The 2007 BIRN AHM will be held in Oct. 15-18 in Bethesda, MD for more information visit the BIRN site 2007MouseDay Mouse Meeting Day is Monday October 15th: October15th2007MouseDay ...

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 ...

Table of Contents TOC 2D Image rendering plugin User Manual Introduction The 2D image rendering plugin allows the user to view and manipulate two-dimensional images ...

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 ...

Discuss methods and issues of reconstructing 2D slices into 3D volumes

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 ...

Table of Contents TOC 3D Volume rendering plugin User Manual Introduction The 3D volume rendering plugin allows the user to view and manipulate volume image data, ...

Discuss methods and issues of 3D to 3D registration

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 ...

Return to previous meetings page Overview of AHM and mouse info: Arthur Mouse Model Updates: Alpha-synuclein model of Parkinson's: Diana EAE model Multiple Sclerosis ...

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

Software Requirement: 1. Python 2.5.1 1. !PythonXML module 1. sudo account AIDB upload script checklist: 1. Install Python on the linux/Mac platfor 1. Install !PyhonXML ...

Table of Contents TOC Allen Brain Atlas (ABA) data source plugin User Manual Introduction The ABA data source plugins allows the user to query the publicly available ...

Alzheimer’s Disease, Tet-off APP Transgenic Mouse Model Alzheimer's disease is thought to arise from the accumulation of a small peptide termed amyloid-beta that ...

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 ...

Table of Contents TOC Animal Imaging Database(AIDB) data source plugin User Manual Introduction The AIDB data source plugins allows the user to query the publicly ...

A mouse brain environment Should have a system of coordinates which can be related to a reference coordinate system (Paxinos Franklin) a reference atlas or brain ...

Things to do here: a) we will send the API and demos around b) review the API and demo communications, to see if it will fit your atlas (Willy and Joshua will help ...

See The original page where exchange of Atlas State was started Overview: Work resumed at the end of 2006 with a focus on setting up an Atlas Server that can be used ...

A mouse brain environment Should have a system of coordinates which can be related to a reference coordinate system (Paxinos Franklin) a reference atlas or brain ...

Atlasing Dynamic atlas labels

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 ...

Atlas definition: Collection of annotations within a coordinate system (ontological) Canvas on which you pin information including the tools and protocols for integrating ...

Mouse meeting presentations welcome.ppt: Overview of AHM and mouse specific information EAE.ppt: Allan's EAE presentation alpha-synuclein.ppt: Diana's Parkinson's ...

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 ...

Planning Atlas workgroup meetings dealing with biological aspects of atlasing 2006 3 08 atlasingissues.doc: Minutes from atlasing WG discussion of structure hierarchy ...

Bio-Ontology References Onto-centric Views of Biological Knowledge: some useful examples The following research articles provide excellent, concrete examples of ontological ...

Meetings and Conferences With a Focus on the Curation and Use of Bio-ontologies Meeting Description Bio-ontologies Special Interest Group at the annual Intelligent ...

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 ...

Documentation for BrainGraph Editor BrainGraphEditorOverview.doc: initial documentation for BrainGraph Editor

Table of Contents TOC Hierarchy Viewer Desired Features Multiple parents per node Multiple root nodes File Formats (mbManagerIO) ILF/BGX (only supports single parents ...

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 AIR Pipeline Workflow Plugin User Manual Introduction The Automated Image Registration (AIR)-based plugin allows the user to create template ...

Carl Gustafson carl.gustafson #64;drexelmed.edu proper noun 1. a member of the Laboratory for Bioimaging and Anatomical Informatics, Drexel University College ...

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 ...

Table of Contents TOC Cell Centered Database(CCDB) data source plugin User Manual Introduction The CCDB data source plugins allows the user to query the publicly available ...

Coding Policies To maintain good team development and coding standards, all developers must adhere to the following policies: 1. Comment all commits 1. Comment code ...

First draft by Seth, Erh-Fang, and Jyl on 3/22/06 as conceptualized by Seth Ruffins and Mike Tyszka Need Documenation of what the goal is of this project including ...

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 ...

Preferred terms for Mouse Strains in BIRNLex Inbred strains BALB/cJ Bonfire ID: C1516114 Jax Stock ID: 000651 BIRN definition: A substrain of BALB/c mouse developed ...

