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User`s Manual The Brain Operation Database BODB (http://bodb.usc

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1. neural region A Delete farea FS FS neural region PRETO Figure 70 The Nomenclature Edit page The Nomenclature Edit page allows administrators to modify the attributes of an existing nomenclature Click on the Save button to save the changes or Close to cancel and close the window To delete the nomenclature click on the Delete button Basic Information To change the nomenclatures name or version edit the data in the Name or Version text field To associate the nomenclature with a reference click on the Search button to pop up the Literature Search page or Add to pop up the Literature Insert page If the nomenclature is already associated with a literature entry clicking on the Edit button next to the entry will open the Literature Edit page BODB 3 0 Manual USC Brain Project September 2010 76 Figures The Figures section lists each figure associated with the nomenclature Clicking on the Add new button will open the Add Figure page and clicking on the thumbnail of a listed figure will open the Edit Figure page Species The Species section lists each species associated with the nomenclature The genus species and common names of each listed species can be edited directly by modifying the data in the appropriate text field To remove a species from the nomenclature click on the Remove link next to it To associate another species with the nomenclature click on the Search link to open
2. Figures Hide bo LA E Caption ait Competitive queuing Edit Delete STR ill pea Figure 12 The expanded Figures section To add a new figure click on the Add new link This will open up the Add Figure window Clicking the Edit link next to an existing figure will open the Edit Figure window while clicking Delete will delete the figure and remove it from the BOP Summaries of Experimental Data SEDs Clicking on the Show link in the Summaries of Experimental Data SEDs section will expand the SEDs section displaying the SEDs linked to the current entry and allowing the user to add new SEDs After expansion the Show link will turn into a Hide link that can be used to collapse the SEDs section Summaries of Experimental Data SEDs Hide Search Add new Name Relationship Description Remove Collapse scene setting Tags Narrative Figure 13 The expanded SEDs section In order to add an existing SED to the current BOP clicking on the Search link will open the SED Search window Clicking Select next to one of the search results will add that SED to the current BOP entry In order to add a new SED and link it to the current BOP entry click on the Add new link which will add a new SED form to the SEDs section The form contains fields for the SED name relationship to the current BOP and description A specific summary datum may be classified as pertaining to the present BOP in 2
3. Summary of Simulation Results Search Summary of Simulation Results SSR entries Search Summary of Summary of Brain A Literature BOPs Models E gt Experimental Data Simulation Results Regions Title r Description Po Tags A Related Brain Region Only my entries L Related Literature Title Author Po Year SS 2 Annotation Results Add new Title Description Discriminative grasp hidden units After training neurons in the hidden layer corresponding to the inferior parietal lobule IPL selectively respond to the observation of specific grasps FS action recognition Simulated FS mirror neurons are trained to recognize hand state trajectories using Fo canonical activity as a training signal They are then able to recognize a grasp before the hand contacts the object FS action recognition Simulated FS mirror neurons are trained to recognize hand state trajectories using FS canonical activity as a training signal They are then able to recognize a grasp before the hand contacts the object FS audiovisual action recogntion Hebbian association of object recognition input with FS mirror activity allows FS mirror neurons to respond to invisible actions when the sound associated with them is perceived o Figure 39 The input form for searching SSR entries Any Field Search for SSR entries that contains this string in any field BODB 3 0 Manual USC Brain Project September 2010 50 Advanced Options
4. 2001 Features Here we list the major features of BODB User Registration and Login Once registering users can login to the site from the main page If the user does not have a login one may be acquired through a self service registration process BODB 3 0 Manual USC Brain Project September 2010 5 Structure of the BODB Site An online description of the layout of the BODB website and an overview of its functionality Insert The insert page provides links for adding new Literature Brain Operating Principle BOP Model and Summary of Experimental Data SED entries Literature Literature Journal Article Book Chapter Conference Thesis and Unpublished information Brain Operating Principles BOPs Brain Operating Principle e g Winner Take All Models Structured description of a model with links to related entities e g Didday Model based on the Winner Take All Principle Summaries of Experimental Data SEDs A summary of experimental data e g brain imaging Search The search page allows the user to search all entries Literature Brain Operating Principle BOP Model Summary of Experimental Data SED Summary of Simulation Results SSR and Brain Region entries Talairach Applet The Talairach Applet allows users to visualize brain imaging SEDs in two dimensional or three dimensional mode Workspace The Workspace provides users an area to manage their Model BOP and SED drafts selected Mode
5. Authors Hide Search Add new First name Middle name Last name Order Brief description Narrative Tags Architecture Show Summaries of Experimental Data SEDs and Simulation Results SSRs Show URLs Show Related Models Show Related BOPs Show Related Brain Regions Show References Show Figure 18 The input form for Model entries Title The name of the Model e g Mirror Neuron System MNS Model The text field has a maximum length of 200 characters It is very important to first search for existing Models to ensure that duplicate entries aren t added BODB 3 0 Manual USC Brain Project September 2010 21 Authors Add New Author To add an author click the Add new link in the Authors section The ordering of authors when the Model entry is listed can be set by setting the Order field of each author appropriately Search Authors In order to link an existing author to the new Model entry click on the Search link in the Authors section An Author Search popup window will appear where authors can be searched by multiple fields Click on the Select link next to an author to link it to the Model entry Search Authors Any field ungerleider First name Middle name Last name Po Email Alias Pl Results Add new First name Middle name Last name Select LG Ungerleider Figure 19 Author search window Brief Description Start with an edited abstract of the ke
6. Display Properties A new window will pop up where the user can click at a checkbox to set or unset visibility click at the color box to select a new color or click on the shape dropdown to change the shape of the coordinate Under each SED coordinate list there are links to check or clear the visibility change the color or change the shape of every coordinate in the SED all at once After a change is made hit Save to save the changes BODB 3 0 Manual USC Brain Project September 2010 55 E ra Regions hippocampus inferior frontal gyrus Coordinates SED asdfadstdastggdsfgtdsg 50 67 26 Right Cerebellum RA 30 60 10 Erodmann area 10 ha al 40 22 4 Erodmann area 45 y a 65 24 6 Erodmann area 21 ha EN a at a 90 52 47 Erodmann area 40 Ix bd E 36 25 6 Hippocampus X 00 29 28 Erodmann area 9 Ix h E 63 37 0 Erodmann area 21 X T Apply toal 2554 woman areas e HO MO Figure 44 The display properties window of the two dimensional version of the Talairach applet Search Functions There are 2 search functions on the applet search for coordinates A and search for regions B The user can click at any location on the slice 2D image in the left hand window of the applet and then click the Search coordinate s button to see what brain regions it is in shown hierarchically A red cross on the image and an exact coordinate value x y z will appear after eac
7. Figures Hide dientes a z b EEn fe Competitive queuing HET Edit Delete Ses a Aedes k lt 1 L r Figure 28 The expanded Figures section To add a new figure click on the Add new link This will open up the Add Figure window Clicking the Edit link next to an existing figure will open the Edit Figure window while clicking Delete will delete the figure and remove it from the SED Related Brain Regions Brain region s that relate to the present SED Clicking on the Show link in the Related Brain Regions section will expand the Related Brain Regions section displaying the Brain Regions linked to the current entry After expansion the Show link will turn into a Hide link that can be used to collapse the Related Brain Regions section Related Brain Regions Hide Name Nomenclature Remove F5 Parma 1 Remove AIP Lewis amp Wan Essen 1 Figure 29 The expanded Related Brain Regions section In order to add an existing Brain Region to the current SED clicking on the Search link will open the Brain Region Search window Clicking Select next to one of the search results will add that Brain Region to the current SED entry Clicking Remove next to a linked Brain Region will remove it from the current SED entry References References to articles books chapters etc relevant to this SED Clicking on the Show link in the References section will expand the References section displaying
8. Title Search the title field of SSR entries Description Search the description field of SSR entries Narrative Search the narrative field of SSR entries Tags Search the tags field of SSR entries Related Brain Regions Search for SSRs related to the given brain regions Only My Entries Search only SSR entries belonging to the current user Related Literature Title Search for SSRs related to Literature with the given text in the title Author Search for SSRs related to Literature with the given authors Year Search for SSRs related to Literature in the given year range Annotation Search for SSRs related to Literature with the given text in the annotation Results The results of the SSR search are displayed here Clicking Add new opens a window to add a new SSR entry Clicking the title of each search result will open a window with the SSR view page Brain Regions Search Brain Region entries BODB 3 0 Manual USC Brain Project September 2010 51 Search Summary of Summary of Brain Hata AER MAGRIS Experimental Data Simulation Results Eume Any field Brodmann Advanced Options Hide Mame Parent Po Nomenclature Po Species Region Type we Can t find the brain region you re looking for Try reguesting a new one Results Region Abbreviation Region Type Parent Region Nomenclature Species Brodmann area 1 BA 1 neural region Talairach Horno 1 sapiens Brodmann area 10 BA 10
9. a notification will be displayed in the to right corner Click on this notification to display the Messages page If the current user has no unread messages a Messages link will instead be displayed that leads to the Messages page Hi jponaluto Logout My Profile You have 1 unread message Help Figure 54 The top right corner of the BODB page displays new mail notifications Viewing Messages The Inbox tab of the Messages page lists all messages read and unread For each message the sender 1s displayed along with their avatar as well as the subject a portion of the text and the date and time 1t was received After selecting messages by clicking on their checkbox the user can delete mark them as read or mark them as unread by clicking on the appropriate button Messages Compose Mail sent L fd Jimmy Test message Hello world 2010 02 01 02 10 11 a Select All None Read Unread Figure 55 The Inbox tab of the Messages page Clicking on a message in the Inbox list will display the message view page containing the entire message The options available from this screen are Back to Inbox Reply Close or Delete BODB 3 0 Manual USC Brain Project September 2010 65 Back to Inbox From a jimmy Date 2010 02 01 02 10 11 Subject Test message Hello world Reniy cose Detete Figure 56 The message view page Replying to Messages Clicking on the Reply button on the message
10. the Species Search page and link an existing species To add a new species click on the Add new link which will add a row with text fields for the genus species and common name Brain Regions The Brain Regions section lists each brain region belonging to the nomenclature The name and abbreviation of each listed region can be edited directly by modifying the data in the appropriate text field and the region type and parent region can be set by selecting their values from the appropriate dropdown box To delete a region click on the Delete link next to it To add a new region to the nomenclature click on the Add new link which will add a new row with text fields for the name and abbreviation and dropdown boxes for the region type and parent region Insert Nomenclature Add Nomenclature Help Name Wersion Reference Figures Hide Add new Species Hide Search Add new Genus name Species name Common name Remove PO Po Brain Regions Hide Name Abbreviation Type Parent Delete neural region BODB 3 0 Manual USC Brain Project September 2010 77 Figure 71 The Nomenclature Insert page The Nomenclature Insert page allows administrators to add new nomenclatures to the system Click on the Save button to save the new nomenclature or Close to cancel and close the window Basic Information To set the nomenclatures name and version enter the data in the appropriate text field To li
11. 16 61 59 4 58 Insula anterodorsal part 43 5 3 305 1 area PE caudal 25 59 66 5 13 l 39 15 3 17 Mins gt _ E J A Tnsula anterodorsal part 43 3 305 Premotor cortex caudal area 6 34 8 63 446 9 15 337 2 4 62 42 Premotor cortex caudal area 6 34 8 63 4 46 Motor cingulate cortex area 6 32 3 1 44 479 da 265 4 62 42 Putamen 28 4 BAH Motor cingulate cortex area 6 32 3 10 44 4 79 Cerebellum 31 49 3 60 IPutamen 20 23 4 51 i Cerebellum 31 49 26 3 69 32 a 36 3 84 3 13 14 437 16 85 5 3 60 46 B 3 78 50 718 3 445 38 80 23 3 70 33 Tl 17 691 Perirhinal cortex area 36 near 20 Subcallosal cortex area 25 Prestriate cortex area 18 Prestriate cortex area 19 Orbital frontal area 47 Perichinal cortex area 36 near 20 ISubcallosal cortex area 25 Prestriate cortex area 18 Prestniate cortex area 19 Dorsal prestriate cortex area 19 Ventral prestriate cortex area 19 Ventral temporooccipital cortex 27 50 11 4 94 area 37 39 61 14 7 25 J b Sub table 1 for the first task coming py BANE control minas hands mental rotation Condition from part A of original table a AA la barame arrim fare TIA T A Mia f 11 A AL l Dorsal prestriate cortex area 19 Ventral prestriate cortex area 19 y Ventral temporooccipital cortex 27 50 11 4 94 _ area 37 39 61 14 7 25 38 80 23 3 70 35 71 17 6 91 AP rer war wae za
12. 2 reinforcement Learning 1 1 Striatum 1 stroop 1 Substantia Nigra Pars Compacta 2 Substantia Nigra Pars Reticulata 1 Subthalamic Nucleus 2 Supplementary Motor Area 1 Thalamus 2 Thalamus 1 conceptual learmimg 1 semantics syntax 1 Wentrolateral Pars Oralis working memory 1 Brain Operating Principle tag cloud coding 4 decision making 5 excitation amp inhibition 6 Lect amp rink faci cedo bodhmodal bench mark Search Talairach Workspace USC Brain Project September 2010 82 BODE Model Benchmarking Q cooe Hi schuler Logout My Profile a Messages Help Admin About Model Benchmarking Models Mirror Neuron System MNS Oztop Arbib Mirror Neuron System 2 MNS2 SEDs Bonaiuto Rosta Arbib STS visual response STS shape selective cells 7b projection to F5 AIP grasp selectivity AIP projection to FS Area 7 is reciprocally connected with STS Area 7b connection to visual areas Area 7b connection with AIP cIPS projection to 7a cIPS projection to AIP F4 reach selectivity FS canonical visual properties FS grasp selectivity F5 mirror broadly congruent F5 mirror strictly congruent FS mirror transitive action selectivity FS mirror properties LIP projection to Ya MIP projection to 7a PIP object selectivity Separation of dorsal and ventral ld id o Display A Figure 12 An example benchmarking report compari
13. AAP eer zee Fa pus 23 4 B 434 Orbital frontal arca 47 a a a eer zee fot id th meal os Pa BODB 3 0 Manual USC Brain Project September 2010 36 a Original Table consisting of two parts ao COOMA A activation information of task 1 Hands Brain area xy z value mental rotation minus hands control Hands control minus hands mental rotation condition Middle temporal cortex area 21 64 26 11 4 45 condition and 66 25 12 3 96 Ventrolateral frontal cortex area 45 46 25 18 353 B activation information of task 2 Hands Posterior dorsolateral frontal cortex 30 20 45 447 control minus hands mental rotation area 8 32 22 51 559 o Dorsolateral frontal cortex area 5 9 40 29 35 4 54 condition Frontopolar cortex area 10 32 56 3 534 63 6 4 95 47 34 45 425 46 37 Gl 432 40 63 44 358 44 66 39 462 55 45 42 3145 1 66 41 4 13 Posterior inferior parietal cortex area 40 39 Inferior parietal cortex area 7 40 ee ee ee el el Fd Inferior parietal cortex area 40 Medial parictal cortex area 7 Posterior paracingulate cortex area 31 R 4 59 26 4 12 Posterior cingulate cortex area 23 L 5 26 27 5 06 b Sub table 2 for the second task coming from part B of original table Figure 5 A table containing results from two tasks aligned vertically Bonda E et al Year The second example is similar to the first one but the results are aligned hori
14. Add new to add a new SED which inserts a new subrow with the following fields Name The name of the SED Description A brief description of the SED SSR the model s simuation results that explain or contradict the SED Name The name of the SSR Description A brief description of the SSR Predictions Predictions made by the model can be entered and optionally linked to Summaries of Simulation Results SSRs Clicking on the Add new link will insert a new row in the Predictions section with fields for the Name and Description Clicking on the Expand link will display fields the Tags and the Narrative SSRs can be added to the prediction by clicking on the Add new link in the SSRs section This will open the Insert SSR window Execution url Documentation url AO Description url Simulation url Figure 22 The model URLs section The URLs section allows the user to add the following hyperlinks Execution URL A URL that points to downloadable code for the present model s executable implementation Documentation URL A URL that points to the present model s documentation Description URL A URL that points to the description of the present model Simulation URL A URL that points to simulation results obtained with the present model s simulation code Related Models Note that Models are documented in separate entries in BODB Your job then is to decide which of the available Models relat
