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1. lt PURPOSE This DTD was developed within the SimBio project It is intended to define a user request on the environment CHANGE HISTORY The list of changes appears at the end of the DTD gt lt A SimBio request consists of a user environment element and a request sequence element Additionally each SimBio request an ID which should be universially unique gt lt ELEMENT SimBio Request user environment request sequence gt lt ATTLIST SimBio Request id ID REQUIRED gt lt The user environment consists of a working directory a log file possibly stderr and stdout files and a an e mail address of the user to be notified when the request has completed gt lt ELEMENT user environment working dir log file notify gt lt ELEMENT working dir PCDATA gt lt ELEMENT log file PCDATA gt lt ELEMENT notify PCDATA gt lt The request sequence consists of one or more requests that are to be executed in the order in which they appear in the file gt lt ELEMENT reguest seguence request gt lt Each request contains all the information needed to run the specified command gt lt ELEMENT request command stdin stdout stderr command line options gt lt ELEMENT command PCDATA gt lt ELEMENT command line options option gt lt ELEMENT option PCDATA gt lt ATTLIST option name CDATA REQUIRED type CDATA IMPLIED gt lt ELEM2. lt option name lh gt BEM lt option gt lt option name lis gt L2 lt option gt lt option name lit gt Truncated_S VD lt option gt lt option name gs gt On_Cortex lt option gt lt option name gh gt BEM lt option gt lt option name ms gt On_Cortex lt option gt lt option name mh gt BEM lt option gt lt option name num gt 4 lt option gt lt option name df gt Moving lt option gt lt option name dh gt BEM lt option gt lt option name di gt Truncated_S VD lt option gt lt option name do gt Simplex lt option gt lt option name dc gt MSError lt option gt lt option name igs gt 0 lt option gt lt option name sveb gt 0 lt option gt lt option name itl1 gt 0 lt option gt lt option name nls gt On_Cortex lt option gt lt option name nlh gt BEM lt option gt SimBio Deliverable D6 b lt command line options gt lt request gt lt request gt lt command gt Drama Sim lt command gt lt command line options gt lt option name f gt out4 lt option gt lt option name out gt out5 lt option gt lt option name np gt 8 lt option gt lt command line options gt lt request gt lt request sequence gt lt SimBio Request gt 29 SimBio Deliverable D6 b Annex 2 Corresponding DTD file simbio request dtd lt xml versionz 1 0 encoding UTF 8 gt eleka Ae PO gt lt SimBio Request DTD rra gt glabra EAE RA O kek gt
3. a new simple icon for menus see application xpm in resources Add include application xpm or the name you choose for your icon in SimbioWindows cpp 5 Add menu button in SimbioMainWindow createSimulationMenu 6 Add toolbar button in SimbioMainWindow createSimulationToolbar 7 Add function SimbioMainWindow addApplication in SimbioWindows hpp 8 Add function SimbioMainWindow addApplication in SimbioWindows cpp 9 1 1 Pon Add function SimbioDocumentWindow addApplication in SimbioWindows hpp 0 Add function SimbioDocumentWindow addApplication in SimbioWindows cpp 1 Add new application parameters in SimbioSimulation initializeKnownApplications Be careful don t forget to update SimbioSimulation nbKnownApplications in this function 12 Add new type of application EN ApplicationKind in SimbioApplication hpp 13 Add new case in SimbioApplication setType 14 Add new case in SimbioApplication updateDialogFromApplication Be careful don t forget any widget 15 Add new case in SimbioApplication update ApplicationFromDialog Be careful don t forget any widget 20 SimBio Deliverable D6 b Simulation Phase General Overview As already described above the SimBio partners agreed to restrict the SimBio environment to a simplified 2 way model The first part of this model constitutes the loca
4. compute server we use the SSL plug in from CORBA This gives as currently a 128 bit encryption security If user decide that the sensitivity of their data is low e g test or junk data encoding and decoding phases can be omitted for performance issues Status of Prototype The first integrated simulation program is the HEAD FEM FE code It expects a mesh file originally generated by the vgrid utility and later partitioned with the DRAMA tool as input parameter Both the partitioning program and the simulation code run in parallel on the same number of processors which allows to do just one resource allocation A predefined batch script is passed to the scheduler that fetches the mesh file and invokes the DRAMA tool on it If this could be successfully completed the actual simulation is carried out 22 SimBio Deliverable D6 b SimBio Pilot Description The SimBio Pilot executes the SimBio requests Normally as mentioned above this program will be started automatically by the so called SimBio Scenario Editor however if the user has an appropriate XML file then it can be started on the command line as simbio pilot file xml Functionality The SimBio Pilot uses the Apache Xerces program to parse the XML request file It then extracts the individual commands which are part of the complete request and executes them sequentially in the order defined by the XML request file Once the request sequence is completed an email message is
