Overview of Progress and Plans MBATmilestonesplans2 iz.ppt: Mouse BIRN progress and plans for 2007

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TOC{title "Table of Contents"} 2008 AHM (Oct.20) !MBAT3.0 Requirements This document lists the required functionality for !MBAT that will be delivered at the 2008 ...

Table of Contents TOC Working plan: June 2009-October 2009 The MBAT team has identified several features for delivery by October 2009 (Society for Neuro Science Annual ...

People: Maryann, Erh-Fang, Bill, Asif, Diana, Van Suggested plan for outlining a Common Data Model (by August 25) Identify data sources Investigate if these APIs ...

Table of Contents TOC 3D Atlas rendering plugin User Manual Introduction The 3D Atlas rendering plugin allows the user to view and manipulate digital atlases in the ...

People: Yoni, Maryann, Allan, Seth, Alexandra, Jeff Suggested plan for outlining a Common Data Model (by August 25) Identify data sources Investigate if these APIs ...

Objective: To integrate the NeuroCommons Google Map API ABA demo into MBAT and if successful, use this same method for other types of data CONCEPT Query Initiation ...

Meeting Minutes of MouseBIRN AHM 21 May 2009 TOC Attendees Main., Main., Main., Main. 1. Critiques More detailed instructions for installing prerequisites (ie: Java ...

jboline 25 Jan 2006 There has been a suggestion for how several different atlas conventions could be created, accessed, and viewed on the Visualization page. It would ...

Go to Mouse BIRN Wiki Table of Contents Atlasing: Table of Contents of Working Pages TOC{"AtlasingUseCases" title "Atlasing Use Case Page"} TOC{"AtlasStateExchange ...

Use Cases AtlasIntegrationScenarios.doc: Expanded version of Mouse BIRN atlas integration scenario Use Case Work Page Atlas Wish List Features from Related Program ...

First drafts for a general way to group all BIRN data for query (also ties in with data upload). Started 2/7/07 General query categories 2.vsd: Microsoft Visio format ...

heng 08 Mar 2006 BrainGraph History BrainGraph was originally developed by Ivo using GML format using a graph display. Then Fotios Konstantinidis developed a HyperTree ...

Table of Contents TOC MBAT 3.0 Build Instructions If you are using Eclipse then all the configuration and build scripts should automatically compile, archive the plugins ...

Table of Contents TOC Cart Manager Cart Manager is the mechanism using which objects are passed in different workspaces in !MBAT. !MBAT !API users can add new plugins ...

Web-Services API Working Page Data-type Work Pages Gene Expression 2D images 3D volumes Supporting Documents MBATSchedule.xls MBAT Tech Guide2.doc MBATdesign.doc ...

Comparison Workspace Features List of desirable features for MBAT Comparison Workspace. Items in italics are open issues. Focus on flexibility and customization 1 ...

Comparison Workspace Mockup The comparison workspace will provide UI components to (1) view and compare several datasets at once and (2) apply analysis tools. The ...

Creating mbat.jar This section gives instructions on how to create the mbat.jar application file using Eclipse. The Ant build file used in these instructions is located ...

Table of Contents TOC Adding Plugins to the !MBAT source code These instructions are for adding and creating a new plugin in the !MBAT source code. General instructions ...

BIRN Mediator Topics Related to Mouse BIRN Source database registration New2 SourceRegistrationRequarements.doc: Document of Mediator Requirements from Vadim SourceRegistration ...

Data Sources Drexel Atlas to MBAT format Concept term mapping DB accessed and used for MBAT data sources Metadata mapping finished for all sites Switch to advanced ...

Attendees: Rob Williams, Arthur Centeno, Zhaohui Sun, Beni Mozhui, Steve Anderson, Queenie Ng, Allan !MacKenzie-Graham, Jyl Boline UTHSC plans to replicate Zapala ...

Attending: Rob, Beni, Arthur, Daniel, Queenie, Steve, Jyl Problems uploading the 20 MB file (34 columns), the original has 50-60 column and failed with 30 columns ...