15. Generic v Title Brief description Narrative Tags Figures Show Related Brain Regions Show References Show save orar save Figure 27 The input form for Summary of Experimental Data entries Type Currently there are two types of SEDs in BODB generic and brain imaging Generic summary data could be a description of experimental data using any technique while brain imaging summary data describes neuroimaging data such as that obtained from MRI or PET experiments Selecting brain imaging will display the form shown in the Brain Imaging Data section Generic Summary Data Title The name of the SED entry Brief Description A brief description of the SED We provide a text input area but in general the entry should be much shorter say 200 words since a full description can be entered in the Narrative field Narrative A full length description of the SED The narrative must be detailed enough to provide rigorous constraints for the design and or testing of models Tags A list of keywords associated with this SED entry Figures BODB 3 0 Manual USC Brain Project September 2010 29 Clicking on the Show link in the Figures section will expand the Figures section displaying figures linked to the current entry and allowing the user to add new figures After expansion the Show link will turn into a Hide link that can be used to collapse the Figures section
16. Globus El Dynamic Neural Field Mirror The Dynamic Neural Field Mirror Neuron System DNF Pallidus 2 Gating 1 Globus Neuron System DNF MNS MNS model combines dynamic neural fields with Hebbian Pallidus 2 grasping 6 Erihagen Mukovskiy learning to provide an account of goal directed matching of Bicho action observation and action execution The model is Imitath Internal Globus Pallid dra tested in an imitation task using actors and observers with 2 language 1 learning 1 memory different embodiments a mirror neurons 4 motor Til Hebbian Mirror Neuron A conceptual model of how Hebbian learning between the Cortex 1 motor development 2 System H MNS Keysers areas STS PF FS allows recognition of the actions of motor learning 2 PBWM 1 Perrett others by associating them with self produced actions Prefrontal Cortex 1 procedural 1 Til Mirror Neuron System MNS The MNS model explains how the mirror neurons are Putamen 1 PYV gl reinforcement Oztop Arbit developed during infancy The main hypothesis of the model is that the temporal profile of the features an infant experiences during self executed grasps provides the training stimuli for the mirror neuron system to develop Thus developmentally grasp learning precedes initial mirror neuron formation This madel shows how the mirror 2 reinforcement Learning 1 semantics 1 Stratum 1 stroop 1 Substantia Nigra Pars Compacta 2 Substantla Nigra
17. Manual USC Brain Project September 2010 27 Related Brain Regions There will be one entry here for every listed brain structure relevant to the model In general a brain structure will be relevant because it is in part modeled by a module or a group of interconnected modules of the model Clicking on the Show link in the Related Brain Regions section will expand the Related Brain Regions section displaying the Brain Regions linked to the current entry After expansion the Show link will turn into a Hide link that can be used to collapse the Related Brain Regions section Related Brain Regions Hide Name Nomenclature Remove FS Parma 1 Remove AIP Lewis amp Van Essen 1 Figure 25 The Related Brain Regions section In order to add an existing Brain Region to the current Model clicking on the Search link will open the Brain Region Search window Clicking Select next to one of the search results will add that Brain Region to the current Model entry Clicking Remove next to a linked Brain Region will remove it from the current Model entry References References to articles books chapters etc relevant to this Model Clicking on the Show link in the References section will expand the References section displaying Literature linked to the current entry and allowing the user to add new Literature entries After expansion the Show link will turn into a Hide link that can be used to collapse the References
18. Model summary data Article E g support contradict Brain Regions Information Theoriza summary of simulation Summary of 1 N Experimental Data Data MN subciass a 3 Brain Behavioral Neurophysiol Imaging Data ogical Data so l p Figure 1 The entity relationship schema of BODB s fundamental entities BODB 3 0 Manual USC Brain Project September 2010 7 Article Information This functions as a bibliography keeping information on publications cited in other entries in BODB Each item is categorized into one of 7 types journal book chapter thesis conference electronic and unpublished Brain Operating Principle BOP This originated from the observation that key concepts concerning brain mechanisms are sometimes implicit in many references but integrated in none The Brain Operating Principle entity is designed to serve as a repository for maintaining structured and succinct concepts about how the brain or a key functional or structural subsystem works whether extracted and generalized from empirical data or exemplified in computational models We designed this entity with the m n relationship linking to Article information since one brain operating principle could be derived from many articles while one article could be a source of information for two or more principles Model This is designed to function as a repository for descriptions of computati
19. Moreover article data files are in various formats such as PDF HTML and Microsoft Word Therefore it is difficult to provide a tool that automatically reads the data file excerpts the whole table and its description then marshals and puts these data into BODB properly Our solution for importing the table is to provide a structured input form for pasting the table s description and data and specifying metadata column configuration The structure of the input form and the metadata will assist the user populate the table data correctly After clicking on the link Summary of experimental data the system will redirect to a page as in Figure 1 BODB 3 0 Manual USC Brain Project September 2010 31 Add SED Type Brain Imaging Title Brief description Narrative Tags Method i a Control condition Experimental cond ition Coordinate System a Core column Brain Region hemisphere x yz rCBF 2 1 header E __ a aa Extra header i Use to separate each column Data Column order Brain Region hemisphere x y z rCBF T Use newline ta separate rows and tab or to separate columns Figures Show Related Brain Regions Show References Show Figure 1 Title The name of the SED entry Brief Description A brief description of the SED We provide a text input area but in general the entry should be much shorter say 200 words since a full descr
20. coordinate Under each SED coordinate list there are links to check or clear the visibility change the color or change the shape of every coordinate in the SED all at once After a change is made hit Save to save the changes BODB 3 0 Manual USC Brain Project September 2010 59 E Regions Show tooltips Region Color Transparency brodmann area 44 brodmann area 45 Coordinates t Show tooltips SED asdfadstdastqggdstgfdsg Region Brodmann area 9 Brodmann area 40 Right Cerebellum Hippocampus Brodmann area 10 40 22 4 Erodmann area 45 63 3 0 Erodmann area 21 Erodmann area 21 Region 25 574 Erodmann area 45 Figure 48 The display properties window of the three dimensional version of the Talairach applet Search Functions The user can input some brain region names and click the Search button to see where they are in 3D space Each area is displayed distinctively by semi transparent colored blobs The size and minimum maximum values of x y z coordinates of brain regions are also given in the search results box Moving the mouse over a blob will popup a tooltip displaying the region name The color and transparency of each blob can be changed in the window shown after clicking Display Properties Color blobs can be removed from the image by clicking on the button Clear region s BODB 3 0 Manual USC Brain Project September 2010 60 Talairach Applet 3D 2D ma LU Input brain regi
21. for use to support the design of a model or to be used in testing a model whose SSRs may explain the SED or be contradicted by SEDs The latter situation may either be used to downgrade confidence in the model or to point the way to further efforts that build on the current model Brain Imaging Experimental Data Currently this entity provides the one specifically structured type of Summary of Experimental Data for BODB It serves primarily as a repository for tables of brain imaging experimental data We adapted the Talairach Daemon TD developed by the San Antonio group as well as ideas from USCBP s own NeuARt project Dashti et al 2001 to enable the user to graphically compare and contrast the experimental data on brain slice images One brain imaging article could have two or more experiment sets and almost every brain imaging experiment will relate to multiple brain regions In addition to the basic entities described so far we added a set of tables that are responsible for maintaining block diagrams for models and anatomical relationships etc with supplementary BODB 3 0 Manual USC Brain Project September 2010 8 information such as box area coordinates and box name These diagrams not only help the user visualize Model entries but also provide connections between Models via hierarchical relations Connections among entities not only allow the user to go back and forth between entries via their relations but provide options f
22. link it to the current BOP entry click on the Add new link which will add a new Model form to the Related Models section The form contains fields for the Model name and description Clicking on the Expand link will make visible fields for Model tags and narrative The Expand link will then turn into a Collapse link that can be clicked to hide the Tags and Narrative fields Clicking on the Remove link next to a linked Model will remove that Model from the current entry Related Brain Regions Brain region s that relate to the present principle For example reinforcement learning has many related brain regions Basal Ganglia Prefrontal Cortex etc Clicking on the Show link in the Related Brain Regions section will expand the Related Brain Regions section displaying the Brain Regions linked to the current entry After expansion the Show link will turn into a Hide link that can be used to collapse the Related Brain Regions section Related Brain Regions Hide Name Nomenclature Remove FS Parma 1 Remove AIP Lewis amp Van Essen 1 Figure 16 The expanded Related Brain Regions section In order to add an existing Brain Region to the current BOP clicking on the Search link will open the Brain Region Search window Clicking Select next to one of the search results will add that Brain Region to the current BOP entry Clicking Remove next to a linked Brain Region will remove it from the current BOP entry Reference
23. neural region Talairach Horno 1 sapiens Brodmann area 11 BA 11 neural region Talairach Homo 1 sapiens Figure 40 The input form for searching Brain Region entries Any Field Search for Brain Region entries that contains this string in any field Advanced Options Name Search the name field of Brain Region entries Abbreviation Search the abbreviation field of Brain Region entries Parent Search for Brain Regions with the given parent region Nomenclature Search for Brain Regions belonging to the given nomenclature Species Search for Brain Regions corresponding to the given species Region Type Search for Brain Regions of the given type fiber tract neural region vesicle Results The results of the Brain Region search are displayed here If the desired brain region is not found the user can request that a new region be added to the database by clicking the given link This will display the New Brain Region Request form Talairach Applet The Research Imaging Center of The University of Texas Health Science Center at San Antonio has given us permission to use the brain templates and database of regional Talairach coordinates from their Talairach Daemon We now describe the Talairach Applet TA that we provide in BODB 3 0 Manual USC Brain Project September 2010 52 BODB It has been improved by incorporating features from an earlier but only partially implemented effort of the USC Brain Project NeuARt the NeuroAnatom
24. of BOP entries Narrative Search the narrative field of BOP entries Parent Search for BOPs whose parent BOPs contain this string Tags Search the tags field of BOP entries Related Brain Regions Search for BOPs related to the given brain regions Building SEDs Search for BOPs with Building SEDs containing the given text Related BOPs Search for BOPs with related BOPs containing the given text Related Models Search for BOPs with related Models containing the given text Only My Entries Search only BOP entries belonging to the current user BODB 3 0 Manual USC Brain Project September 2010 45 Related Literature Title Search for BOPs related to Literature with the given text in the title Author Search for BOPs related to Literature with the given authors Y ear Search for BOPs related to Literature in the given year range Annotation Search for BOPs related to Literature with the given text in the annotation Results The results of the BOP search are displayed here Clicking Add new opens a window to add a new BOP entry Clicking the title of each search result will open a window with the BOP view page Models Search Model entries BODB 3 0 Manual USC Brain Project September 2010 46 Search summary of summary of Brain r iteratur OPS ci i i E BEELER MEE Experimental Data Simulation Results Regions Any field Tite O autor AA Tags O Building SED Po Prediction Po Related Brain Region Po Relat
25. output layer is fully connected to the recurrent input layer and the output of the HS audio recurrent network is fully Is rr Public photographs will public be displayed in the default views Tags Separate tags with ns spaces put quotes around multiple word tags Figure 73 The Edit Figure window Click the Browse button next to the Image field to select a different image to upload The current image is displayed to the right as a thumbnail The Crop from field determines how the image 1s cropped when thumbnails are generated Possible choices are Top Right Bottom Left and Center default The title and title slug can be edited in the appropriate text field The title slug will be automatically generated as the title is entered but can be changed by the user A warning will be shown if the entered slug is not unique The user can modify the description of the figure in the Caption field The figure can be set to public which allows other users to view it or not in which case it will only be visible to the user who added it Keywords for the figure can be modified in the Tags field Click the Save button to save the figure and close this window Workspace The Workspace section provides an area for users to manage drafts of models in progress selections of other models and selections of TD coordinates When a user adds a new model and BODB 3 0 Manual USC Brain Project September 2010 80 subsequently saves a dr
26. region area F5 F5 neural region Figure 69 The Nomenclature View page The Group View page displays all of the nomenclature s information including the version and the literature reference that the nomenclature was described in The figures section displays a thumbnail and caption of each figure associated with the nomenclature Click on a thumbnail to view the full size image The Species section lists the genus species and common name of the species that the nomenclature applies to The Brain Regions section lists the name abbreviation region type and parent region of each brain region in the nomenclature To edit the nomenclature s information click on the Edit button This will open the Nomenclature Edit page To delete the nomenclature click on the Delete button Clicking on the Close button will close the current window BODB 3 0 Manual USC Brain Project September 2010 75 Edit Nomenclature Edit Nomenclature Help m E Name Parma Version 1 Reference search edit Matelli et al 1985 Patterns of cytochrome oxidase activity in the frontal agranular cortex of the macaque monkey Add new Species Hide Search Add new Genus name Species name Common name Remove Macaca fascicularis Icrab eating mal Remove Macaca Inemestrina southern pig ta Remove O Brain Regions Hide Add new Name Abbreviation T YPE Delete farea F2 Fz neural region R Delete area FA F4
27. responsive for the observation of actions associated with characteristic noises are just as responsive for the sounds of these actions FS mirror broadly congruent Some FS mirror neurons the congruence between preferred observed and performed actions is quite loose For example a mirror neuron may fire during performance of precision pinches and observation of power grasps Figure 38 The input form for searching SED entries Any Field Search for SED entries that contains this string in any field Advanced Options Title Search the title field of SED entries Description Search the description field of SED entries Narrative Search the narrative field of SED entries Tags Search the tags field of SED entries Related Brain Regions Search for SEDs related to the given brain regions Only My Entries Search only SED entries belonging to the current user BODB 3 0 Manual USC Brain Project September 2010 49 Related Literature Title Search for SEDs related to Literature with the given text in the title Author Search for SEDs related to Literature with the given authors Year Search for SEDs related to Literature in the given year range Annotation Search for SEDs related to Literature with the given text in the annotation Results The results of the SED search are displayed here Clicking Add new opens a window to add a new SED entry Clicking the title of each search result will open a window with the SED view page
