NeuroLOG Client User Guide
Contents
1. Next Search returned 2 result s Clicking on the Next button opens an additional Subject oo query column on the right Identifier of the first one This new E Common identifier o column will help continue the browsing process one jin _ progress Type gt level ahead in the 2002 04 01 I browsing tree With examination Manual hem domir i anual hem dominance In this new column the Language hem dominance drop down list proposes Born between O and types of the second level of the browsing tree in Figure 1 1Y any 35 i yes f no Search aided annotation of cortex structures aat importation study Follow the same process again in the second column select the entity type note that the status bar changes on each selection to describe the type of query this will perform Fill in the criteria and click on Search button Select results and proceed with the next step by clicking on the Next button Ultimately you will get to a leaf of the browsing tree like on the example branch Study gt Subject gt Dataset Once datasets are retrieved the Next button is no longer availbable Instead use the pop up menu in the results list to add selected datasets to the cart as shown below Refer to sections 4 2 for datasets management from the cart h Subject Dataset result of a study ha Search Criteria Searc2. alban gaignard i3 s unice fr Accept Reject This tab display the list of all pending requests for role subscription An administrator can either wait accept or reject a request by selecting a user and selecting the action to perform in the Register column All requests are finally processed when the administrator clicks on the Validate button Selected requests can be removed but do it carefully because the user won t receive any notification iii Study access control management This last tab displays the access control policy of the site Each line corresponds to an authorization rule triplet StudyID Role Permission Authorization rules can be modified by clicking on the role or on the permission or can be removed by selecting a rule and by clicking on the remove button Access control f Users management User requests Resource ID admin write NI SS 3 Study NI SS 3 fe Study ID Role a pas arao a O oyi NESS 2 NESS 1 Study RE SS 1 RE SS 2 Study RE SS 2 A new rule can be constructed by selecting an element for each column studyID role and permission When the administrator clicks on the ok button the window is closed and the new rule is added to the access control policy 4 2 2 Data retrieval Before data files can be visualized they should be downloaded onto the user workstation From the cart pop up menu select the Downl
3. Search Criteria Identifier Name Status Started after e Ended before E Clinical Tip each type you change the selection the status bar displays a With examination description of the query you will perform at this stage i any i any yes cf no yes C no the set of search criteria depending on the type of entity Search f f the search result list will display a synthetic results list entity identifier and possibly a name or common identifier Tip A drop down menu allows to view or explore entities or to select all of them Once some results are selected the Next button opens a new query column to go on browsing 4 1 3 Usual browsing process From the drop down list select the type of entity you would like to query first Note that the search criteria panel is refreshed based on the selected type of entity Status a Started after cal bdid Dt a j Fill in the search criteria then click on the aa in_progress al Search button a 2002 04 01 i After a few seconds the results are Ended before e displayed in the results list while the TENE T status bar displays the number of results any yes Select the result you re interested in and B then click on the Next button any i yes i no Search NI 55 2 Computer aided annotation of cortex structures NI 55 3 DICOMFormat importation study
4. Ma The list of operations that can be invoked is displayed in a selection list Clicking on the Execute button cause the selected operation to be invoked on the site server side and the output is displayed in a new area at the bottom of the window If the service has input parameters one line appears for each of them in the Parameters area T x MA x Wa x Execute echo 1 0 0 Service echo 1 0 0 Operation local Parameters text string hello world i Cet from cart Execute The user can enter the parameter value manually or select it amongst the dataset expressions available from the cart if some datasets where previously selected by performing queries see section 4 A tool wrapped with the generic web service tool wrapper as documented above will typically produce file as result of its processing The file identifiers then appear in the Output area after execution P y j Execute echo 1 0 0 Service echo 1 0 0 Operation loca ey Parameters text string a Get from cart Output file Users johan data 1241703364374 std out f file Users johan data 12417033643 74 std err i F Execute 5 4 Workflow edition and invocation To open a workflow tab use the Tools gt Workflow engine menu or the workflow icon The workflow panel is an empty panel that can be used to load or edit a new workflow and then follow on its execution Use the oad button in the bottom right corner of the