5. Cascade Tie home cj SIMBIO SOURCES SimBioProject samples exampleComplet xmi wt home cj SIMBIO SOURCES SimBioProject samples aaaa xmi Figure 5 Windows Menu e Cascade All existing scenario windows are displayed one by one above the others e Tile All existing scenario windows are displayed one by one beside the others e Window 1 n The selected window is displayed in front of the others and becomes active The red sign shows the current active window Help Functionality Functions used to manage SimBio Scenario Editor help About Fi About Qt What s This Shift F1 Figure 6 Help Menu e About Display a dialog with a very simple definition name short description authors and version of the SimBio Scenario Editor About OT Display a dialog with a simple definition remembering QT usage e What s this The current icon becomes Click on a menu or a button to display a short description of its functionality 14 SimBio Deliverable D6 b Applications functionality Here is the list of functions used to manage SimBio Scenario Editor components The user could choose the components he want to use during its simulation he is also requested to set every parameter Once the user selects one component the corresponding property panel is displayed and needs to be validated If the current component is already inserted in the current simulation the operation is cancelled For the moment only 4 appli
6. ENT stdin PCDATA gt lt ELEMENT stdout PCDATA gt lt ELEMENT stderr PCDATA gt Document Type Definition 30 SimBio Deliverable D6 b lt Change history rra gt lt 18 12 2000 kohring Ammended the stdin stdout and stderr definitions to be consistent with the definition for logfile 07 12 2000 janvrais Replaced request with request in request sequence definition This prohibits one from generating XML files without a request 24 10 2000 kohring initial version gt 31
7. T PROPERTIES PANEL rru FIGURE 9 VSEGMENT SEGMENTATION COMPONENT PROPERTIES PANEL FIGURE 10 UIF3 INVERSE TOOLBOX COMPONENT PROPERTIES PANEL FIGURE 11 DRAMA SIM COMPONENT PROPERTIES PANEL rra FIGURE 12 EDIT MENU iten preki ag Eat aak AA BNG BABABA aa aie AN DAANAN ABA reen SimBio Deliverable D6 b Introduction Summary This document describes the first prototype of the WP6 SimBio project The purpose of this package is to allow all SimBio codes and also in the future external codes to interact between each other inside the SimBio environment The interoperability of the environment s components will be realised using a portable object oriented interoperable architecture such as CORBA The purpose of this document is gt To present current status of the WP6 prototype gt To describe WP6 prototype functionality and uses gt To describe future plan of WP6 The SimBio Project The central objective of the SimBio project is the improvement of clinical and medical practices by the use of numerical simulation for bio medical problems The project builds on significant expertise and prior developments for specific applications to construct a generic environment running on parallel and distributed computing systems capable of handling a range of important problems relevant to the target community of clinical and medical service providers This innovative development is an enabling technology for advanced clinical practi
8. The IST Programme Project No 10378 information society technologies SimBio SimBio A Generic Environment for Bio numerical Simulation http www simbio de Deliverable 6b Preliminary Component Interaction CI Definition Status Final Version 1 3 Security Public Responsible ESI Authoring Partners ESI and NEC Release History Version Date 1 0 24 04 2001 11 27 04 2001 1 2 02 05 2001 1 3 16 05 2001 The SimBio Consortium NEC Europe Ltd UK MPI of Cognitive Neuroscience Germany A N T Software The Netherlands Biomagnetisches Zentrum Jena Germany CNRS DR18 France ESI Group France Sheffield University UK Smith amp Nephew UK 2001 by the SimBio Consortium SimBio Deliverable D6 b Contents US BUSAREN AM Ka 1 IO LE MP 24 EEE 2 INTRODUCTION 05 4344441442 LG AKIRA LALABANAN 3 SUMMARY ss e SA V AJA NA RE NANANA SANTANA BADA NAG NUNG e PHESSIMBIO Biei GARATEA THE COMPONENT INTERACTION WORK PACKAGE DEFINITION SOME DEFINITIONS SCENARIOS CASE 1 A SIMPEE GERNIKA aek ka iake 5 CASE 2 A MORE AMBITIOUS SCENARIO sr aaa 6 WP6 PROTOTYPE DEFINETION sissccssssoicctesinesssesnsncconsuseseassbetcesnsvnesigusn sects siecetessvedbeassibestsbonniseonsusecese oja boben 7 DESCRIPTION a sijo i na AN NANA AS III DES NADIN a FIT TO PREDEFINED REOUIREMENTS ni FIT TO PREDEFINED GONSTEAINTE rrura BO BO GO XML SIMULATION REQUEST FILE DESCRIPTION rrura 9 USER S MANUA Lara AGA
9. aeeie APA ANA GAAN GG 10 SIMBIO SCENARIO PDI DR epi ee EEA NANG BLIND NI ara 10 Description ii A NT ler ara ar AN a ai aaa ais 10 Technical Description 10 SimBio Scenario Editor Main Interface File EGTTOO IE e si bes si Window Eunice Help F ncnonality gian Adana ANG An BANGS NAPAGANA WANG AKDANG NANG pna Napa GANG AA does Applications functionality Applications Management dT A GAZA 20 SIMULATION PHASE AA 21 GENERAT OVERVTE Weed ideas 21 INTRODUCTION da 21 IMPEEMENTATION DESIGNS islas ABG 21 Request Initiation Reguest Storing AE E a a ia RN a NEA ae A i o E ULA Reg est Execution aa AE ka o a ra on a SECURITY agarrar STATUS OF PROTOTYPE NS EGO GE OO E NANA INAANAK aN GUO a erk arka a arie eer ek ae ar arretik RELEASE NOTES reen SIMBIO SCENARIO EDITOR SIMBIO PILOT FUTURE PANA 26 GAIEK 26 MIM BIO PIRO K sie SEN O bab Aa NA Na Ban Npa ANA Pa a NG 27 ANNEX 1 XML SIMULATION REQUEST EXAMPLE BUL Ko 28 ANNEX 2 CORRESPONDING DTD FILE SIMBIO REQUEST DTD cccsssssssssssssssssessssessssssssssesssssseees 30 SimBio Deliverable D6 b Figures FIGURE 1 SIMPLE SCENARIO COMMUNICATION rr FIGURE 2 SIMBIO SCENARIO EDITOR MAIN WINDOW sr FIGURE 3 BIE MENU ar EAE at ba A E Nela GIN NA AE FIGURE 4 SIMULATION REQUEST PROPERTIES DIALOG sa FIGURE 5 WINDOWS MENU sr FIGURE 67 HELP MENU a nag RNGA ii an Soria EU NI BIGURE INSERT MENU co dirt FIGURE 8 VGRID MESH GENERATOR COMPONEN
