization Standard menu items added File gt Save File gt Save As and Edit e New plugins available for SBSIVisual Access to the rule based modelling framework Kappa via the SBSIVisual up date site see the SBSIVisual website for details 11 A graphical SBML editor VisualBiology is now available from the SBSI update site Written by Dimitrios Milios at CSBE this plugin provides a viewer and editor for SBML files Don t forget you can also get information from our Sourceforge Help Tracker at https sourceforge net projects sbsi forums forum 1048774 which provides solutions and work arounds for current usage issues 1 6 6 Bug fixes e The inability of Windows versions of SBSIVisual to self update has been fixed e More informative error messages should now be generated in the event of any problem
19. ceed The file chooser wizard keeps a history of the chosen files for any given model The history is saved at the moment the next button is pressed and the wizard navigates to the next page If a data file is moved from its historical location or deleted then an 18 error message will be displayed until this file is removed from the selection or replaced by browsing to its current location in the workspace Note that when configuring cost functions the configuration is saved to the header files matching the data files chosen on this file browser page Should you move the data files but wish to keep the same cost function configuration for a given model you will need to remember where in order to browse to them again Obviously if you change the data files used it follows that you will also use a dif ferent cost function configuration This is in contrast to all other configuration of the optimization process which is linked solely to the model A selection list of optimization methods is present at the bottom of this page It currently only includes PGA or simulated annealing PGA is chosen by default The choice made here affects the display and validation on the next page the parameter configuration page 2 3 Configure Parameters Every parameter present in the model is displayed on this page in a checked table Each row in the table represents one parameter with a checkbox to toggle whether to use that paramete
20. data Run As Debug As Profile As Team Compare With Replace With Data scaling FWFFFrFrrFr Animate Simulation data Properties Vw Assuming the path to the model is correct a view should open showing a simple view of the reaction pathway Time course progress ale Save e E a aa s 1 E I am P AN In this view reactions are small blue nodes and species are larger pale nodes You 44 can rearrange the nodes if the layout is not clear To animate the nodes press the play icon on the top right of the view If the column names in the data match precisely the animation will start If not a mapping dialog will appear AO Map exp data columns to species identifiers Species name Mapping Column Data Column ld EmptySet EmptySet EmptySet ld PX PX PX Id PY PY PY ld PZ PZ bd KX x Id YY Id Z Z Z Just drag and drop experimental columns from the right hand side of the dialog into the central section to match up with the model IDs in the left hand section Only matching elements will be animated Once you re done click OK and the animation will start Nodes resize according to their normalized levels through the time course E g if a node has minimum value 20 0 and maximum value 300 then if at a given time the value is 160 the node will appear to be 50 of its maximal size This functionality is also available from the slid
21. dels Model ID abc_1 Model name SBMLErrors Compartments Function Definitions Parameters Reactions Species 2 Objective Functions Other Resources Ee abc_1_1277080073595 s abc_1_1277080073595 sl ee eZ 6 6 Updating SBSIVisual 6 6 1 Updating SBSI This page provides information on how to update SBSIVisual and install additional functionality Once you have downloaded and installed SBSIVisual once we can provide minor updates via the update mechanism To begin the process click Help gt Check for 94 updates If updates are available choose what you want to update and follow the wizard instructions setting defaults If you want to receive automated notification of updates you can configure this in the preference pages Click Options gt preferences and then expand the Help update gt automatic update section 6 6 2 Installing new software To install new software click Help gt Install New software It may be that SBSI is already aware of its own update site click Work with drop down list to see if a site with http www sbsi ed ac uk update is mentioned If not you will need to fill in the form below using the URL http www sbsi ed ac uk update Ea oy a Preferences S gt n type filter text Available Software Sites lt P Gr Cache b Dispatcher Server b Ce Li cal type filter text Help Name 4 Location Enabled Y install Update Automatic U
22. e for example 1 First of all select the project you want to export in the System View and right click to get the context menu choose the Export menu item New p o Copy C i 1 MX Delete E e sa Rename F2 t Import 13 Export 5 Refresh FS Close Project Close Unrelated Projects Team Compare With gt Restore from Local History Properties Ye 37 2 In the subsequent dialog choose export to File System then click Next eno _ Select A Export resources to the local file system i Select an export destination 2 General Archive File L File System E Preferences 2 Team Team Project Set lt Back Next gt Finish 3 Then choose the projects you want to export the destination folder and select op tions The default Create only selected directories is normally sufficient Finally click Finish File system Export resources to the local file system de DS_Store gt S abel M El project se b21stochastic gt 8 bmd21 b fe bz To directory Users radams Desktop Browse l Options C Overwrite existing files without warning O Create directory structure for files Create only selected directories i i lt Back Mext gt Finish gt Cancel A To import a project into the workspace 1 Right click anywhere in the System View and choose Import from the context menu 38 d New i 1 Il