Facilitation of Data Exchange in Mouse BIRN Mapping of Mouse BIRN Metadata Mouse XCEDE Working page Controlled Vocabularies View a draft of the complete BIRNLex, ...

Mouse Data Federation Working Group Tele-conferences Tuesday, 2006-08-01 Tuesday, 2006-08-08 Tuesday, 2006-08-15

Go to Mouse BIRN Wiki Table of Contents Data Federation: Table of Contents of Working Pages TOC{"DataFedTCons" title "Data Federation Working Group Teleconferences ...

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 ...

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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 ...

Table of Contents TOC Electronic Lab Notebook (ELN) data source plugin User Manual Introduction The ELN data source plugins allows the user to query the Caltech Electronic ...

Meeting Minutes of Test1, 22 May 2008 TOC Dial-in Domestic Dial-in Number: 888-... International Dial-in Number: 608-... Participant Code: ... Attendees person1. ...

EMAP (submitted by Seth) The Edinburgh Mouse Atlas Project(EMAP) is essentially composed of two major sections. An anatomy browser and gene expression database (EMAGE ...

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 ...

Functional Specifications: Graph manager

Table of Contents TOC Graph Manager The Graph Manager presents hierarchical anatomical structure information using a radial tree display that is synchronized with ...

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

TOC File menu options Introduction This page describes the functional specifications for "File" menu items. The File menu contains following menu options: File Open ...

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

GeneExpression

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 ...

http://www.genenetwork.org/ LeiYan 01 May 2009

Table of Contents TOC GeneNetwork (GN) data source plugin User Manual Introduction The GN data source plugins allows the user to query the publicly available GeneNetwork ...

General Standards and Tools for Formalized Representation of Information Below is a list of wide-spread, general efforts to create formal schemes for representing ...

Table of Contents TOC GENSAT(Rockefeller) data source plugin User Manual Introduction The GENSAT (Rockefeller) data source plugins allows the user to query the publicly ...

Table of Contents TOC GENSAT Entrez data source plugin User Manual Introduction The GENSAT (Entrez) data source plugins allows the user to query the publicly available ...

Potential schema items that arise from the queries (some are already part of the current global conceptual schema) Global Conceptual Schema Previous Global Conceptual ...

Modification of HID for AIDB The Mouse BIRN group works with many types of images and deals with multiple data sources. Many of the groups work with 3D volumes (mostly ...

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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 ...

Visit the Mouse BIRN Workflows page to see how this example evolved EAE example Workflow Based Questions Based on EAE example workflowfor data sharing between CIT ...

How To Use the Wiki We encourage you to change the contents of a Wiki web page and to add your own web page topics that is what a Wiki is all about ! Edit a Wiki ...

Individual site Schemas Caltech Caltech DB link Caltech ER Diagram Overview.pdf: Overview of schema Caltech ER Diagram Detailed..pdf: Detailed diagram caltech birn ...

In-Person Programmer Meeting General Information Dates: June 25-26, 2007 Location: UCSD — BIRN-CC 9500 Gilman Drive Mailcode 0715 Holly Building La Jolla, CA 92093 ...

Table of Contents TOC JxBrowser Eclipse Setup 1. Set the native library locations for jniwrap. 1. Run Configurations Environment tab . Set the appropriate environmental ...

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Requirements AHM Plan (Oct. 20) Mockups 1 Workflows 1 Workspace 1 Workspace 1 Terms Feature Requests Data Sources Registration View BrainGraph Viewer Search Plugin ...

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 ...

Table of Contents TOC Landmark Warp Registration Plugin User Manual Introduction The landmark-based registration plugin allows the user to align 2D or 3D images using ...

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 ...

Lei Yan leiyan2000@gmail.com IT Specialist II Department of Anatomy and Neurobiology College of Medicine University of Tennessee Health Science Center

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

20 Apr 2007 Introduction of the issue For the past couple months, we have been trying to adopt MAGE as our standard, and make our existing BIRN Micro-array database ...

- 20 Apr 2007 Working Page to standardize some of the MAGE entries across Mouse BIRN or BIRN test beds 1. the identifier prefix: To identify where the data is from ...

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 ...

Working group: Jeff, Seth, Jyl

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 ...

