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CNS*14 Tutorial on Neuronal Model Parameter Search Techniques
by Cengiz Günay July 24, 2014

July 24, 2014

Dear colleagues, You are invited to attend our shortly upcoming full-day tutorial session at CNS*2014 in Quebec City. *Where:* Organization for Computational Neurosciences (OCNS) Conference, Quebec City Conference Center, Room 2105 *When:* Saturday July 26, 2014 between 9am - 4:30pm *T9: Neuronal Model Parameter Search Techniques* Parameter tuning of model neurons to mimic biologically realistic activity is a non‐trivial task. Multiple models may exhibit similar dynamics that match experimental data – i.e., there is no single “correct” model. To address this issue, the ensemble modeling technique proposes to represent properties of living neurons with a set of neuronal models. Several approaches to ensemble modeling have been proposed over the years, but the two most prevalent parameter tuning methods are systematic “brute‐force” searches [1, 2] and various evolutionary algorithms‐based techniques [3, 4, 5, 6]. Both approaches relay on traversing a very large parameter space (with thousands to millions of model instances), but utilize diametrically different ways to accomplish that. In both cases, however, entire collections of biologically realistic models are generated, whose neural activity characteristics can then be cataloged and studied using a database [1, 2]. The tutorial covers “tips and tricks,” as well as various pitfalls in all stages of model construction, large‐scale simulations on high performance computing clusters [S2], database construction and analysis of neural data, along with a discussion about the strengths and weaknesses of the two parameter search techniques. We will review software implementations for each technique: PANDORA Matlab Toolbox [7][S1] for the brute force method and NeRvolver (i.e., evolver of nerve cells) for evolutionary algorithms. PANDORA was used in recent projects for tuning models of rat globus pallidus neurons [2][M1], lobster pyloric network calcium sensors [8][M2], leech heart interneurons [9][M3,S3] and hippocampal O‐LM interneurons (Skinner Lab, TWRI/UHN and Univ. Toronto). NeRvolver is a prototype of a computational intelligence‐based system for automated construction, tuning, and analysis of neuronal models, which is currently under development in the Computational Intelligence and Bio (logical) informatics Laboratory at Delaware State University [10]. Through the utilization of computational intelligence methods (i.e., Multi‐Objective Evolutionary Algorithms and Fuzzy Logic), the NeRvolver system generates classification rules describing biological phenomena discovered during the process of model creation or tuning. Thus in addition to producing neuronal models, NeRvolver provides–via such rules–insights into the functioning of the biological neurons being modeled. In the tutorial, we will present basic functionalities of the system and demonstrate how to analyze the results returned by the software. We will allocate enough time for Q&A and if participants bring a laptop pre‐loaded with Matlab, they can follow some of our examples. *Lecturers/Organizers:* Cengiz Günay, Anca Doloc-Mihu (Emory University, USA) Vladislav Sekulić (University of Toronto, Canada), Tomasz G. Smolinski (Delaware State University, USA) *References * [1] Astrid A. Prinz, Cyrus P. Billimoria, and Eve Marder. Alternative to hand‐tuning conductance‐based models: Construction and analysis of databases of model neurons. J Neurophysiol, 90:3998–4015, 2003. [2] Cengiz Günay, Jeremy R. Edgerton, and Dieter Jaeger. Channel density distributions explain spiking variability in the globus pallidus: A combined physiology and computer simulation database approach. J. Neurosci., 28(30):7476–91, July 2008. [3] Pablo Achard and Erik De Schutter. Complex parameter landscape for a complex neuron model. PLoS Comput Biol, 2(7):794–804, Jul 2006. [4] Tomasz G. Smolinski and Astrid A. Prinz. Computational intelligence in modeling of biological neurons: A case study of an invertebrate pacemaker neuron. In Proceedings of the International Joint Conference on Neural Networks, pages 2964–2970, Atlanta, GA, 2009. [5] Tomasz G. Smolinski and Astrid A. Prinz. Multi‐objective evolutionary algorithms for model neuron parameter value selection matching biological behavior under different simulation scenarios. BMC Neuroscience, 10(Suppl 1):P260, 2009. [6] Damon G. Lamb and Ronald L. Calabrese. Correlated conductance parameters in leech heart motor neurons contribute to motor pattern formation. PLoS One, 8(11):e79267, 2013. [7] Cengiz Günay, Jeremy R. Edgerton, Su Li, Thomas Sangrey, Astrid A. Prinz, and Dieter Jaeger. Database analysis of simulated and recorded electrophysiological datasets with PANDORA’s Toolbox. Neuroinformatics, 7(2):93–111, 2009. [8] Cengiz Günay and Astrid A. Prinz. Model calcium sensors for network homeostasis: Sensor and readout parameter analysis from a database of model neuronal networks. J Neurosci, 30:1686–1698, Feb 2010. NIHMS176368,PMC2851246. [9] Anca Doloc‐Mihu and Ronald L. Calabrese. A database of computational models of a half‐center oscillator for analyzing how neuronal parameters influence network activity. J Biol Phys, 37(3):263–283, Jun 2011. [10] Emlyne Forren, Myles Johnson‐Gray, Parth Patel, and Tomasz G. Smolinski. Nervolver: a computational intelligence‐based system for automated construction, tuning, and analysis of neuronal models. BMC Neuroscience, 13(Suppl 1):P36, 2012. -Cengiz -- Cengiz Gunay Postdoctoral Fellow, Dept. of Biology Visiting Faculty, Dept. of Math & CS Emory University cgunay(a)emory.edu http://www.biology.emory.edu/research/Prinz/Cengiz/