10. cations are available vgrid vsegment uif3 and drama sim VSegmeni3D Ciri 0 VGrid Ctri Drama Sim Ciri 2 uit Ctri 3 Figure 7 Insert Menu Here are each Properties Dialog Box the user has to fill to define component parameters that correspond to the current status of development for each application See below images to have more information on this parameter that corresponds to the command line option of the described component 15 SimBio Deliverable D6 b Figure 8 vgrid Mesh Generator Component Properties Panel 16 SimBio Deliverable D6 b Figure 9 vsegment segmentation Component Properties Panel 17 SimBio Deliverable D6 b Figure 10 uif3 Inverse Toolbox Component Properties Panel Figure 11 drama sim Component Properties Panel 18 SimBio Deliverable D6 b Applications Management Functions used to manage SimBio Scenario Editor editing Undo Ctri U Cut Ctri X Copy Ctri C Paste Ctri V Deselect Properties Figure 12 Edit Menu Undo Not yet implemented Should cancel the last operation done only one level e Cut Remove selected component from the current simulation but keep it in the SimBio Scenario Editor clipboard e Copy Copy selected component from the current simulation to the SimBio Scenario Editor clipboard e Paste Copy SimBio Scenario Editor clipboard to the current simulation Deselect Remove component selection In this case Cut and Copy becomes n
11. ce and health care leading to improvements in non invasive prognosis and diagnosis pre operative planning design and implantation of prostheses and postoperative verification and evaluation of treatment success The application evaluations in the project will demonstrate the effectiveness of the SimBio environment and thus accelerate the take up of this IT technology within the medical area SimBio Deliverable D6 b The Component Interaction Work Package Definition The goal of this Component Interaction Module is to organise interaction between all SimBio components The object oriented implementation of the SimBio environment will allow to simply sending requests to the SimBio server that will organise a solution by calling the appropriate components The component based SimBio environment will offer the ability of distributed heterogeneous execution of its components The Common Object Request Broker Architecture CORBA is the most appropriate client server middleware for the object oriented implementation of the SimBio system CORBA provides a high flexibility and enables the user to optimally exploit the computer resources being at his disposal A CORBA object bus defines the shape of the SimBio components that reside within the bus and also fixes how these components inter operate Beyond interoperability CORBA specifies an extensive set of bus related services for creating and deleting objects accessing them by name externalising their
12. date the permission for inserting into a table Furthermore the values for requested time and procs are checked whether they are in allowed range If all relevant parameters are matching the requirements the actual insertion will be done After the successful completion of this first transmission phase the client starts to send the large binary file The servant in charge receives this file chunk by chunk and stores it into the targetdir If no problems occurred a special flag is updated in the corresponding line of the database table indicating the completeness of the simulation request At this point the client program terminates and the established network connection shuts down Request Execution The job scheduling system is instrumented to check periodically the contents of the SimBio request database If it detects a simulation request ready for execution and the required resource contingents are available it will automatically schedule the request for a batch queue Every user gets an e mail acknowledgement at starting and termination time of the job In those cases where automatic transfer of result data is possible the scheduler will invoke the corresponding client program The request will be taken out of the request table and shifted to an accounting table The information stored here could be taken for various things e g statistics on machine usage or preparation of invoices Security For the data exchange between user site and the
13. e D6 b SimBio Scenario Editor Main Interface Simbio Environment Editor fhome cySIMBIOSOURCESSimBioPraject samples aaaa ans D File Edit insert Windows De HZ DK HEN b Figure 2 SimBio Scenario Editor Main Window Fach component is represented with a simple square and the component name We hope to replace this with application icons as soon as they will become available Selected component appears in red others in green The first toolbar on the left contains some tool buttons with important often used functionality such as New Open Save Print Properties Run and Help The second toolbar on the right contains list of available components It is exactly the same contents than Insert Menu 11 SimBio Deliverable D6 b File Functionality Here is the list of all file menus available from this SimBio Scenario Editor D New Cirle gt Open Cirt 0 El Save Cirl S Save As Ciri A S Print Ctri P MM Properties Ciri T IN Run CirlaR Close CiriaW Quit Citri Q Figure 3 File Menu e New Create a new empty scenario A new empty Scenario Window appears and becomes the one active Next calls to save save As Print Close Edit menus and Insert menus will concern this new active window Open Open a file selector where user can select a file Then this file is loaded and a new window will appear to display its content If the load operation failed an error message is displayed and no new wi
