Stephen Larson

Stephen Larson
OpenWorm.org

Ph.D in Neuroscience

About

59
Publications
10,059
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1,167
Citations
Additional affiliations
January 2008 - December 2012
University of California, San Diego

Publications

Publications (59)
Article
Full-text available
Computational models are powerful tools for exploring the properties of complex biological systems. In neuroscience, data-driven models of neural circuits that span multiple scales are increasingly being used to understand brain function in health and disease. But their adoption and reuse has been limited by the specialist knowledge required to eva...
Article
Full-text available
The OpenWorm project has the ambitious goal of producing a highly detailed in silico model of the nematode Caenorhabditis elegans. A crucial part of this work will be a model of the nervous system encompassing all known cell types and connections. The appropriate level of biophysical detail required in the neuronal model to reproduce observed high-...
Article
It has been 30 years since the ‘mind of the worm’ was published in Philosophical Transactions B (White et al . 1986 Phil. Trans. R. Soc. Lond. B 314 , 1–340). Predicting Caenorhabditis elegans ' behaviour from its wiring diagram has been an enduring challenge since then. This special theme issue of Philosophical Transactions B combines research fro...
Article
Full-text available
The adoption of powerful software tools and computational methods from the software industry by the scientific research community has resulted in a renewed interest in integrative, large-scale biological simulations. These typically involve the development of computational platforms to combine diverse, process-specific models into a coherent whole....
Article
Full-text available
To better understand how a nervous system controls the movements of an organism, we have created a three-dimensional computational biomechanical model of the Caenorhabditis elegans body based on real anatomical structure. The body model is created with a particle system–based simulation engine known as Sibernetic, which implements the smoothed part...
Preprint
Full-text available
Computational models are powerful tools for investigating brain function in health and disease. However, biologically detailed neuronal and circuit models are complex and implemented in a range of specialized languages, making them inaccessible and opaque to many neuroscientists. This has limited critical evaluation of models by the scientific comm...
Conference Paper
Full-text available
Place cells in hippocampus exhibit sharp spatially-related firing fields, which are formed when the animal explores new environments and are retrieved, as memories, each time the rat is placed back in those specific settings. Knowledge of the environment-specific set of place fields (map) allows for the application of Bayesian statistics to infer t...
Conference Paper
Full-text available
We simulate C. elegans' forward crawling with a cell network composed of the AVB interneuron pair, 18 B-type and 19 D-type motorneurons and 95 body muscles, considering three key hypotheses; I. AVB interneurons get activated from their upstream neurons, and excite B-type motor neurons. II. Simultaneously, a central pattern generator (CPG) in the he...
Preprint
Full-text available
The growth of the software industry has gone hand in hand with the development of tools and cultural practices for ensuring the reliability of complex pieces of software. These tools and practices are now acknowledged to be essential to the management of modern software. As computational models and methods have become increasingly common in the bio...
Preprint
Full-text available
The growth of the software industry has gone hand in hand with the development of tools and cultural practices for ensuring the reliability of complex pieces of software. These tools and practices are now acknowledged to be essential to the management of modern software. As computational models and methods have become increasingly common in the bio...
Article
A prerequisite for simulating the biophysics of complex biological tissues and whole organisms are computational descriptions of biological matter that are flexible and can interface with materials of different viscosities, such as liquid. The landscape of software that is easily available to do such work is limited and lacks essential features nec...
Article
Full-text available
The nematode C. elegans is historically one of the most studied model organism in biology and the only one to have its full connectome mapped. OpenWorm [1] is a project dedicated to recreating the C. elegans nematode as a virtual organism in a computer. The project takes an Open Science approach to development, relying on volunteer contributions an...
Article
Full-text available
The growth of the software industry has gone hand in hand with the development of tools and cultural practices for ensuring the reliability of complex pieces of software. These tools and practices are now acknowledged to be essential to the management of modern software. As computational models and methods have become increasingly common in the bio...
Preprint
Full-text available
The growth of the software industry has gone hand in hand with the development of tools and cultural practices for ensuring the reliability of complex pieces of software. These tools and practices are now acknowledged to be essential to the management of modern software. As computational models and methods have become increasingly common in the bio...
Article
Full-text available
OpenWorm is an international collaboration with the aim of understanding how the behavior of Caenorhabditis elegans (C. elegans) emerges from its underlying physiological processes. The project has developed a modular simulation engine to create computational models of the worm. The modularity of the engine makes it possible to easily modify the mo...
Article
Full-text available
Development is a complex process that, under normal circumstances, proceeds in a stable and patterned fashion. Developmental morphogenesis (called embryogenesis) can tell us a great deal about the function and structure of an adult organism. One of the most important aspects of development to understand is the progression of cell division and diffe...
Article
Full-text available
The ability to transmit, organize, and query information digitally has brought with it the challenge of how to best use this power to facilitate scientific inquiry. Today, few information systems are able to provide detailed answers to complex questions about neuroscience that account for multiple spatial scales, and which cross the boundaries of d...
Article
Full-text available
The number of available neuroscience resources (databases, tools, materials, and networks) available via the Web continues to expand, particularly in light of newly implemented data sharing policies required by funding agencies and journals. However, the nature of dense, multifaceted neuroscience data and the design of classic search engine systems...
Conference Paper
Full-text available