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Announcement: GENESIS 2.4 beta tutorial at CNS
by Hugo Cornelis July 23, 2014

July 23, 2014

This is a public announcement of the GENESIS-2.4 tutorial at the Computational Neuroscience meeting (CNS) in Quebec City and the official public beta release of GENESIS 2.4. This new release includes support for spike-timing dependent plasticity in large networks of multicompartmental cells, bug fixes, comes with new python utilities and tutorial materials. The "Ultimate GENESIS Tutorial Distribution", included in this release, contains updated course materials for the tutorial Constructing biologically realistic neuron and network models with GENESIS. The tutorial brings together material that is available as separate downloads from the GENESIS web site and through the GENESIS Users Group. It includes several simulator-independent tutorials on biologically realistic neural modeling, as well as both tutorial and research simulations that have been implemented with GENESIS. The latest version of this GENESIS tutorial distribution will be available at http://genesis-sim.org/GENESIS/UGTD.html. The GENESIS tutorial at the CNS meeting is introductory and aimed at people who are new to or have only elementary knowledge about the GENESIS-2 simulator, as well as those who have used GENESIS in the past and would like to learn of new developments in cortical network modeling with GENESIS. * introduction and overview ** Why are we doing this? ** resources ** installation and configuration overview * single neuron modeling and visualization * debugging model and script * fast simulations with hsolve * network modeling * spike-timing dependent plasticity During the last hour of the tutorial, I will show in detail how to technically debug models, scripts and source code, at various levels of implementation. The latest news can always be found at http://genesis-sim.org/GENESIS/ -- Hugo -- Hugo Cornelis Ph.D. GENESIS-3 -- lead architect http://www.genesis-sim.org/ Neurospaces Project Architect http://www.neurospaces.org/

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Brian tutorial at CNS meeting in Québec City
by Marcel Stimberg July 23, 2014

July 23, 2014

**Brian tutorial at CNS meeting in Québec City** Everyone interested in simulating spiking neural networks is invited to join us for a tutorial on the "Brian simulator": 9am-4.30pm, Saturday, 26th July 2014 in Québec City The tutorial is part of the OCNS meeting's tutorials (http://www.cnsorg.org/cns-2014-tutorials) and takes place in room 2101 of the Québec City Conference Center. It will demonstrate the use of Brian 2, a major update of the Brian simulator which further improves its flexibility and adds exciting new code generation abilities. We will provide an introduction to Brian in the morning (no prior knowledge of Brian necessary) and discuss more advanced topics (including the new code generation features) in the afternoon. We recommend participants to install the current version of Brian 2 beforehand; installation instructions, the schedule and additional material can be found here: http://briansimulator.org/brian-tutorial-at-cns-2014/ Best regards, Marcel Stimberg

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Faculty Position in Computational Neuroscience at the University of California, Irvine
by Jeff Krichmar July 22, 2014