5. Program Files Java jdkl 6 0 06 Depending on your OS you may have to update the PATH environment variable by adding the bin directory of all JDK OpenSSL and Graphviz applications On a Windows system add the following to the PATH or Path variable C Program Files OpenSSL bin C Program Files Graphviz2 22 bin JAVA HOME bin 2 1 3 Validate the installation To validate the installation of these components do the following commands and make sure they do not return any error OpenSSL execute command openssl x509 h and see the usage of the command Graphviz execute command dot h JDK execute command keytool help command Do not proceed with the next section if this one is not completed successfully 2 2 NeuroLOG client software installation The client version documented in this guide is version 0 4 0 Download the client bundled archive from the NeuroLOG web site htto neurolog polytech unice fr doku php id public namespace prototyoe v0 4 0 and follow the instructions There exists one archive per supported platform linux macosx and windows Expand this archive in your user home directory The archive expands all files in the neurolog sub directory It contains e The startup Script neurolog nlog client MacOS and Linux or neurolog nlog client bat Windows e The client jar archive neurolog lib e The visualizer neurolog viewer In addition the Windows archive contains addi
6. panel to load and display an existing workflow To create a new workflow right click anywhere on the panel and use the contextual menu to add workflow inputs outputs and computing processors TEE m New inputs outputs and processors appear in the workflow panel at the place poena of the mouse click Double ETT output click on the processor box voice ak to change its name with a meaningful value or select the rename contextual menu item Load Save Simulate Empty workflow a 12 To create a link between processors move the mouse over the source processor use in the contextual menu item edge from and orem select the source output port from the configure processor in the sub menu delete node P Then move the mouse over the target processor and select the target input port i from the processor in the menu A link is then created The graph is re laid out automatically after each link addition for optimizing the graph readability it is normal b for the processor to be redistributed in the EE panel during this process new workflow ee new workflow edge from gt rename i configure delete node m a Li i new workflow Processor Q configuration Ports iterators Processor x j F re Once the workflow has been edited it can be saved through the save button in the bottom right corner of the panel The workflow can then be
7. that corresponds to the tool to wrap into the system by clicking the browse button Additional information can be entered such as a name mandatory the default is the binary name a description of the service licensing information etc The input outputs of the executable being wrapped then need to be described Use the button in the Argument tab at the bottom of the window Add new tool Executable bin echo Browse Service name echo Version 1 0 0 Description Vendor Copyright CeCILL B Key Address a E Argumen RESNI Label IO l Input Option Type File H Value Space Yes f Pia ma 5 D 1 a Crid Configuration Create Service k A dialog box enables to specify an I O label human readable I O field description the corresponding command line option e g c and an optional value The kind of argument input output and the type integer double string or file also needs to be specified Labels of arguments specified are listed in the Argument tab When the all arguments have been specified the Create Service button cause the service to be created and registered a Web Service interface is created the service is packaged into a jar archive that will be hosted by the middleware web service container and this archive is transferred to the site server the client depends on for deployment 5 2 Tools listing Use the Tools gt Browse processing tools menu o
8. I 55 145 f has same sampling grid as datasets al 0 is result of MR dataset acquisition 4 2 1 Data access rights For the normal user user point of view i e not a site administrator data can be retrieved only if the good role has been beforehand assigned the user by an administrator We will see later how an administrator can grant access right to hosted data through roles A role subscription process has been integrated within the client application Using Data Subscribe to role the user can select the role she wants to subscribe to the role names should be enough explicit such as for instance partnerlnStudyXX Then the system retrieves the coordinator site of the role only one site is responsible for a given role and stores a role subscription request in the administration panel of the application a mail notification is also sent to each administrator If an administrator approves the request the role is assigned to the user and consequently she can retrieve data whose access has been granted through this particular role The data access authorization manager is only accessible to site administrators The normal users do not have access to the menu and icon Use Administration gt Authorizations manager menu or the administration icon Q Administration is divided into three main activities which correspond to the three tabs of the administration panel users management requests management and finally st