TOC{title "Table of Content"} Required Software 1 Java SDK 1.6: http://java.sun.com/javase/downloads/index.jsp 2 JOGL JSR231-1.1.1: 3 Eclipse: http://www.eclipse ...

File Formats The following file formats are currently supported by MBAT. Image volume files Analyze(tm) ( .img, .hdr): http://www.mayo.edu/bir/PDF/ANALYZE75.pdf Nifti ...

Table of Contents TOC MBAT 3.0 File Formats Atlas File Format The .atlas file format is an XML based file format to specify a labelled atlas object which consists ...

Table of Contents TOC Registration workspace Using registration workspace, users can align a source image with respect to a template image. Following diagram shows ...

Gene Expression Migration Plan Migration Plan Overview Architecture Diagram OriginalOutput.xml: Original MBAT Gene Expression XML ConvertedOutput MAGE.xml: Mouse ...

12/1/06: Review status of MBAT. UCLA and UTHSC 12/18/06: Updates on GE DB and infrastructure progress. UCLA and UTHSC

Recommendation for BIRN MAGE : Started 4/07 People: Rob, Daniel, Jintao, Steve, Hongqiang, Bill Minutes for follow up meetings Suggested plan for outlining a Common ...

sruffins 16 Apr 2009 MBAT Future Development This document is a list of suggestions for the future MBAT development. Although the direction of MBAT development within ...

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LONI Subversion Repository Structure The LONI Subversion repository location is svn+ssh://cvs.loni.ucla.edu/cvs/map . The following is the directory structure under ...

Supporting Large 3D Datasets in MBAT We need to pick at least one data format for large (larger than available RAM, larger than a 32-bit address space) 3D image volumes ...

Table of Contents TOC Large Volume Atlas Plugin User Manual Introduction The Large Volume Atlas plugin provides support for large volumes in the MBAT 3D Atlas Viewer ...

Table of Contents TOC Large Volume Rendering Plugin User Manual Introduction The Large Volume Viewer (LVV) plugin allows the user to view volume image data, such as ...

Literature Search Plugin Desired Features Search multiple websites based on config.xml PubMed, Google Scholar, etc. Display options Embed browser in MBAT (JDIC; MacOS ...

ABOUT THE MOUSE BIRN ATLASING TOOLKIT (MBAT) GENERAL DESCRIPTION: Reference biological/biomedical imagery has always been critically important for providing context ...

MBAT 3.0 Architecture The !MBAT 3.0 Architecture is an extensible design built on a scalable plugin architecture. It consists of a core framework (utlity libraries ...

MBAT Client Documentation Modules Supported Formats Volumes Viewing Gene Expression Brain Graph Surface Rendering CCDB Search Development Environment Requirement ...

Current Data Types to be Displayed in !MBAT Image2DSeries An ordered list of references to one or more 2-D image files. The following image file formats are supported ...

JylBoline^? 26 Jun 2007

jboline 01 Mar 2006 Image Files .hdr This is the binary header file of an Analyze(tm) image volume. An image volume contains two files, a header file (.hdr) and a ...

Mouse BIRN Atlasing Toolkit (MBAT) Forum Please feel free to post to the Mouse BIRN MBAT forum. You must have an account to post to this space. 2/07 General information ...

TOC Introduction This page describes the functionality provided by the !MouseBIRN Atlasing Toolkit (MBAT) application. It is developed as a bioinformatics framework ...

Main Data Classes in the MBAT Metadata Interface DataSourceRef Metadata information about a particular data source. SearchParam A search parameter class supplied ...

Minutes from All MBAT Programmer Meetings Link to Mouse BIRN Programmers Working Page General decisions: 03/09/06: Decided that in general, people will work on modules ...

Minutes meetings 2006 January 19, 2006 (look and feel) 2006 1 19.doc: January 20, 2006 (MBAT demo) 2006 1 20.doc: January 24, 2006 (Usability meeting) Demo of how ...