23. e see our website http www sbsi ed ac uk Copyright Centre for Systems Biology Edinburgh 2010 Chapter 1 Getting started Welcome to this SBSIVisual user manual This is a print version of the integrated Help pages contained within SBSIVisual itself This documentation is valid for the 1 4 2 release of SBSIVisual 1 1 Starting the application Welcome to the Help pages for the SBSIVisual application If you are a new user you will have probably downloaded this application in order to run parameter optimizations of your biological model This document describes the features of the SBSI Visual client application but if you want more detailed information about the optimization procedure then please consult the SBSINumerics user manual that you can find in SBSIVisual s installation folder When you download and unzip the application open the extracted folder and you should see some files like this artifacts xml gt 3 configuration gt MM features Launch_mac command p Lal plugins README txt SBSINumericsUserManual_1 0 0 pdf E SESIVisual SbsiVisualUserManual pdf vw The README file will have the platform specific information necessary to open the application 1 2 Creating a workspace The first time SBSIVisual is run you are presented with a dialog inviting you to choose a workspace i AAN Switch Workspace Pick Workspace Your workspace is where settings project files and resources will be s
24. er this will proceed frame by frame through the animation For a non trivially small model you ll probably need to edit the layout to make all the nodes visible Once you ve arranged the layout click on the Save animation layout button and the layout will be preserved The layout information is saved directly into the SBML model file 5 8 Visualizing time series data 5 8 1 Inbuilt data display To view time series data select a file ending in dat or sbsidata in the workspace and choose Visualize data from the context menu The following dialog appears 45 Graph title _ Title Species list Select all Deselect all Select Independent variable default is time Axis information X axis name Time X axis units unknown Y axis name textField Y Y axis units nM Ca Ga Using this dialog you can configure the title axes and units of the graph A chart will open Simulation results for Pokhilko_At_2010_SBML_v2 xml You can use the Arrow keys to scroll the axes If the Ctrl key is held down while using the up down arrow the graph will be zoomed in out Dragging the mouse with the Shift key held down will zoom to the selected rectangle A number of context menu items are available restoring the original plot and showing hiding the individual data points on the chart There is also a basic SVG export for data sets viewed via the Visualize Data menu For graphs with
25. erfaaia332112413 E Refresh F5 Alog runl 268237416 Team b Compare With P Replace With b Plot Cost Function LA Plot all files Plot this file Properties Xx The user has two options in order to plot the cost function values He can either plot the full span of the simulation or he can plot a portion of it By selecting the Plot all files action the user will have a plot with all the values of the plot function that cover all the generations of the simulation In the case of the Plot this file action the plot will contain a range of the generations generally those that are included in the selected file The following image is a sample plot for the whole span of the generations E hoper D Gie E parchear tra LO ika Cost function a ma DE i Cost Maroti SeRPRUE HBETRaAE 5 6 Visualizing optimisation results To quick view the result data you have to navigate inside the RESULTS folder and right click on one of the files that resemble the following Best_Tseries MODEL _NAME_XXX dat 41 ALBA Jels Ei PA cosi Default Perspective E tens View E Diagrams 7 gt jobFolder Y 5 ABBA 1268237419744 b 2 config data PIABCO_2 sbsibeoder Time A B C LI e Caba 10000007 2 01940499 0 473265 2 02040808 8 841442 v gt RESULTS 2 23000308 a 8279445 E gt ckpoint ARAS BBL SIE A A 060900999 A 217394 Fo oxo data ASA 886000208 0 813639f m RA 8 4r000004 0 810175 EE Best Tseries 1
26. es gt and then select SBSIVisual gt SBSINumerics preferences Alternatively you can access the CVODE solver via a web service This is useful to run prior to submitting an optimization job since it will confirm whether or not SBSI can simulate your model properly For a fully featured simulation tool that handles stochastic and ODE based models you can install the Biopepa plugin In the output configuration page you can choose log axes whether you want to save the simulation data in a file and which variables you want plotted You can also choose to post process the simulation results by entering a mathematical expression 28 Configure your simulation results Configure the required presentation for your simulation results Choose output types Axes M 2D plot D DataSet Log X Log Y Dependent variable Species ID name Include Optional processing x prey wi x x y y predator iwi ty f x yji Select all Deselect all Restore Defaults M Export to SED ML If you choose to save the data and want to look at it again you can use the Visualize data menu item to do this If you want store your simulation configuration for archival purposes or for run ning in another software tool you can export your simulation configuration in SED ML format To do this you just need to choose an export file and location and whether you want to export just the description or include the model as well in a sel
27. f contained archive a SED ML archive 800 Choose export options for SED ML archive Choose your preferred export format and location for your SEDML file SED ML export type O Miase archive XML Save SED ML file to lotkaVolterra Models File name mySEDML Optional annotation note in HTML Basic time course of Lotka NV Al If you do the former you will need to edit the generated XML file to add in an appropriate URI for the source field of the model element If you export the archive the model will be included The archive is in zip format but with an extension sedx 29 and you can access the original files in the future by unzipping the archive A history of simulation runs and the ability to monitor the progress of running simulations is available in the Progress view SED ML files can be used as a way to run simulations as well and SBSIVisual offers some support for doing this To do this right click on a SED ML file and choose the menu Execute SED ML simulation A dialog will appear with a choice of Outputs described in the file for you to reproduce At present in SBSIVisual we do not support 3D visualizations so only 2d plots and reports tables of data can be generated You can also view the contents of a SED ML file by selecting it and choosing the View in Browser menu item which will open an HTML view of the SED ML file Once an output is chosen SBSIVisual