14. e corresponding Document Type Definition DTD file at the end of the document For more information about XML format please consult http www xml org http www w3 org XML or http xml apache org index html SimBio Deliverable D6 b Fit to predefined requirements In the previous deliverable D6a we listed some requirements for this WP6 such as Genericity Heterogeneity Security Authentication in Distributed Environments User Interaction and Data Reuse We could see that the previous description of the current work done inside WP6 continue to fit with this requirement gt Genericity we will see in the following description of work that adding new components in this prototype will be as simple as possible Facility to do a such thing remains one of the main objective of the future job Heterogeneity same remark Components of SimBio environment will come from a lot of partners in very different platform and should be included easily Security Authentication in Distributed Environments In the local phase no security problems could occur In the remote phase use of securized option inside Corba will assure this security User Interaction The end user will be completely responsible of its simulation through the SimBio Scenario Editor He is also responsible of tools he wants to use and of course on the way to use it Data Reuse For the moment no connection to result database will be done the only reuse of data that we
15. e the scenario through the SimBio Pilot The ultimate goal of this GUI should be to provide each class of users a means to automatically generate the corresponding SimBio request The SimBio request describes the complete pre and or post processing The ideal GUI should be capable to reflect a dynamically changing pool of services However since we are aware of the fact that the generation of such a tool is extraordinary complex on the one hand and imposes a significant overhead to the majority of static cases on the other we propose to deal with this issue in the following way 1 Step 1 currently done Development of a GUI for controlling the fixed set of tools which currently constitute the backbone of the project The GUI should generate an XML file that serves as a control file for pre and or post processing Thus every user gets an elegant and efficient tool for driving the environment 2 Step 2 Due to the fact that we cannot assume that the set of tools remains constant in the future a professional GUI should be able to dynamically adapt itself to changes For this advanced tool we propose to base the generation of the GUI on an XML file containing the explicit descriptions of all participating tools However the development of this GUI should NOT be mandatory for the scope of WP6 Anyway the reflection about this step has already started at ESI and depending on the job to do during the next month of the project improvement debuggi
16. esh of the patient s knee 3 The doctor s assistant then selects a standard mesh for the meniscus prosthesis and instructs SimBio to prepare a simulation of the knee movement 4 SimBio sends the data to a computing centre where the simulation is performed Once it is completed the doctor s clinic is notified of the results 5 The doctor then examines the simulation results and makes any recommendations to his or her assistant regarding changes to the selection of prosthesis design While this scenario may sound far fetched today it is in the realm of what is possible within the next decade In addition to the requirements already mentioned this scenario yields one further point which need to be taken into consideration Namely not all users will be experts in the field of bio numerical simulations or Ph D level scientists or even computer experts therefore the SimBio environment must be easy to use SimBio Deliverable D6 b WP6 Prototype Definition Description After a lot of discussions with every partners involved in the SimBio project depending on their needs it has been decided the following Partners asked WP6 to develop a simple design concept for the Component Interaction The basic idea was to have something with a complexity similar to shell scripts but easier for the novice to use Furthermore the SimBio environment should be comprised of two sites gt At the first site the complete pre computing will be perfo