28. the nomenclature s name will pop up the Nomenclature View page while clicking on the literature reference will open the Literature View page Clicking on the Edit link next to the nomenclature name will pop up the Nomenclature Edit page and clicking on the Delete link will delete the nomenclature To add a new nomenclature click on the Add new link which will open the Nomenclature Insert page BODB 3 0 Manual USC Brain Project September 2010 74 View Nomenclature Momenclature Parma Help Version 1 Reference Matelll et al 1985 Patterns of cytochrome oxidase activity in the frontal agranular cortex of the macaque monkey Figures Hide Figure 1 Matelli 85 figs Cytochrome oxidase maps of the agranular frontal cortex Four hemispheres of 3 monkeys are presented IT4 6 and IT6 4 were Macaca irus SII 1 was a Macaca nemestrina The borders between the areas are marked by the dotted lines and each area is indicated by its name Asterisks show the transition zones Hatched areas indicate those parts of the cortex that were Impossible to define either because of the orientation of the cutting SII 1 left parasagittal cutting or because of the sulci pattern IT6 4 Species Hide Genus Species Common Name Macaca fascicularis crab eating macaque Macaca nemestrina southern pig talled macaque Name Abbreviation Region Type Parent area Fl Fi neural region area F2 FZ neural region area F3 F3 neural region area F4 F4 neural
29. the World Wide Web As one contribution to channeling this flood we are developing BODB to facilitate the interchange between those developing new brain models and those developing new experiments The current ideas are that the system houses capsules of neuroscientific literature information that will facilitate comparison and integration of original articles provides a standard form and repository for entering BOPs provides a standard form and repository for entering Model summaries supplies a sharing point for the data in 1 2 3 among users to enhance knowledge development provides a repository of experimental data with a standard structure and the experimental data and cross experiment data analysis tools currently our focus is on brain imaging data and provides a means to connect related documents together with practical search tools to enhance the accessibility of information These features are intended for use by both brain modelers and brain experimenters The experimental data and analysis tools will be used by the brain modeler in extracting knowledge and developing new models and by the experimenter in designing further experimental protocols Furthermore the BOP and Model entries will supply knowledge for the modeler to construct new models and provide the experimenter suggestions to contrive new experiments Consequently the implementation and integration of these features would enhance a theory experiment cycle Arbib
30. the image navigator or selecting a slice from the dropdown list to the right of the image navigator The view can be changed by selecting one of Axial Coronal or Saggital from the topmost dropdown list to the right of the image navigator BODB 3 0 Manual USC Brain Project September 2010 53 Talairach Applet 2D 3D 30 10 00 10 30 oo A Click on coordinates to see the brain regions they belong to Otherwise input coordinates below Format is x y z CO OO B Input brain region name s to see the blobs representing their extent Use acommato separate names hippocampus inferior frontal gyrus Clear all region s Search region s TD coordinate y 2 28 1 E5 70 4 Image Navigator Slice Index 27 Significance Threshold 0 00 Significance Metric Mt Score lJ z Score Figure 42 The two dimensional version of the Talairach applet in coronal view mode Talairach Applet 2D 3D A Click on coordinates to see the brain regions they belong to Otherwise input coordinates below Format is x y z L O B Input brain region name s to see the blobs representing their extent Use acommato separate names hippocampus inferior frontal gyrus Search Results or inferior frontal gyrus ound 16476 coordinates x ranges from 64to 65 ranges from 4to 60 ranges from 5to 19 41 TD coordinate x y 7 41 28 4 5 70 4 Image Navigator Slice Index 06 Significance Threshold 0 00 Significance Metr
31. with spaces put quotes around multiple word tags Figure 72 The Add Figure window Click the Browse button next to the Image field to select an image to upload The Crop from field determines how the image is cropped when thumbnails are generated Possible choices are Top Right Bottom Left and Center default Each image must be given a title and title slug which must be unique The title slug will be automatically generated as the title is entered but can be changed by the user A warning will be shown if the entered slug is not unique The user can enter a description of the figure in the Caption field The figure can be set to public which allows other users to view it or not in which case it will only be visible to the user who added it Keywords for the figure can be entered in the Tags field Click the Save button to upload the figure and close this window Edit Figure The Edit Figure window allows the user to edit an existing figure BODB 3 0 Manual USC Brain Project September 2010 79 Edit Figure Help image Browse i a Crop Center Default w from Title IMNS2 2 Title Imns2 2 slug 1ail Caption The main recurrent network at the heart of the mirror neuron system II MNS model The visual and recurrent input Layers are fully connected to the hidden layer which is fully connected to the external and recurrent output B layers The recurrent
32. 0 Manual USC Brain Project September 2010 61 Model tag cloud affordances 2 computational 5 conceptual 2 dectaratres 1 dynamic neural held 1 grasping 5 THES I anquage 1 mirror neurons 4 moor declonmera 11 moia bese 41 procedural 1 roomer 1 semantics l syntax 1 Brain Operating Principle tag cloud coding 4 decision making 5 excitation amp inhibition 6 learning 8 maps amp frames 5 memory 6 motor control 9 processing principles 8 sensory perceptual processing 10 Summary of Experimental Data tag cloud action recognition 7 action election 415 afordances 2 connectivity 21 meca sedard Grasping 14 mirror neurons 7 object ecognition 314 population code 11 reaching 4 sequences 2 sound recognition 2 target location 1 bombie a working memory 4 Prediction tag cloud affordances 6 grasping 6 mirror neurons 6 Summary of Simulation Results tag cloud action recognition 12 affordances 4 firing rate 15 grasping 16 mirror neurons 14 Figure 50 The tag cloud displayed in the sidebar Clicking on a tag in a tag cloud displays the tag view page which lists all of the entries of a particular type Model BOP SED Prediction or SSR associated with that tag Also listed on this page 1s a list of tags related to that tag BODB 3 0 Manual USC Brain Project September 2010 62 Models Tagged with computational Related Model tags affordanc
33. 1996 Divergent projections from the anterior inferotemporal area TE to the perirhinal and entorhinal cortices in the macaque monkey Edit Delete Schall et al 1 Schall et al 1995 Topography of visual cortex connections with frontal eye field in macaque convergence and segregation of processing streams Edit Delete Schwarz amp 1 Schwarz amp Fredrickson 1971 Rhesus monkey vestibular cortex a bimodal primary projection field Fredrickson Edit Delete Seltzer amp Pandya 2 Seltzer amp Pandya 1986 Posterior parietal projections to the intraparietal sulcus of the rhesus monkey Edit Delete Seltzer amp Pandya 1 Seltzer amp Pandya 1978 Afferent cortical connections and architectonics of the superior temporal sulcus and surrounding cortex in the rhesus monkey Edit Delete Stanton et al 1 Stanton et al 1989 Cytoarchitectural characteristic of the frontal eye fields in macaque monkeys Edit Delete Talairach 1 Talairach amp Tournoux 1988 Co Planar Stereotaxic Atlas of the Human Brain Edit Delete Wogtetal 1 Wogt et al 1987 Cingulate cortex of the rhesus monkey I Cytoarchitecture and thalamic afferents Edit Delete Woolsey et al 1 WOOLSEY et al 1952 Patterns of localization in precentral and supplementary motor areas and their relation to the concept of a premotor area Figure 68 The Nomenclatures tab of the Administration page Each nomenclature 1s listed on this along with its version and literature reference Clicking on
34. 4 370 50 29 28 DLPFE Middle Temporal Gyrus 5 760 65 24 6 Auditory activation Middle Temporal Gyrus 6 420 63 37 0 Auditory activation Figure 9 Formatted data Add SSR Title Brief description Narrative Tags Figures Hide Add new References Hide Search Add new Authors Year Title Figure 34 The input form for SSR entries Title The name of the SSR e g F5 mirror response to altered kinematics The text field has a maximum length of 200 characters Brief Description A brief description of the simulation results Narrative BODB 3 0 Manual USC Brain Project September 2010 41 An extended description of the simulation results Tags A list of keywords associated with this SSR entry Figures Clicking on the Show link in the Figures section will expand the Figures section displaying figures linked to the current entry and allowing the user to add new figures After expansion the Show link will turn into a Hide link that can be used to collapse the Figures section Figures Hide Add new pr Ba Caption l l abst Competitive queuing Edit Delete ee ai st Figure 31 The expanded Figures section To add a new figure click on the Add new link This will open up the Add Figure window Clicking the Edit link next to an existing figure will open the Edit Figure window while clicking Delete will delete the figure and remove it from the SSR References References to a
35. 996 43 1 2 Brain Res Mol Activation of nitric oxide synthase gene Premkumar DR Kumar GK Brain Res expression by hypoxia in central and peripheral Kalaria AN neurons Import Zhou FC Xu Y Bledsoe 5 1996 43 1 2 Brain Res Mol Serotonin transporter antibodies production Lin R Kelley MR Brain Res characterization and localization in the brain Import Yan der Schyf CJ Dormehl 1996 43 1 2 Brain Res Mol Long term treatment with the tetrahydropyridine IC Oliver DW Hugo HN Brain Res analog HPTP of haloperidol influences Keeve R M ller G rtner HW dopamine ligand binding in baboon brain An Pond SM Castagnoli N Jr 123IJiodobenzamide IB2M SPECT study Import Ilyin SE Plata Salam n CR 1996 43 1 2 Brain Res Mol Molecular regulation of the brain interleukin 1 Brain Res beta system in obese fa fa and lean Fa Fa Zucker rats Import Okuda Ashitaka E 1996 43 1 2 Brain Res Mol Identification and characterization of an Tachibana S Houtani T Brain Res endogenous ligand for opioid receptor Minami T Masu Y Nishi M homologue ROR C its involvement in allodynic Takeshima H Sugimoto T response to innocuous stimulus Ito 5 Import Johnston JA Norgren 5 1996 43 1 2 Brain Res Mol A new quantitative solution hybridisation RNase Anner n G Cowburn RF Brain Res protection assay for APP and APLP2 mRNA Lannfelt L Impert Lin YJ Bovetto 5 Carver JM 1996 43 1 2 Brain Res Mol Cloning of the cDNA for the human NMDA Giordano T Brain Res receptor N
36. Edit User Help Username jimmy Password Last name First name Pl E mail address jbonaiuto gmail com Active Ml Staff status O Admin status C Groups lUSCBP Lab Members Add Another Hold down Control or Command on a Mac to select more than one Q A E 1 Change Literature Models Modules BOPs SEDs SSRs Predictions FHSAA EHR eSeeee OooOooooag nm Nomenclatures Figure 62 The User Edit page The User Edit page allows administrators to modify the attributes of an existing user Click on the Save button to save the changes or Close to cancel and close the window Basic Information To change the user s username password first name last name or email address edit the data in the appropriate text field The user s active status can be changed by checking or unchecking the Active checkbox Inactive users cannot login to the system The Staff status field is currently unused by the system The admin status of the user can be changed by checking or unchecking the Admin status checkbox Only admin users can access the Administration Page The groups that the user belongs to can be modified by selecting or unselecting groups from the Groups list Hold down control or command on a Mac to select more than one group BODB 3 0 Manual USC Brain Project September 2010 69 Security Permissions The user s security permissions can be set in the Permission
37. Literature linked to the current entry and allowing the user to add new Literature entries After expansion the Show link will turn into a Hide link that can be used to collapse the References section References Hide Authors Year Title Edit Remove Amari amp Arbib 1977 Competition and cooperation in neural nets Edit Remove Barto 2003 Reinforcement Learning in Motor Control Figure 30 The expanded References section To link an existing Literature entry to the current SED click on the Search link This will open the Literature Search window where Select link next to any search result can be clicked to link it to the current SED entry To add a new Literature entry click on the Add new link This will BODB 3 0 Manual USC Brain Project September 2010 30 open up the Insert Literature window Clicking the Edit link next to an existing Literature entry will open the Edit Literature window while clicking Remove will remove the Literature entry from the SED Brain Imaging Summary Data BODB is intended to serve also as an experimental data repository In addition to the generic SED entry form it provides an explicit storage and user interface for tables of brain imaging data based on Talairach coordinates Although brain imaging data are often supplied in table format different articles may differ in the number labeling and layout of columns and differ in the freeform description of the experimental conditions of that table
38. P object selectivity Many cells in AIP demonstrate object specific activity However itis important to note that some cells actually respond to several different objects with varied activity levels Most often cells are actually selective to varying degrees for several objects that often share some common characteristics Some cells demonstrate specificity toward the size of the object to be grasped while showing a certain degree of independence from the type of object other cells demonstrate independence from the size of the object Taira et al 1990 Sakata and Kusunoki 1992 Murata et al 1993 FS canonical visual properties Some FS cells respond to the observation of graspable objects Rizzolatti et al 1988 Murata et al 1997 Predictions Hide Name Brief Description AIP and FS response to multiple If an object can be grasped in one of two ways but information about which grasp to select is delayed FS and affordances AIP neurons should represent both possibilities during the delay period Once the instruction stimulus is given the population of cells in each region not corresponding to the selected grasp will be inhibited AIP response to different objects with Iftwo objects are grasped in an indentical manner motor related cells in AIP will respond identically but the same affordances visual related cells can appear to have an object specific code AIP selectivity for grasp relevant AIP will only represent parameters relevant for progr
39. Pars Reticulata 1 Subthalamic Nucleus 2 system may learn to recognize actions already in the Supplementary Motor Area 1 syntax 1 repertoire of the F5 canonical neurons Thalamus 2 Ventrolateral Pars Oralls Thalamus 1 working memory 1 Benchmark de Display a menu A Figure 11 The Workspace view for Model Selections In order to benchmark models the user must first search for the models and select the models of interest Then she must proceed to the Model Selections tab of the Workspace From there she selects the models to be benchmarked BODB may take several seconds to generate the benchmarking report This will display a screen similar to that shown in Figure 12 comparing the summary data entries associated with each selected model The screen allows a visual analysis of which summary data entries set the scene for support are explained by are predicted by and contradict each model BODB 3 0 Manual BODB Insert Model tag cloud affordances 3 basal ganglia 3 computational 6 Computational Model 1 2 Cortex 1 D1 receptors 1 D2 receptors 1 declarative 1 dynamic neural field 2 External Globus Pallidus 2 Gating 1 Globus Pallidus 2 grasping 6 Imitatlan 1 Internal Globus Pallidus 2 language 1 memory 1 mirror neurons 4 motor Cortex 1 motor development 2 motor learning 2 PBWM 1 Prefrontal Cortes 1 procedural 1 Putamen 1 PVLV 1 reinforcement
40. R2C subunit and its expression in the central nervous system and periphery impor White MJ DiCaprio MJ 1996 70 2 J Neurosci Assessment of neuronal viability with Alamar Greenberg DA Methods blue in cortical and granule cell cultures Import Wolfman Viola H Marder 1996 3181 Eur J Anxioselective properties of 6 3 dinitroflavone a M Wasowski Ardenghi F Pharmacal high affinity benzodiazepine receptor ligand Izquierdo I Paladini AC Medina JH Import Suzuki Y Shimozawa M 1996 804 Ann N Y Acad Peroxisomal disorders clinical aspects Takahashi Y Imamura A Sci Kondo N Orii T 1 10 of 9410 Figure 9 Pubmed search tool Given keywords and or a year range the PubMed tool will list the most relevant articles from PubMed Database The user can click on the Import link next to a search result to transfer the entry into BODB Save Clicking on the Save button will save the entry in the BODB database and redirect to the Literature view page BODB 3 0 Manual USC Brain Project September 2010 15 Bonaiuto et al 2007 Title Extending the mirror neuron system model I Audible actions and invisible grasps Authors Bonaluto J J Rosta E Arbib M Year 007 Journal Biol Cybern Volume 96 Issue 1 Pages 9 38 URL http www ncbi nlm nih govpubmed 17028884 Language English Figure 10 Literature view page Insert BOP In BODB a Brain Operating Principle is a generalized description of an opera