28. iment reaction units value minvalue Wi Yes K K Yes No Global substance 1 0 0 0 Wi Yes Kd Kd Yes No Global substance 0 13 0 0 WI Yes Km km Yes No Global substance 0 5 0 0 Mi ves vd Vd Yes No Global substance 1 4 0 0 Wi Yes Vm Vm Yes No Global substance 0 505 0 0 Mi Yes V5 Vs Yes No Global substance 1 6 0 0 Wi Yes k1 kl Yes No Global substance 0 5 0 0 Mi Yes k2 ke Yes No Global substance 0 6 0 0 M Yes ks ks Yes No Global substance 0 5 0 0 la e delselect all It s also possible to set the constraints globally as a multiplier of the original value in the model For example to set the constraints to 90 and 110 of the parameters current value type 1 1 into the max textbox and 0 9 into the min text box Clicking Apply will set these constraints globally This approach is useful when there are many parameters you wish to set constraints for at once 20 2 4 Configure optimization This page enables configuration of an optimization run As this is a complex topic please refer to the SBSI Numerics user manual for a detailed description However the page itself is designed to help and contains much of the relevant information describing each configurable item on it Clicking on the information symbol next to any text field spawns a pop up with help text Text fields on the page are greyed out and disabled based on choices either made previously i e PGA versus simulated annealing or o
29. ktop WS2 stochastic test Users radams Desktop WSs2 test test Users radams Desktop WS2 test1 tnf Users radams Desktop W52 tnf treenut Users radams Desktop WS52 treenut iw Copy projects into workspace Working sets 1 Adda nrniart ta imerbinn ratr Finally click finish and the project should appear in the System View 5 4 Searching Searching functionality is provided by the Search menu 40 5 5 Visualizing cost function history v gt RESULTS DARIO VALI Es ckpoint a 06000009 4 813 i l a 2740000 2 819 PG exp data 5 28900000 4 206 v gt results 4 2300000d 2 003 El Bast_Tserits_ABCO_100 dak 19400005 4 809 Best_Tseries_ASCO_100 4bs header 0 11000000 9 736 5 A AAAAARAA A 793 Best_Tseries_ABCO_L50 dax Bost_Tserles_ABCO_150 sbsibeadeor EM hest_Tseries_ABCO_173 dat Bost_Tseries_ABCO_L 3 sbsiheader No operations to display ES Gest_Tseries_ABCO_50 dar Bese_Tseries_ABCO_50 sbsiheader BestCost_ABCO ext 100 beseCost ABCO 150 1 BestiCost_ABCO xt 173 BostCost_ABCO tt 50 Progress Data vie Besitos 100 BostCost txt 150 BostCostit_ 17 BestCoston 50 i PGA Sopla New n PGA Stapir PCA Stopir Open PCAStopi OPEN With b E PGALeg Fi a Copy sc i PGALOG FI El PGA Log 1 al PGALOG FI M Delete mb E abe_1 1312 Move b Es ABC_1_with_log_12680 Rename F2 b G Rewisitinabe_ 1267706 gag Import ey Export 5 Downs jobrold
30. lying file system Via the context menu you can perform standard move copy paste operations and create new files and folders 6 5 Installation test Try downloading the application from Sourceforge Extract the download go into the application folder and launch the application On Windows this should just be double clicking the launch icon on Mac Linux please read the README file If you ve never downloaded SBSIVisual before you should see a dialog asking you to choose a workspace folder choose an empty folder and accept defaults then the application should open If you have downloaded SBSIVisual before the application should just open and you should see something like ol No operations to display at this time O items selected a ia The purpose of this test is to see if the libSBML library included in the application is working properly Click File gt New gt SBSISystem and in the ensuing dialog 2 Le New SBSI System Mew SESI System Create a new SBS modelling project Projeet name ral Create default directory structure Directory Structure Models Diagrams Objective Functions Data Simulations Experiments Other Data jobFolder Other Resources ED es Cae Ga dh enter any name for the project and click Finish You should see the project created and visible in the System View 92 Diagrams jobFolder Models Objective Functions Other Resources a Prog
31. many data points tens of thousands performance is much better 46 if data points are not displayed 47 Chapter 6 Reference 6 1 Miscellaneous features This page provides information on various basic functions provided by SBSIVisual e Reset perspective e Preferences 6 1 1 Reset perspective If you wish to reset the appearance of views and editors in your application click Help le Other Reset Perspective E Show perspective from the Window menu This will reset the appearance of the application to its default state No data is lost during this process it is purely cosmetic 6 1 2 Preferences Preferences allow configuration of application wide settings and are accessible by Preferences Preferences can be contributed by any SBSIVisual plugin By default SBSIVisual includes the following e Preferences to set your SBSI Dispatcher login credentials e Preferences to set the extent of SBML validation applied to SBML models e Preferences to set the local installation of SBSINumerics if you have it installed 6 2 Problems view The Problems view shows errors and warnings on the format or content of editable documents Support is provided for e SBML documents e SBSI data format data and header files e SED ML simulation archive files 49 The Problems view can be opened via Window gt Other which opens the following dialog F co RS Y A b i LI en Li El Console na E Markers
