BIRN Community

New BIRN Capability: nihmaps.org

cristina — Fri, 20 Apr 2012 15:46:04 +0000

We are pleased to announce that we have just added a new capability to our list! This web application (which is available at www.nihmaps.org) provides a “topic map” that enables all grant proposals funded by NIH in a particular year to be queried in several ways. The map shows the similarity of topics between grants, providing an intuitive, interactive clustered representation. Users may view grant patterns based on changing coloring schemes, overlays and other viewing options. Future developments will include creating subject-specific MEDLINE maps for specific scientific communities and comparing these maps with others derived from CRISP.

The project is lead by Ned Talley (a program officer at NINDS) with support from Chalklabs, Indiana University, UC Irvine, U Mass and BIRN. For an overview of the methodology, see Database of NIH grants using machine-learned categories and graphical clustering, published in Nature Methods, May 2011.

To use this capability, go to www.nihmaps.org and click “Database”.

BIRN’s Pathology Paper accepted for HealthGrid 2012

cristina — Thu, 22 Mar 2012 19:01:25 +0000

BIRN is happy to announce another paper accepted for HealthGrid 2012. The Pathology project is a joint effort between BIRN and the California and Oregon National Primate Research Centers (NPRCs) to provide a decentralized network that allows the sharing of very high resolution images among distributed pathology laboratories. “A Flexible, Open, Decentralized System for Digital Pathology Networks” provides details about the resulting system including an active testbed involving two primate research centers with thousands of virtual microscopy slides at sizes over 15GB. This paper will be part of the HealthGrid Conference this May in Amsterdam.

For more information see healthgrid.org.

XNAT Workshop in St. Louis June 25-29

cristina — Tue, 06 Mar 2012 23:09:19 +0000

The 2012 XNAT Workshop will be held in St. Louis, MO, on the Washington University School of Medicine campus June 25-29. Registration is now open.

The workshop will be led by the XNAT developers at Washington University along with several invited speakers and includes three separate tracks designed to interest both technical and non-technical attendees.

For more information, please go to:

http://www.xnat.org/workshop.

BIRN’s CTSI Short Imaging Profile Paper accepted for HealthGrid 2012

cristina — Tue, 28 Feb 2012 20:35:58 +0000

As a result of BIRN’s work with Clinical Translational Science Institutes (CTSIs) at USC and UCI, a paper was written and accepted by HealthGrid 2012. A System Architecture for Sharing De-Identified, Research-Ready Brain Scans and Health Information Across Clinical Imaging Centers was put together by members of a pilot project that have set up a successful pilot that allows the exchange of clinical data between hospitals at USC and UCI at Irvine. This paper will be part of the HealthGrid Conference this May in Amsterdam.

For more information see healthgrid.org.

LONI Pipeline Workshop with BIRN Genomics capability in Cincinnati on March 2012

cristina — Tue, 21 Feb 2012 18:58:35 +0000

An upcoming workshop will be held in Cincinnati in March that will include the BIRN Genomics Graphical Pipeline capability.

For more information about the workshop, see http://pipeline.loni.ucla.edu/training/cchmc2012/.

Nature Genetics paper describes ISA format related to BIRN Knowledge Engineering efforts

cristina — Thu, 02 Feb 2012 22:50:08 +0000

The BioSharing initiative is a large-scale international collaboration
concerned with developing methods for sharing data. In February 2012,
Nature Genetics published a paper describing the isacommons.org
community which are based on systems developing interoperable
approaches based on the emerging ‘ISA’ (‘investigation, study, assay)
format. BIRN are active participants in this effort and are developing
knowledge engineering systems and general methods designed to leverage
this approach in order to create interoperable technology with these
other efforts.

You can view the paper here: http://www.nature.com/ng/journal/v44/n2/full/ng.1054.html

BIRN Genomics Pipeline paper leads on BMC Bioinformatics site

cristina — Wed, 30 Nov 2011 20:47:00 +0000

A paper published in the journal BMC Bioinformatics by a team of BIRN researchers led by Ivo D. Dinov of UCLA and Fabio Macciardi at UC Irvine has been downloaded 1,825 times since July, making it one of the most accessed papers on the journal’s site.

You can view the paper here: http://www.biomedcentral.com/1471-2105/12/304

New Paper: Knowledge synthesis with maps of neural connectivity

cristina — Tue, 01 Nov 2011 20:06:15 +0000

Congratulations on another paper from the Knowledge Engineering Working Group: Knowledge synthesis with maps of neural connectivity. Please see the link here for more information:

http://www.frontiersin.org/neuroinformatics/10.3389/fninf.2011.00024/abstract

Below is the abstract:

This paper describes software for neuroanatomical knowledge synthesis based on neural connectivity data. This software supports a mature methodology developed since the early 1990s. Over this time, the Swanson laboratory at USC has generated an account of the neural connectivity of the sub-structures of the hypothalamus, amygdala, septum, hippocampus, and bed nucleus of the stria terminalis. This is based on neuroanatomical data maps drawn into a standard brain atlas by experts. In earlier work, we presented an application for visualizing and comparing anatomical macro connections using the Swanson third edition atlas as a framework for accurate registration. Here we describe major improvements to the NeuARt application based on the incorporation of a knowledge representation of experimental design. We also present improvements in the interface and features of the data mapping components within a unified web-application. As a step toward developing an accurate sub-regional account of neural connectivity, we provide navigational access between the data maps and a semantic representation of area-to-area connections that they support. We do so based on an approach called “Knowledge Engineering from Experimental Design” (KEfED) model that is based on experimental variables. We have extended the underlying KEfED representation of tract-tracing experiments by incorporating the definition of a neuronanatomical data map as a measurement variable in the study design. This paper describes the software design of a web-application that allows anatomical data sets to be described within a standard experimental context and thus indexed by non-spatial experimental design features.

BIRN Presentations to NIH

cristina — Wed, 21 Sep 2011 21:13:37 +0000

This week members of BIRN’s Executive and Steering Committees made several presentations to many members of NIH describing what we’re doing. The slides have been posted on the wiki and you can check them out here (scroll down to the ‘Slides’ section:

https://wiki.birncommunity.org/x/SgNrAQ

New BIRN Video Introductions

cristina — Tue, 13 Sep 2011 03:02:41 +0000

Please check out these new videos where Dr. Carl Kesselman describes BIRN and answers key questions newcomers may have:

http://www.birncommunity.org/about/birn-video-intro/