SteveAnderson^? 07 Feb 2008 Creating an MBAT Build from the Subversion Repository A full MBAT build currently consists of several separate modules that are included ...

MBAT/SHIVA SVN Repository Check-in Policy To make sure the code being checked into the source code repository meeting some standards: Only check-in code that contains ...

MBAT Search The MBAT Search module provides the ability to query external data sources. The module is maintained as a separate package in the MouseBIRN repository ...

Data Source Searching Algorithm Used in MBAT The following is a description of the high-level "algorithm" that summarizes the MBAT search behavior as implemented ...

Created on 26 Jun 2007 MBAT Upcoming Features Data Collaboration Conceptual Query Dynamically access data from multiple modalities. Access data from one central location ...

Overview This page is a working page for the continued development to the Mouse BIRN Atlasing Toolkit (MBAT). Any suggestions are welcome. Goals Collaborative software ...

ABOUT THE MOUSE BIRN ATLASING TOOLKIT (MBAT) General Description The Mouse BIRN Atlasing Toolkit is designed to view multiple types of multiscale data, access and ...

ABOUT THE MOUSE BIRN ATLASING TOOLKIT (MBAT) Version 1.1.0 Release Date November 2007 GENERAL DESCRIPTION: The Mouse BIRN Atlasing Toolkit is designed to view multiple ...

ABOUT THE MOUSE BIRN ATLASING TOOLKIT (MBAT) GENERAL DESCRIPTION: The Mouse BIRN Atlasing Toolkit is designed to view multiple types of multiscale data, access and ...

ABOUT THE MOUSE BIRN ATLASING TOOLKIT (MBAT) GENERAL DESCRIPTION: The Mouse BIRN Atlasing Toolkit is designed to view multiple types of multiscale data, access and ...

Table of Contents TOC mbManagerCart Design This section describes how to access and retrive data from the !MBAT cart, the mechanism that allows the sharing of objects ...

Table of Contents TOC MBAT Common Datatype Class Interface The fundamental datatype that can be exchanged among all the workspaces and all the core libraries is defined ...

Table of Contents TOC mbSecurity Design Overview mbSecurity framework is a singleton class that can be called by all workspace plugins. Its goal is to provide the ...

Table of Contents TOC Comparison Viewer Overview The Comparison Viewer workspace in !MBAT3.0 is built on the concept of layers which can be composited together. Each ...

MBAT Plugins API Specify well-defined Input/Output data model for plugins TOC I. !DocManager Core 1. File reader plugin Input: Classtype: metafile,2D/3D Image, numeric ...

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Meeting Minutes of {SESSIONNAME HERE} 30 May 2008 TOC Attendees Willy, Queenie, Daren 1. !MBAT cores effected DocManager/Search/Viewer/Analysis 3D-image API link ...

Features List 29 May 2008 TOC Attendees MouseBIRN AHM 1. Desired Features List High priority (Oct 2008) 1. Plugin infrastructure 1. ImageJ plugins (evaluate) 1. image ...

Meeting Minutes of Mediator/Concept Term Mapper 30 May 2008 TOC Attendees Vadim Astakhov, Brian Sanders, Steve Anderson, Jeff Grethe 1. !MBAT cores effected DocManager ...

Meeting Minutes of Registration Workflow 30 May 2008 TOC Attendees Asif, Daren 1. !MBAT cores effected DocManager/Search/Viewer/Analysis Analysis core (Spatial Registration ...

Meeting Minutes of SmartAtlas 30 May 2008 TOC Attendees Asif, Daren 1. !MBAT cores effected DocManager/Search/Viewer/Analysis Viewer core 2. Plugin input requirements ...

Meeting Minutes of BIRN AHM 20 Oct 2008 TOC Attendees Rob W, Ilya, Seth, Willy, Asif, Josh, Davit, Queenie, Steve, Daren 1. Plugins ImageJ IO Integration (Nov 30 ...

Minutes of !MouseBIRN Programmers Meeting 30 May 2008 TOC Attendees Main., Main., Main., Main. 1. !MBAT cores effected DocManager/Search/Viewer/Analysis 2. Plugin ...