9. NeuroLOG ANR 06 TLOG 024 Software technologies for integration of process data and knowledge in medical imaging NeuroLOG Client User Guide PE LEOTE U Pi allan J 1 T T 1 T D a Authors F Michel IRISA F Ahmad IRISA A Gaignard I3S J Montagnat I3S D Godard Visioscopie J Rojas Balderrama 13S Version V0 04 NeuroLOG client version 0 5 1 Date Mar 19th 2010 Summary This document is the NeuroLOG client software installation and usage guide 1 2 3 4 6 T NeuroLOG ANR 06 TLOG 024 Document layout Architecture OVE E Woese aAA EE E A 4 Software installation and start up nnnenennnnnennnenennnnnnnnnnsnnnnnrnnrrnnnnrrnnenrrenenrreennne 5 2a Prorcdu SeS ernea runny Mahansdacueiesseamsnaienessieevaials 5 2 1 1 Needed third party SOWALES ccccccssccccseeeeceeseecseseecseeeeeseeeessaeeessaaees 5 Ak2 ENVronmMentvanaplES posoan a lad ancusndadsa le 5 2 1 3 Validate the installation cccccccccccsseccseeeseeeeceeeseeeeeeeeseeeseesseeeseeeeaeeess 5 2 2 NeuroLOG client software Installation cccccccccssecccesseeeceeeeeseeeeeeeeeeesseeeeeseeeeees 6 eas Meo E Gla 01 9 emer Meee Re eee APT ee ORR OCR Creo A A E E ner me Ro meee eee ene 6 CQUIGK SLANT GUIGE ay scscearcntacecereienctanzctieiaiesseaenansere a eee 7 3 14 Firstconfigurahon Ste Deinsea eh E E 7 372 SECOMNG COMMNGUNALION SIC Drai ates teen ctuet daciateteu bert a tues eejoneueiaitaialan
10. RM OU GIN ASCLEPIOS C FR O INRIA OU SOPHIA 5 The next panel requires to enter the path the graphviz executable file Check that the path is correct then click next The user certificate now needs to be signed by the server CA The certificate request will be transferred to the CA administrator You will be notified directly when the certificate is ready for retrieval and you can restart the client installation procedure to retrieve it 6 The next panel indicates the end of the first step of the configuration process Clicking on terminate will cause the necessary information and your certificate signature request to be sent to the site administrator for validation Cancel lt Previous Terminate First step succeded 7 Upon correct transfer of this data you will receive a confirmation message Your certificate has successfully been delivered Wait for the notification from the CA administrator and start the setup again You now need to wait for the administrator validation Once you receive the successful notification email restart the client and proceed with the second configuration step next section 3 2 Second configuration step Login Once you have been notified by phone or email that your user registration request has been validated you can restart the client to finalize the installation procedure On start up the client will prompt you with a login window enter your selected login and passwor
11. This document first describes how to install the client application and to configure it for proper communication with the I3S site server It then documents the use of the NeuroLOG platform accessible through the client 2 Software installation and start up 2 1 Pre requisites 2 1 1 Needed third party softwares The client application depends on third party software packages that should be pre installed on the client machine prior to the NeuroLOG software installation e OpenSSL tools to generate user identification certificates OpenSSL is installed on most standard OS distributions It can be downloaded from http Awww openssl org or http Awww slproweb com products Win320penSSL html for Windows e Java6 Development Kit JDK to run the core application software http java sun com javase downloads e Mono for non Windows OS virtual machine to run the images visualizer hitp Awww go mono com mono downloads download html You should also be able to validate the command mono version e Net for Windows htip www microsoft com net Download aspx e Graphviz graph visualizer dot tool for workflows visualization and edition http www graphviz org Download php e OpenGL libraries for 3D visualization This should be pre installed with the graphic card drivers on any modern distribution 2 1 2 Environment variables Set the JAVA HOME variable to the JDK path Typically on Windows this will be like C
12. ay then select the check box and use buttons at the bottom of the Downloads section to either visualize the dataset see section 4 3 for a description of the visualization tool or remove a download and its temporary files from the user workstation 4 3 Data visualization Visioscopie image viewer is in a beta status with limited functions This guide will include a description of this tool later on Fow now please contact David Godard for any issue on this matter david godard visioscopie com 4 4 Semantic data querying In semantic querying section of current version of NeuroLOG client available functionality is 1 Fetching data from RDBMS and generating RDF files 2 Querying this generated file and displaying result in XML format Step 1 is an automatic procedure and each time on the launch of window system updates its files from the database Results in tabular format and query builder will be available in next releases To launch semantic window either use Semantic gt semantic query or icon In semantic window there are 3 major sections as shown in figure below Semantic Search Select Result Format Available Queries Select Result Format Results a Results in XML Format lt xml version 1 0 encoding Cp1252 gt lt cos result xmins cos http l www inria Friacacia corese gt lt cos tquery gt lt I CDATA select list display xml where x rdFitype y gt lt cos tquery gt