41. User s Manual The Brain Operation Database BODB http bodb usc edu Version 3 0 September 2010 James Bonaiuto Anon Plangprasopchok Nantana Tinroongroj Michael A Arbib University of Southern California Brain Project USCBP Feedback welcome Please send comments and questions to James Bonaiuto bonaiuto usc edu Robert Schuler schuler isi edu and Michael Arbib arbib usc edu Development of BODB was supported in part by the National Science Foundation under Grant No 0924674 Any opinions findings and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation BODB 3 0 Manual USC Brain Project September 2010 2 Contents DSA OLELE KTO i PAETAE E E E E E EA AE EA ENA A EAE ET 2 Conceptual OV IVI N oe E E E 4 Ir E E E E A E AA A E E 4 Coneco nte AAA EE E EE EE OERE 6 Resistrationcand LODI ica end E 8 SAE o 31 PROA POE SE EOI IN cenaseensase E 9 A O AEN EEE E e eee sadece es OON 10 AAA E E desis sewesuanaceaincsn se tesuanaceoscsiosucesuaneceonee 10 a A E OO A 15 aa AAA ee o 20 Im A PP OO oo oo EET al ss R e E E E E ee E 34 S o E A 41 PP RR A 42 DAUR AWG POP iO OE O o E 42 RR 43 A ro o A 45 Summary of Experimental Data ooooooonncnnnnnnnnnnnnnocnnnnnnnnnononnnonnnnnnnnnnnnnnnonnnncnnnnnnnnnnaninnnss 47 Summary of Simulation Results oooonccnnnnccnnnnnnocnnnnnnnnnnnnnononnnnnnnnonononnnnnnn
42. a Simulation Results Regions Advanced Options Hide Tags y y Only my entries LI Literature Results Hide Add mew Select All None Pormat Endrta Y Export Selected Authors Sztop amp Arbib E Kohler et al Keysers et al C Bonaiuto et al BOP Results Hide Add new Title Corollary Discharge Cross Body Mirroring Year 2002 2002 2003 2007 Title Schema design and implementation ofthe grasp related mirror neuron system Hearing sounds understanding actions action representation in mirror neurons Audiovisual mirror neurons and action recognition Extending the mirror neuron system model I Audible actions and invisible grasps Description This principle involves the sending of a copy known as the corollary discharge or efference copy of motor command to other processing centers so that knowledge of current actions may be integrated with ongoing perception and the coordination or planning of subsequent actions The ability to map the structure of another whether body or object to ones own body structure Figure 34 The input form for searching entries Any Field Search for any entry that contains this string in any field Advanced Options Title Search the title field of any entry Description Search the description field of any entry Narrative Search the narrative field of any entry Tags Search the tags field of any entry Only My Entries Search onl
43. aft of the new model BODB saves the draft to the users workspace At a later time the user can go to her workspace and find the model under the Drafts tab apno BODE Workspace 3 hup bodb usc edu bodb workspace Qr Google CO H Taiwan Games Work Finance Neuro Globus My Yahoo nas Admin Router Popular 612 Programming orials com Kyron Horman su Hi schul L t My Profil pate aga ri Insert Search Talairach Workspace Admin About Model tag cloud affordances 3 basal ganglia 3 computational 6 Fes Model Selections Coordinate Selections Computational Model 1 conceptual Workspace 2 Cortex 1 Ol receptors 13 D2 Models receptors 1 declarative 1 dynamic Title Description neural field 2 External Globus Edit Delete Stroop Model A model of the Stroop effect This model simulates the Stroop Pallidus 2 Gating 1 Globus effect and matches the empirical results of the classic color word Pallidus 2 grasping 6 Stroop experiment stimulus onset asynchrony variants and imitation 1 Internal Globus Pallidus semantic variation 2 language 1 learning 1 memory y mirror neurons 4 motor Cortex 1 motor development 2 motor learning 2 PBWM 1 Prefrontal Cortex 1 procedural 1 Putamen i PYLV fi reinforcement 2 reinforcement Learning 1 semantics 1 Stratum 1 stroop 1 Substantia Nigra Pars Compacta 2 Substantia Nigra Pars Reticulata 1 Subthalamie Nu
44. ag indicates the number of entries it 1s associated with and this number is also displayed in parenthesis after the tag name Clicking on a tag opens a page listing all the entries associated with it The tag cloud section can be hidden by clicking on the lt link in the middle to the right of the column When hidden this will change to a gt link that can be clicked on to display the section again The new entries section displays the five most recently added Model BOP SED and SSR entries For each section the orange RSS icon to the left of the section header can be clicked on for the RSS subscription feed This can be used in any news ticker or news reading program such as Google Reader to get automatic updates of the latest BODB entries Insert Insert Literature Literature Journal Article Book Chapter Conference Thesis and Unpublished Information Brain Operating Principle Brain Operating Principle e g Winner Take All Model Structured description of a model with links to related entities e g Didday Model based on the Winner Take All Principle Summary of Experimental Data A summary of experimental data Figure 5 BODB insert page The insert page provides links for adding new entries Literature Literature Journal Article Book Chapter Conference Thesis and Unpublished Information Brain Operating Principle Brain Operating Principle e g Winner Take All Model Structured description of a mod
45. amming grasps parameters Effect of explicit attordance coding on If object affordance information is explicitly available to mirror neurons it can in some cases overwhelm the mirror neuron response to hand state influence of the hand state trajectory when itis not appropriate for the object affordance trajectory affordance mismatch Mirror neuron response to grasp object Mirror neurons should not respond when the orientation of the grasp does not match the axis of the object axis mismatches Temporal effect of explicit affordance If object affordance information is explicitly available to mirror neurons they should respond faster when the coding on mirror neuron response grasp matches the observed affordance Summaries of Simulation Results SSRs Hide Name Brief Description AIP population response to different AIP population response in fixation task is object specific while there is no object specificity in the grasp in objects in light dark fixation task the dark task FS mirror response to different sized When objects of different sizes are grasped with the same precision pinch hand state trajectory the mirror objects with same hand state trajectory neurons can recognize it as a pinch However with explicit affordance encoding ifthe object is big enough the influence of the affordance information can overwhelm that of the hand state and cause the power grasp mirror neurons to be activated FS mirror response to different sized When a precisio
46. as a new entries section that is only visible on the main page The toolbar contains the options Insert Search Talairach Workspace About and depending on the user s level of access Admin Insert leads to a page where the user can insert new Literature Brain Operating Principle BOP Model or Summary of Experimental Data SED records Search allows the user to search all BODB records Talairach opens the Talairach Atlas allowing the Talairach coordinates associated with Brain Imaging SEDs Workspace opens the user s workspace where entry drafts are listed and model and Talairach coordinate selections can be managed About leads to a description of the history of BODB and its implementors Admin allows administrators to manage other users and brain atlases The user information section displays the user s avatar this can be set on the User Profile page and provides the following options Logout My Profile Messages and Help If there are any unread messages in the user s inbox the number is displayed here Logout logs the user out of the system BODB 3 0 Manual USC Brain Project September 2010 10 My Profile allows the user to view and modify their profile Messages allows the user to read and write messages to other BODB users Help opens the appropriate help page The tag cloud section displays the tags associated with Model BOP SED Prediction and Summary of Simulation Results SSR entries The relative font size of each t
47. ater development into a computational model but which is not yet specific enough to reach an implementation level BODB 3 0 Manual USC Brain Project September 2010 4 A Summary of Experimental Data SED encapsulates a fragment of knowledge in a particular domain encapsulating empirical findings from one or more studies in a form that is amenable for use in the support or testing of a certain model or BOP Note that a summary datum could encapsulate any set of related experimental results along with the associated protocol Thus brain structure connectivity neurophysiological or neurochemical data or a table in Talairach coordinates from an fMRI brain imaging study could be presented in this way An issue with this paradigm would be when scientist A works on his model and inserts SED A to support his model while scientist B inserts SED B to support her model If SED A is in fact the same as or a minor variant of SED B they or an editor will have to discover this fact and replace each of these SEDs by the same integrated version A Summary of Simulation Results SSR summarizes a basic set of simulation results from a model A Model entry should include explicit analysis of appropriate SEDs either with design features of the model or with SSRs for the model Conceptual Overview Advances in neuroscientific research have led to a flood of information that can only be structured and navigated with the aid of databases and the technology of
48. chael amp Price 1994 Architectonic subdivision of the orbital and medial prefrontal cortex in the macaque monkey Edit Delete Jones et al 1 Jones etal 1978 Intracortical connectivity of architectonic fields in the somatic sensory motor and parietal cortex of monkeys Edit Delete Lewis amp Van Essen 1 Lewis amp Wan 2000 Mapping of architectonic subdivisions in the macaque monkey with emphasis on parieto occipital cortex Edit Delete Morel et al 1 Morel et al 1993 Tonotopic organization architectonic fields and connections of auditory cortex in macaque monkeys Edit Delete Pandya amp Seltzer 1 Pandya amp Seltzer 1982 Intrinsic connections and architectonics of posterior parietal cortex in the rhesus monkey Edit Delete Parma 2 Matelli et al 1991 Architecture of superior and mesial area 6 and the adjacent cingulate cortex in the macaque monkey Edit Delete Parma 1 Matelli et al 1985 Patterns of cytochrome oxidase activity in the frontal agranular cortex of the macaque monkey Edit Delete Pons amp Kaas 1 Pons amp Kaas 1986 Corticocortical connections of area 2 of somatosensory cortex in macaque monkeys a correlative anatomical and electrophysiological study Edit Delete Preuss amp 1 Preuss amp Goldman Rakic 1991 Architectonics of the parietal and temporal association cortex in the Goldman Rakie strepsirhine primate Galago compared to the anthropoid primate Macaca Edit Delete Saleem Tanaka 1 Saleem amp Tanaka
49. cleus 2 Supplementary Motor Area 1 syntax 1 Thalamus 2 Ventrolateral Pars Oralls Thalamus 1 working memory 1 rI Figure 10 The Workspace view for Model Drafts Likewise while searching for models a user may identify several models of interest Instead of searching for the same models repeatedly the user may select the models he wishes to review immediately or at a later time The model selections are recorded to the users workspace At any time the user can go to the Model Selections tab of the workspace to find the results of his earlier searches To remove an entry from the current selections click the checkbox next to the model The next time the user visits the workspace the unselected model will no longer be seen in the listing BODB 3 0 Manual USC Brain Project September 2010 81 606 BODB Workspace http bodb usc edu bodb workspace G Oy Google CO NH Taiwany Gamesy Worky Financer Neuroy Globus My Yahoo nas Admin Router Popular 612 Programming orials com Kyron Horman Hi schuler Logout My Profile JSC BO D a Messages Help Insert Search Talairach Workspace Admin About Model tag cloud affordances 3 basal ganglia 3 computational 6 Drafts EROS lt H aC Coordinate Selections Computational Model 1 conceptual Workspace 2 ortex i i receptors ij D Select All receptors 1 declarative 1 dynamic Unselect All Name Description neural field 2 External
50. cortex Motor and premotor cortex Primary motor area 4 R 39 15 63 7 14 Primary motor area 4 R L 42 18 66 655 L Lateral premotor area 6 R 42 3 60 5 67 Lateral premotor area 6 R 42 6 57 5 69 L 36 3 66 5 19 L 42 3 51 5 35 Medial premotor area 6 Medial premotor area 6 Pre SMA R 6 6 57 5 11 Pre SMA R 3 6 69 6 29 L 9 9 51 4 37 L 3 6 69 5 81 Post SMA R 3 3 66 459 Post SMA R L 3 3 66 6 01 L 6 3 69 4 61 Parietal area Parietal area Primary sensory area 1 2 3 R 42 33 60 5 03 Primary sensory area 1 2 3 R 54 21 39 43 L 48 24 57 4 94 L 60 21 39 5 18 Superior parietal area 7 R 35 36 66 4 Superior parietal area 7 R 24 54 51 3 6 L 30 42 66 3 66 L 27 60 54 4 63 Inferior parietal area 40 R Inferior parietal area 40 R 36 30 42 4 53 L 45 36 60 4 95 L 36 42 48 4 73 S ll area 40 43 R 60 9 15 3 95 SII area 40 43 R L 60 15 21 3 93 L Other cortical areas Other cortical areas Middle temporal area 21 R Middle temporal area 21 R L L 60 57 6 4 65 Subcortica regions Subcortica regions Caudata nucleus R Caudate nucleus R 15 9 15 4 81 L L 18 9 21 4 3 Anterior part of the putamen F 24 18 6 47 Anterior part of the putamen R 27 9 1 5 47 L 30 6 6 5 73 L 27 6 12 5 57 Posterior part of the putamen R 2 9 12 3 25 Posterior part of the putamen R L 33 3 6 42 L Thalamus R 15 12 9 4 83 Thalamus R L 18 15 9 4 67 L Cerebellum E 21 45 18 535 Cerebellum R L 27 45 18 6 23 L b A table of task 1 extracted from
51. cture section Diagrams Since the model may be hierarchical you may choose to use several diagrams Use at least one to present the overall structure of the Model In some cases a diagram will explicitly show not only the immediate submodules but also the further decomposition of some of these In other cases BODB 3 0 Manual USC Brain Project September 2010 23 you will need a separate diagram to show how a module shown as a unit of an earlier diagram is expanded to reveal the structure of 1ts submodules In order to add a diagram click on the Add new link in the Diagrams section This will open the Add Diagram window Clicking on the Edit link next to a diagram already linked to the model will open the Edit Diagram window and clicking on the Delete link will delete the diagram and remove it from the Model Inputs The Name DataType i e Image Vector Scalar and Description of all inputs to the model Outputs The Name DataType 1 e Image Vector Scalar and Description of all outputs of the model States The Name DataType i e Image Vector Scalar and Description of all states of the model In general the state of a module comprises the state of all the submodules which comprise it It is thus a matter of judgment by the collator whether the state of a module whose decomposition is presented should be described or left implicit Submodules New submodules can be added by clicking on the Add new link in the Subm
52. different ways 1 Scene setting Background information that is not specifically used in developing or assessing the principle 2 Support These are data that are examples of the principle BODB 3 0 Manual USC Brain Project September 2010 18 After the user links an existing SED or adds a new one she should specify the relation between the present BOP entry and the SED as one of Scene Setting or Support This will aid in clarifying how the summary data relate to the principle Clicking on the Expand link will make visible fields for SED tags and a narrative The Expand link will then turn into a Collapse link that can be clicked to hide the Tags and Narrative fields Clicking on the Remove link next to a linked SED will remove that SED from the current BOP entry Related BOPs This allows listing of principles related to the present principle Clicking on the Show link in the Related BOPs section will expand the Related BOPs section displaying the BOPs linked to the current entry and allowing the user to add new BOPs After expansion the Show link will turn into a Hide link that can be used to collapse the Related BOPs section Related BOPs Hide Search Add new Name Relationship Description Remove Collapse Parent Tags Narrative Figure 14 The expanded Related BOPs section In order to add an existing BOP to the current BOP clicking on the Search link will open the BOP Search window Clicki
53. e the configuration Brain region T x y z N A N A y yields the same result as the configuration brain region T N A N A x y z After specifying the header the user then has to paste the data into the text area in Data using tabs to separate columns and using linefeed new line to separate rows One may do this symbol by symbol or simply copy and paste a table from Microsoft Word or Excel Figure 4 displays this step in inserting the present example data BODB 3 0 Manual USC Brain Project September 2010 35 Data Column order Brain Region T x y z Comments Mid temporal g BA 21 6 42 63 37 0 Auditory activation Mid temporal q BA 21 5 76 65 24 6 Auditory activation Mid frontal q BA 9 4 37 50 29 28 DLPFC Cerebellum 4 07 50 67 26 Inferior parietal BA 40 4 02 50 52 47 Superior frontal q BA 10 3 8 30 60 10 Hippocampus 3 78 36 25 6 Inferior frontal g BA 45 3 65 40 22 4 Similar to midazolam Use newline to separate rows and tab or to separate columns Figure 4 Pasting text The screen shows the pasted data after copying a Microsoft Word table Note the columns in the text area in this step may or may not be graphically aligned It depends on the length of each word in a certain column As we shall see in Figure 9 once the table is entered it will be formatted properly Dealing with complex tables One table in a published articl
54. e aspect of model design e g an SED showing an inhibitory connection between 2 brain regions would support the decision to constrain the connection between Model modules representing those brain regions to be inhibitory To link an existing SED to the model click on the Search link in the SEDs Used to Build the Model section This will open the SED Search window where the Select link can be used to link a search result to the current model In this case the user only then has to select the relationship between the SED and the model support or scene setting Alternately a new SED can be added by clicking on the Add new link This will add a new form to the section including fields for the SED Name Relationship to the model and Description Clicking on the Expand link next to the new form will make visible additional fields for Tags and a Narrative SEDs Used to Test the Model BODB 3 0 Manual USC Brain Project September 2010 25 SEDs used to test the model s performance can be linked to Summaries of Simulation Results SSRs that either explain or contradict them Clicking the Add new link under the SEDs used to test the model will add a new row to the form with the following fields Name The name of the the association between the SED and SSR Relationship Explanation or Contradiction Description A brief description of the association SED the SED used to test the model Click Search to open the SED Search page or