AllanMackenzieGraham^? 07 May 2007

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 ...

Mapping Across Data Models This section deals with using the Common Data Models, the Global Conceptual Schema, and BIRNLex to specify Mouse BIRN metadata for upload ...

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List of Suggested Required Metadata: See http://en.wikipedia.org/wiki/Minimum Information Standards#External Links for more information Based on: MIAME misfishi MIBBI ...

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 ...

Overview This project is in collaboration wiht Joanna Jankowsky at Caltech to examine the Tet-off APP model. Goals Planning Plans and Action Items Bulleted list of ...

Overview The mouse BIRN Alpha Synuclein mouse model of Parkinson's Disease is a collaborative project spearheaded by Diana Price at NCMIR with Dr. Eliezer Masliah ...

From the BIRN Cooperative Guidelines Authorship: Summary: The guidelines for authorship are not completely consistent but do follow the general principle: Everyone ...

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 ...

Atlasing Resources $ Edinburgh Mouse Atlas Project (EMAP) : Digital atlas of mouse development and spatially registered gene expression data $ Allen Brain Atlas ...

Mouse BIRN Data Federation Tcon 2006-08-15 minutes Attendees: CIT: Seth, Edriss Duke: Jeff, Sally UCLA: Daniel, Allan, Karen, Steve, Jyl Drexel: Bill Too many technical ...

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 ...

These are some of the multiscale mouse brain data collection protocols used by the members of the Mouse BIRN. MR Microscopy Submitted by G. Allan Johnson, 4/10/02 ...

Mouse BIRN data for download BIRN Data Sharing Policy Version 1.0, November 2005 Data will be openly shared and made available with no restrictions other than subject ...

Overview The goals of the Data Federation workgroup are to develop multiscale databases and tools to aid in storing, managing, sharing, expanding, and visualizing ...

Mouse BIRN participants offer tools that aid in data management. Data query $ UTHSC (Rob Williams): Modified search commands that facilitate mouse BIRN integration ...

Mouse BIRN AHM, otherwise known as "All Paws Meeting": May 29-30th 2008, Santa Barbara Inn BIRN AHM: October 20-22nd 2008, UCSD Society for Neuroscience, November ...

Overview The mouse BIRN EAE mouse model of Multiple Sclerosis is a collaborative project spearheaded by Allan MacKenzie-Graham at LONI at UCLA. Goals Goals here Planning ...

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? : ...

Overview This project is headed by Rob Williams to create a genetic reference population (GRP). The GRP that will be used by the Mouse BIRN is the !BxD family of ...

Mouse BIRN models of neurodegenerative disease We have chosen mouse models for three devastating and common human neurological diseases—multiple sclerosis, Alzheimer ...

Mouse BIRN All Hands Meeting Logistics Upcoming Mouse All Hands meeting Meeting information Dates: Tuesday May 31-Wednesday June 1 Location: UCLA Laboratory of Neuro ...

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 ...

2005 Mouse All Hands meeting Meeting information Dates: Tuesday May 31-Wednesday June 1 Location: UCLA Laboratory of Neuro Imaging (LONI) Register at: http://www ...

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 ...

Semantic Bio-Ontology Topics of General Interest To Mouse BIRN Participants To access manuscripts directly related to Mouse BIRN sponsored research, go to the topic ...

Gene Symbol (mouse; human): Park7; PARK7 Gene Name: Parkinson disease (autosomal recessive, early onset) 7 Function (from UniProt): Acts as positive regulator of ...

The BIRN currently consists of three "test bed" projects that are conducting structural and functional studies of neurological disease: Mouse BIRN studying animal ...

Table of Contents TOC MouseBIRN Partner Plugins This page contains the documentation and functional specifications for the plugins developed by the MouseBIRN partners ...

Go to Mouse BIRN Wiki Table of Contents 2007 Presentations by members of the Mouse BIRN at the 2007 SfN meeting Presentations at the 2007 Mouse BIRN meeting 2006 ...

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 ...

Go to Mouse BIRN Wiki Table of Contents Mouse BIRN Projects Overview Mouse BIRN (mBIRN) is a research and development effort funded by the National Center for Research ...

Mouse BIRN Sample Queries The Data Integration team and the data base developers need to have some idea of the types of questions scientists are likely to ask of ...