13. basic properties like the identifier name type status dates etc But it does not display relations of the entity with others typically a subject will not be displayed with the studies he s involved in or his datasets The following presents an example of the View selected window for some subjects n View Subject Identifier Type Sex O Manual Hemisphe Language Hemis Birth Date Common Identifier Inissi Patet Mae Left he O hooro Ee23771196399 Nissa Patient Mae het he fioa60r01 JAR B6BF 654771 NESS 12 Patient Mae he O ossoa faoeos1037E12 Nrss 18 Patient Male O OOOO hoooron eraz Explore selected menu The Explore selected menu allows for a more in depth presentation of a single entity that is check the context of one entity how it is related with others The entity properties are displayed on the right pane along with a tree like view of its relation to other entities on the left pane For instance a study will provide data about the centre in which it is hosted the involved subjects the datasets either produced or used as input of the study etc Each such related entity is presented as a node that can be expanded in which case a request to the NeuroLOG server may be needed to retrieve the properties of the related entity The example below presents a study tree alolx Study NI 55 2 Properties G takes place in centres with main investigator kh Centre NI SS 1 E A Investigator NI 55 3 yj has for coordina
14. ch textual entries in order to identify contributors If you want to benefit from mail notification please ask a personal account to alban gaignard i3s unice fr Tickets will be then prioritized and grouped in order to enhance and define next development phases 3 trac Integrated SCM amp Project Management logged in as gaignard Logout Settings Help Guide About Trac pki f Tmeine Roadmap Browse Source View Tickets New Ticket Create New Ticket Short summary Typa Full description you may use WikiFormatting here BIA 8 amp 8 amp E fT uz Ticket Properties Priority Milestone C W Component Keywords Assign to Cc Q I have files to attach to this ticket Preview Submit ticket Note See TracTickets for help on using tickets at amp ie OR ER EH
15. d login jlapin lesseoe password On successful login the client contacts its server and imports a security certificate that will guarantee the protection of all subsequent communications This certificate transfer is unprotected since the client and server have not already exchanged the necessary elements The user is prompted to validate this exchange This will only be needed once on the first login The server certificate is validated through a hash signature similar to the one given in the example window below 1A 4D 0F 6F 1B 47 E3 C5 You can verify this signature from you site administrator The signature is typically published on a public web site for checking It is important that this signature is trusted before you continue If the signature does not match the expectation click No Only otherwise click yes Validate Site CA certificate Carefully validate the Neurolog CA certificate retrieved The certificate downloaded distinguish name is CN NeuroLOG Root CA OU ANR 06 TLOG 024 NeuroLOG O CNRS C FR and its signature is 14 10 03 94 7 8 ED F7 74 2A4EL D 2C 9 4 8D C8 BE95 9F 57 0E after counter checking these values with your site administrator DO YOU TRUST THIS CERTIFICATE Once the signature is validated the client interface will be started Any further transaction between the client and server will be secure The interface main window provides access to all the middleware functionality data manag
16. e View selected menu in section 4 1 4 as shown in the following picture To open the cart select the User Cart icon from the top icons bar Datasets Identifier NI S5 145 NI S5 146 f Explored Entity Processed Type Nature Modality Type Creation Date T Result OF Study Anatomical Dataset ReconstructedDataset MR Dataset 2008 05 30 00 NI 55 3 NI 55 18 Anatomical Dataset ReconstructedDataset MR Dataset 2008 05 30 00 NI S5 3 NI S5 18 Anatomical Dataset ReconstructedDataset MP Dataset 2008 05 30 00 ND SS 3 NI 55 18 From the cart pop up menu the entity Explore menu provides the ability to dataset ReconstructedDataset MR Dataset explore a dataset as already Dataset ReconstructedDataset MR Dataset described in section 4 1 4 Dataset Reconstr Dataset Cre 200 200 Processed Type Nature Modality Type Download Files From expression Explore details of the selected dataset Remove from cim As a result a window of the following type pops up B Entity Viewer MF Dataset NI 55 145 o is result of piana r re a ee oe EME concerns subject he Subject NI 55 18 concerns experimental groups of subjects EI gt has dataset expressions Dataset Expression NI 55 146 E G is expression of dataset 43 has parent dataset expression a Dataset Expression NI 55 145 3 ce 9 Dy Dataset Expression N
17. e next panel is empty Please fill in your complete name first name and last name your desired login when accessing the system your desired password your phone number and your email contact information for your site administrator to be able to contact you back Click next to continue 3 The next panel describes the site server you will be connecting to Change the parameters corresponding to your site as listed below Server neurolog unice fr Port 8445 not 8444 as on the picture Unses Server Unses Port Server Port Unses Server Unses Port Server Port Unsec Server Unsec Port 8080 Server Port Unses Server Unses Port Server Port Unses Server Unses Port ee Client setup Enter user certificate distinguish information Tcl i Organization Organization unit 35 User name Jeannot Lapin Client setup What is the path to the Graphviz executable file graphviz exe fusr local bin dot 4 The next panel gathers information that will be integrated into your X509 user certificate namely country code C 2 letters organization name OJ organization unit OU and complete user name CN Fill in the organization name and organization unit and click next For now the following conventions have been applied C FR O CNRS OU I3S IFR49 C FR O INSERM OU IFR49 or C FR O INSERM IMPC U UMR_S 678 LIF O IRISA C FR O INRIA OU IRISA C C FR O INSE
