Donald Doherty's blog

Category: Brain Science

  • Viewing the Fly Brain Connectome with Brainbow

    Figure 1. About 2,000 neurons in the fruit fly implicated in male courtship behavior are grouped into many lineage based subpopulations identified by different colors using Brainbow techniques. Figure 4 j and k from “Drosophila Brainbow: a recombinase-based fluorescence labeling technique to subdivide neural expression patterns” by Stefanie Hampel, Phuong Chung, Claire E McKellar, Donald Hall, Loren L Looger and Julie H Simpson. Nature Methods Advance Online Publication, February 6, 2011.

    The fruit fly (Drosophila melanogster) brain is composed of about 100,000 neurons. This makes their brains complex enough to support interesting behavior and, therefore, makes the fruit fly an excellent candidate for clarifying principles governing how brains work. The new paper “Drosophila Brainbow: a recombinase-based fluorescence labeling technique to subdivide neural expression patterns” (published February 6, 2011 in Nature Methods Advance Online Publication) describes the authors’ application of a multicolor labeling technique known as Brainbow in conjunction with genetic targeting tools to enable the identification of individual neurons in the same fruit fly brain. In addition to identifying individual neurons, the team was able to trace the ancestry – the cell lineage – of individual neurons, enabling them to address questions about how cell lineages contribute to neural circuits.

    Other related blog posts:

    How the Brain Works, Flies, and the FlyBase Online Data Repository

  • NIH and Other Major Funding Biomedical Research Institutions Call for Sharing Research Data

    “As funders of public health research, we need to ensure that research outputs are used to maximize knowledge and potential health benefits. In turn, the populations who participate in research, and the taxpayers who foot the bill, have the right to expect that every last ounce of knowledge will be wrung from the research.”

    The above statement concludes the first paragraph of a comment “Sharing research data to improve public health” published January 7, 2011 in the Lancet and signed by 17 major biomedical research funding institutions from across the globe. The published comment goes on to state that data are often treated as private property by investigators “who aim to maximize their publication record at the expense of the widest possible use of the data.”

    Note: Excerpts of a joint statement of purpose are published in the comment. The full statement is available online here.

    Since taxpayers foot most of the bill for research, the data are really owned by the public. Nevertheless, the competition is intense for the biomedical researcher working to build his or her career. The main determining factor for getting ahead is the number of papers that the individual has published. Funding agencies have an obligation to maximize data use – an obligation to both the people footing the bill and also to the subjects that participate in the research – but they also have an obligation to the research scientists who put so much of their life into time consuming, difficult, and extremely important research.

    Meeting all of these apparently contradictory obligations may be less than the impossible task that it seems at first glance. Transition the biomedical research culture – the funders, the university administrations that promote their scientists, etcetera – to appreciate and fund the scientists’ producing solid data and producing the largest impact on their field. Not by counting their direct publications. This is the easiest thing to do but has lead to a massive amount of literature that is redundant or worse. With current technology we can easily quantify the amount of data scientist contributes to online data repositories. We can also easily track the use of those data. Perhaps these measures could help to replace the old measure of the number of papers published.

  • International Effort to Design and Create a Brain Atlas-based Data Sharing Framework

    Last year a new coordinate system named Waxholm Space (WHS) for the mouse brain was published (see “WHS: The Standard Mouse Brain Coordinate System?“). The space was named after the Swedish city Waxholm where, in February of 2007, a group of scientists was assembled through the International Neuroinformatics Coordinating Facility (INCF) to discuss what they might do to help coordinate mouse brain research data. They decided on establishing a reference atlas of the mouse brain that would act as a universal coordinate system for mouse data. A new paper “Digital Atlasing and Standardization in the Mouse Brain” (published February 3, 2011 in PLoS Computational Biology) describes the goals of the INCF Digital Atlasing Infrastructure team to create a framework that not only enables interoperability between existing and future mouse data resources but also provides the tools for the discovery and publishing of data aggregated from distributed resources.

    Figure 1. The International Neuroinformatics Coordinating Facility (INCF) Digital Atlasing Infrastructure enables interoperability between existing and future mouse brain data resources. Figure 3 from “Digital Atlasing and Standardization in the Mouse Brain” by Michael Hawrylycz, Richard A. Baldock, Albert Burger, Tsutomu Hashikawa, G. Allan Johnson, Maryann Martone, Lydia Ng, Chris Lau, Stephen D. Larsen, Jonathan Nissanov, Luis Puelles, Seth Ruffins, Fons Verbeek, Ilya Zaslavsky and Jyl Boline. PLoS Computational Biology Volume 7, Number 2, February 3, 2011.

    To achieve their goals, providing a common mouse brain coordinate system was just one step. They also needed to provide a collection of distributed services that would support publication, discovery, and the aggregate use of different distributed atlas resources. The prototype version of the INCF Digital Atlasing Infrastructure is released and supports mapping between WHS reference space and the following online resources:

    Kudos to the coordinating organization INCF and all of the people from organizations around the world that are working hard together to make a global atlas-based data sharing framework a reality! Their work will have a huge impact on the future of neuroscience, including the application of research data for medical purposes, and should be supported by everyone.

    Other related blog posts:

    Whole Brain Catalog: the Google Earth for the Brain

    WHS: The Standard Mouse Brain Coordinate System?