The Experts below are selected from a list of 2598 Experts worldwide ranked by ideXlab platform
Wibe A. Jong - One of the best experts on this subject based on the ideXlab platform.
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nwchem a comprehensive and scalable Open Source Solution for large scale molecular simulations
Computer Physics Communications, 2010Co-Authors: Marat Valiev, T P Straatsma, Karol Kowalski, Edoardo Aprà, Eric J. Bylaska, Theresa L. Windus, Jarek Nieplocha, Niranjan Govind, D. Wang, Wibe A. JongAbstract:The latest release of NWChem delivers an Open-Source computational chemistry package with extensive capabilities for large scale simulations of chemical and biological systems. Utilizing a common computational framework, diverse theoretical descriptions can be used to provide the best Solution for a given scientific problem. Scalable parallel implementations and modular software design enable efficient utilization of current computational architectures. This paper provides an overview of NWChem focusing primarily on the core theoretical modules provided by the code and their parallel performance.
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NWChem: A comprehensive and scalable Open-Source Solution for large scale molecular simulations
2010Co-Authors: Marat Valiev, T P Straatsma, Karol Kowalski, H. J J Van Dam, Edoardo Aprà, Eric J. Bylaska, Theresa L. Windus, Jarek Nieplocha, Niranjan Govind, D. Wang, Wibe A. JongAbstract:The latest release of NWChem delivers an Open-Source computational chemistry package with extensive capabilities for large scale simulations of chemical and biological systems. Utilizing a common computational framework, diverse theoretical descriptions can be used to provide the best Solution for a given scientific problem. Scalable parallel implementations and modular software design enable efficient utilization of current computational architectures. This paper provides an overview of NWChem focusing primarily on the core theoretical modules provided by the code and their parallel performance. ?? 2010 Elsevier B.V.
Balazs Hangya - One of the best experts on this subject based on the ideXlab platform.
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opeth Open Source Solution for real time peri event time histogram based on Open ephys
Frontiers in Neuroinformatics, 2020Co-Authors: Andras Szell, Sergio Martinezbellver, Panna Hegedus, Balazs HangyaAbstract:Single cell electrophysiology remains one of the most widely used approaches of systems neuroscience. Decisions made by the experimenter during electrophysiology recording largely determine recording quality, duration of the project and value of the collected data. Therefore, online feedback aiding these decisions can lower monetary and time investment, and substantially speed up projects as well as allow novel studies otherwise not possible due to prohibitively low throughput. Real-time feedback is especially important in studies that involve optogenetic cell type identification by enabling a systematic search for neurons of interest. However, such tools are scarce and limited to costly commercial systems with high degree of specialization, which hitherto prevented wide-ranging benefits for the community. To address this, we present an Open-Source tool that enables online feedback during electrophysiology experiments and provides a Python interface for the widely used Open Ephys Open Source data acquisition system. Specifically, our software allows flexible online visualization of spike alignment to external events, called the online peri-event time histogram (OPETH). These external events, conveyed by digital logic signals, may indicate photostimulation time stamps for in vivo optogenetic cell type identification or the times of behaviorally relevant events during in vivo behavioral neurophysiology experiments. Therefore, OPETH allows real-time identification of genetically defined neuron types or behaviorally responsive populations. By allowing ‘hunting’ for neurons of interest, OPETH significantly reduces experiment time and thus increases the efficiency of experiments that combine in vivo electrophysiology with behavior or optogenetic tagging of neurons.
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opeth Open Source Solution for real time peri event time histogram based on Open ephys
bioRxiv, 2019Co-Authors: Andras Szell, Sergio Martinezbellver, Panna Hegedus, Balazs HangyaAbstract:Abstract Single cell electrophysiology remains one of the most widely used approaches of systems neuroscience. Real-time feedback during electrophysiology experiments is important to guide experimental decisions that eventually determine the quality of recording, duration of the project and value of the collected data. We present an Open-Source tool that enables flexible online visualization of action potential alignment to external events, called the peri-event or peristimulus time histogram (OPETH). Based on the Open Ephys Open Source data acquisition system, we developed a Python interface for real-time plotting of neuronal spike times and evoked waveforms with respect to external events represented by digital logic signals. These digital inputs may signal photostimulation time stamps for in vivo optogenetic identification of cell types or the times of behaviorally relevant events during in vivo behavioral neurophysiology experiments. Therefore, OPETH allows real-time identification of genetically defined neuron types or behaviorally responsive populations. By allowing ‘hunting’ for neurons of interest, OPETH may significantly increase the efficiency of experiments that combine in vivo electrophysiology with behavior or optogenetic tagging of neurons.
Marat Valiev - One of the best experts on this subject based on the ideXlab platform.
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nwchem a comprehensive and scalable Open Source Solution for large scale molecular simulations
Computer Physics Communications, 2010Co-Authors: Marat Valiev, T P Straatsma, Karol Kowalski, Edoardo Aprà, Eric J. Bylaska, Theresa L. Windus, Jarek Nieplocha, Niranjan Govind, D. Wang, Wibe A. JongAbstract:The latest release of NWChem delivers an Open-Source computational chemistry package with extensive capabilities for large scale simulations of chemical and biological systems. Utilizing a common computational framework, diverse theoretical descriptions can be used to provide the best Solution for a given scientific problem. Scalable parallel implementations and modular software design enable efficient utilization of current computational architectures. This paper provides an overview of NWChem focusing primarily on the core theoretical modules provided by the code and their parallel performance.
