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 ...

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

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 ...

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

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 ...