July 22, 2014

Dear Computational Neuroscientists, The following job position may be of interest to many of you. ************************** University of California, Irvine Faculty Position in Computational Neuroscience The Department of Cognitive Sciences (www.cogsci.uci.edu) at the University of California, Irvine (UCI) invites applications for a faculty position at the Associate or Full Professor level. We are especially interested in candidates who use mathematical, computational, or robotics approaches to study the neural basis of cognition in any of these areas: (1) vision, hearing, and attention; (2) memory and decision-making; (3) learning and development; (4) language. Applicants whose research relates to human behavior are preferred. A strong record of publications and extramural funding is essential. Exceptional candidates at the Assistant Professor level will also be considered. The online application includes: A cover letter, CV, research and teaching statements, 3 recent publications, and contact information for 3-5 referees. Interested candidates can apply for the position at: https://recruit.ap.uci.edu/apply/JPF02452. To ensure full consideration, please complete the application by November 15, 2014. The University of California, Irvine is an Equal Opportunity/Affirmative Action Employer committed to excellence through diversity. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, age, protected veteran status, or other protected categories covered by the UC nondiscrimination policy. ************************** Best regards, Jeff Krichmar Department of Cognitive Sciences 2328 Social & Behavioral Sciences Gateway University of California, Irvine Irvine, CA 92697-5100 jkrichma(a)uci.edu http://www.socsci.uci.edu/~jkrichma

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GENESIS 2.4 beta release and modeling tutorials
by Dave Beeman July 22, 2014

July 22, 2014

There is now a stable public beta release of GENESIS 2.4 available on the web site for the GENESIS neural simulator. Although there have been development releases of GENESIS 3, this is the first new release of GENESIS 2 since the March 2006 release of GENESIS 2.3. This new release was made necessary by the many improvements and user contributions over the past few years, and the incorporation of new objects for efficiently modeling synaptic plasticity in large networks of realistic multicompartmental cells. The final release will be in November 2014. There is also a new July 2014 version of the "Ultimate GENESIS Tutorial Distribution", a complete self-paced GENESIS modeling course, combined with GENESIS binary and source distributions and installation instructions. It provides an easy way to get everything by downloading a single package. This was prepared as course materials for the tutorial "Constructing biologically realistic neuron and network models with GENESIS" to be given on July 26th at CNS 2014. These may be downloaded from the GENESIS 2 home page at http://genesis-sim.org/GENESIS/ Those who wish to follow or contribute to the development of the final release can get the latest versions at the github repository: https://github.com/dbeeman/genesis-2.4beta-files Dave Beeman ------------------------------------------------------------ Prof. David Beeman, GENESIS Users Group Dept. of Electrical, Computer, and Energy Engineering University of Colorado, Boulder, CO 80309 email: genesis(a)genesis-sim.org - dbeeman(a)colorado.edu GENESIS 2 WWW site: http://genesis-sim.org/GENESIS/ ------------------------------------------------------------

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CNS-2014 - Workshop on Cortical Oscillations: Computational Models and Dynamic Mechanisms
by Horacio G. Rotstein July 22, 2014

July 22, 2014

Dear colleague, We would like to bring to your attention the forthcoming Workshop on "Cortical Oscillations: Computational Models and Dynamics Mechanisms" as part of the Computational Neuroscience Meeting, Juy 26 - 31, Quebec City, Canada. The detailed program including the list of speaker and talk titles can be found in the following link: http://web.njit.edu/~horacio/CNS-2014/CNS-2014_WorkshopCorticalOscillations… Sincerely, Mark Kramer and Horacio Rotstein -- Horacio, NY/NJ area. "Az di bobe volt gehat beytsim volt zi geven mayn zeide" (Yiddish expression) Horacio G. Rotstein Associate Professor Department of Mathematical Sciences New Jersey Institute of Technology Newark, NJ, 07102, USA. Graduate Faculty Behavioral Neuroscience Program Rutgers University (NWK) and Federated Department of Biological Sciences Rutgers / NJIT tel: (1-973) 596-5306 e-mail: horacio(a)njit.edu horacior(a)andromeda.rutgers.edu <horacio(a)njit.edu> http://web.njit.edu/~horacio

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Videos online: Workshop on Cortical Spreading Depression (CSD) and Related Neurological Phenomena
by Markus A Dahlem July 22, 2014