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Synopsis and Documentation of the 2006 Mouse Mouse AHM 2006mAHMreport.doc: Report from the 2006 Mouse AHM Synopsis.xls: Synopsis of items needed as pointed out at ...

March 7th, 2007 Ontology Working Day Plans and what was discussed Bug, Grethe: Ontology working day March 8, 2007 PI Progress/Plans What we did and what we will do ...

sruffins 26 May 2009 DRAFT AGENDA Thursday, May 21: 7:30-9:00 Breakfast 9:00-9:15 Seth Ruffins: (UCLA) Welcome and the Evolution of MBAT 9:15-9:30 Arthur Toga: ...

Go to Mouse BIRN Wiki Table of Contents Mouse BIRN News and Events Important Dates for Mouse BIRN Meetings Upcoming Meetings Previous Meetings The BIRN All Hands ...

Overview This workgroup has been formed to tackle creating a neuroinformatics framework using multimodal digital atlases to coordinate access to disparate forms of ...

Attendees: Duke: Jeff B., Sally UCLA: Karen, Allan, Erh-Fang, Steve, Jyl Drexel: Bill UCSD: Van, Willy, Joy, Jeff G. CIT: Seth, Edriss Status update: CIT: EAE mice ...

Frequently Asked Questions $ What is Mouse BIRN? : See the overview of the Mouse BIRN project at the Mouse BIRN Projects page. $ Who is involved in Mouse BIRN? : ...

Go to Mouse BIRN Wiki Table of Contents Mouse BIRN Acknowledgement Guidelines Mouse BIRN Publications Mouse BIRN PRESS Neurology Today Article, April 06 Mouse BIRN ...

Presentations from the meeting Return to previous meetings page Milestones for the meeting Hierarchy finalized and data in Mark up of data bases done Mediator-functioning ...

Return to Mouse BIRN Announcements Page PRESENTATIONS from the 2007 MOUSE AHM Milestones for the meeting Go here to REGISTER for the 2007 Mouse BIRN All Hands Meeting ...

Go here to REGISTER for the 2008 Mouse BIRN All Paws Meeting Need to share rides to the Airport or get suggestions about the best hotels or restaurants? Go here to ...

Mouse BIRN Programmers Pages 1. Architecture MBAT 3.0 Framework Overview Class Hierarchy Design Design Design Data Viewer Design workspace Design 1. Plugins Plugins ...

Mouse BIRN Progress This is an area where we can keep track of items that move directly towards some of goals of the Mouse BIRN project (details/busy work have been ...

MouseBIRN Site Map Background Data Acquisitions and Processings Atlasing Data Federation Applications Resources Meetings and Events Background a. MouseBIRN i. About ...

BIRN Software License To Access other Tools Offered by the BIRN Community: BIRN Tools Mouse BIRN: Tools offered from the collaborative efforts of Mouse BIRN $ Mouse ...

The needs of Mouse BIRN group from the BIRN project and infrastructure guides much of our work. How these wants and needs are expressed has evolved over time with ...

Table of Contents TOC Spring 2009 AHM Deliverables (May 21, 2009) This document lists the deliverables for each institution to be delivered by the Spring !MouseBIRN ...

Table of Contents TOC Fall 2009 Deliverables (Oct 21, 2009) This document lists the deliverables for each institution to be delivered by Oct 21, 2009. CalTech Goal ...

Mouse BIRN Data Federation WG Tcon: Tuesday, 2006-08-01 Admin Time : 1PM PST/3PM CST/4PM EST Call-in Tcon # : 858-678-5580 Call-in VTC IP : 132.239.1.216 (BIRN-CC ...

Mouse BIRN Data Federation WG Tcon: Tuesday, 2006-08-08 Admin Time : 11AM PST/1PM CST/2PM EST Call-in Tcon # : 858-678-5580 Call-in VTC IP : 132.239.1.216 (BIRN-CC ...