32. merics Particle swarm algorithms can now run multiple loops previously they could only be run in one loop 436 A new configuration parameter ReportInterval is introduced which specifies the interval between time points in the Best time series result files This will limit the size of the output files 303 Negative values now accepted for the cost function t_init argument 392 e SBSIVisual new features Upgrade of Copasi API library to 4 7 includes event handling Persistence of data animation layouts 384 Models and data can now be obfuscated on SBSI servers to improve privacy Performance of parameter constraint table greatly improved 445 Optimization jobs update automatically in the Dispatcher Database view Potential for smaller and hence faster downloads of result files by specifying larger intervals for the report interval 4303 Improved feedback during the result download process 4438 Model files in the result folders containing modified parameters now change their ID to contain the job name in which they were run 441 When configuring parameter constraints default ranges for constraints can be applied globally to all parameters 445 Previously defaults were fixed at 0 min and 100 the current value max The CVODE simulator used by the Numerics optimization framework is now available as a simulation provider via the Simulation menu requires network connection and an SBSI login
33. meters to optimize and con straints Provide a location in which the optimization can be run Configure the optimization process A wizard takes you through these steps and ensures all files are in the correct format before submitting the job to be run See the tasks Choose data and models Configure parameters Configure optimization Configure cost functions Choose job output folder 14 for guidance on using the wizard pages The Problems View can help you resolve prob lems with data formatting You can view the progress of an optimization job in the Progress View This shows the current best cost function value and an indication of how long the job will run for if it runs until the MAX NUM GEN cut off point is reached After a successful run many files are present in the folder in which the optimization was run The results can be found in a subdirectory runtimeFolder results results and include several files e A time course of a simulation with the best found parameters e A file containing the values of parameters which give the lowest cost e A run log e A modified version of the model with the new parameters 2 1 1 Viewing results All the resources results and configuration data from an optimization run are stored in a single folder To get an overview of the results go into the config_data subfolder and select the file ofwconfig xml From the context menu choose Show Summary In Browser LI
34. ms that are already installed Wi Group items by category What is already installed mi Contact all update sites during install to find required software C lt a ES enna dh 3 Click Finish accept any prompts for licence agreements then install Installation 36 will download about 50Mb of new code After this accept the invitation to restart In the restarted application the BioPEPA perspective should be enabled in the Window gt Show Perspective view For help with using BioPEPA see the project webpages at www biopepa org 5 2 Creating a new SBSI project You can create a new project by clicking File gt New gt SBSI System or Ctrl N gt SBSI System A wizard dialog pops up which needs an alphanumeric name for the project You can also choose whether you want the default project directory structure set up In the next page of the dialog you can optionally import an SBML file into your file system Before importing SBSI attempts to validate the file and shows a validation report On finish the resources are created in the workspace and made visible in the System view 5 3 Importing and exporting projects This page tells you how to import and export projects into and out of SBSIVisual Files and folders can be dragged and dropped into the workspace Projects on the other hand can be imported and exported via a dialog e Exporting projects e Importing projects To export a project to share with a colleagu
35. n the page itself ie use SobolSelect or SobolUnselect If invalid data is entered an error is displayed In contrast to the other wizard pages data is not saved until the save button is pressed No validation happens until this time either Invalid data will be left in the text field awaiting correction This is again in contrast to the other pages where invalid data will immediately be replaced with the original data upon attempting to finish an edit of the text field If multiple text fields have become invalid then only 1 error message will be displayed As soon as the field matching that message is fixed then the another error message will be displayed and so on until all invalid fields are fixed and the wizard can proceed to the next page The message save complete is displayed when all errors on the page have been fixed The Use defaults button will revert the page to the default setting for each field and save these values at the same time There are two fields on the page tFinal and popsize which depend on choices made on previous pages Specifically tFinal depends on the maximum time value of a data point in the data sets chosen for this optimization Popsize is calculated as 50 multiplied by the number of processor cores on the platform which will run the optimization For remote optimizations the number of processor cores the tasks value configured in the remote server configuration section If the s
36. n optional field and its contents will be backend machine specific Once you have completed the first login page configuring an optimization job is exactly the same as configuring it to run locally You can view the progress of a remote optimization job by choosing the Optimize gt Query Database menu item This opens a new view the Dispatcher Database view which tracks the status of running jobs Name Status Running Stage Download Log De ion Server Start Time End Time bgl FINISHED FINISHED Download Normal finish stopped after maximum Generation bgl bluegene 2009 12 11 11 05 15 0 2009 12 14 15 23 37 0 bgl FINISHED FINISHED Download Normal finish stopped after maximum Generation bgl sbsidevl 2009 12 11 11 04 32 0 2009 12 11 11 05 20 0 ff FINISHED FINISHED Download Normal finish stopped after maximum Generation ff sbsidevl 2009 12 11 11 02 51 0 2009 12 11 11 05 45 0 ff FINISHED FINISHED Download Normal finish stopped after maximum Generation ff sbsidevl 2009 12 11 10 59 54 0 2009 12 14 15 23 37 0 testl FINISHED FINISHED Download Normal finish stopped after maximum Generation test bluegene 2009 11 24 12 28 55 0 2009 12 11 11 00 05 0 demo2 FINISHED FINISHED Download Normal finish stopped after maximum Generation demo bluegene 2009 11