17. he near future 1 high Adding work package ST4 2 application called uif3 that is not yet fully achieved 2 high Manage automatically adding new components into Editor This will probably be done using some kind of XML configuration file that described each new component Each new component will be described at least with the following Information e Application name executable name e Application description e Application parameters For each parameter we need at least the following information e Parameter description e Command line name like np for instance e Type of parameter input output option or help e Type of parameter value filename string Boolean integer real enumerated range This information will be used to generate an automatic interface for the component e Default value e Application small icon to be used for toolbar e Application large icon to be used for drawing This evolution needs to be discussed again to be sure to do not forget any important information These informations will be read and used to generate a simple Dialog box that allows user to set every parameters of his new component We cannot expect to have an extraordinary beautiful dialog box but only simple one using some kind of simple OT widget such as label text slider checkbox and list box 3 medium Changing application menus toolbar by using 16x16 icons Needs to get icon for each component that is part of
18. ilable Following functions that are not currently implemented Print nothing done for the moment Undo not yet finished Binary versions are available for the following operating systems 1 SGIIRIX 6 5 with QT Dynamic or OT static 2 SUN OS 5 5 has been tested once but have to be redone 24 SimBio Deliverable D6 b SimBio Pilot e 11 04 2001 Version 0 1 1 fixes a bug that can occur due to certain incompatibilities between versions 18 12 2000 and 24 10 2000 of the simbio request dtd files e 01 04 2001 Beta Version 0 1 0 is completed The SimBio Pilot incorporates the following features Reads XML files covered by the simbio request dtd version 18 12 2000 or 24 10 2000 Executes the user s request in exactly the order given Creates a log file containing a list of all requests along with any error messages Notifies the user via e mail when the entire request sequence has finished Binary versions are available for the following operating systems 3 SGI IRIX 6 5 4 Linux 2 2 At the moment only dynamically linked versions are available for SGI systems 25 SimBio Deliverable D6 b Future Plan SimBio Scenario Editor First of all this editor will be distributed to partners involved in the project that they can evaluate it Depending on their comments the following list of priority could be modified Anyway here are future developments in order of priority we would like to emphasis on in t
19. ion of a request and it s completion an e mail will provide information on the termination status of the request to the user Implementation Design Request Initiation The Pilot invokes the client program after having successfully generated the mesh grid file It simply passes the name of the grid file and additional control values as command line parameters to the executable The client tries first to transfer the RD to the server Currently the RD consists of the following IDL entries 21 SimBio Deliverable D6 b struct SimReg Account user Account password Path email FileName mesh Path workdir Path targetdir short time short procs bi Listing 1 RD s Idi Representation The call might fail due to several reasons On the one hand the complete compute server service may not be active Here the client is unable to connect to the naming service or the actual SimBio server due to hardware network problems Another possibility would be a rejection of the service due to invalid access permissions While in the first case the users have to postpone their actions in the latter one they could check their user password pairs and re try or ask the SimBio service administrator for further information Request Storing The server program running on a system in the parallel compute server environment enters some data from the RD into a relational database currently MySQL The delivered user and password entries are used to vali
20. l environment Here all non simulation tools are installed and controlled by our SimBio Editor The other part of this model is the so called remote or compute server site Many discussions have been held about the way local and remote tools should interact within medical environments cf D6a Finally we agreed on using the middleware layer CORBA to handle the required data exchanges and authorisation steps Since the use of CORBA imposes a client server logic onto our environment we have to install server daemons on the compute server site which permanently listen for incoming SimBio requests Apart from very few exceptions the vast majority of parallel systems are under the control of management programs One central part of these suites is the job scheduler The SimBio server has to interact directly with the scheduler for starting simulation requests and receiving information about the current job status queued running terminated Since the server has to do these actions in name of all legal SimBio users it needs additional permissions for their execution However it is very unlikely that external computing centres would allow the installation of such daemons Furthermore the interaction possibilities with classical batch queuing systems e g NQS are rather limited Thus it is only feasible to provide a comfortable and user friendly compute server environment on systems that are fully under our control The negative impact on SimBio partne