Go to Mouse BIRN Wiki Table of Contents Resources Offered by BIRN BIRNLex Draft Version: The BIRN Project lexicon will provide entities for data and database annotation ...

Please see Mouse BIRN Resources to access the resources shared by Mouse BIRN. The mouse BIRN is a research and development effort that will result in a distributed ...

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

Individual Site Subject IDs Caltech Drexel Duke Each project initiated at CIVM, and each specimen processed here, is assigned a unique (within CIVM) identifier. These ...

TOC{"MouseBIRNAnnouncements" title "Announcements"} TOC{"MouseBIRNProjects" title "Projects"} TOC{"MouseBIRNResources" title "Available Resources Tools"} TOC{"MouseBIRNManuscripts ...

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 ...

Download Version 1 of the LONI Pipeline and it's help manual pipelinev1 use.zip: Version 1 of the LONI Pipeline (zipped) LONI Pipeline.pdf: Version 1 help manual Download ...

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 ...

Go to Mouse BIRN Wiki Table of Contents Important Dates for Mouse BIRN Mouse BIRN Progress Page Mouse BIRN Wants from the BIRN Project

Go to Mouse BIRN Wiki Table of Contents MouseBIRN Atlasing: Atlasing Working Pages Table of Contents The tool integration and prioritization taskforce has interoperable ...

Generalized Workflow GeneralWorkflow.pdf: Generalized workflow for mouse BIRN Workflow Expt.pdf: Experimental setup: diagram with questions and answers Workflows ...

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 ...

Table of Contents TOC Mouse Brain Library section viewer plugin User Manual Introduction The Mouse Brain Library (MBL) viewer plugin is designed to allow easy browsing ...

Directions to the hotel can be found at http://www.santabarbarainn.com/directions/. Recommendations for how to get to Santa Barbara: 1. Fly into Santa Barbara Airport ...

Converting investigator-provided descriptive terms for describing research data into BIRNLex OWL/RDF concepts Links The semi-automated process for mapping source ...

Overview The goal of this area is to act as a resource area for mouse registration issues. Goals Discuss and solve practical issues of registration of atlases within ...

First Mouse group meeting to be held May 1, 20006: This meeting is to focus on what people have been doing in terms of registration of Nissl and MRI 3D volumes and ...

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 ...

Review of Mouse MBIRN Testbed Local Data Models to XCEDE mapping Duke, UCLA, !CalTech, and UCSD have all been reviewing the means they would use to map the elements ...

Multiple Sclerosis, the EAE Mouse Model The pathology of Experimental Autoimmune Encephalomyelitis (EAE) is characterized by lymphocytic and mononuclear cell infiltration ...

TOC{title "Table of Contents"} GUI Builder Java 1.5 Compatibility 1. Look at form in design view. 1. Go to Inspector panel. Click on Form. Right-click and go to properties ...

Table of Contents TOC Neuroterrain Atlas Client plugin User Manual Introduction The Neuroterrain Atlas Client plugin is a viewer for data sets hosted on Neuroterrain ...

Ontology Curation Tools Onto-Centric Viewers Construction and Maintenance Tools Oriented Toward the Ontology Curator Please send your comments and suggestions to ...

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

Parkinson’s Disease, the Alpha Synuclein Mouse Model The project efforts are focused on the development and application of correlated imaging approaches (confocal ...

Subject ID species strain age gender weight breeding info genetic manipulation(appropriate here?) Model disease model/normal stage of disease gene or protein manipulated ...

2006 BIRN AHM The 2006 BIRN AHM was held at UCSD October 23-25th. Click here for the Mouse BIRN presentations and notes from the meeting. MouseBIRN 2006 Mouse AHM ...

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 19 Nov 2008 TOC Attendees Asif, Willy, Jeff B, Carl, Davit, Seth, Queenie, Steve, Daren 1. Agenda Reviewed AHM tasks/timelines ...

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 Feb 2009 TOC Attendees Willy, Carl, Jeff, Edriss, Seth, Queenie, Steve, Nikhil, Daren 1. Action Item Updates Seth/Edriss ...

Meeting Minutes of MouseBIRN Programmers' Meeting 25 Feb 2008 TOC Attendees Asif, Willy, Will, Carl, Jeff, XiaoDong, Seth, Steve, Queenie, Nikhil, Daren 1. Action ...