18. egistration request Only when the site administrator validated this request can the client actually connect to the middleware This validation is a manual process that can take some time depending on the site administrator availability When the request is validated or rejected the client owner is notified by email She he can then run the client a second time to complete the configuration process and run the middleware see next section 3 1 First configuration step Client setup 1 One the first run the configuration This assistant will help you set up a NeuroLOG procedure with this screen client A user account and a server connection During the rest of the procedure the user Will be created as l will have to fill in the information requested by the system in the following panels for proper configuration Most requested fields are pre filled and should not be changed Click next to continue Client setup Enter new user information User name Jeannot Lapin Login lapin wesss O Confirmation esses O Phone 123456789 es tstsisisidCY jeannot lapin org Password chent setup Which is the NeuroLOG Site Server to connect oe tps ooo Serer Ineurolog unice Fr Basa o Unsecure access protocol m ss Bosz NeuroLOG_Middleware 1 0 SNAF Access protocol Port number Service path Service name Unsecure server Unsecure port number Unsecure service path Unsecure service name 2 Th
19. ement processing workflows Each function will operate in a different window tab On start up a single tab displaying the content of the user cart the result of former data selection It is empty on first start up as illustrated below NeuroLloG I3SDEV client V0 3 2 Jeannot Lapin Data Tools Semantic Help SP Dx amp OF Datasets identifier Modality Type Explored Entity Processed Type Creation Date Result Of Study Downloads visualize Remove The button bar and the menu will cause specific tabs to be added to the main window containing specific interfaces for each function The following sections describe each function available Tip At any time the user carticon can be used a to display the cart tab content e 4 Data Management The data management is the set of features that allow a user to gather datasets into the cart in order to later visualize these datasets or use them as input of processing tools and workflows This process of gathering datasets is performed through the querying of metadata attached with datasets in a metadata browsing manner A future version of the NeuroLOG software will allow to fill in fields of pre defined multi criteria complex queries 4 1 Metadata querying 4 1 1 Understanding the browsing tree Browsing the metadata is performed by following the branches of a predefined browsing tree This tree which
20. executed Prior to real execution it is usually useful to control the data flow that will be generated during execution by simulation Click the simulate button in the bottom right corner of the panel This causes two dummy data items to be pushed inside each workflow input and cause all processors that received data items to be activated just producing an output string trace of the simulated invocation rather than performing a real computation The data flow is thus dynamically resolved and the progress of the Reset strategy Each processor created has a default structure with one input port labeled in one output port labeled out and no computing content defined To configure a processor right click on it and select the configure menu item The configuration widget enables the definition of processor ports first tab the definition of iteration strategies second tab for processors with 2 inputs or more and the processor content third tab To edit an iteration strategy you can e Change ports order by dragging ports names vertically e Right click on an iteration strategy operator to change it e Select a group of ports right mouse click and drag around ports to create a new iteration operator computation is visualized in the workflow interface EH ape The number of runs of each aa ee Workflow production processor is displayed in Output out the processor box The Type String proce
21. ferent purposes Add query To add a new query type query in query operations and click add query button It will validate the query If query is valid then it will ask for query name Query will be available for execution in available queries Remove selected query To remove a query from available queries select query and click remove selected query Load query Load query will validate and load an already available query from a file Save query Save query will save a query from available queries in a file By default file name will be the same as per query name Execute query To execute any query first add query in the list of available queries After addition of query in the list of available queries select query to execute Due to limitation of resources we only display first 100 results in XML format Save results in file To save results in a file select location and provide file name Results will be available in the file for later processing 5 Tools management 5 1 Tools registration New tools can be registered by a system administrator through an admin specific menu Use the Tools gt Add new tool menu The tools registration interface is shown in the figure below Add new tool Executable Browse Service name Version 1 0 0 Description Vendor Copyright CeCiLL B Key Address ak Category Application Argument Dependency The user first need to select an executable