55. e current entry and allowing the user to add new figures After expansion the Show link will turn into a Hide link that can be used to collapse the Figures section BODB 3 0 Manual USC Brain Project September 2010 33 Figures Hide dere gt Captian 3 ea fe Competitive queuing Edit Delete Ss ts ail Prete iF L H Figure 31 The expanded Figures section To add a new figure click on the Add new link This will open up the Add Figure window Clicking the Edit link next to an existing figure will open the Edit Figure window while clicking Delete will delete the figure and remove it from the SED Related Brain Regions Brain region s that relate to the present SED Clicking on the Show link in the Related Brain Regions section will expand the Related Brain Regions section displaying the Brain Regions linked to the current entry After expansion the Show link will turn into a Hide link that can be used to collapse the Related Brain Regions section Related Brain Regions Hide Name Nomenclature Remove FS Parma 1 Remove AIP Lewis amp Van Essen 1 Figure 32 The expanded Related Brain Regions section In order to add an existing Brain Region to the current SED clicking on the Search link will open the Brain Region Search window Clicking Select next to one of the search results will add that Brain Region to the current SED entry Clicking Remove next to a linked Brain Region will remove it f
56. e may contain experimental results for different tasks providing the equivalent of several tables of the kind described in the previous section In this case the user has to break the table into sub tables one sub table for one task each in BODB s standard format This reformatting makes experimental results more readily searchable Here are some examples of complex tables and how to break them The first example is a table with the results of 2 different tasks aligned vertically Results of task 1 lie above results from task 2 They share column names which are brain region Talairach coordinates x y Z and t value In this case users can easily copy and paste text the first half of the table to use as sub table 1 experimental result of task 1 Similarly the other half is used as sub table 2 experimental result of task 2 The table and its sub tables are shown inFigure 5 Table 1 Significant CBF changes in the hands mental Stereolaxic coordinate Stereolaxic A e coordinate Brain area x y z value Hands mental rotation minus hands control condition A SS E Anterior intraparietal sulcus area PF L 46 30 42 6 10 Hands mental rotation minus hands control condition Middle intraparietal sulcus 34 50 59 353 Anterior intrapartetal sulcus arca PF L 46 30 42 6 10 Caudal superior parietal lobule 16 61 39 458 Middle intraparietal sulcus 36 50 39 353 area PE caudal 35 59 66 513 Caudal superior parietal lobule
57. e to the way the present Model works You can search BODB for related models and link them to the current one or add a new model Clicking on the Show link in the Related Models section will expand the Related Models section displaying the Models linked to the current entry and allowing the user to add new Models After expansion the Show link will turn into a Hide link that can be used to collapse the Related Models section BODB 3 0 Manual USC Brain Project September 2010 26 Related Models Hide Mame Descnption Augmented Competive Queueing Figure 23 The Related Models section Edit Remove In order to link an existing Model to the current Model entry clicking on the Search link will open the Model Search window Clicking Select next to one of the search results will add that Model to the current Model entry In order to add a new Model and link it to the current Model entry click on the Add new link which will open a Insert Model window Clicking on the Edit link next to a linked Model will open the Edit Model window and clicking on the Remove link will remove that Model from the current entry Related BOPs This allows listing of principles related to the present Model Note that BOPs are documented in separate entries in BODB Your job then is to decide which of the available BOPs describe general principles that help us map the way the present Model works You can search for existing BOPs to link to the cu
58. e user group s information The Permissions section displays 1ts security permissions These permissions are inherited by each user belonging to the group but are overridden by their personal security permissions To edit the group s information click on the Edit button This will open the Group Edit page To delete the group click on the Delete button Clicking on the Close button will close the current window Edit Group Edit Group Help Name USCBP Lab Members Change Delete Literature Models Modules BOPs SEDs SSRs Predictions ET Nomenclatures Figure 66 The Group Edit page The Group Edit page allows administrators to modify the attributes of an existing user group Click on the Save button to save the changes or Close to cancel and close the window To delete the group click on the Delete button Basic Information To change the group s name edit the data in the Name text field Security Permissions The group s security permissions can be set in the Permissions section Checking or unchecking the Add Change or Delete checkbox for a given entry type grants or removes permissions for user s in this group to perform that action on entries of that type These security permissions are inherited by each user in this group but are overridden by each user s personal security permissions BODB 3 0 Manual USC Brain Project September 2010 72 Insert Group Add Group Mame P
59. ed BOP E Related Model A Only my enties Related Literature Title Pf Author C Results Add new Select All f Unselect Aii eee il Dynamic Neural Field Mirror Neuron The Dynamic Neural Field Mirror Neuran System ONF MNS System ONF MNS Erlhagen model combines dynamic neural fields with Hebbian learning to Mukowskiy Bicho provide an account of goal directed matching of action observation and action execution The model is tested in an imitation task using actors and observers with different embodiments E Hebbian Mirror Neuron System A conceptual model of how Hebbian learning between the areas H MNS Keysers Perrett STS PF FS allows recognition of the actions of others by Figure 37 The input form for searching Model entries Any Field Search for Model entries that contains this string in any field Advanced Options Title Search the title field of Model entries Description Search the description field of Model entries Narrative Search the narrative field of Model entries Tags Search the tags field of Model entries Building SEDs Search for Models with Building SEDs containing the given text Testing SEDs Search for Models with Testing SEDs containing the given text BODB 3 0 Manual USC Brain Project September 2010 47 Predictions Search for Models with Predictions containing the given text SSRs Search for Models with SSRs containing the given text Related Brain Regions Search for Models rela
60. el with links to related entities e g Didday Model based on the Winner Take All Principle Summary of Experimental Data A summary of experimental data Insert Literature After the user clicks Literature from the Insert page the following screen will appear BODB 3 0 Manual USC Brain Project September 2010 11 Add Literature To avoid having redundant references in the database we recommend first searching for a desired reference and then using the result if found before adding a new reference Type Journal y Title Authors Hide Search Add new First name Middle name Last name Order Year Journal Issue Pages Volume Url Language English Annotation Figure 6 The Literature insert page The form provides 6 types of article information Journal Book Chapter Thesis Conference and Unpublished Each type has appropriate fields Six types of article forms are available and these can be selected by changing the value of the Type dropdown Add New Author To add an author click the Add new link in the Authors section The ordering of authors when the Literature entry is listed can be set by setting the Order field of each author appropriately BODB 3 0 Manual USC Brain Project September 2010 12 Add Literature To avoid having redundant references in the database we recommend first searching for a desired reference and then using the re
61. ermissions Hide Literature O 4 L Models L Modules B C BOPs O LI SEDs C SSRs Predictions Nomenclatures O Figure 67 The Group Insert page The Group Insert page allows administrators to add new user groups to the system Click on the Save button to save the new group or Close to cancel and close the window Basic Information To set the group s name enter the data in the Name text field Security Permissions The group s security permissions can be set in the Permissions section Checking or unchecking the Add Change or Delete checkbox for a given entry type grants or removes permissions for users in this group to perform that action on entries of that type These security permissions are inherited by each user belonging to this group but are overridden by each user s personal security permissions Nomenclatures The Nomenclatures tab allows administrators to add edit and delete brain nomenclatures BODB 3 0 Manual USC Brain Project September 2010 73 Administration Users Groups Add new Name Version Reference Edit Delete Akbarian et al 1 Akbarian et al 1994 Corticofugal connections between the cerebral cortex and brainstem vestibular nuclei in the macaque monkey Edit Delete Biittner Buettner 1 Biittner amp Buettner 1978 Parietal cortex 2v neuronal activity in the alert monkey during natural vestibular and optokinetic stimulation Edit Delete Carmichael amp Price 1 Carmi
62. es dynamic neural field grasping imitation mirror neurons motor development motor learning reinforcement Add new Name Brief Description Dynamic Neural Field Mirror Neuron System The Dynamic Neural Field Mirror Neuron System DNF MNS model combines dynamic neural fields with Hebbian learning to provide an DNF MNS Erlhagen Mukovskiy Bicho account of goal directed matching of action observation and action execution The model is tested in an imitation task using actors and observers with different embodiments FARS Fagg Arbib A model of cortical control of grasping that focuses on the interaction between anterior intraparietal area AIP and ventral premotor area FS Based on input from the dorsal visual stream area AIP represents the possible affordances for grasping Area FS uses this information along with task constraints to select and program a grasp to an affordance Infant Learning to Grasp Model Oztop The Infant Learning to Grasp Model ILGM models how motor parameters for grasp can be learned through trial and error with Bradley Arbib reinforcement Mirror Neuron System MNS Oztop The MNS model explains how the mirror neurons are developed during infancy The main hypothesis of the model is that the Arbib temporal profile of the features an infant experiences during self executed grasps provides the training stimuli for the mirror neuron system to develop Thus developmentally grasp learning precedes initial mirro
63. ext annotation and 111 a repository for Talairach based brain imaging experimental data along with a visualization tool for brain imaging data analysis A brain operating principle BOP presents some general operational principle that will provide a unifying principle embodied in usually a wide range of neural systems and the corresponding models Examples include winner take all somatotopic layered computation and Hebbian learning to name just a few In general a given BOP will be supported by many experimental and simulation data though of course such data may be used to refine and bound the validity of specific BOPs Brain Operating Principles capture the gist of the brain mechanisms that abstract away from their heterogeneities as a way to organize experiments models and technological spin off of brain mechanisms We define a brain model as either a an explicit computational model at e g the level of biologically realistic brain regions and neural networks of how a particular brain system operates or b a more abstract conceptual model To be more specific the former tries to emulate the function of a biologically established brain system matching simulation results to data from experimental protocols The simulation results will be used to contrast and compare with a certain collection of experiments as well as predict results for further ones By contrast a conceptual model may provide diagrams and comments suitable for l
64. h click and can be erased by clicking the Clear all coordinate s button On the other hand the user can input some brain region names and click the Search region s button to see where they are on 2D images Each area is displayed distinctively by different color blobs in all three views The color blobs also appear on the image navigator in order to help the user see the brain regions clearly The size and minimum maximum values of x y z coordinates of brain regions are also given in the search results box The color of each blob can be changed in the window shown after clicking Display Properties Color blobs can be removed from the image by clicking on the button Clear region s BODB 3 0 Manual USC Brain Project September 2010 56 Talairach Applet 2D 3D A Click on coordinates to see the brain regions they belong to Otherwise input coordinates below Format is x y z Clear all coordinate 5 Search coordinate 5 B Input brain region names to see the blobs representing their extent Use acommato separate names hippocampus inferior frontal qyrus Clear all region s Search region s Search Results or inferior frontal gyrus ound 16476 coordinates x ranges from 64to 65 ranges from 4to 60 z ranges from 5to 19 Image Navigator Slice Index 08 Significance Threshold 0 00 Significance Metric JM t Score J z Score Figure 45 The two dimensional version of the Talairach applet when using the search regions
65. he name of the structure is a synonym for one already in the master list In addition if the table contains only coordinates not brain region names the system will search for possible brain region names in the database that match a coordinate of each row and let the user select one This will be useful later on when the user wants to compare parts of several tables according to brain region names After entering the data cf Figure 4 the user will be prompted with the page showed in Figure 8 Clean SED Coordinate Hemisphere Errors Brain Region Errors The named brain region Inferior frontal g BA 45 does not match any region in the Talairach atlas o Match region by name 40 22 4 Qe al a Match region by coordinate Inferior Frontal Gyrus 2 The named brain region Superior frontal g BA 10 does not match any region in the Talairach atlas o Match region by name 30 60 10 sana a Match region by coordinate Superior Frontal Gyrus E The named brain region Inferior parietal BA 40 does not match any region in the Talairach atlas o Match region by name 50 52 47 Pp gt a Match region by coordinate Inferior Parietal Lobule The named brain region Cerebellum does not match any region in the Talairach atlas o Match region by name 50 67 26 ps 5 a Match region by coordinate Right Cerebellum The named brain region Mid frontal q BA 9 does not match any region in the Talairach atlas o Match regi
66. how Related BOPs Show Related Models Show Related Brain Regions Show References Show Save Ort Figure 11 The input form for Brain Operating Principle entries Title The name of the principle e g Winner Take All It is very important to first search for existing BOPs to increase the utility of BODB by helping collators gather similar BOPs into a single entry where this is appropriate Parent The BOP entry with a parent relationship to this one For example Reinforcement learning would be the parent of Temporal difference learning In order to link to an existing BOP click on the Search button which will open the BOP search window Clicking on the Add button will open another Add BOP window in order to add a new BOP as the parent Brief Description A brief description of the principle We provide a text input area but in general the entry should be much shorter say 200 words since a full description can be entered in the Narrative field Narrative A full length description of the present principle BODB 3 0 Manual USC Brain Project September 2010 17 Tags A list of keywords associated with this BOP entry Figures Clicking on the Show link in the Figures section will expand the Figures section displaying figures linked to the current entry and allowing the user to add new figures After expansion the Show link will turn into a Hide link that can be used to collapse the Figures section
67. ic Ff t Score J z Score Figure 43 The two dimensional version of the Talairach applet in saggital view mode BODB 3 0 Manual USC Brain Project September 2010 54 Viewing Coordinates Selected coordinates are displayed in the slice image if they fall within the bounds of the current slice and the image navigator The blue and green sliders control the thickness of the slice by increasing or decreasing the lower and upper bounds on coordinates to display in the current slice image Typically brain imaging coordinates are given along with a measure of their statistical significance usually scores for a t or z test When these values are entered with coordinates the significance threshold for the Talairach Daemon can be set such that only coordinates with a statistical significance above that threshold will be shown The current significance threshold is shown below the image navigator The significance metric used to determine significance can be selected by checking either t Score or z Score All coordinates that do not have a value for the selected metric will be displayed regardless of the threshold value The threshold value can be adjusted by clicking and dragging the black slide bar the maximum threshold is the highest significance level in the current set of selected coordinates given the chosen significance metric In addition a user can select not to see some coordinates or change the color or shape by clicking the button