Background / Purpose: The goal of the International Neuroinformatics Coordinating Facility (INCF) digital atlasing program is to facilitate data sharing via an atlasing infrastructure. The work is primarily in rodents at this stage. Main conclusion: Workflows for registering data to atlas references and adding to the INCF digital atlasing infr...
Thesis
Full-text available
We have merged and extended the C. elegans connectome (Varshney et al., 2006) and a three-dimensional cellular anatomy model (Grove & Sternberg, 2011) in the context of the OpenWorm project, an open source project to build a data integration and simulation framework for the C. elegans. To do so, we have leveraged the NeuroML standard (Gleeson et al...
Article
The nematode C. elegans is the only animal with a known neuronal wiring diagram, or “connectome”. During the last three decades, extensive studies of the C. elegans have provided wide-ranging data about it, but few systematic ways of integrating these data into a dynamic model have been put forward. Here we present a detailed demonstration of a vir...
Article
Full-text available
An initiative of the NIH Blueprint for neuroscience research, the Neuroscience Information Framework (NIF) project advances neuroscience by enabling discovery and access to public research data and tools worldwide through an open source, semantically enhanced search portal. One of the critical components for the overall NIF system, the NIF Standard...
Article
The numbers of available neuroscience resources (databases, tools, materials and networks) on the web have, and continue to expand; particularly in light of newly implemented data sharing policies required by funding agencies and journals. However, the nature of dense, multi-faceted neuroscience data and the design of classic search engine systems...
Article
Sensory information may be represented in the brain by stereotyped mapping of axonal inputs or by patterning that varies between individuals. In olfaction, a stereotyped map is evident in the first sensory processing centre, the olfactory bulb (OB), where different odours elicit activity in unique combinatorial patterns of spatially invariant glome...
Article
Full-text available
[This corrects the article on p. e1001065 in vol. 7.].
Conference Paper
The goal of the INCF Digital Atlasing Infrastructure (DAI) Task Force is to develop scientific and technical foundations and to support implementation of a distributed system of brain atlas resources that can be published, shared and integrated based on spatial characteristics of the information. These spatial characteristics can include different...
Article
Full-text available
The scientific community has invested heavily in the creation of genetically modified organisms, other model systems, and large genetic screens because they greatly inform our understanding of human disease. However, it remains difficult to identify organisms suitable for one's research because information about them is not readily accessible. The...
Conference Paper
Digital atlases of rodent brain contain large volumes of 2D and 3D imagery, gene expression, electrophysiological and other information. Federating these atlases is one of the goals of the INCF Digital Atlasing Infrastructure (INCF-DAI) Task Force. To enable such federation, we rely on a collection of spatial and semantic translations that convert...
Article
Full-text available
Current information technology practices in neuroscience make it difficult to understand the organization of the brain across spatial scales. Subcellular junctional connectivity, cytoarchitectural local connectivity, and long-range topographical connectivity are just a few of the relevant data domains that must be synthesized in order to make sense...
Article
Full-text available
A critical component of the Neuroscience Information Framework (NIF) project is a consistent, flexible terminology for describing and retrieving neuroscience-relevant resources. Although the original NIF specification called for a loosely structured controlled vocabulary for describing neuroscience resources, as the NIF system evolved, the requirem...
Article
Databases have become integral parts of data management, dissemination, and mining in biology. At the Second Annual Conference on Electron Tomography, held in Amsterdam in 2001, we proposed that electron tomography data should be shared in a manner analogous to structural data at the protein and sequence scales. At that time, we outlined our progre...
Article
This chapter focuses the application of brain cartography to the problem of multiscale integration of brain data in the context of the Biomedical Informatics Research Network (BIRN) project.The BIRN project focuses on creating a grid infrastructure for integrating data on brain morphology and function obtained by different researchers to support co...
Conference Paper
Full-text available
We present the semantic data model for an ontological database for subcellular anatomy for Neurosciences. The data model builds upon the foundations of OWL and the Basic Formal Ontology, but extends them to include novel constructs that address several unresolved challenges encountered by biologists in using ontological models in their databases. T...
Article
Full-text available
The complexity of the nervous system requires high-resolution microscopy to resolve the detailed 3D structure of nerve cells and supracellular domains. The analysis of such imaging data to extract cellular surfaces and cell components often requires the combination of expert human knowledge with carefully engineered software tools. In an effort to...
Conference Paper
Full-text available
We have demonstrated the use of OWL-based ontologies to infer novel facts from existing knowledge. Using an ontology developed for subcellular anatomy of the nervous system, the SAO, merged with a terminological resource for gross neuroanatomy (Brain Architecture Management System; Bota and Swanson, 2005), we have inferred the existence of axons fr...
Conference Paper
Full-text available
The nervous system, perhaps more so than any other tissue, requires the fine spatial resolution of high resolution microscopy to resolve the intricate structure of individual nerve cells and supracellular domains. The analysis of such imaging data often involves the extraction of cellular surfaces and cell components. The resulting geometries are u...
Conference Paper
Full-text available
If we are to understand human-level intelligence, we need to understand how meanings can be learned without explicit instruction. I take a step toward that understanding by showing how symbols can emerge from a system that looks for regularity in the experiences of its visual and proprioceptive sensory systems. More specifically, the implemented sy...
Article
Full-text available
The grand goal in neuroscience research is to understand how the interplay of molecular, and electrical signals in nervous tissue gives rise to behavior. Experimental advances of the past decades have given scientists an increasingly powerful arsenal for obtaining data across scales, from the level of molecules to nervous systems. The next challeng...

Projects

Projects (5)
Archived project
Creating and using artificial connectomes, allows us to create artificial intelligence capable of unsupervised learning in domain agnostic environments (aka: AGI)