22. h Criteria Identifier P Identifier Common Identifier o Mature s55 Type Patient Processed dataset type J1 e Sex Maes Modality j Manual hem dominance ft Explored entity CaN Language hem dominance O any Born between 1965 01 01 Ca and a yes C no Search Search Search artex structures DERA NI 55 147 MR Dataset N1 55 146 MR Dataset NI 55 145 MR Dataset View selected Explore selected Select all Next Next Add to cart Next Add selected datasets to your cart Tips You may rerun this process again following any other branch of the browsing tree until you have collected required datasets You may open any number of Browse Metadata panels or continue browsing on the same panel note that clicking on the Search button will remove any query column on the right 4 1 4 Viewing entities details A i ren During the browsing process it may be al necessary to review entities in more details Wpic than simply getting their identifier For this epaitan purpose a pop up menu is available from ar era View selected the results list whatever the selected type of INI S5 17 EA 22F2 1 Explore selected CJA f 219370 View mi details of enti ty NI 55 18 E1 31233 Select all iew more details o Meat View selected menu The View selected menu displays a set of entities in a tabular form Columns of the tab represent the entity
23. lt cos info gt lt CDATAL Stop query after 100 projections 0 00 s for 100 projections J gt lt cos info gt lt sparql xmins http www w3 org 2005 sparql results xmins rdf http fwww w3 org 1999 02 22 rdF syntax ns gt lt head gt lt variable name x gt lt variable name y gt Results in Table Query Operations select where x rdf type y Add query lt head gt lt results ordered false distinct false gt lt result gt R pdb a lt binding name x gt lt uri gt DBIOL NI 55 19 lt uri gt lt binding gt lt binding Load query name y gt lt uri gt http fwww mis u picardie fr lando ontologi es dataset OWL Lite owl dataset lt uri gt lt binding gt lt result gt lt binding name x gt lt uri gt DBIOL NI 5S 20 lt uri gt lt binding gt Execute query seta lt binding name y gt lt uri gt http fwww mis u picardie fr lando ontologi es dataset OWL Lite owl dataset lt uri gt lt binding gt lt fresult gt lt result gt lt 4 4 1 Available queries This section provides a list of available queries for execution To view any query available in this section just double click the query and it will be visible in the query operations window 4 4 2 Query operations Purpose of this section is available to view or addition a query 4 4 3 Result window Result window is to display results of executed query We have following set of buttons for dif
24. may evolve along with users feed back helps query metadata step by step and ultimately gather datasets Typically a user may want to query studies matching some criteria then get some subjects involved in these studies and finally get the datasets of those subjects produced within these studies outlined in red in the figure below The figure below describes the current status of the browsing tree at the time this document is written Level Subject lt Leyej2 Dataset Dataset Subject Experimental input of study result of study group of subjects Dataset input of study Dataset Dataset input of study result of study Level 3 Dataset Dataset input of study result of study Figure 1 Metadata browsing tree Thus the metadata browser will help browse through this tree starting by a query on an entity of level 1 possibly going on with level 2 etc 4 1 2 Using the query column Select the Data gt Browse Metadata menu or select the Browse Metadata icon SH The browse metadata panel is initially displayed with one query column on its left side Several such query columns may be later displayed along with the browsing process The query column is always composed of the same parts The entity selection drop down list allows to select the type of entity to search at this stage of the browsing process the first query column lists entities in level 1 of the browsing tree and so on Study
25. oad files from expression menu From the sub menu select the dataset expression which files must be downloaded Each dataset expression is given by its identifier format type oe Nifti etc and record date as depicted below Creation Date T Result OF Stuc Identifier Explored Entity Processed Type Nature Modality Type Anatomical Dataset ReconstructedDataset pM R Dataset 2008 05 30 00 if NI S5 145 NISS 146 Anatomical Dataset ReconstructedDataset ee R Dataset 2008 05 30 00 i JC WIR 2008 05 30 00 Anatomical Dataset Reconstr As a result a new download entry is added to the Downloads section of the car panel The download entry section provides the identifiers of both the dataset and its dataset expression the dataset expression format type DICOM Nifti etc and the record date Result OF Study Creation Dake Time Datasets Identifier NT S5 145 NI 55 146 NI S55 147 Explored Entity Frocessed Type NI 55 a Dataset _ReconstructedDat a Dataset 2008 05 30 00 00 NI 55 MR Dataset 2008 05 30 00 00 NI 55 3 MI S 35 18 CPePeOCOOTOePOPeererreererertterereererterrererenrs Downloads MP Dataset NI 55 145 expression NI 55 145 DICOM 2009 01 20 MR Dataset NI 55 146 expression NI 55 147 DICOM 2009 01 20 Visualize Remove Once the progression bar reaches 100 the selection check box becomes active You m