Mouse BIRN Data Federation WG Tcon: Tuesday, 2006-08-15 Admin Time : 11AM PST/1PM CST/2PM EST Call-in Tcon # : 858-678-5580 Call-in VTC IP : 132.239.1.216 (BIRN-CC ...

TOC{title "Table of Contents"} MouseBIRN Schedule This document lists the major tasks, the organizations responsible for leading the efforts, and the timeline for ...

Presentations at the 2006 SFN meeting by members of Mouse BIRN MBAT 2006.pdf: A Digital Atlas and Neuroinformatics Framework for Query and Display of Disparate Data ...

Package Organization of MBAT Search The MBAT Search package is found in the MouseBIRN repository described in MBATProjectCheckoutFromSVNServer . The package is currently ...

Meeting Minutes of Programmer VTC Meeting 02 Jul 2008 TOC Attendees Asif Memon, Brat Vesdly, Daren Lee, Queenie Ng, Seth Ruffins, Steve Anderson, Willy Wong MBAT ...

Meeting Minutes of Programmer VTC Meeting 16 Jul 2008 TOC Attendees Asif Memon, Brad Vesely, Daren Lee, Jeff Brandenburg, Queenie Ng, Steve Anderson, Willy Wong 1 ...

Meeting Minutes of Mouse BIRN Bi-Weekly Programmer Meeting 30 JUL 2008 TOC Attendees Asif Memoms, Brad, Carl, Daren Lee, Davit, Jeff Brandenburg, Queenie Ng, Steve ...

Meeting Minutes of Programmer's Mtg 10 September 2008 TOC Attendees Davit, Jeff B, Willy, Carl, Asif, Daren, Steve, Queenie Updates 1. Davit: Finish the registration ...

Meeting Minutes of Programmer's Meeting 24 Sept 2008 TOC Attendees Carl, Jeff B, Willy, Seth, Steve, Daren. Updates 1. Willy AIDB development continuing; migrating ...

Meeting Minutes of MouseBIRN Demo Day 8 Oct 2008 TOC Attendees MaryAnn M, Jeff G, Willy, Asif, Jeff B, Carl, Davit, Seth, Daren, Queenie 1. Demo Day to showcase MouseBIRN ...

Meeting Minutes of MBAT Programmers' Mtg 15 Oct 2008 TOC Attendees Willy, Asif, Carl, Jeff B, Daren, Queenie, Steve 1. Agenda Covered architecture review of MBAT3 ...

Meeting Minutes of Programmers' Meeting 03 Dec 2008 TOC Attendees Willy, Asif, XiaoDong, Lei Yan, HongQiang, Rob W., Seth, Steve, Queenie, Daren 1. Updates AIDB Willy ...

Meeting Minutes of Programmer Meeting Dec 17 2008 TOC Attendees Carl, Jeff, Willy, Davit, Seth, Queenie, Daren 1. Updates Willy: working with Seth and Rob Williams ...

Meeting Minutes of Programmers' Mtg 14 Jan 2009 TOC Attendees Jeff, Carl, Edriss, Willy, Asif, Seth, Steve, Queenie, Daren 1. Action Items Updates Seth: AIDB data ...

Meeting Minutes of !MouseBIRN Programmer Meeting Minutes 28 Jan 2009 TOC Attendees Asif, Willy, XiaoDong, Lei Yan, Jeff B, Seth, Steve, Queenie, Nikhil, Daren 1. ...

Meeting Minutes of Programmers' Meeting 11 March 2008 TOC Attendees Willy, Jeff, Carl, XiaoDong, LeiYan, Asif, Seth, Steve, Queenie, Nikhil, Daren Action Item Updates ...

Meeting Minutes of Programmers' Meeting 22 Apr 2009 TOC Attendees Jeff, Asif, XiaoDong, LeiYan, Willy, Seth, Steve, Queenie, Nikhil, Daren Action Item Updates Willy ...