37. nu option can now be exported to SVG format via the context menu Export to SVQ The FFT cost function can now be configured with an end time after which the FFT will not be fitted 1 6 2 New features in 1 4 1 Tracker numbers for features and bugfixes are included in parentheses e SBSIVisual new features An SBML Validation Preference page is added you can now choose what errors and warnings you want to see listed for your SBML file 460 When running a parameter fitting on the SBSI server you can choose whether or not to compress the log files of the search making the download shorter 459 e SBSIVisual bugfixes Testing model compilation can now proceed even if there are SBML errors as these may be unimportant for SBSINumerics 460 New SBSIVisual users can now access a simulation menu without an SBSI login 464 Dialog history for TestModelCompilation added 463 Current Cost Function text box resized to view the results better e SBSIDispatcher To cut down on the size of the downloaded job contents only time series data sets from the the last 1 2 checkpoints will now be returned e SBSINumerics bugfixes SBSINumerics now ignores SBML errors pertaining to unit consistency by default It should not now fail if these errors are present in an SBML model 1 6 3 New features in 1 4 0 Tracker numbers for features and bugfixes are included in parentheses e SBSINu
38. ose the files to visualize ABC_dat dat Copy of _ABCO_50 dat _ABCO_50 dat Below we see the plot of one of the tabs The tab contain all the species that are common between the experimental and the result data These are being plotted in pairs experimental against result data The user has the ability to quickly browse though the species of the model by using the controls on the top right of the view 42 E Progress Data view DisparcherDarabas ee S _ABCO Soda El im Help A umpro i o gt _ABCO_50 dat ESC tuo ro lt gt gt i ee ae C 5 7 Visualizing a time series on a network diagram SBSIVisual contains a prototype functionality to display a layout of an SBML file and overlay time series data on top of it This functionality is available as an animation In order for this to work you need an SBML model and an experimental data file relevant to your model To begin with you need to add a line in the annotation section of the data s header file which links the data to a model Annotation Model Models repressilator xml The path to the model file can be absolute path on your folder system or a path relative to your data file Now select the data file in the SystemView and select Animate Simulation data from the context menu 43 New gt Open Open With p Copy aC E Paste de Y X Delete Move Rename F2 2 Import ei Export 2 Refresh FS Validate Visualize
39. pdates Available Software Sites f Edit le Run Debug A oro le SBSIWisual leTeam Validation le XML Location http www sbsi ed ac uk update eee AGO SITE Remove f Test Connection Enable i lmmort 1 Once you have done this you can Test Connection to check all is well Now choose click Work with and choose the SBSI update site Choose your plugin and follow the installation procedure Make sure that the option Contact all update sites during install is checked This enables SBSI to locate any other required plugins You will need to restart the application after updating so it s best not to do this if you are running a long process e g a parameter optimization process on your machine 55
40. pe top again and the process should no longer appear 2 2 Choose data and Models To run an optimization you must browse the local workspace and choose in order a project a model in that project and finally dataset s in SBSI data format You may choose 1 or more SBSI data sets To select multiple data sets use Ctrl click Windows or cmnd click Mac You will receive validation warning messages warnings do not block progress of the wizard and are displayed next to a yellow exclamation mark if there is any inconsistency between the species in the data set and those in the model You will also receive warnings if the chosen model contains SBML errors Note however that the latter is very common and may not adversely affect the optimization You cannot choose 2 data sets with the same name This creates an error displayed next to a red cross and blocks progress of the wizard Choosing a data set that does not have a valid header reference will also produce an error Header references are found at the top of an SBSI data file in the format of path to header hdr When they are invalid there will be a warning marker a yellow exclamation mark in the margin of the file to the left of the header reference If you enter a valid path to a header file and save the data file the warning exclamation mark next to the previously invalid header reference will disappear You may then return to the optimization wizard and pro
41. r in optimization or not Parameters are colour coded parameters in light grey are not being used for optimization but may be toggled to being used Parameters in dark grey are not being used and may not be toggled This is because they are present in the experimental data Parameters which are not constant are toggled to off by default and appear in light grey A minimum of three parameters must be selected Parameters have constraints for max and min an initial value and if simulated annealing was chosen on the previous page an initial step All data on this page is saved to history as soon as it is edited It is also validated at this time invalid data is not saved to the history of the model An attempt to enter invalid data generates an error message Data is valid if min lt initial value lt max for PGA or min lt initial value initial step lt max for simulated annealing Data can begin with a and may have one instance of a decimal point Attempts to enter any other characters are ignored However it is possible to paste in copied data that uses scientific notation For example its not possible to type 1 0E 10 for a value but it is possible to copy this string from a text editor and paste it into a cell in the table Note that parameter data from this page is saved in two places One is the history of the model The other is to the model itself The reason that data is simply not j