68. ical Registration viewer There are two versions of the Talairach applet two dimensional and three dimensional The default version is two dimensional but this can be changed in the User Profile When clicking on the Talairach link in the main toolbar the default applet is loaded Two Dimensional Talairach Applet The Two Dimensional Talairach Applet provides 3D brain information via 2D brain images in 3 views axial coronal and saggital Talairach Applet 2D 3D A Click on coordinates to see the brain regions they belong to Otherwise input coordinates below Format is x y z 22 50 4 01 22 34 01 B Input brain region name s to see the blobs representing their extent Use acommato separate names Search Results For 22 50 1 Right Cerebrum Superior Frontal Gyrus White Matter For 22 34 1 Right Cerebrum Dis play Properties 50 10 LO ah oir m j Image Navigator Slice Index 10 Significance Threshold 0 00 Significance Metric IM t Score J z Score TD coordinate 6 y 2 22 34 01 17 38 1 i 06y 2 22 34 01 Save Slice Generate Report _ Print Region labels Figure 41 The two dimensional version of the Talairach applet Navigation The two basic navigation actions that can be performed are changing the slice and changing the view The current slice can be changed by three methods dragging the red slider to the right of the slice image clicking anywhere in
69. ing the mouse scroll wheel The Reset button will return the 3D view to the default initial position The slice in each view can be changed by dragging the appropriate slider at the bottom of the applet This will move the slice plane as well as change the slice image BODB 3 0 Manual USC Brain Project September 2010 58 Talairach Applet 3D 2D Input brain region name s Separated by commas to see blobs representing their spatial extent Search Clear Region s Search Results J U 30 A 50 20 28 Right Cerebrum Frontal Lobe Middle Frontal Gyrus Display Properties Axial i 30 20 10 6 4 14 24 34 44 54 64 Coronal l 95 85 75 65 55 45 35 25 15 5 5 15 25 35 45 95 65 Sagittal 61 51 41 31 21 11 1 g 19 29 39 49 59 Figure 47 The three dimensional version of the Talairach applet after rotating the view and zooming in Viewing Coordinates Selected coordinates are displayed in the 3D view as colored three dimensional shapes Moving the mouse over a coordinate shape will popup a tooltip displaying the coordinate and hierarchical brain regions it is part of The user can select not to see some coordinates or change the color or shape by clicking the button Display Properties A new window will pop up where the user can click at a checkbox to set or unset visibility click at the color box to select a new color or click on the shape dropdown to change the shape of the
70. iption can be entered in the Narrative field Narrative A full length description of the SED The narrative must be detailed enough to provide rigorous constraints for the design and or testing of models BODB 3 0 Manual USC Brain Project September 2010 32 Tags A list of keywords associated with this SED entry Method The imaging method used currently PET or fMRI Control Condition A description of the control condition 1f applicable that the activity in the experimental condition is being compared to Experimental Condition A description of the task in the experimental condition Coordinate System The system that the coordinates are reported in MNI or Talairach Coordinates in the MNI system will converted to Talairach coordinates for visualization in the Talairach Applet Core Column Header The mandatory core columns for brain imaging data consists of Brain Region Hemisphere the X Y Z Talairach coordinates rCBF and T The user has to specify these columns corresponding to the columns and their order of the present table Extra Header The user can specify optional extra columns by inserting the column names separating each one with a Tab character and ordering by the column sequence in the present table Data The user has to paste the data into the text area Figures Clicking on the Show link in the Figures section will expand the Figures section displaying figures linked to th
71. l i IIi 3 30 a 45g L l 45 3i 60 495 11 36 42 48 473 l 3 ll area 40 43 R y 5150 49 15 3 95 11 l l L 1 50 15 21 3 93 Il I Other cortical areas I I l i i Middle temporal area 21 R l i l l i E L 1 ra 60 57 B 46 l Subcortical regions tt 11 Caudate nucleus A ry TE g 15 a y l L pol poa l y 21 43 l Anterior part ofthe putamen F 1 12 13 6 47 i 2 q 12 547 i L 30 i 6 573 aT 6 12 55 y 1 Posterior part of the putamen F 12 B 12 3 25 i l I L 1 Laa 3 6 42 Se See ee aS eS Se ae Thabmus Fi 1 15 12 a 483 i L y 1 48 15 q 4 67 Cerebellum R 1 172 ai 18 535 l 7 L lay 45 18 623 1 a Original table with its three parts A brain regions and hemispheres column B BODB 3 0 Manual USC Brain Project September 2010 37 activated coordinates of task 1 executed movement compared with rest and C activated coordinates of task 2 imagined movement compared with rest Hemisphere imagined movement with rest compared Anatomic Areas Brodmann area Hemisphere Executed movement with rest compared Anatomic Areas Brodmann area X Y Z Z score X Y Z Z score Prefrontal cortex Prefrontal cortex Dorsolateral prefrontal area 9 46 R Dorsolateral prefrontal area 9 46 R L L 54 42 15 3 76 Rostral prefrontal area 10 11 R Rostral prefrontal area 10 11 R 30 51 24 4 58 L L Inferior frontal area 44 45 R 57 18 24 5 62 Inferior frontal area 44 45 R 48 24 6 4 75 L L 54 12 12 4 31 Motor and premotor
72. ls for benchmarking and selected coordinates Tags Each BODB entry can be associated with a list of tags or keywords that can be used to group and search for related entries Report Generation Reports for Model and BOP entries can be generated in either RTF or PDF format by clicking on the appropriate button at the bottom of the Model View or BOP View page The report will contain all of the information on the view page including any expanded subsections Information in collapsed subsections will not be included User Profile The User Profile page allows the user to manage their account information and preferences BODB 3 0 Manual USC Brain Project September 2010 6 Messaging BODB s internal messaging system allows users to send and receive messages with other users Administration The Administration section allows BODB administrators to manage users user groups and their permissions as well as brain regions and nomenclatures Conceptual Overview Our current version of BODB combines features of an SDB Summary Database and Model Repository as in Brain Models on the Web BMW Bischoff Grethe Spoelstra amp Arbib 2001 supplemented with a variety of new features The system provides data entities for storing article information brain operating principles models generic summary data brain imaging experimental data and finally their relations Model sub modules Models Use instantiate
73. n pinch planned for a medium sized object is directed towards object of different sizes the objects with same hand state trajectory model mirror neurons can still recognize it as a pinch However with explicit affordance encoding the power grasp neurons become more and more activated as the object size increases eventually switching the network grasp classification F5 mirror response to precision pinch With explicit affordance encoding the mirror neuron selective for precision pinches was activated earlier when with explicit affordance encoding the observed pinch was directed toward smaller objects Figure 52 The tag page BODB 3 0 Manual USC Brain Project September 2010 63 User Profile The user profile page allows users to view and change their BODB preferences and account information Edit User Profile Jbonatuto First name Jimmy Last name Bonaiuto Email Ibonaiuto usc edu Email new message wi notifications Default Talairach Applet ET version 2D Talairach Applet size 1950 x 1550 3D Talairach Applet size 950 X 550 New password New password again Avatar Add new Notification Type Entry Type Keywords Delete email y Medel mirror Figure 53 The user profile page Profile Settings First name The user s first name Last name The user s last name Email Valid email address where system notifications are to be sent to Email new message
74. ng Select next to one of the search results will add that BOP to the current BOP entry In order to add a new BOP and link it to the current BOP entry click on the Add new link which will add a new BOP form to the Related BOPs section The form contains fields for the BOP name relationship to the current BOP and description Clicking on the Expand link will make visible fields for BOP parent tags and a narrative The Expand link will then turn into a Collapse link that can be clicked to hide the Parent Tags and Narrative fields Clicking on the Remove link next to a linked BOP will remove that BOP from the current entry Related Models This will list any models that use this principle Clicking on the Show link in the Related Models section will expand the Related Models section displaying the Models linked to the current entry and allowing the user to add new Models After expansion the Show link will turn into a Hide link that can be used to collapse the Related Models section BODB 3 0 Manual USC Brain Project September 2010 19 Related Models Hide Search Add new Name Descnpton Delete Collapse Tags Narrative Figure 15 The expanded Related Models section In order to add an existing Model to the current BOP clicking on the Search link will open the Model Search window Clicking Select next to one of the search results will add that Model to the current BOP entry In order to add a new Model and
75. ng the MNS1 and MNS2 models in BODB
76. nk the nomenclature to an existing reference click on the Search button to open the Literature Search page To link the nomenclature to a new reference click on the Add button to open the Literature Insert page Figures To add a new figure to the nomenclature click on the Add new link This will open the Add Figure page Species To associate an existing species with the nomenclature click on the Search link to open the Species Search page To associate the nomenclature with a new species click on the Add new link This will add a new row with text fields for the genus species and common name The new species will be saved and linked to the new nomenclature when the Save button is clicked To remove a species click on the Remove link next to it Brain Regions To add a new brain region to the nomenclature click on the Add new link This will add a new row with text fields for the name and abbreviation and dropdown boxes for the region type and parent region To delete a brain region click on the Delete link next to it Figures Add Figure The Add Figure window allows the user to add a new figure to the record that opened the window BODB 3 0 Manual USC Brain Project September 2010 78 Add Figure Help Image Browse Crop Center Default w from _ Title Po Title slug ee Caption Is public 7 Public photographs will be displayed in the default views Tags Separate tags
77. nnnnnnnnnnnnnnnnnss 49 Bat AKC PIOUS e Po 05U E E E E E E 50 E A A ses anhenaesssees 31 Two Dimensional Talairach Applet cccccooononnnnnnnnnnnnononononnnnnnnnnnnnnnnnonnncnnnnnnnnnnnannncnnnnns 52 Thres Dimensional Talairach Applet msi iaa E E 56 T OU II A 60 SS PTO I E E cen secesstacterentucaraestasieresinsecu 63 PEO TUE SUMING CAPARO OPA UPON Ue A e PE o 63 DCP O A A o o o phot A mboeshccneioi 64 MESS ACM ote 64 NI Ys AS 64 FRC PI 1 ropa E T e A A E E o un A 65 Viewing SCAU IVS SCS ticos 65 Compose a INC W IVC SSAC oracion E 66 PCIE CAI OM A eno E o E O o O A 66 a o E 66 O A e e rio o A EA E 70 NomenclatUlOs staba dedicada oi cniusbiar reia N 12 PoU A A ss sue saaunetuesbdudesseaecehedess sees TI Add T 11 eea e E E A E E Oo Un pototaseearnetemes 11 POCE U ee Ue E E III 78 e IU E TE E E A E 79 BODB 3 0 Manual USC Brain Project September 2010 3 Introduction Advances in neuroscientific research have led to a flood of information that can only be structured and navigated with the aid of databases and the technology of the World Wide Web As one contribution to channeling this flood we are developing BODB in which the aim is to facilitate the interchange between those developing new brain models and new experiments The current ideas are that the system 1 houses capsules of neuroscientific literature information that will facilitate comparison and integration of original articles 2 provides a standard form and its
78. notifications When checked emails will be sent to the email address above alerting the user whenever messages are received in BODB s messaging system Default Talairach Applet version The version of the Talairach Applet to display by default 2D Talairach Applet size Width and height of the 2D Talairach Applet 3D Talairach Applet size Width and height of the 3D Talairach Applet New password New user password must be entered twice Avatar The user avatar Click the Add button to popup an image upload window Click the Change button to change the existing avatar image BODB 3 0 Manual USC Brain Project September 2010 64 Subscriptions BODB allows users to set up subscriptions to be automatically notified when new entries with certain keywords are added to the system To add a new subscription click the Add new link in the Subscriptions section This will add a new subscription row Set the notification type email for only email notifications message for notifications using BODB s messaging system or both The Entry Type can be Model BOP SED Prediction or SSR and the Keywords field takes a list of keywords separated by spaces If these keywords appear anywhere in a new entry of the specified type a notification will be sent to the user using their preferred method Messaging The BODB messaging system allows users to send and receive message to and from other users When the currently logged in user has unread messages
79. odules section This will add a new form containing fields for the Name and Description of the submodule Clicking on the Expand link next to the new submodule form will make visible the Narrative field To delete the submodule and remove it from the model click on the Delete link Related SEDs and SSRs Summaries of Experimental Data SEDs and Summaries of Simulation Results SSRs are documented in separate entries in BODB BODB 3 0 Manual USC Brain Project September 2010 24 Summaries of Experimental Data SEDs and Simulation Results SSRs Hide SEDs used to build the model Hide Search Add new Name Relationship Description Remove Collapse scene setting Tags Narrative SEDs used to test the model Hide Add new Name Relationship Description Remove Expand explanation SED Search Add new Name Description Expand SSR Name Description Expand Predictions Hide Add new Name Description Remove Collapse Tags Narrative Name Description Figure 21 The Related SEDs and SSRs section SEDs Used to Build the Model When reading about a Model you may find that some of the empirical data that are cited are not actually used either in defining or testing the model In most cases you will not document such data in BODB But in some cases you may decide that they strengthen the Model Entry by setting the scene for the actual modeling Alternately SEDs may support som
80. on by name 50 29 28 pe al a Match region by coordinate Middle Frontal Gyrus The named brain region Mid temporal g BA 21 does not match any region in the Talairach atlas o Match region by name 65 24 6 pa a Match region by coordinate Middle Temporal Gyrus 4 The named brain region Mid temporal g BA 21 does not match any region in the Talairach atlas o Match region by name 63 37 0 Ps 1 a Match region by coordinate Middle Temporal Gyrus Submit Figure 8 In Figure 8 for each brain region entered the page gives warning messages indicating that new names are entered thus the user has to select one option either Match region by name or Match region by coordinate For the first choice a list box containing all brain region names in the database is provided For the second choice a list box containing all brain region names that occupy the input coordinate is provided Once everything is done the user can click on the Submit button to enter all data and relationships between names This will be of benefit for growing the database dynamically The formatted data will look as in Figure 9 BODB 3 0 Manual USC Brain Project September 2010 40 Data Brain Region T x y z Comments inferior Frontal Gyrus 3 650 40 22 4 Similar to midazolam Hippocampus 3 780 36 25 6 Superior Frontal Gyrus 3 800 30 60 10 Inferior Parietal Lobule 4 020 50 52 42 Right Cerebellum 4 070 50 67 26 Middle Frontal Gyrus
81. on name s separated by commas to see blobs representing their spatial extent Brodmann 4rea 44 Brodmann Area 45 Hippocampus search Cleat Regions D Search Results ranges from 2 to 18 z ranges from 6 to 21 ound 4156 coordinates x ranges fram 61 to 63 ranges from 10 to 40 z ranges from Oto 21 _ or Hippocampus 2 ound 1673 coordinates Brodmann Area 45 po e x ranges from 34 to 35 m E ranges from 41 to 10 a z ranges from 22 to 5 Axial i 36 26 16 6 14 24 34 44 54 64 Coronal 95 85 75 65 55 45 35 25 15 5 5 15 25 35 45 55 65 Sagittal l 61 51 41 31 21 11 1 9 19 249 39 49 59 Figure 49 The three dimensional version of the Talairach applet when using the search regions function Export Function The current 3D view including selected coordinates and regions can be saved in a variety of image formats by clicking on the Save Snapshot button Tags Forms for Model BOP SED Prediction and SSR entries include a field for tags or keywords This field takes a list of comma separated keywords These tags can be used to find related entries The tags are used to generate a tag cloud displayed in the sidebar Each tag cloud contains all of the tags associated with entries of that type Model BOP SED Prediction or SSR The relative size of each tag is determined by the number of entries it is associated with the exact number is shown in parentheses BODB 3