Query Terms Responses to Jyl's Mockup of Query Terms: http://ahammond.updatelog.com/projects/1174317/project/log 1 How to fit CCDB "products" into MBAT query terms ...

Suggestions for interface: User is polled for what type of data they want to register Popped into a default for that type of data 2 image views, one of atlas, and ...

Registration Features List of desirable features for MBAT Registration. Items in italics are open issues . More details and illustrations about the registration steps ...

TOC{title "Table of Content"} Registration Workspace Mockup 1 Registration Frame The registration workspace will provide UI components to select (1) source and template ...

TOC Overview This page describes the design and technical details of "Save/Open workspace" functionality. We have used XStream library for implementing this functionality ...

TOC{title "Table of Contents"} Search Datasource Plugin This document describes the search datasource plugin architecture and how to create and add a datasource plugin ...

Table of Contents TOC Search workspace In the search workspace, users can specify a single query that searches across multiple data sources. Searches can be by keyword ...

Server Protocols ArcIMS ArcXML Programmer's Reference Guide for ArcIMS 9.1 Neuroterrain Atlas Server Network Protocols Web Services Description Language (Axis Client ...

Posters presented at Society for Neuroscience 2007 MBAT SfN 2007.pdf: Mouse BIRN Atlasing Toolkit (MBAT) poster

TOC{title "Table of Contents"} Spatial Registration Plugin This document describes the registration plugin architecture and how to create and add a new spatial registration ...

Current terminologies Currently, MBAT has been released with two structure hierarchies that Allan adapted along with the BAMS group. These are the MAP2003S 256.ilf ...

Table of Contents TOC Trouble Shooting Below are some common problems you may encounter when building and running !MBAT: 1 SVN error: org.tigris.subversion.javahl ...

TOC{title "Table of Content"} Uniform Web Services API Background Web services is a standard way to access remote functionality cross-platform, and assemble applications ...

TOC{title "Table of Contents"} Upload Data Plugin This document describes the upload plugin architecture and how to create and add a new upload plugin to the !MBAT ...

Table of Contents TOC Comparison Viewer Rendering Plugin This document describes the comparison viewer rendering plugin architecture and how to create and add a new ...

Comparison Viewer Workspace In the comparison viewer workspace, users can view one or more images and perform various image manipulation tasks. The viewer workspace ...

jboline 25 Jan 2006 This idea has arisen in the past but is becoming more concrete: We've been wrestling with how to make sure everything is connected within an atlas ...

Meeting Minutes of VTC Meeting Minutes 24 June 2008 TOC Attendees !MaryAnn, Willy, Asif, Edriss, Seth, Queenie, Steve, Daren Topics discussed 1. AIDB (interim solution ...

Meeting Minutes of MouseBIRN Conference Call 12 Aug 2008 TOC Attendees MaryAnn, Yani, Ilya, Carl, Jeff, Edriss, Brian, Davit, Willy, Brad, Seth, Queenie, Steve, Daren ...

VTC Meeting Minutes 20080827 27 Aug 2008 TOC Attendees Asif Memons, Carl Gustafson, Daren Lee, Davit Janvelyan, Jeff Bradenburg, Queenie Ng, Steve Anderson, Seth ...

Minutes of !MouseBIRN VTC 7 Jul 2009 TOC Attendees Yoni, Russ Jacobs, Rob Williams, Carl, Willy, Asif, !XiaoDong, !LeiYan, Seth, Nikhil, Queenie, Daren 1. Review ...

Mouse Biomedical Informatics Research Network (BIRN) Mouse BIRN Wiki Table of Contents $ MouseBIRN Partner Institutions: Collaborating research groups. $ MouseBIRN ...

Web Services Providers used by MBAT 1. BIRN Miroarry DB API Methods: URI: http://microarray.nbirn.net/get data.php? Parameters: 1. cmd get probes get my probes 1 ...

Statistics for MouseBIRN Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and uploads: Nov 2009 15495 ...

TOC{title "Table of Contents"} Workspace Plugin This document describes the workspace plugin architecture and how to create and add a new workspace plugin to the ...