42. ress de PR No operations to display at this time anyName Now download this simple model right click on the link and click Download linked file then drag the file into any folder in your new project Click on the file to select and expand you should see something like this Y anyName Data jobFolder Y Models Y SB abc_1 xml Model ID abc_1 Model name P SBMLErrors Compartments Function Definitions b Parameters le Reactions Species 2 Objective Functions Other Resources If the file doesn t have the SBML logo decorating it and doesn t show internal details of the model then this is a problem The aim of this test is to check that the Copasi library for running simulations is working properly Select the abc_1 xml model file from the previous step Now right click and choose the Simulation menu item or Ctrl R keyboard shortcut and choose the deterministic LSODA option then click LAUNCH E g 93 Select project anyName Executable model file abc_l xml Save Results to Choose simulation type Standard parameters Duration 1 Intervals 100 Interval size 0 01 Cutoff 30 E tauneH gt fe The simulation should run and produce some sort of visible time series plot E g y na a Pe Ff E SBSI Defa ult Perspective CF System View ses anyName b Data Diagrams jobFolder Mo
43. rom the client This is the initial state before any processing occurs e VALIDATED basic validation of submitted resources is successful I e this checks that all necessary files are available for the job e COMPILED the model has been converted to C and a test compilation was successful e SUBMITTED_TO_REMOTE_SERVER the job has been submitted to the server that will run the job e LAUNCHED the job has now started executing e PARTIAL RESULTS the job is still running but has produced some interim results e FINISHED the job has stopped running either successfully or with error From any point from SUBMITTED_TO_REMOTE_ SERVER onwards then some download should be available Before the job is launched this may be useful to get some indication of an error for example or to examine log files Once PARTIAL_ RESULTS stage is reached some optimisation results will be available The frequency which this is updated depends on the configuration of the optimisation every numGen generations an interim set of results checkpoint will be produced The job is FINISHED when the optimisation has finished perhaps because the target cost has been reached or the MAXGEN number of generations has been reached 2 6 2 Cancelling jobs Running Jobs can be cancelled by clicking on a cell in the Status column which enables a Cancel button This will stop the remote job and update the running stage to be correct at
44. rompted and you should see the following projects imported 800 to 4 Ej H SBS Default Perspective CF System View E T be ses ABC example_initial gt i ABCFinal sus GoldbeterFinal gt ses GoldbeterTutorial In the Models subfolder of the ABC_example_initial project you can find an example SBML model representing the simple reaction system A gt B gt C From here you can run a simulation In the Data gt Experiments folder there are example time series data sets in SBSI Data format You can visualize a basic plot of the data or see an animation of the data on a pathway diagram In the Job Folder you can see the results of a pre run optimization The Help pages describing viewing optimization results provide links to how to visualize some of the result files If you have any question please contact the SBSI team 1 4 Creating a new project When you run SBSIVisual for the first time you will find an empty workspace The first step you will probably take is to create a new SBSI system This is essentially a specialized folder on your file system in which data models and simulations can be managed To create a new Project click File gt New gt SBSI System The following dialog should appear MN New 5651 System New SBSI System Create a new SBSI modelling project vi Create default directory structure Directory Structure Models Diagrams Objective Functions Y Data Simulations
45. s importing the SBML model on the server 12 Chapter 2 Running parameter optimisations 2 1 Run optimization locally In order to run an optimization locally on your own machine the SBSI Numerics frame work and its dependent libraries need to be installed Instructions for this can be found in the SBSINumerics user manual Once it is installed you need to point SBSIVisual to the install location of SB SINumerics You can do this by selecting the Options gt Preferences menu and then selecting the SBSIVisual gt SBSINumerics option AC Preferences type filter text SBSI Numerics Preferences Dr Dpr w Cache Tani b Dispatcher Server 585 Numerics General SESI Numerics folder Users radams Desktop SBSINumReleases install Help le Run Debug Browse y W5BS Wisual SBSI Numerics Preferences Restore Defaults Apply Team Validation he XML So for example if you installed SBSINumerics into home sbsi then that is the folder you would choose in the Preferences Running local optimizations can be activated by or clicking on the Optimize gt Lo A 2 4 5 cal optimization menu To configure an optimization you need to Provide a model file from the workspace in SBML format Provide one or more experimental data files and header files in SBSI data format See chapter 4 of the SBSINumerics user manual for details of this data format Configure the initial parameter values which para
46. se seo 5 8 1 Inbuilt data display ua add bd 4 eGR a 6 1 Miscellaneous features 6 1 1 Reset perspective o 6 1 2 Preferences 0 0000 eee De RRB eRe RAO Ae ee ee eee eee eee ee 6 3 Progress View 4 ee ae eb ew dw ee AOR REE EGE eK ED BS 0A System VieWl ex sser ee ee heey ross 6 5 Installation test oa ee 6 6 Updating SB5SIVisuall LL 6 6 1 ias PARE 6 6 2 Installing new software Acknowledgements Funding This work was supported by funding awarded to the Centre for Systems Biology at Edinburgh a Centre for Integrative Systems Biology CISB by the BBSRC and EPSRC reference BB D019621 1 Contributors SBSI is primarily the work of Neil Hanlon Nikos Tsorman Shakir Ali Azusa Yamaguchi Allan Clarke and Richard Adams Others have contributed to this project most of whom are listed below If anyone who should be on is missing we apologize and please let us know so we can rectify the omission Galina Lebedeva provided example models and helped with testing the software Andrew Millar and members of the Circadian Clock modelling group provided di rection support and requirements to the project Liz Elliot and the CSBE admin team have provided a great deal of behind the scenes support to the project This project was led firstly by Prof Igor Goryanin and currently by Prof Stephen Gilmore For up to date information about help and contacts pleas