21. logfile lt log file gt lt notify gt toto Otiti de lt notify gt lt user environment gt lt reguest seguence gt lt reguest gt lt command gt V Segment3D lt command gt lt command line options gt lt option name in gt out1 lt option gt lt option name out gt out2 lt option gt lt option name nc gt 4 lt option gt lt option name correct gt 1 lt option gt lt option name opt gt 0 lt option gt lt option name lambda1 gt 500 lt option gt lt option name lambda2 gt 2 00E 06 lt option gt lt option name min gt 5 lt option gt lt option name max gt 33 lt option gt lt command line options gt lt request gt lt request gt lt command gt V Grid lt command gt lt command line options gt lt option name in gt out2 lt option gt lt option name out gt out3 lt option gt lt option name elem gt tetra6a lt option gt lt option name file gt gridfile lt option gt lt option name format gt kaskade lt option gt lt option name min gt 5 lt option gt lt option name max gt 7 lt option gt lt option name smooth gt marching lt option gt lt option name shift gt 0 05 lt option gt lt command line options gt lt request gt lt request gt lt command gt uif3 lt command gt lt command line options gt lt option name in gt out3 lt option gt lt option names out gt out4 lt option gt lt option namez Is gt On Cortex lt option gt
22. managed will be reuse of already existing result file managed by the end user Fit to predefined constraints Also in the previous deliverable D6a we listed some constraints for this WP Not all applications that we want to inter operate have their source code available which means we have to find a solution to create some kind of encapsulation above the executable gt By the fact we will use direct calls to application from the SimBio pilot as we could do with scripts no needs to source code is necessary Only executable and users manual are necessary to add new application inside SimBio environment The SimBio applications work on different platforms like Unix Linux or Windows based systems gt By the fact that we will work on local machine end users will be responsible to get the correct application he wants to use platform and version If he wants to use remote version of a given application he will be responsible for writing remote access using script for instance or any other solution Since we cannot provide solutions for every local environment and we won t be granted with sufficient access permissions at large independent computing centres we will exclusively focus our remote site environment work on compute servers that we are able to control ourselves Not all applications run at the same site They are located at many different sites on remote computers not close to each other gt Same remark than the previous c
23. ndow is created 9 Save Save the current XML scenario file If no save has already been done a name and location are asked and the new file is created otherwise the current file is updated Save As A name and location are asked and the new file is created Print Not yet implemented We are currently thinking about that function print the XML file print the graphical part of the interface or something else To be discussed 12 SimBio Deliverable D6 b e Properties Display the properties filename simulation name working directory error log file and notify address of the current simulation request See below Figure 4 Simulation Request Properties Dialog Run Call the SimBio Pilot to run the current simulation If modifications have been done save function is called before Default called application is the one defined with environment variable called SIMBIO PILOT PROG if no variable is defined script simbio pilot csh is called The only parameter to this application or script is the name of the XML Simulation Request file A Close If modifications have been done save function is called and the current window is closed otherwise current window is simply close e Quit Same than close function but applied to all windows of the editor Once all windows are closed the application is exiting 13 SimBio Deliverable D6 b Window Functionality Functions used to manage SimBio Scenario Editor windows
24. ng modifications partners need after the evaluation phase it will be possible to achieve this step Technical Description This application is written in C and used OT library http www trolltech com products index html to define GUI and Xerces C http xml apache org xerces c index html for XML read and write QtTM is a GUI software toolkit Qt simplifies the task of writing and maintaining GUI graphical user interface applications Qt is written in C and is fully object oriented It has everything you need to create professional GUI applications And it enables you to create them quickly Xerces C is a validating XML parser written in a portable subset of C Xerces C makes it easy to give your application the ability to read and write XML data A shared library is provided for parsing generating manipulating and validating XML documents Xerces C is faithful to the XML 1 0 recommendation and associated standards DOM 1 0 DOM 2 0 SAX 1 0 SAX 2 0 Namespaces The parser provides high performance modularity and scalability Source code samples and API documentation are provided with the parser For portability care has been taken to make minimal use of templates no RTTI no C namespaces and minimal use of ifdefs Official Description Please have a look on official WEB site for more information 3 Official Description Please have a look on official WEB site for more information 10 SimBio Deliverabl