July 22, 2014

*18 VIDEOS online available: * *Workshop on Cortical Spreading Depression (CSD) and Related Neurological Phenomena* http://www.fields.utoronto.ca/video-archive/event/294/2014 Organizers: K. C. Brennan (Neurology,U Utah), Markus A. Dahlem (Physics, Humboldt U, Berlin), Huaxiong Huang (Math. & Statistics, York U), Robert M. Miura (Math. Sci. and Biomedical Eng, NJIT) This workshop brought together a group of researchers from the areas of mathematical modeling and clinicians and experimentalists in neuroscience to address some of the fundamental issues related to neurovascular coupling and cortical spreading depression (CSD) and related neurological phenomenon. 1. Bernice Grafstein: Spreading depression as a holistic process: A historical perspective 2. Cenk Ayata: Spreading depression and the biological heterogeneity of cerebral blood flow response: clues for modeling 3. Huaxiong Huang: Modeling cortical spreading depression and related phenomena 4. Steven Schiff: Unification in the Observation and Control of Spikes, Seizures, and Spreading Depression 5. Jessica Seidel: Cerebral Venous Potassium Efflux During Spreading Depression 6. David Terman: Blocking spreading depolarizations in a neuron/astrocyte network model 7. Jed Hartings: Spreading depolarizations in acute brain injury: mathematical dynamic instability of cerebral cortex? 8. Béla Joós: The Nav coupled left shift model of axon damage: how minor damage can cause major grief 9. Ghanim Ullah: Towards a model-based control of neuronal systems 10. Jorge Manuel Mendez: In vivo cellular dynamics in cortical spreading depression 11. Ernest Barreto: Ion Concentration Dynamics and its Effects on Neuronal Excitability and Bursting 12. Bas-Jan Zandt: Dynamics of single neurons and populations during spreading depolarization 13. Niklas Hübel: Dynamics from seconds to hours in HodgkinHuxley model with time- dependent ion concentrations and buffer reservoirs 14. Markus A. Dahlem: Ghost behavior: Transient localized patterns of CSD in the gyrified human cortex 15. K.C. Brennan: Minimum conditions for the induction of CSD 16. Edward Dudek: Perinatal hypoxic-ischemic encephalopathy: electrographic seizures vs background supression 17. David Andrew: Spreading depolarization strength during ischemia determines higher brain susceptibility and lower brain resistance to acute injury 18. Yoichiro Mori: Modeling ionic electrodiffusion and osmosis in spreading depression If you are interested in updates and upcoming events on this topic, please sent an email to dahlem(a)physik.hu-berlin.de -- Dr. Markus A. Dahlem Humboldt-Universität zu Berlin AG NLD Cardiovascular Physics Robert-Koch-Platz 4 10115 Berlin Germany phone: +49 (0)30 2093 99185 email: dahlem(a)physik.hu-berlin.de skype: markus.dahlem web: https://sites.google.com/site/markusadahlem

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OCNS Workshop on Modeling of Neuron-Glia Interactions, Quebec City, July 30-31.
by Maurizio De Pittà July 22, 2014

July 22, 2014

Dear Sirs, I would kindly ask you to please forward the following message to the comp-neuro mailing list, and further encouraging you to share it with your colleagues. Thanks in advance for your consideration of the matter. Sincerely, Maurizio De Pitta' -------------------------------------------------------------- Dear colleague, we would like to bring at your attention the forthcoming OCNS workshop on "Computational Methods and Modeling of Astrocyte Physiology and Neuron-Glia Interactions". The workshop will take place in Quebec City (Canada) on July 30th-31st, following the main OCNS meeting. The workshop brings together a representative pool of theoreticians involved in modeling of several aspects of astrocyte physiology and neuron-glia interactions, aiming at providing a rare and original occasion to familiarize with the current state of research on the challenging topic of the functional role of neuron-glia interactions. Topics covered by this workshop include: 1. -- Calcium signaling in astrocytes (from subcellular/compartmentalized to network levels); 2. -- Neuron-glia interactions, regulation of synaptic transmission, plasticity and neuronal responses by astrocytes; 3. -- Astrocyte role in homeostasis and neurotrasmitter clearance; 4. -- Information processing by astrocytes. For the detailed program and the list of speakers, you are kindly invited to visit the workshop homepage: https://team.inria.fr/beagle/ocns-2014-workshop/ We encourage you to share this mail with your colleagues and whoever could be interested to attend our workshop. Thanks for your attention. Kind regards, Maurizio De Pitta' Hugues Berry -------------------------------------------------------------------------------- Maurizio De Pitta' - https://sites.google.com/site/mauriziodepitta Hugues Berry - http://www.inrialpes.fr/Berry -------------------------------------------------------------------------------- Project-Team BEAGLE INRIA Rhone-Alpes Université de Lyon LIRIS UMR5205 Antenne INRIA de La Doua Batiment CEI-1 66 Blvd Niels Bohr CS 52132 69603 Villeurbanne cedex France