47. t Refresh Validate Visualize data Run As Debug As Profile As Team Compare With Replace With Data scaling rrrrTrrr r Animate Simulation data Properties Me 33 Chapter 5 Miscellaneous Tasks 34 5 1 BioPEPA integration 5 1 1 BioPEPA BioPEPA http www biopepa org is a stochastic modelling framework based on pro cess algebras It is an independent software effort but can be run within SBSIVisual SBSIVisual may have been distributed with or without BioPEPA This page describes how to install BioPEPA if you don t already have it If you re not sure if you have BioPEPA installed or not click Window gt Show Perspective if the BioPEPA per spective is listed then you have BioPEPA installed and can skip this section The installation process uses SBSIVisual s update facility which is a mechanism to install new functionality in a straightforward manner You will need to be networked in order to download the BioPEPA plugins New features can be downloaded and installed from update sites It may be that your installation already knows about the update sites it needs to contact to test this Click Help gt Install New Software and expand the Work with dropdown list and see if the BioPEPA update site is listed If it is you can skip this first section If not we need to add in the URLs of the BioPEPA update site and two other update sites on which it depends To install BioPEPA the following steps are
48. t be used Error messages are displayed at the top of the page and progress in the wizard is disabled until inconsistencies in the data are resolved you may have to use the previous job configuration page to do this as values here can conflict with values on the cost function page For FFT cost function a warning is displayed to you if your start time plus 2 period for a state is less than the tFinal value set on the previous page This is just intended as a helpful pointer that the framework will have little possibility of finding cycles For both FFT and X2 Cost functions click on the use in setup checkbox in order to include or exclude them from the setup phase of optimization although you must use at least 1 cost function in this phase Interval must be greater than zero and greater than the solver interval defined on the job configuration page The start time t_init for an X2Cost Function is actually an offset from the start time in the dataset The default value O means that the data time points should be compared with the equivalent simulation time points An offset of 5 would compare data with simulation data at t 5 The corresponding value tFinal determines the simulation end point and set on the job configuration page as it is global for all cost functions The Weight term is an optional configuration to scale the relative importance of X2 and FFT cost functions when both are selected By default the costs for chi sq
49. the time of cancellation If results are available at the time of cancellation these can still be obtained by the Download mechanism described above 25 2 7 Test model compilation remotely Before configuring an optimization job it is a good idea to check that SBSI will be likely to run your model Using the Optimize gt Test Model Compilation menu item it is possible to do this Select project Browse Projects Browse SEML models Browse Models Choose output 0 Please return the C code of the model to my model folder No thanks just tell me if the model will run O gt dl If you like you can also download the generated C code This could be useful if you are interested in developing your own custom cost functions for your model After running a dialog should appear reporting on the success or otherwise of the test compilation E po Ra ai IT est compilation of model file was successful Console output Template is home sbsi disp_dev sbsi_optimisation Template Goldbeter1991_MinMitOscil_1j1_2 3e 4 1269043663611 Goldbeter1991_MinMitOscil xml home sbsifdisp_dev jobs radams Goldbeter1991_MinMitOscil__1j1_2 3e 4 i 1269043663611 rm rf Goldbeter1991 MinMitOscil_1jl_ 2 3e 4 i 126904366361 1 exe Goldbeter1991_MinMitO name E name M name X src DeCodeSBML cppDeCode Goldbeter1991_MinMitOscil__1jl__2_3e_4_i 1269043663611 Goldbeter1991_MinMitOscil__1jl__2_3e_4_i 1269043663611 Goldbeter1991_
50. tored Workspace Root Path Users radams Desktop SESIVisualDemoWs Browse ral Remember workspace L Clone Cancel xu listens to changes in workspace files and performs validation error checking and dynamic provision of functions based on changes A good choice for the location of the workspace is e A writeable location in your own user space e Quite near to the file system root to avoid problems with file path lengths if using Windows e Not easily modifiable by accident from outside the application The workspace files and resources should only be accessed from SBSI Visual ma nipulating resources through the regular file system tools may result in the application not working properly 1 2 1 Multiple workspaces It is possible to have multiple workspaces on your filesystem This is enabled by the File gt Switch Workspace action Simulation Of l Fy New b Exit Switch workspace which opens the workspace chooser dialog 1 3 Working with the example project On Sourceforge you can access an example workspace containing example projects and results to illustrate the sort of things you can do with SBSIVisual 1 3 1 Installing the example workspace Once you have SBSIVisual running download and unzip the SBSIVisualDemo WS zip workspace Now in SBSIVisual click File gt Switch Workspace and choose the folder SBSIVisualDemo WS that you just downloaded Restart the application when p