25. o more available e Properties Open the Properties Panel Dialog corresponding to the selected component 19 SimBio Deliverable D6 b Adding new components To be really generic users must be able to easily add new components inside the SimBio Scenario Editor To do such as thing we propose to deal with this issue in the following way 1 Adding new components by source code modification 2 Reading components definition inside configuration file probably XML format too For the moment only step 1 is available the SimBio Scenario Editor contains a fixed number 4 of components and we have defined a list of steps to do to add a new component This adding manual has already been tested successfully when adding the fourth component Inverse Toolbox component Step 2 will be the next emphasis work and will be defined in the Future Plan section For the moment to add new component by source code modification you have to follow the next 14 steps You can also have a look on source code and search for vgrid for instance to see how this component has been added Please use variables name files name functions name which contain the name of the component you add to be able to find it again easily in the source code 1 Create properties dialog box using QT designer See examples in designer ui You can also created by hand but it will be more difficult Add references into Makefile and designer Makefile Create
26. onstraint Not all applications have a GUI so we have to execute the application directly or create a simple wrapper GUI gt Each application must be able to run with command line options then the SimBio Scenario Editor will provide GUI to allow settings all parameters of every application Component Interaction CI Report SimBio Deliverable D6 b XML Simulation Request File Description You will find one XML Simulation example file on the Annexes in this document and the corresponding Document Type Definition DTD file The XML Simulation Request file contains the following information in addition to the requested XML heading 1 Simulation Request ID 2 User Environment description Working directory Log file Notify address person to prevent when simulation is finished Request Sequence list of application to be run Fach Request called application contains the following parameters Application name command name Standard input filename Standard output filename Standard error filename Command line parameters each parameter is made of option name command line name and corresponding value Some additions will be made during the development phase if necessary SimBio Deliverable D6 b User s Manual SimBio Scenario Editor Description This is a simple GUI application which allows creating scenarios by selected desired components application to define application parameters and then execut
27. or example SimBio Deliverable D6 b Scenarios Many scenarios could be envisaged and the end user will have the possibility to imagine as many scenarios as he wants However to clarify the SimBio environment somewhat we will define two scenarios and will try to see how each will work inside the SimBio environment First of all we will consider a simplified SimBio environment made of five applications 1 Raw data 2 Image Segmentation software 3 Mesh Generator 4 Numerical Simulation engine 5 Visualisation software In the following sections we make references to these scenarios Case 1 A Simple scenario The user has already generated their mesh before calculation and wants to visualise it before running their simulation So the scenario will be 1 Translate the mesh file to Vista format 2 Send Vista data to the Visualisation tool MRI Raw Data Visualisation Tool Figure 1 Simple Scenario Communication SimBio Deliverable D6 b Case 2 A More Ambitious Scenario An ultimate post project end user scenario in the case of meniscus replacement might look like the following 1 The patient s knees are scanned at some scanning facility and the data is inserted into the SimBio environment 2 At the clinic of the patient s doctor which may be in the same building or across the street or as is often the case in Germany across town a doctor s assistant uses SimBio to access the scanned data and prepare a m
28. rmed To be more precisely independent on the employed tools and their interactions the output of this phase is the corresponding mesh We will call this phase local gt The other site we call it a compute server or remote site is responsible for performing the designated simulations The output of the compute server is the final visual data set All those users who do NOT intend to use these dedicated compute server have to take care about the simulation phase themselves To generate the SimBio reguest that will describe the user s simulation we will provide to the end user an editor This editor will be used to define the user needs application and parameters and then will generate a SimBio Reguest or Simulation reguest File This editor will be called SimBio Scenario Editor and developed by ESI The contents of the Reguest will be analysed by a special application This program launches the programs seguentially according to their appearance in the reguest It is also in charge of initiating the calls for the compute server related part This application is called SimBio pilot and was developed at NEC The implementation of the compute server functionality has also been taken over by NEC The File format used for this Simulation Reguest file is XML eXtended Marked Language format You will find short descriptions of the SimBio Reguest XML file in the following sections There is also an XML Simulation example file with th
