A5056393081- Biomedical Text Mining and Ontologies
- Semantic Web and Ontologies
- Genetics, Aging, and Longevity in Model Organisms
- Cell Image Analysis Techniques
- Bioinformatics and Genomic Networks
- Spaceflight effects on biology
- Gene Regulatory Network Analysis
- Evolution and Genetic Dynamics
- Scientific Computing and Data Management
- Digital and Cyber Forensics
- Advanced Malware Detection Techniques
- Ecosystem dynamics and resilience
- Trypanosoma species research and implications
- Software Engineering Techniques and Practices
- Information Systems Education and Curriculum Development
- Genetics, Bioinformatics, and Biomedical Research
- Knowledge Management and Sharing
- Advanced Text Analysis Techniques
- Experimental Learning in Engineering
- Neural dynamics and brain function
- Personal Information Management and User Behavior
- Innovations in Educational Methods
- Research on Leishmaniasis Studies
- Insect symbiosis and bacterial influences
- AI in Service Interactions
Slippery Rock University
2009-2021
George Washington University
2020-2021
George Mason University
2020
Open Geospatial Consortium
2018-2019
Open Society Foundations
2018
Hainan Normal University
2015
University of California, San Diego
2007-2013
Virginia Commonwealth University
2011
University of Pennsylvania
2010
University of California, Berkeley
2007
A critical component of the Neuroscience Information Framework (NIF) project is a consistent, flexible terminology for describing and retrieving neuroscience-relevant resources. Although original NIF specification called loosely structured controlled vocabulary neuroscience resources, as system evolved, requirement formally ontology with sufficient granularity to describe access diverse collection information became obvious. This led standardized (NIFSTD) ontology, comprehensive common...
OpenWorm is an international collaboration with the aim of understanding how behavior Caenorhabditis elegans (C. elegans) emerges from its underlying physiological processes. The project has developed a modular simulation engine to create computational models worm. modularity makes it possible easily modify model, incorporate new experimental data and test hypotheses. modeling framework incorporates both biophysical neuronal simulations novel fluid-dynamics-based soft-tissue for physical...
Computational models are powerful tools for exploring the properties of complex biological systems. In neuroscience, data-driven neural circuits that span multiple scales increasingly being used to understand brain function in health and disease. But their adoption reuse has been limited by specialist knowledge required evaluate use them. To address this, we have developed Open Source Brain, a platform sharing, viewing, analyzing, simulating standardized from different regions species. Model...
The ability to transmit, organize, and query information digitally has brought with it the challenge of how best use this power facilitate scientific inquiry. Today, few systems are able provide detailed answers complex questions about neuroscience that account for multiple spatial scales, which cross boundaries diverse parts nervous system such as molecules, cellular parts, cells, circuits, tissues. As a result, investigators still primarily seek their in an increasingly densely populated...
An initiative of the NIH Blueprint for neuroscience research, Neuroscience Information Framework (NIF) project advances by enabling discovery and access to public research data tools worldwide through an open source, semantically enhanced search portal. One critical components overall NIF system, Standardized Ontologies (NIFSTD), provides extensive collection standard concepts along with their synonyms relationships. The knowledge models defined in NIFSTD ontologies enable effective...
The OpenWorm project has the ambitious goal of producing a highly detailed in silico model nematode Caenorhabditis elegans . A crucial part this work will be nervous system encompassing all known cell types and connections. appropriate level biophysical detail required neuronal to reproduce observed high-level behaviours worm yet determined. For reason, we have developed framework, c302, that allows different instances networks generated incorporating varying levels anatomical physiological...
Current information technology practices in neuroscience make it difficult to understand the organization of brain across spatial scales. Subcellular junctional connectivity, cytoarchitectural local and long-range topographical connectivity are just a few relevant data domains that must be synthesized order sense brain. However, due heterogeneity produced within these domains, landscape multiscale is fragmented. A standard framework for needed bridge existing digital resources help...
The nematode C. elegans is the only animal with a known neuronal wiring diagram, or "connectome". During last three decades, extensive studies of have provided wide-ranging data about it, but few systematic ways integrating thes
<ns4:p>The growth of the software industry has gone hand in with development tools and cultural practices for ensuring reliability complex pieces software. These are now acknowledged to be essential management modern As computational models methods have become increasingly common biological sciences, it is important examine how these can accelerate improve research quality. In this article, we give a focused case study our experience unit testing test-driven in<ns4:italic>...
To better understand how a nervous system controls the movements of an organism, we have created three-dimensional computational biomechanical model Caenorhabditis elegans body based on real anatomical structure. The is with particle system-based simulation engine known as Sibernetic, which implements smoothed particle-hydrodynamics algorithm. includes elastic body-wall cuticle subject to hydrostatic pressure. This then driven by muscle cells that contract and relax, whose positions shape...
The complexity of the nervous system requires high-resolution microscopy to resolve detailed 3D structure nerve cells and supracellular domains. analysis such imaging data extract cellular surfaces cell components often combination expert human knowledge with carefully engineered software tools. In an effort make better tools assist humans in this endeavor, create a more accessible permanent record their data, aid process constructing complex computational models, we have created core...
The Basics of Digital Forensics: Primer for Getting Started in Forensics is well-named–it really very basic. And it should be, as the book’s intended audience includes entry-level digital forensics professionals and complimentary fields such law enforcement, legal, general information security. Though copyright 2012, some data from 2009, there mention estimates 2010.
Trypanosoma brucei is an early branching protozoan parasite that causes human and animal African trypanosomiasis. Forward genetics approaches are powerful tools for uncovering novel aspects of trypanosomatid biology, pathogenesis, therapeutic against Here, we have generated a T. cloned ORFeome consisting >90% the targeted 7,245 genes used it to make inducible gain-of-function library broadly applicable large-scale forward genetic screens. We conducted proof-of-principle screen identify whose...
It has been 30 years since the 'mind of worm' was published in Philosophical Transactions B (White et al 1986 Phil. Trans. R. Soc. Lond. B314, 1-340). Predicting Caenorhabditis elegans' behaviour from its wiring diagram an enduring challenge then. This special theme issue combines research neuroscientists, physicists, mathematicians and engineers to discuss advances neural activity imaging, quantification multiscale simulations, how they are bringing goal whole-animal modelling at cellular...
The diversity of modeling approaches in computational neuroscience makes model sharing, retrieval, reuse and reproducibility difficult even sometimes impossible. To address this problem, standardized languages have been developed by for the community, such as NeuroML[1], PyNN [2] NineML (http://software.incf.org/software/nineml). Although these enable software interoperability therefore reproducibility, they lack semantic information that would facilitate efficient sharing retrieval. In...
Abstract Computational models are powerful tools for investigating brain function in health and disease. However, biologically detailed neuronal circuit complex implemented a range of specialized languages, making them inaccessible opaque to many neuroscientists. This has limited critical evaluation by the scientific community impeded their refinement widespread adoption. To address this, we have combined advances standardizing models, open source software development web technologies...
Abstract Development is a complex process that, under normal circumstances, proceeds in stable and patterned fashion. Developmental morphogenesis (called embryogenesis) can tell us great deal about the function structure of an adult organism. One most important aspects development to understand progression cell division differentiation what will become worm. This where DevoWorm project both address multiple outstanding theoretical issues provide graphical clarity embryogenetic process. As...