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 Minutes 25 Mar 2009 TOC Attendees Willy, Carl, Edriss, Seth, Steve, Queenie, Nikhil, Daren 1. Action Items updates Daren: ...

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

Meeting Minutes of Programmers' Meeting Minutes 06 May 2009 TOC Attendees Carl, Jeff, Willy, Lei Yan, XiaoDong, Seth, Queenie, Nikhil, Daren 1. Updates Seth reviewed ...

Minutes of !MouseBIRN Programmers Meeting 10 June 2009 TOC Attendees Carl, XiaoDong, LeiYan, Willy, Asif, Seth, Queenie, Nikhil, Daren Minutes Discussed the upcoming ...

Minutes of !MouseBIRN AHM Meetings New topic: (Must be WikiWord: two or more words with initial capitals, run together) SEARCH{"^ MeetingMinutes " scope "topic" type ...

Query 3D Query AIDB Duke CalTech webservices

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 ...

Sample Workflows Use Case #1: Query Register Compare 1 Open Concept Query Workspace Enter query terms In Results Page: Add results to cart 1 Open Registration Workspace ...

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 ...

Organizations and Academic Departments With a Special Focus on Developing and Using Semantic Biomedical Ontologies list in process Please send your comments and suggestions ...

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

Defining "atlas" 1. Where can you access your atlas/program? 1. What coordinate system does your atlas use? 1. What terminology do you use to map your data? 1. What ...

JylBoline^? 27 Apr 2006

Biomedical Ontologies Relevant to Mouse BIRN Data Management/Integration and Systems Interoperability The following is a list of existing ontologies encapsulating ...

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 ...

Normalizing Mouse Strain Names Strain-Subject-Genotype-Phenotype data model Link to the list of current strains used by Mouse BIRN Overview On Mouse BIRN, we need ...

svn+ssh on command line (Windows) Required Software 1. PuTTY, Plink, Pageant: 2. svn.exe: http://subversion.tigris.org Installation 1. Setup ssh (see http://tortoisesvn ...

25 Apr 2007 Note: This page is based on the definition from the tab2MAGE spreadsheet notes. We've modified some of the requirement for BIRN MAGE standard. Experiment ...

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 ...

Uploading

jboline 13 Jul 2005 In Maryann's document, she lists several potential user workflows. I've tried to separate them into different functions: AtlasingWorkshopDay Visualization ...

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 June 10, 2008 TOC Attendees Willy, Brian, Asif, Jeff G, Mark Ellisman, Seth, Queenie, Steve, Allan, Daren 1. Agenda Items CCDB/AIDB UCSD folks ...

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 ...

INCLUDE{" TWIKIWEB .WebChanges"}

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

SEARCH{"\. " scope "topic" regex "on" nosearch "on"} See also the faster WebTopicList

INCLUDINGWEB Web INCLUDINGWEB Web Home Changes Index Search Webs WEBLIST{" $name" separator ""} INCLUDE{" MAINWEB . WIKINAME LeftBar" warn "Create personal sidebar ...

This is a subscription service to be automatically notified by e-mail when topics change in this MouseBIRN web. This is a convenient service, so you do not have to ...

MouseBIRN Web Preferences The following settings are web preferences of the MouseBIRN web. These preferences overwrite the site-level preferences in TWIKIWEB . WIKIPREFSTOPIC ...

TWiki's MouseBIRN web SCRIPTURL /view SCRIPTSUFFIX /MouseBIRN The MouseBIRN web of TWiki. TWiki is a Web-Based Collaboration Platform for the Corporate World. INCLUDE ...

INCLUDE{" TWIKIWEB .WebSearch"}

INCLUDE{" TWIKIWEB .WebSearchAdvanced"}

No permission to read topic MouseBIRN.WebServer perhaps you need to log in?

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 ...

WIKINAME DATE

TOPICLIST{" $name "} See also the verbose WebIndex.

Functional Specifications: Welcome workspace On starting the application, the user gets directed to this workspace by default. Following diagram shows the welcome ...

Using XCEDE, SRB, Portlet UI to augment workflow automation Overview The research groups within the Mouse BIRN testbed have done a significant amount of effective ...

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 ...