26. r the tools icon b a Registered tools are listed in a two columns window On the left is shown the list of existing services On the right appears detailed information on the service its endpoint WSDL interface the list of operations exposed by this service and the input parameters for each operation In the example below the echo 1 0 0 service has 2 operations output and local The first operation has no parameter while the second one has a single string input parameter echo 1 0 0 Authe nticationService Registry Version FileManagementService service echo 1 0 0 RetrieveMetadataService Attps 157 169 100 16 8443 axis2 services echo 1 0 0 jgaswPortawsal operations output a local l text string Refresh 6 tools found On the first selection of a service the information may take a little time to display since the remote web service container is queried for the detailed description of the service First access to a web service typically takes some time as the service has to be loaded by the container 5 3 Single tool invocation Use the Tools gt Perform processing menu By double clicking on a tool name in the tools list or by selecting the appropriate menu when a tool is selected a new panel with an execution interface appears eH Va Va psa Execute Version Service Version Operation getVersion Parameters Output Hello am Axis2 version service My version is 1 4 1 G Execute
27. s prototype is far from being complete and many improvement will be included in future versions It is really important for user who test the prototype to give feedback about any issue encountered playing with the software To ease the gathering of this feedback please use the TRAC portal https nyx unice fr projects neurolog with neurolog guest neurolog guest for login password User feedback is stored through tickets A ticket is textually described files like logs or screenshots may be attached to the ticket by a reporter and can represent issues such as bugs or enhancement requests The reporting procedure is as follow 1 Login into in the TRAC portal 2 Search for a similar issue using the search box 1 Ifa ticket describing the same issue already exists add some information to it and contribute to its description or resolution 2 If not continue this procedure 3 Click on the New Ticket button 4 Describe your ticket 1 Give a short summary 2 Type your ticket with the more appropriate label defect enhancement or task 3 Give a full description of the issue 4 Assign a component to your ticket in the ticket properties area The project is actually decomposed into several components administration data metadata semantic processing tools security administration and user interface 5 Finally submit your ticket gt Because all reporters will use the neurolog guest account please personally sign ea
28. seeeeeseueesseesseeees 29 INGE AVAIADICS YOU sazietety trea rete sete eaie ae teeta ines oc toh Bacterial sate ihe 33 Reporting DIOCCOUIRG saracii enre E A E 34 2 35 Document history V0 01 May 26 2009 Creation S o V0 02 Oct 21 2009 Modification Additions in the pre requisites section V0 03 Nov 2009 Modification Add details in the client installation procedure V0 04 Mar 19 2010 Modification Add connection data for site ASCLEPIOS 1 Architecture overview The NeuroLOG middleware is a collaboration of services operating on different sites There are 3 main components part of the middleware e A unique federation registry deployed and maintained on the federation server e A site server deployed and maintained on each participating site e User clients deployed on each user workstation The federation registry is only used for site coordination and it is not visible from the end users It is deployed at I3S on host neurolog unice fr Each user accesses the middleware functionality through a local client application which is affiliated to one specific site server In the middleware version 0 3 0 presented in this document there is a single site server deployed at I3S on host neurolog unice fr All clients are therefore configured to communicate with this server as exemplified in the following figure Federation registry neurolog unice fr host Site server Client Client Client User A User B ae User X
29. ssor color changes _ Q_out P_out in_0 R_out in_0 when they are running and T Q out P_out in_1 R_out in_1 they complete execution The simulation will end when no processor can fire anymore It is then possible to check for the workflow production by selecting the view production menu item on the contextual menu of workflow outputs The production window displays the data item received as exemplified on F this figure out view production executed 1000633085 Note that you can get information on any processor by moving the mouse cursor over it and wait for two second until a tip window appears The following items are documented in this window e Processor input and output ports with Processor R type and depth Input ports e Data item received in input ports Workflow editor 1 new workflow in type String depth 0 Baten Goris e Data item produced through output out type String depth 0 ports Received Produced list R_outtin_ 1 R_outtin_O Real enactment of processors and connection between the data management system and the workflow input outputs still need to be integrated in the workflow manager 6 Not available yet More functionality will be available in future versions of the middleware In particular the following important functionality was not yet implemented e Annotating produced data e Registering computation results 7 Reporting procedure Thi