82. onal models of brain mechanisms with fields available to provide linkages to actual implementations simulations documentation and descriptions We designed this entity too with the m n relationship to Article information Another m n relationship links the Model and Brain Operating Principle entities because one model could be derived from many principles while one principle could be exemplified in many models Since one model could be synthesized from other models the m n self relationship is also supplied to this entity Brain Region This entity contains names and hierarchies of regions of the human brain currently based on data from the Research Imaging Center The University of Texas Health Science Center at San Antonio These brain region names are used to categorize entries related to specific human brain regions enhancing entry search capability Summaries of Empirical Data and Simulation Results BODB provides forms for two types of summaries one for summarizing experimental data SED and the other for summarizing simulation results SSR For SEDs BODB currently provides generic forms to contribute to a repository for summarizing related facts experimental settings and results from one or several publications A specific form for brain imaging experimental data see below is also provided For SSRs BODB provides only a generic form for use in documenting each related set of key findings associated with a model Each SED is amenable
83. option Export Functions The current slice image including selected coordinates and regions can be saved in a variety of image formats by clicking on the Save Slice button A full report including an image of each slice in each view can be generated by clicking on the Generate Report button If the Print Region labels checkbox is selected the images will contain a key describing the color and name of each selected brain region Three Dimensional Talairach Applet The Three Dimensional Talairach Applet allows the user to view selected coordinates brain regions and a slice in each view Axial Coronal Saggital in three dimensional space This applet requires Java3D to be installed on the user s system BODB 3 0 Manual USC Brain Project September 2010 57 Talairach Applet 3D 2D Input brain region name s Separated by commas to see blobs representing their spatial extent AAA xIoo gt gt Clear Region s Search Results Save Snapshot Display Properties Axial A 36 26 16 6 4 14 24 34 44 54 64 Coronal 295 83 753 65 55 45 35 25 15 5 5 15 25 35 45 55 65 Sagittal 61 51 41 31 21 11 1 9 19 29 39 49 59 Figure 46 The three dimensional version of the Talairach applet Navigation The brain can be navigated by changing the current 3D view as well as changing the slice in each view The 3D view can be rotated by left clicking and dragging panned by right clicking and dragging or zoomed by us
84. or cross search as well e g to search models by related brain operating principles Registration and Login To access the BODB website use http bodb usc edu When you first go to the BODB page you will be presented with a prompt to login to the site or register for an account Login or Register SC BODB Heb Insert Search Talairach Workspace About usemame Ld Password or Register for an account Figure 2 Login page Clicking Help will open a new window with this page If you already have an account enter your username and password and click Login If not click on the Register link which will take you to the following form Login or Register l BODB Insert Search Talairach Workspace About Username a t CsSCs CON Address passnord sd ane LC SY again Figure 3 Registration page Enter your desired username email address and password twice An email will be sent to this address with an activation link Clicking on the activation link will activate your account and take you back to BODB where you can login as described above BODB 3 0 Manual USC Brain Project September 2010 9 Site Layout BODB So rin Model tag cloud a rca it EST Wekome to the Brain Operation Database System BODB Beau Dee Bee This Recently Added Models grasping 4 mirar neurons system ES a repository for modek brain operating principles and Senma of ei ac AS i non axper men
85. ps Nomenclatures Add new Username Active Staff Admin Groups Real Name Email Edit jbonaiuto hdl il Wi USCBP Lab Members Jimmy Bonaiuto bonaiuto usc edu Edit jimmy il O O jbonaluto Mqmail com Figure 60 The Users tab of the Administration page BODB 3 0 Manual USC Brain Project September 2010 67 Each BODB user is listed on this tab including their status active staff or admin the groups they belong to as well as the real name and email address To change a user s status simply click on the appropriate checkbox Clicking on the user s username will pop up the User View page Clicking on the Edit link next to the username will pop up the User Edit page To add a new user click on the Add new link This will open the User Insert page View User jimmy Help Username jimmy First name Last name Email jbonaiute gmail com Active X Staff status Admin status Groups Add Change Delete Literature Models Modules BOPs SEOs SSRs Predictions Nomenclatures Figure 61 The User View page E A A S s SAS The User View page displays all of the user s information The Permissions section displays their security permissions These permissions override those of groups that the user belongs to To edit the user s information click on the Edit button This will open the User Edit page Clicking on the Close button will close the current window BODB 3 0 Manual USC Brain Project September 2010 68 Edit User
86. r neuron formation This model shows how the mirror system may learn to recognize actions already in the repertoire of the FS canonical neurons Mirror Neuron System 2 MNS2 Bonaiuto The MNS2 model extends the MNS model of the macaque mirror system to address data on audio visual mirror neurons and mirror Rosta Arbib neurons that respond to the observation of partially hidden grasps Figure 51 The model tag view page Clicking on the tag at the top of the tag view page displays a page which lists all of entries of any type that are associated with that tag as well as a list of related tags Tag affordances Related tags action recognition computational firing rate grasping mirror neurons motor development motor learning reinforcement Models Hide Add new Name Brief Description FARS Fagg Arbib A model of cortical control of grasping that focuses on the interaction between anterior intraparietal area AIP and ventral premotor area FS Based on input from the dorsal visual stream area AIP represents the possible affordances for grasping Area FS uses this information along with task constraints to select and program a grasp to an affordance Infant Learning to Grasp Model Ciztop The Infant Learning to Grasp Model ILGM models how motor parameters for grasp can be learned through Bradley Arbib trial and error with reinforcement Summaries of Experimental Data SEDs Hide Add new Name Brief Description AI
87. raft will also be available to edit at a later time and will be listed in the Workspace for convenience Example To illustrate this process we show how to insert Figure 2 into BODB Talairach T Y Comments Region value X BA 21 activation BA 21 activation Mid frontal g BA 4 37 50 29 28 DLPFC 9 Cerebellum 4 07 50 67 26 Inferior parietal 4 02 50 BA 40 Superior frontal 3 8 30 g BA 10 Hippocampus 3 6 ae Inferior frontal g 3 65 40 Similar to BA 45 midazolam Figure 2 An example of brain imaging data Veselis et al 2002 The header of Figure 2comprises the core headers and an extra header The core headers are Talairach Region Brain Region T X Y Z while the extra header consists of one column Comments Therefore we have to configure the header corresponding to the present core header and the extra header respectively Figure 3 demonstrates the header configuration for the present example data Coordinate System Talairach q Core column header Brain Reglon T xyz na _ na dl Extra header Comments Figure 3 The column configuration for importing data as from Figure 2 In Core column header we set N A if there is no such column in the present data The user has to set a column sequence corresponding to the sequence of columns in the present data Note the presence of N A will not affect the sequence of columns For exampl
88. repository for entering BOPs Brain Operating Principles the gist of the brain mechanisms that abstract away from their heterogeneities as a way to organize experiments models and technological spin off of brain mechanisms 3 provides a standard form and its repository for entering Model summaries 4 supplies a sharing point for the data in 1 2 3 among users to enhance the knowledge development 5 provides a repository of experimental data with a standard structure and the experimental data and cross experiment data analysis tools currently our focus is on brain imaging data and 6 provides a means to connect the related documents together and a practical entry searching tool to enhance the accessibility of information We describe the basic features of an online integrated environment for neuroscientists the Brain Operation DataBase BODB pronounced Beau DB http bodb usc edu The Brain Operation Database is explicitly designed to provide a framework for the linkage of neurobiological data and computational modeling via the general operating principles of the brain which provide a unifying perspective on a host of diverse studies The 3 main conceptual entities to be stored in BODB are models brain operating principles BOPs and summary data SD The system currently provides 3 main features 1 a repository for article information in bibliography format 11 a repository for BOPs and Models enhanced with discussion based t
89. rom the current SED entry References References to articles books chapters etc relevant to this SED Clicking on the Show link in the References section will expand the References section displaying Literature linked to the current entry and allowing the user to add new Literature entries After expansion the Show link will turn into a Hide link that can be used to collapse the References section References Hide Authors Year Title Edit Remove Amari amp Arbib 1977 Competition and cooperation in neural nets Edit Remove Barto 2003 Reinforcement Learning in Motor Control Figure 33 The expanded References section To link an existing Literature entry to the current SED click on the Search link This will open the Literature Search window where Select link next to any search result can be clicked to link it to the current SED entry To add a new Literature entry click on the Add new link This will open up the Insert Literature window Clicking the Edit link next to an existing Literature entry will open the Edit Literature window while clicking Remove will remove the Literature entry from the SED BODB 3 0 Manual USC Brain Project September 2010 34 Insert SSR The form for inserting SSRs 1s shown after clicking on the Add new link in a SSR section of the Insert Model page Click on the Save button to save the SSR or the Save Draft button to save a draft of the present SSR to the BODB database The d
90. rrent Model or add new BOPs In either case you should explain why this BOP is relevant to the current Model in the Relationship field e g because it applies to the operation of a specific module or set of connections Clicking on the Show link in the Related BOPs section will expand the Related BOPs section displaying the BOPs linked to the current entry and allowing the user to add new BOPs After expansion the Show link will turn into a Hide link that can be used to collapse the Related BOPs section Related BOPs Hide Search Add new Name Relationship Description Remove Collapse I Parent Tags Narrative Figure 24 The Related BOPs section In order to link an existing BOP to the current Model clicking on the Search link will open the BOP Search window Clicking Select next to one of the search results will add that BOP to the current Model entry In order to add a new BOP and link it to the current Model entry click on the Add new link which will add a new BOP form to the Related BOPs section The form contains fields for the BOP name relationship to the current Model and description Clicking on the Expand link will make visible fields for BOP parent tags and a narrative The Expand link will then turn into a Collapse link that can be clicked to hide the Parent Tags and Narrative fields Clicking on the Remove link next to a linked BOP will remove that BOP from the current entry BODB 3 0
91. rticles books chapters etc relevant to this SSR Clicking on the Show link in the References section will expand the References section displaying Literature linked to the current entry and allowing the user to add new Literature entries After expansion the Show link will turn into a Hide link that can be used to collapse the References section References Hide Authors Year Title Edit Remove Amari amp Arbib 1977 Competition and cooperation in neural nets Edit Remove Barto 2003 Reinforcement Learning in Motor Control Figure 33 The expanded References section To link an existing Literature entry to the current SSR click on the Search link This will open the Literature Search window where Select link next to any search result can be clicked to link it to the current SSR entry To add a new Literature entry click on the Add new link This will open up the Insert Literature window Clicking the Edit link next to an existing Literature entry will open the Edit Literature window while clicking Remove will remove the Literature entry from the SSR Search The search page provides tabs for searching all entries Literature BOP Model SED SSR and Brain Region records It is displayed after clicking on the Search link in the main toolbar BODB 3 0 Manual All Search for all types of entries Search Literature BOPs USC Brain Project September 2010 42 Meda Summary of summary of Brain PO Experimental Dat
92. s References to articles books chapters etc relevant to this principle Clicking on the Show link in the References section will expand the References section displaying Literature linked to the current entry and allowing the user to add new Literature entries After expansion the Show link will turn into a Hide link that can be used to collapse the References section BODB 3 0 Manual USC Brain Project September 2010 20 References Hide Cormsthon and cooperabon newal mets Reinforcement La srimg im Motor L ont nl Figure 17 The expanded References section To link an existing Literature entry to the current BOP click on the Search link This will open the Literature Search window where Select link next to any search result can be clicked to link it to the current BOP entry To add a new Literature entry click on the Add new link This will open up the Insert Literature window Clicking the Edit link next to an existing Literature entry will open the Edit Literature window while clicking Remove will remove the Literature entry from the BOP Insert Model The form for inserting Models is shown after clicking on the Model link in the Insert page Click on the Save button to save the Model or the Save Draft button to save a draft of the present Model to the BODB database The draft will also be available to edit at a later time and will be listed in the Workspace for convenience Add Model Title
93. s 11 The Dominey and Arbib 1992 model of the control of saccades The superior colliculus is modeled as a WTA for selecting among a set of retinotopically coded targets 111 Self Organizing feature Maps Kohonen 1982 At each training trial the WTA selects the neuron that responds best then provides a Hebbian adjustment to nearby neurons in relation to the current stimulus with the size of the synaptic change decaying with distance from the winner iv The Taxon Affordance Model Guazzelli et al 1998 Premotor cortex combines maps of affordances incentives and expected reinforcement and then applies a WTA to choose a particular affordance v The basal ganglia based model Redgrave Prescott and Gurney 1999 for selecting one of several competing actions vi The Itti amp Koch 2000 model of visual attention which applies WTA to a sum of feature maps to locate the most location in a given scene A form for populating BODB with BOPs will be described here that is shown after clicking on the Brain Operating Principle link in the Insert page Click on the Save Draft button to save a BODB 3 0 Manual USC Brain Project September 2010 16 draft of the present principle to the BODB database The principal draft will also be available to edit at a later time and will be listed in the Workspace for convenience Add BOP Title Parent Brief description Narrative Tags Figures Show Summaries of Experimental Data SEDs S
94. s 12 17 15 A L Caudate 11 5 18 A 5 L Anterior IPC 32 40 44 A L Anterior IPC 32 40 44 A Anterior PE 324944 R Antenor IPC 38 35 41 A R Anterior IPC 38 35 41 A 2 i 3 35 steri a gt 25 R Pestener PO _23__ 6___29__B R Pesterier PE B 69 gt gt gt b Task 1 s table We see c Task 2 s table We see d Task 3 s table We see which rows are activation areas of task 1 only by crossing out each row that has D or a blank value in the EM gt Rest Activation deactivation column which rows are activation areas of task 2 only by crossing out each row that has D or a blank value in the IM gt VI Activation deactivation column which rows are activation areas of task 3 only by crossing out each row that has D or a blank value in the EM gt IM Activation deactivation column Figure 7 A table contains results from three tasks Dechent P et al Dealing with multiple names for brain regions Experimental data from the literature may contain brain region names that are slightly different from ones in the database for that region or even names for regions not yet in the database If you wish to have a new brain structure added to BODB s list email arbib usc edu with BODB 3 0 Manual USC Brain Project September 2010 39 documentation of the case for this addition including species brain location preferably with diagram and link to a supporting e resource and whether or not t