29. rs is that it s only possible to use the NEC s PC cluster for their simulation automatically If they require other platforms instead they will get no further support from the generic environment However if partners would install compatible clusters they could straightforwardly port our compute server related software to them Introduction Depending on the local security environment under which a user is working the simulation part consists of either one or two client server pairs The first client program is responsible for transferring to the target machine the description of the simulation the so called request descriptor RD along with the corresponding mesh grid file On the target machine a servant listens for matching incoming requests It checks the validity of the RD and if all security aspects are successfully matched stores it in a database The status of the transmission success or error value is returned to the client program On those sites that allow for callbacks an additional server program is launched in the local environment of the user Its purpose is to process the incoming result data from the simulation and to store it in a certain directory The server on the simulation site launches an appropriate client for handling the transfer If security restrictions on the user site prohibit the automatic exchange users are in charge of fip ing the data on their own Since big time differences may occur between the initiat
30. sent to the user containing a status report on each individual request In addition the status messages are written to the log file specified by the user in the XML request file 23 SimBio Deliverable D6 b Release Notes SimBio Scenario Editor 24 04 2001 Version 0 1 1 fixes the following bugs and errors 1 nA o b Adding new application called uif3 Inverse Toolbox application with corresponding properties panel raw data used for testing was removed Memory Fault core dumped with New menu in OT static version Memory Fault core dumped when inserting a vgrid application within an empty simulation Call to SimBio Pilot is now done using environment variable called SIMBIO PILOT PROG instead of calling directly a script If this variable does not exist default value simbio pilot csh is called The parameter is still the scenario XML file 15 04 2001 Beta Version 0 1 0 is completed The SimBio Scenario Editor incorporates the following features 1 2 It contains 4 applications rawdata vgrid vsegment and drama sim Each application has its own properties panel that allows user to set application parameters Following functions are currently working New Open Save Save As Properties Run Close Quit Cut Copy Paste Deselect Properties and Insert applicationl to 4 It is able to manage several scenarios at the same time and all windows manipulation tile cascade and so on from QT are ava
31. states and defining ad hoc relationships between them To make use of CORBA for SimBio an interface has to be specified for each component These specifications are written in the Interface Definition Language IDL and define a component s boundary i e a contractual interface with potential clients A particular example of the need for interacting components arises with the simulation of a prosthetic implant where close interactive links between the visualisation package the material database an external prosthesis database and the biomechanical solvers are required The portability of CORBA will allow the SimBio internal and SimBio to external interactions to take place in a seamless manner The platform independence of this approach is of decisive advantage in the clinical field as hospitals are often equipped with very heterogeneous computer clusters Some Definitions 1 SimBio Environment set of all applications tools products etc developed inside the SimBio project or used by SimBio applications 2 SimBio Application tools developed or used inside the SimBio project such as the mesh generator solver and so on 3 SimBio Component each application and its interface GUI CORBA Web Access developed inside the SimBio Environment each component provides a list of services inside the SimBio Environment 4 SimBio Service functionality provided by a SimBio component such as mesh generation mesh visualisation cropping etc f
32. the SimBio Scenario Editor 4 low Changing application drawing by using 100x100 icons Needs to get icon for each component that is part of the SimBio Scenario Editor 5 medium Create a configuration file XML again that could allow user to change SimBio Scenario Editor parameters such as user name user email address SimBio pilot name colour widget size widget position XML reading and writing option with or without DTD for instance 26 SimBio Deliverable D6 b Compute Server Development In the second year we will integrate the missing simulation applications into our compute server environment Another important issue is the implementation of solutions for the interaction of applications and the inverse tool box which has not been addressed yet Since the transfer of huge binary data files between user and compute server site can become a significant bottleneck possibilities for optimising the transfer should be considered 27 SimBio Deliverable D6 b Annex 1 XML Simulation Request Example File This simulation request called New Simbio Simulation is made of 4 application vgrid vsegment uif3 and drama sim each application contains an important number of parameters called option lt xml version 1 0 gt lt DOCTYPE SimBio Request SYSTEM simbio request dtd gt lt SimBio Request id New_Simbio_Simulation gt lt user environment gt lt working dir gt lt working dir gt lt log file gt
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