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NWChem: A comprehensive and scalable Open-Source Solution for large scale molecular simulations
2010Co-Authors: Marat Valiev, T P Straatsma, Karol Kowalski, H. J J Van Dam, Edoardo Aprà, Eric J. Bylaska, Theresa L. Windus, Jarek Nieplocha, Niranjan Govind, D. Wang, Wibe A. JongAbstract:The latest release of NWChem delivers an Open-Source computational chemistry package with extensive capabilities for large scale simulations of chemical and biological systems. Utilizing a common computational framework, diverse theoretical descriptions can be used to provide the best Solution for a given scientific problem. Scalable parallel implementations and modular software design enable efficient utilization of current computational architectures. This paper provides an overview of NWChem focusing primarily on the core theoretical modules provided by the code and their parallel performance. ?? 2010 Elsevier B.V.
Andras Szell - One of the best experts on this subject based on the ideXlab platform.
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opeth Open Source Solution for real time peri event time histogram based on Open ephys
Frontiers in Neuroinformatics, 2020Co-Authors: Andras Szell, Sergio Martinezbellver, Panna Hegedus, Balazs HangyaAbstract:Single cell electrophysiology remains one of the most widely used approaches of systems neuroscience. Decisions made by the experimenter during electrophysiology recording largely determine recording quality, duration of the project and value of the collected data. Therefore, online feedback aiding these decisions can lower monetary and time investment, and substantially speed up projects as well as allow novel studies otherwise not possible due to prohibitively low throughput. Real-time feedback is especially important in studies that involve optogenetic cell type identification by enabling a systematic search for neurons of interest. However, such tools are scarce and limited to costly commercial systems with high degree of specialization, which hitherto prevented wide-ranging benefits for the community. To address this, we present an Open-Source tool that enables online feedback during electrophysiology experiments and provides a Python interface for the widely used Open Ephys Open Source data acquisition system. Specifically, our software allows flexible online visualization of spike alignment to external events, called the online peri-event time histogram (OPETH). These external events, conveyed by digital logic signals, may indicate photostimulation time stamps for in vivo optogenetic cell type identification or the times of behaviorally relevant events during in vivo behavioral neurophysiology experiments. Therefore, OPETH allows real-time identification of genetically defined neuron types or behaviorally responsive populations. By allowing ‘hunting’ for neurons of interest, OPETH significantly reduces experiment time and thus increases the efficiency of experiments that combine in vivo electrophysiology with behavior or optogenetic tagging of neurons.
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opeth Open Source Solution for real time peri event time histogram based on Open ephys
bioRxiv, 2019Co-Authors: Andras Szell, Sergio Martinezbellver, Panna Hegedus, Balazs HangyaAbstract:Abstract Single cell electrophysiology remains one of the most widely used approaches of systems neuroscience. Real-time feedback during electrophysiology experiments is important to guide experimental decisions that eventually determine the quality of recording, duration of the project and value of the collected data. We present an Open-Source tool that enables flexible online visualization of action potential alignment to external events, called the peri-event or peristimulus time histogram (OPETH). Based on the Open Ephys Open Source data acquisition system, we developed a Python interface for real-time plotting of neuronal spike times and evoked waveforms with respect to external events represented by digital logic signals. These digital inputs may signal photostimulation time stamps for in vivo optogenetic identification of cell types or the times of behaviorally relevant events during in vivo behavioral neurophysiology experiments. Therefore, OPETH allows real-time identification of genetically defined neuron types or behaviorally responsive populations. By allowing ‘hunting’ for neurons of interest, OPETH may significantly increase the efficiency of experiments that combine in vivo electrophysiology with behavior or optogenetic tagging of neurons.
T P Straatsma - One of the best experts on this subject based on the ideXlab platform.
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nwchem a comprehensive and scalable Open Source Solution for large scale molecular simulations
Computer Physics Communications, 2010Co-Authors: Marat Valiev, T P Straatsma, Karol Kowalski, Edoardo Aprà, Eric J. Bylaska, Theresa L. Windus, Jarek Nieplocha, Niranjan Govind, D. Wang, Wibe A. JongAbstract:The latest release of NWChem delivers an Open-Source computational chemistry package with extensive capabilities for large scale simulations of chemical and biological systems. Utilizing a common computational framework, diverse theoretical descriptions can be used to provide the best Solution for a given scientific problem. Scalable parallel implementations and modular software design enable efficient utilization of current computational architectures. This paper provides an overview of NWChem focusing primarily on the core theoretical modules provided by the code and their parallel performance.
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NWChem: A comprehensive and scalable Open-Source Solution for large scale molecular simulations
2010Co-Authors: Marat Valiev, T P Straatsma, Karol Kowalski, H. J J Van Dam, Edoardo Aprà, Eric J. Bylaska, Theresa L. Windus, Jarek Nieplocha, Niranjan Govind, D. Wang, Wibe A. JongAbstract:The latest release of NWChem delivers an Open-Source computational chemistry package with extensive capabilities for large scale simulations of chemical and biological systems. Utilizing a common computational framework, diverse theoretical descriptions can be used to provide the best Solution for a given scientific problem. Scalable parallel implementations and modular software design enable efficient utilization of current computational architectures. This paper provides an overview of NWChem focusing primarily on the core theoretical modules provided by the code and their parallel performance. ?? 2010 Elsevier B.V.