51. type filter text SBSI WebService dm leGeneral Plasmo Prefs Please enter a username a password and the URL for the SBSI web service SESI Numerics Preferences Mame 5851 WebService ada Team Password eee Server URL https sbsidevl inf ed ac uk 8083 sbsiservices Restore Defaults Apply Cancel You server preferences mx can click Test Connection to validate your credentials Once you ve done this you should be good to go this is a one time operation and SBSIVisual will remember what you ve set 1 6 New this version 1 6 1 New features in 1 4 2 Tracker numbers for features and bugfixes are included in parentheses e SBSIVisual new features Viewing optimization results when downloading results you can opt to view an HTML report summarising the run which will open in a browser 469 You can see this report subsequently by selecting the file ofwconfig xml in the sub folder config_data in your folder and choosing the Show Summary In Browser action SED ML files can now be viewed in HTML by selecting a SED ML file then selecting the Show in Browser menu option Data view tabs are now labelled with the data set s underlying file name rather than the generic Data View Also by default all species are selected and the chart s title is derived from the data file s name 474 Data views that are visualised by the Visualize Data me
52. uared and FFT functions are simply summed if there is a difference in scale between these values then the smaller contribution will be masked Increasing the weight for the smaller value would counter this effect See section 6 7 of the SBSINumerics manual for a complete explanation For FFT cost function the state data can have a start value and expected period set for each individual state in the model Uncheck the use checkbox to exclude the state from optimization From v1 3 5 we have introduced an option to configure the FFT cost value based on a function of amplitude Used State Start Period fncAmplitude Myes A 0 0 25 0 None 7 Eyes B 0 0 25 0 Eyes C 0 0 25 0 Functional ReciprocalSgrtAmp FI ReciprocalSgrtLogAmp vr ii r The details of this are explained in the SBSINumerics user manual section 6 7 2 but there are 3 options e None the FFT cost is not scaled with respect to the amplitude of the peak and is therefore amplitude agnostic e Functional synonym ReciprocalSqrtAmp the FFT cost is scaled by 1 sqr tamp where amp is the amplitude of the peak 22 e Max synonym ReciprocalSqrtLogAmp the FFT cost is scaled by 1 sqrt log amp 2 6 Run optimisation remotely In order to run an optimization remotely no installation of the SBSINumerics optimiza tion framework is required However you will need to be registered to run on a remote machine For example if you want to run optimi
53. ust saved to the model is that in SBML we currently cannot save constraints to nested parameters Nested parameters are present inside reactions and are only visible within those reactions This is in contrast to global parameters The existence of nested 19 parameters also explains the parameter names which are displayed on the parameter page in the wizard Multiple parameters may have the same parameter ID however they will all be nested inside different reactions The parameter table is sortable by any of the column headers including the use column Note that when sorted by the use column toggling parameters on and off will cause them to move position in the table as toggling causes an instant re sort of the table rows CirCl_new xml Configure parameters unchecked data is not used for optimisation click headers to sort the table Enter values to override default scaling for parameter constraint ranges the value entered will be multiplied by the parameter s value to create a constraint value Caution this will overwrite existing constraint values for that particular constraint for ALL parameters whose value is not 0 To alter constraint values for parameters whose value is zero edit the min default max default and step default fields 0 0 min default apply 100 0 max default apply 0 1 step F app y 0 1 0 step default apply f save changes y use parameter id name constant lin exper
54. will attempt to run the simulation The success of this will depend on many factors e The model language Currently SBSI will only simulate SBML models e The simulation type as described in the Algorithm element of the SED ML file e Whether the model file can be found In SED ML models are referenced by a source attribute in the SEDML model element Currently the actual model file needs to be on your computer and the value of the source attribute should be either an absolute path or a relative path to the model file relative to the SEDML file In future we hope to provide support for resolving models from common model repositories using web services If you choose to reproduce a Plot2D output a graph should appear If you choose to reproduce a Report output you will be prompted for a file location to save the report Any problems or failures will be logged and displayed 30 Chapter 4 Concepts 31 4 1 Model Configuration History The model configuration history includes all of the necessary information to repeat a model s last optimization run Furthermore any given optimization job can be re run using the precise configuration which it originally used The mechanism is designed to maintain this history if you copy move or delete a model whether SBSIVisual is running at the time or not Models which are copied will get a copy of the configuration history of the original They will not subsequently overwrite
55. zation on a remote supercomputer you will need to have set up an account independently on that supercomputer If you want to run jobs on our SBSI server then please get in touch and we ll send you login details Once you have completed this first login page configuring an optimization job is exactly the same as configuring it to run locally To set up your login click on Options gt Preferences gt SBSIWebService and enter the login credentials Then click Apply you will get confirmation if the login details are correct Ane Preferences l type filter text SESI WebService Dr Dr General Plasmo Prefs Please enter a username a password and the URL for the SESI web service SBSI Numerics Preferences Name SESI WebService radams b Team Password ERAS Server URL https sbsidevl inf ed ac uk 8083 sbsiservices Restore Defaults Apply Running remote optimizations can be activated by or clicking on the Optimize gt Remote optimization menu The first wizard page asks you to give a name description for your optimization that you can use to identify it Optionally you can choose to obfuscate the model when it is sent to the server as an additional security step This garbles all the identifiers in your model and data so that there will be no way to identify the biological context of the model while it is run on a backend server When the results are subsequently downloaded the files are
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