30. tional third party softwares that need to be installed prior to running the client 2 3 Start up Running the startup script initializes the NeuroLOG client This script is configured to properly operate when the software has been installed in the neurolog sub directory of the user home It needs to be modified otherwise On Linux and MacOS X At the prompt enter Ped S Oa 2 deuro log aleve ie Is eine On Windows From a file browser go to the neurolog directory in your home directory This will typically be C Documents and Settings username neurolog Then double click on nlog client bat When the client first starts it detects that it was not configured before It displays the message Information i The client was not initialized before Proceeding with the client configuration Click OK to run the configuration procedure see next section for details The configuration procedure will create the client specific configuration files under the directory named neurolog in the current user home directory e g SHOME neurolog under Linux or SUSERPROFILE neurolog under Windows Note that this default location may be changed with the c option of the nlog_ client start up script 3 Quick start guide The client configuration is a two stages procedure On the first run the client environment is created and a request is sent to the site administrator in order to validate the new client and the associated user r
31. tor Subject type Patient e a involves subjects n Subject NI 55 3 3 Sex Male i Subject NI 55 4 A Subject NI 55 5 Birth date 1946 01 01 bo Subject NI SS 6 has input datasets Manual hemispheric dominance Left Sa produced result datasets 7 ee Language hemispheric dominance Left oh Dataset MI 55 38 ol Dataset NI 55 35 lt Dataset NI SS 34 oh Dataset NI S5 30 i Dataset NI 55 29 ot Dataset NI 55 28 ot Dataset NI 55 26 ot Dataset NI 55 25 fe Dataset NI 55 37 Common identifier AA B6BF 654771 The icons in the tree structure have the following meaning Any entity like a study dataset or centre Properties are displayed on the right pane by simply clicking on the entity Any entity like a study dataset or centre Getting its properties will require a query to the NeuroLOG server Once it is retrieved the icon will be changed into Folder depicting a certain relation to other entities Click on the to expand im Folder depicting a certain relation to other entities but currently with no entity 4 2 Using the cart for data retrieval Section 4 1 describes the process of how to browse metadata in order to collect datasets into the cart Once datasets are collected their actual data files can be handled in different manner The cart panel is made up of two parts Datasets and Downloads described in section 4 2 2 The Datasets part provides a tabular view of collected datasets very similar to th
32. tuted 10 Data Manageme Plstenie a T E AT 12 A Ne Metadata GUGINO useriiiegn e i TE 12 4 1 1 Understanding the browsing tree ccccessseceeseseseseeeeeneeeeenseeeeesenesenes 12 Adee WSING Me guer ColuM siriene a es acetone 13 4 1 3 Usual browsing ProCeSS cccccccccseeeecceeseeceneecsaeeeeseueeeesuaseesseeessageeeeas 13 4 1 4 Viewing entities detallS cccccccccsseecccseeecseeeecceeeesseeeeeseaeeesegeesseneeeeas 15 A 2 Using Ine Carl ior data rewevVall cee es ee ee Ga ee 17 Ale ADJAPAACCESS OMS cates eE AER E codhacedteetenieeitalc 19 4 2 2 WALATCUICV Aliss sycicsstintenGunit cee daiienagameSariconehcee adel acnntteliesngand Saadeste aa 22 AS Bata visuali Zaio sa a a aE ta catna a notuiediulamamennoian 23 4 4 SEMaANntc Cala QUELYING arri a r a 24 4 4 1 Available queries 0 nn00annnennnannnnaneosnnnornrensrrernnresnrerrnnrennrersnrrrnnrereneer 24 442 QUERY operations sccs cscese nti cd shes ooh ocavieeeeeeedceatwalsiedesabaholbiataeed sce eealedied 24 AaB TAOS WIMGOW ceinion Pores ae a a atch cae 24 TOOS Manage meN ssotscauesereseninsumecendienusauner anos vanedusieunensuasiaiaabolncuea en tidantbaumeobueihold 26 Hil WOOIS registral Oea Gibson iat det thee tati renee ane E iiGawoenetbeai atts 26 DA OOS NS NT CN estar ad Sea eran ceca a E 27 5 Sr OINGIS LOOM INVOC IUO Merni E tacke aeatieiett ie ciedeeeu into 28 5 4 Workflow edition ANd INVOCATION ccccecccceececeeeeeeeeeeeeeeeceeceseeee
33. udy access control management i Users management Arni __ NeuroLOG 135 client v0 3 0 Alban Sale administrator cuir ye Labs Ge Cal TS _ ens gt lt i Access control Users management User requests Studies access control Users Assigned roles Assignable roles admin admin Study NI SS 3 studyl Study NI SS 3 a ae MyStudy ICN Aiban Gaignard OU I3S O CNRS C FR Once a user certificate has been signed by the site administrator the corresponding user identified by its distinguished name i e the DN of its certificate is registered in the system The list of registered users in a particular site is shown on the left part of the users management tab When the administrator select a user the center column of the tab displays the roles which have been already assigned to her The last column displays the roles managed by this site and thus assignable to users To assign a role to a user the administrator selects both user and roles to assign then by clicking on the left arrow button selected roles are effectively assigned to the user Roles can be dropped by selecting an assigned role and by clicking then on the right arrow button ii User requests management IAO gt NeurotOG 135 client v0 3 Access control Users management Userrequests Studies access control ey User DN User email Study name Register CN Alban Gaignard OU 13S O
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