95. s section Checking or unchecking the Add Change or Delete checkbox for a given entry type grants or removes permissions for the user to perform that action on entries of that type These security permissions override those of any groups the user belongs to Insert User Add User Help Username Password First name Last name E mail address Active a Staff status L Admin status LJ Groups USCEP Lab Members A contre Add Another Hold down Control or Command on a Mac to select more than one eL Change Delete Literature Models L Modules BOPs SEDs SSRs Predictions MOmWOmWoOuWoOn mimin jn u inj u ju BUS Ejn 2 ee Nomenclatures Figure 63 The User Insert page The User Insert page allows administrators to add new users to the system Click on the Save button to save the new user or Close to cancel and close the window Basic Information To set the user s username password first name last name or email address enter the data in the appropriate text field The user s active status 1s set to Active by default but can be changed by BODB 3 0 Manual USC Brain Project September 2010 70 checking or unchecking the Active checkbox Inactive users cannot login to the system The Staff status field 1s currently unused by the system The admin status of the user can be set by checking or unchecking the Admin status checkbox Only admin
96. section References Hide Authors Year Title Edit Remove Amari amp Arbib 1977 Competition and cooperation in neural nets Edit Remove Barto 2003 Reinforcement Learning in Motor Control Figure 26 The References section To link an existing Literature entry to the current Model click on the Search link This will open the Literature Search window where Select link next to any search result can be clicked to link it to the current Model entry To add a new Literature entry click on the Add new link This will open up the Insert Literature window Clicking the Edit link next to an existing Literature entry will open the Edit Literature window while clicking Remove will remove the Literature entry from the Model Insert SED The current version of BODB allows the user to insert generic or brain imaging Summary of Experimental Data SED in addition to BOP and Model entries The summary could be any facts hypotheses or experimental settings and results in a particular domain from one or several publications A form for populating BODB with SEDs will be described here that is shown after clicking on the Summary of Experimental Data link in the Insert page Click on the Save Draft button to save a draft of the present SED to the BODB database The SED draft will also be available to edit at a later time and will be listed in the Workspace for convenience BODB 3 0 Manual USC Brain Project September 2010 28 Add SED a Type
97. sult if found before adding a new reference Title Pd Authors Hide Search Add new First name Middle name Last name Order Remove Expand ss Joy Year Journal Y Volume Oo Issue Pages Url Language English E o Figure 7 A new author added to a new Literature entry Search Authors In order to link an existing author to the new Literature entry click on the Search link in the Authors section An Author Search popup window will appear where authors can be searched by multiple fields Click on the Select link next to an author to link it to the Literature entry BODB 3 0 Manual USC Brain Project September 2010 13 Search Authors Any field ungerleider First name Middle name Last name Email Alias Results Add new First name Middle name Last name Select LG Ungerleider Figure 8 Author search window PubMed Search In general the user can enter the information manually However for journal articles Journal we provide a tool for automatically retrieving article information from PubMed which can also be accessed directly at http www ncb1 nlm nih gov entrez query fcg1 DB pubmed BODB 3 0 Manual USC Brain Project September 2010 14 Search PubMed Help Any f o chellim cae cerebellum Year 1992 1996 range o gt S U OS Results 1 10 of 9410 Authors Year Vol Issue Joumal Tite Import Prabhakar NR Pieramici SF 1
98. tal data The current versi n includes the following function and E y premotor 4 7 Model Ortop Bradley E El Insert Update Debt Article Information BOP Modely Experimental data Search e Mirror Neuron System 2 Brain Operating Principe tag Advanced Coordinate Data Visualizer Talairach Daemon MNS Bona cloud Rosta Arbab coding 14 decision making 15 BODE amp designed as a development environment for computational and s Minor Neuron System excitation amp inhibitio 5 experimental neurmeciontists and we wakoma active data entry as well as MAS Orton 1 learning 8 mags yT feedback on system design e FARS Fagg A 5 memory 6 motor i control 9 processing Recently Added Erain p ray Operating Principles Tag clouds rcs HA New entries sensory perceptual i Palem in processing 10 a Corsolidal j Summary of Experimental a E Data tag cloud 7a 7 Fb 6 action Recently Added 14 i Summaries of Experimental AIP 7 auditory Data cortex 3 4 cls y connectivity 19 e FS mirror partially FS 12 ra 1 oe 3 grasping 6 ha ae El Recently Added we 4 Summaries of Simulation da 7 Results a FS mirar responsa La a F5 hidden grasp ventral a ES pantomined amar premotor 11 vie a F5 audiovisual actio Oram mema Summary of Simulation Results tag cloud Figure 4 BODB main page The main page contains toolbar user information and tag cloud sections which are visible on every page as well
99. ted to the given brain regions Related BOPs Search for Models with related BOPs containing the given text Related Models Search for Models with related Models containing the given text Only My Entries Search only Model entries belonging to the current user Related Literature Title Search for Models related to Literature with the given text in the title Author Search for Models related to Literature with the given authors Year Search for Models related to Literature in the given year range Annotation Search for Models related to Literature with the given text in the annotation Results The results of the Model search are displayed here Clicking Add new opens a window to add a new Model entry Clicking the title of each search result will open a window with the Model view page Clicking on the checkbox next to each result will add the Model to the current selection in the workspace Summary of Experimental Data Search Summary of Experimental Data SED entries BODB 3 0 Manual USC Brain Project September 2010 48 Search Summary of ENE a Brain All Literature BOPs Models ieee Simulation Sats Experimental Data PAS Regions Results Advanced Options Hid Tags ag IS Region Only my entries Related Literature _ Results Add new Title Description FS audiovisual mirror neurons Kohler et al 2002 found that some of the mirror neurons in area FS of the macaque premotor cortex that are
100. the c A table of task 2 extracted from the original original Figure 6 A table containing results from two tasks aligned horizontally Gerardin E et al 2000 The third example emphasizes how idiosyncratic the table could be The table consists of results from 3 different tasks Results from these 3 tasks share all columns including brain region L R or x P A or y I S or z and Activation deactivation The last column is special It is used as task identifier It has sub columns for task 1 2 and 3 There are 3 possible values for this column which are D deactivated A activated or blank For better understanding how the Activation deactivation column works at a specific row if D appears for a sub column task 1 it means the row is not a part of task 1 s result On the other hand if A appears that row 1s a part of task 1 Also if it is blank it means that row is not considered in task 1 Using the Activation deactivation column the user can easily build sub tables for the 3 tasks Figure 7 shows the sub tables Activation deactivation column may not need to be kept in the database after the table is split BODB 3 0 Manual Table 1 USC Brain Project September 2010 Brain regions mvolved in motor execution EM and imagery IM Region Talamrach coordinates Activation deactivation L R P A I S EM gt Rest IM VI EM gt IM SMA l 52 A A A Antenor cingulum 0 M0 25 D D Medial cingulum l 47 A A A Posterior cing
101. the Literature search are displayed here Clicking Add new opens a window to add a new Literature entry Clicking the title of each search result will open a window with the Literature view page The results can be exported in either Endnote or Bibtex format by clicking the checkbox next to the desired results and clicking Export Selected BOPs Search BOP entries BODB 3 0 Manual USC Brain Project September 2010 44 Search summary of summary of Brain Experimental Data Simulation Results Regions All Literature Models Any field Tit o Description Po Marrative fo parent N Tags Po Related Brain Region lA Building SEDs Related BOPs Po Related Models Only my entries Related Literature Author gt Annotation Results Add new Title Description Corollary Discharge This principle involves the sending of a copy known as the corollary discharge or efference copy of motor command to other processing centers so that knowledge of current actions may be integrated with ongoing perception and the coordination or planning of subsequent actions Cross Body Mirroring The ability to map the structure of another whether body or object to ones own body structure Figure 36 The input form for searching BOP entries Any Field Search for BOP entries that contains this string in any field Advanced Options Title Search the title field of BOP entries Description Search the description field
102. ting principle common to a range of functions schemas or structures regions circuits neurons etc of the brain At the micro level the principle could describe electro chemical dynamics at the macro level it might describe the activity of multiple groups of cells achieving some task by competitive and or cooperative means In general a principle specific to the operation of a single model does not count as a BOP Rather it should simply be part of the description of the relevant model The same applies to a principle describing a single functionality of a brain region as modeled by a set of alternate models The whole idea of BOPs is to let one search for models which are related by how they work a functional ontology rather than by the brain regions they model a structural ontology Clearly a principle specific to one model or to very similar models does not serve this purpose though there may be very rare exceptions One example of a Brain Operating is the Winner Take All WTA Principle which asserts that A Winner Take All network responds after a delay to an array of inputs of different intensity with an output array which encodes which input had the greatest intensity This BOP applies to aspects of the operation of a varied range of models These include 1 The Prey Selector Model of Didday 1976 which models the frog s tectum as a Winner Take All network that selects one of several visually presented prey object
103. ulum 2 46 21 D D L FMd 25 12 53 A A R PMd 28 11 56 A A L FMv MU 2 23 A A R PMv 56 7 24 A A L MI 35 27 51 A A R MI 37 18 45 D LSI 42 34 53 A RS 53 21 43 A L 52 48 3l 25 A A A R 52 60 y 27 A A A L Putamen 23 4 16 A A L Thalamus 12 17 15 A A L Caudate 11 5 18 A Precuneus l 23 D D L Antenor IPC 32 40 H A A R Anterior IPC 38 35 41 A A L Posterior IPC 25 T2 32 D D R Postenor IPC 23 76 29 D D 38 a Original Table which contains information of 3 tasks EM gt Rest IM gt VI and EM gt IM Region Talairach coordinates Activation Region Talairach coordinates Activatior Region Talairach coordinates Activatior L R P A 1 S EM gt Rest L R P A 1 S IM gt VI L R P A 1 S EM gt IM SMA l 2 52 A SMA l 2 52 A SMA l 2 52 A Medial cingulum l l 47 A Medial cingulum l l 47 A Medial cingulum l l 47 A L PMd 25 12 53 A L PMd 25 12 53 A EPMd __ a 2 R PMd 28 11 56 A R PMd 28 11 56 A PMH 6 L PMv 50 2 23 A L PMv 5 2 23 A PM R PMv 56 7 24 A R PMv 56 7 24 A Mm LMI 35 27 51 A EMMA S LMI 35 27 51 A LSI 42 34 53 A ESA ESA RSI 53 21 43 A Rt SO a RSA cst _ __ L S2 4 amp 8 3l 25 A L S2 4 amp 8 3l 25 A L S2 48 3l 25 A R S2 6 29 27 A R S2 60 29 27 A R S2 60 29 27 A L Putamen 23 4 16 A Putin 6 L Putamen 23 4 16 A L Thalamus 12 17 15 A 5 2 7 A L Thalamu
104. users can access the Administration Page The groups that the user belongs to can be set by selecting or unselecting groups from the Groups list Hold down control or command on a Mac to select more than one group Security Permissions The user s security permissions can be set in the Permissions section Checking or unchecking the Add Change or Delete checkbox for a given entry type grants or removes permissions for the user to perform that action on entries of that type These security permissions override those of any groups the user belongs to Groups The Groups tab allows administrators to add edit and delete BODB user groups Administration Users Nomenclatures Add new Name Edit Delete USCBP Lab Members Figure 64 The Groups tab of the Administration page Each BODB group is listed on this tab Clicking on the group s name will pop up the Group View page Clicking on the Edit link next to the group name will pop up the Group Edit page and clicking on the Delete link will delete the group To add a new group click on the Add new link which will open the Group Insert page View Group USCBP Lab Members Help Name USCBP Lab Members Add Change Delete Literature X X X Models X X Modules X X X BOPs X X X SEDs x X X SSRs X X X Predictions X X X Nomenclatures X X X Figure 65 The Group View page BODB 3 0 Manual USC Brain Project September 2010 71 The Group View page displays all of th
105. view page will display a form for a message reply Fill in the subject and body and click the Send button to send the message or Cancel to cancel Back to Inbox From ad jimmy Date 2010 02 01 02 10 11 Subject Test message Hello world Subject Re Test message Body Hi back Figure 57 The message view page while replying Viewing Sent Messages Sent messages can be viewed in the Sent tab of the Messages page Click on the message in the list to view it in its entirety BODB 3 0 Manual USC Brain Project September 2010 66 Compose Mail Inbox jimmy Re Test message Hi back 2010 02 01 02 18 32 Figure 58 The Sent tab of the Messages page Composing a New Message To compose a new message click on the Compose Mail link on the Messages page This will display a blank form for writing the message The To drop down box will contain a list of all the other users in the system Selecting a user will display that user s avatar image Fill in the subject and body and click Send to send the message or Cancel to cancel Back to Inbox To jimmy gt swe OO Body Figure 59 The message compose page Administration The Administration page allows administrators to manage BOBD users user groups and brain nomenclatures It is accessed by clicking on the Admin link in the main toolbar Users The Users tab allows administrators to add and edit BODB users Administration Grou
106. y entries belonging to the current user Literature Search Literature entries BODB 3 0 Manual USC Brain Project September 2010 43 Search 2 Summary of Experimental Summary of Simulation All BOPs Models ae Data Results Brain Regions Advanced Options Hide Title Author Type m Year Annotation Only my entries L Results Add new Select All None Format Endnote w Export Selected Authors Year Title 0 Oztop amp Arbib 2002 Schema design and implementation of the grasp related mirror neuron system C Kohler et al 2002 Hearing sounds understanding actions action representation in mirror neurons 7 Keysers et al 2003 Audiovisual mirror neurons and action recognition C Bonaiuto et al 2007 Extending the mirror neuron system model I Audible actions and invisible grasps Figure 35 The input form for searching Literature entries Any Field Search for Literature entries that contains this string in any field Advanced Options Title Search the title field of Literature entries Author Search the author field of Literature entries Type Search for Literature entries of a particular type Journal Book Thesis Conference Unpublished Year Search for Literature entries in a particular year range Annotation Search the annotation field of Literature entries Only My Entries Search only Literature entries belonging to the current user Results The results of
107. y paper but update it to summarize key points as you write the Narrative Narrative The Narrative reviews how the model works and what the model does It will thus refer to the diagrams associated with the model and the linked SEDs and SSRs Note 1 Part of your success a collator here and in presenting the SEDs and SSRs is to be judicious in what you highlight and what you omit The BODB entry is not meant to replace the article s which document the Model but rather to help the user assess the Model in relation to available empirical BODB 3 0 Manual USC Brain Project September 2010 22 data and modeling goals Note 2 Insert citations of references in Author Year style here and in SEDs below with formal bibliographic entries below You should ensure that the reference is included in the Literature section of BODB perhaps as a result of using the PubMed Tool Tags A list of keywords associated with this Model entry Architecture The Architecture section allows the user to upload diagrams of the Model as well as define Model inputs outputs states and submodules Architecture Hide Diagrams Tour of diagram agate A Jordan type recurrent network Inputs Add new Name DataType Descnpton Remove Outputs Add new Mame DataType Descnption Remove States Add new Name DataType Descnpton Remove SubModules Add new Name Descnpton Delete Collapse Narrative Figure 20 The model Archite
108. zontally Results of task 1 and task 2 have their separate columns for x y z and Z score They share only brain regions In this case the user can easily create a sub table for task 1 by copying and pasting the columns of task For task 2 the user has to reassemble the sub table using brain region column from the left of the published table and the x y z and Z score columns of task 2 before inserting this revised table into BODB Figure 6 illustrates this example in more detail Ne 1 I I l Pi I l Prefrontal cortex E i1 l Dorsdlateral prefrontal area 9 461 A p 11 I l L i pi od d2 15 376 Rostralprefrortal area 10 11 R l TEE 51 24 4 58 L l Inferior frontal area 44 45 R i BF 18 2d 5 62 de 2d 6 4 75 1 L 1 11 54 12 12 da l l l 1 I y Moor and premotor cortex io i I Primary motor area 4 R 13 15 63 7 14 11 l L 1 142 18 66 655 Il I Lateral premotor area 6 R I d 3 60 5 67 I 7 5 69 l I L R36 3 66 518 ji 42 3 5 535 1 I Medial premotor area 6 1 1 I Pre SMA R I 1 6 6 57 511 11 3 6 69 BD L 1 4 9 g 51 says 23 6 69 581 l Foat SMA R I 13 3 lila 459 1 l I L La 3 lila 6 01 II HG 3 6a abr l l l 1 I Pa etal area pol i l l Primary sensory area 1 2 3 R 1 142 3 60 5 03 pi od 21 ag 43 l I L l 48 24 57 4 04 1 I 60 21 ag 518 Superior parietal area 7 R 1 3 36 66 4 II a 5d 51 38 l L y 30 A 66 3 66 pa e H0 sd 463 1 I Inferior parietal area 401 R

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