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Journal of Mathematical Neuroscience - recent articles
by Stephen Coombes July 18, 2014

July 18, 2014

Dear all, The Journal of Mathematical Neuroscience publishes research articles on the mathematical modeling and analysis of all areas of neuroscience. The current list of journal articles is available at http://www.mathematical-neuroscience.com/ : Frequency Preference Response to Oscillatory Inputs in Two-dimensional Neural Models: A Geometric Approach to Subthreshold Amplitude and Phase Resonance Rotstein HG http://www.mathematical-neuroscience.com/content/4/1/11 Network Symmetry and Binocular Rivalry Experiments Diekman CO and Golubitsky M http://www.mathematical-neuroscience.com/content/4/1/12 Effects of Synaptic Plasticity on Phase and Period Locking in a Network of Two Oscillatory Neurons Akcay Z, Bose A and Nadim F http://www.mathematical-neuroscience.com/content/4/1/8 Approximate, not Perfect Synchrony Maximizes the Downstream Effectiveness of Excitatory Neuronal Ensembles Börgers C, Li J and Kopell N http://www.mathematical-neuroscience.com/content/4/1/10 Identification of Criticality in Neuronal Avalanches: II. A Theoretical and Empirical Investigation of the Driven Case Hartley C, Taylor TJ, Kiss IZ, Farmer SF and Berthouze L http://www.mathematical-neuroscience.com/content/4/1/9 All articles are Open Access. Best regards, Steve ------------------------------------------------------- Stephen Coombes Professor of Applied Mathematics School of Mathematical Sciences Nottingham, UK Tel: 0115 846 7836 http://www.maths.nott.ac.uk/~sc/ ------------------------------------------------------- This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Post-doc openings for theoretical neuroscience at UCSF and UCB
by Friedrich Sommer July 18, 2014

July 18, 2014

Post-doctoral fellow in computational/theoretical neuroscience The Chang Lab at UCSF and the Sommer Lab at UCB are jointly seeking two (2) post-doctoral fellows in computational/theoretical neuroscience. Our groups are developing and applying novel computational methods to understand population neural data. The positions have the specific focus on understanding the dynamics of neural population data collected directly from the cortical surface of humans during the perception and production of speech at multiple temporal resolutions. These positions are fully funded as part a collaborative effort between University of California San Francisco, University of California Berkeley, and Lawrence-Berkeley National Laboratory. This Bay Area collaboration combines UCSF's strong clinical and experimental neuroscience experience with in vivo cortical electrophysiology, UCB's expertise in theoretical neuroscience, statistical learning and data analysis, and LBNL's supercomputing and applied mathematics together with electronics and microfabrication. Successful applicants will have access to the full range of facilities and expertise uniquely allowed by this collaboration. Applicants should have a Ph.D. (or equivalent degree) in a quantitative field such as computer science, electrical engineering, physics, or applied mathematics/statistics with a strong publication record. Expertise in theoretical/computational neuroscience or the analysis/modeling of complex dynamical systems is recommended; experience in analyzing the dynamics of population neural recordings is preferred. Applicants must be able to work in a collaborative, multi-disciplinary environment and exhibit good communication skills. Experience with scientific programing languages (e.g. C/C++, python, Matlab) is required. Expertise in speech/language and/or high-performance computing is not required, but is beneficial. To apply, please submit a CV and three letters of reference to: changed(a)neurosurgery.ucsf.edu fsommer(a)berkeley.edu ----------------------------------------------------------------------------------------------------------------- Friedrich T. Sommer, Ph.D, Adjunct Professor Redwood Center for Theoretical Neuroscience & Helen Wills Neuroscience Institute UC Berkeley 575A Evans Hall, MC #3198 Berkeley, CA 94720-3198 http://redwood.berkeley.edu/wiki/Fritz_Sommer -----------------------------------------------------------------------------------------------------------------

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