- Comp-neuro - lists.cnsorg.org

OpenWorm for scientists

by Stephen Larson

Hi all, OpenWorm <http://openworm.org/> is an open source project and open science community dedicated to creating the world’s first whole organism in a computer, a C. elegans nematode<https://en.wikipedia.org/wiki/Caenorhabditis_elegans>, via bottom-up computational modeling. It is an association of highly motivated scientists, engineers, coders, and curious citizens from around the world who believe in open science and open access. While our ultimate goal is to simulate every cell in the c. elegans, we are starting out by building a model of its body and environment, its nervous system, and its muscle cells. At the center of this is an incrementally improving detailed multi-compartmental representation of the c. elegans nervous system<http://docs.openworm.org/en/latest/Projects/datarep.html#neuroml-connectome>. You can read more about our neuromechanical modeling approach in our online documentation<http://docs.openworm.org/en/latest/modeling.html#closing-the-loop-with-neur…> . We've recently pulled together a page<http://www.openworm.org/science.html> that focuses content that is relevant to experimental biologists and other scientists in a single place online. http://www.openworm.org/science.html This outreach effort is aimed at creating a conversation between biologists collecting data and making observations and computational modelers building models and validating them against real data. We invite the comp-neuro community to have a look, provide feedback, and join the conversation! Thanks, Stephen Larson, Ph.D Project coordinator http://openworm.org

April 19, 2014

Postdoc/engineer positions in Parkinsons/DBS and Neuroprosthetics

by Dawn Taylor

We currently have multiple openings for Postdocs and/or engineers for two newly funded studies. Detailed descriptions of each study are listed below. If interested, please send a CV to Dr. Dawn Taylor at dxt42(a)case.edu. 1) The goal of the *Parkinson's* project is to understand how Parkinson's disease alters cortical network processing and how *Deep Brain Stimulation (DBS)* can be improved to better re-normalize motor processing. Cortical network activity will be recorded in monkeys via intracortical electrode arrays before and after making the animals hemi-Parkinsonian via injections of the selective neurotoxin MPTP (note this toxin is initially applied in such a way that the animal only develops parkinsonian symptoms on one half of its body so the animal can still groom, ambulate, and take care of itself). DBS will then be applied to two subcortical regions (subthalamic nucleus and globus pallidus) to alleviate Parkinsonian symptoms. Computational models of the cortical microcircuit will be developed that accurately reflect the recorded cortical activity in the normal and Parkinsonian states as well as under the influence of different DBS patterns. The model parameters that need to be changed to make the network computational model behave like the recorded experimental data under the different conditions will be informative regarding the underlying mechanisms of DBS. The refined computational model will also be used to rapidly screen for new DBS patterns that are more effective at restoring normal cortical network processing. The improved DBS patterns suggested by the computational model will then be validated by testing those novel patterns in the monkeys. This project is being done in conjunction with Dr. Cameron McIntyre who will oversee the computational modelling part of the study. We are looking for multiple post docs that can focus on either the animal work, the computational modeling, or both depending on their skills and interests. 2) The long-term goal of the *Neuroprosthetics* project is to enable paralyzed individuals to use their brain signals to control their upper limb via implanted muscle stimulators. Most labs working on brain-controlled neuroprosthetics decode intended limb kinematics (e.g. velocity, joint angles, etc.) from the recorded brain signals. However, that approach still requires converting those kinematic commands into the appropriate stimulation patterns required to generate the desired limb motion. That conversion process has not been resolved for the upper limb due to the limb's complex dynamical nature and the fact that the limb is subject to unknown external forces during use. We bypass this obstacle by retraining the brain to control muscle stimulators directly. We have come up with some novel, but clinically feasible ways of mapping neural signals directly to muscle stimulators. Our methods can enable the user to have good control over both limb motion and stiffness. To demonstrate and refine our methods, we are training monkeys to control the movements of a realistic musculoskeletal model of a paralyzed limb activated via implanted muscle stimulators. The paralyzed limb simulator (developed by the lab of Robert Krisch) provides real-time visual feedback to the animal of the limb motion that would result from stimulating the paralyzed muscles based on the animal's neural signals decoded in real time. The use of this real-time paralyzed arm simulator allows us to test and refine our process of brain-controlled muscle stimulation in monkeys without actually having to paralyze any animals. -- Dawn M. Taylor, Ph.D. Assistant Professor of Neuroscience, Cleveland Clinic Researcher Scientist, Cleveland VA Medical Center, Functional Electrical Stimulation Center Assistant Professor of Biomedical Engineering & of Molecular Medicine, Case Western Reserve University The Cleveland Clinic Lerner Research Institute 9500 Euclid Ave. / NC30 Cleveland, OH 44195 email: dxt42(a)case.edu or taylord8(a)ccf.org Phone: (216) 636-0140 Fax: (216) 778-4259

April 18, 2014

Major change in NIH Policy regarding Revision (Amended) Applications -- NOT-OD-14-074

by Glanzman, Dennis (NIH/NIMH) [E]

I am writing to let the community know that effective immediately, NIH no longer limits applicants to a single Revision Application (A1). >From today's Notice: "... following an unsuccessful resubmission (A1) application, applicants may submit the same idea as a new (A0) application for the next appropriate due date." See the full Notice online at: http://grants.nih.gov/grants/guide/notice-files/NOT-OD-14-074.html Dennis L. Glanzman, Ph.D. Chief, Theoretical and Computational Neuroscience Program National Institute of Mental Health, NIH, DHHS 6001 Executive Boulevard Room 7192; MSC 9637 Bethesda, MD 20892-9637 Telephone: (301) 443-6429

April 17, 2014

Postdoctoral position in systems neuroscience at the University of Manchester

by Mark Humphries

We seek an electrophysiologist to join a team investigating the neural basis of perception. This is a BBSRC-funded project led by Dr Rasmus Petersen in collaboration with Dr Mark Humphries at the University of Manchester, UK. The project is a multidisciplinary team effort involving both experimentalists and computational modellers. Your primary role will be experimental. You will be using state-of-the-art electrophysiological methods to investigate active perception in an awake, behaving in vivo model, using a whisker-guided sensory discrimination task. You will also have the opportunity to develop your skills in data analysis. You will hold a Ph.D. in neuroscience and experience of electrophysiological recording in vivo. Experience with data analysis is an advantage. The position is immediately available and will be for up to 3 years. For more details and to apply, please visit: https://www.jobs.manchester.ac.uk/displayjob.aspx?jobid=7514 Informal enquiries can be made to Dr Rasmus Petersen. Email r.petersen(a)manchester.ac.uk<mailto:r.petersen@manchester.ac.uk> Dr Mark Humphries MRC Senior non-Clinical Research Fellow AV Hill Building Faculty of Life Sciences University of Manchester http://www.systemsneurophysiologylab.ls.manchester.ac.uk/

April 17, 2014

Fully funded combined theoretical and experimental neuroscience PhD at UCL

by Peter Latham

We are looking for an exceptional candidate to carry out a combined theoretical and experimental PhD. The student will receive training from two labs: Professor Peter Latham (Gatsby Computational Neuroscience Unit; theory) and Professor Michael Hausser (Wolfson Institute for Biomedical Research; experiment). The candidate will initially be based at the Gatsby Unit with Professor Latham, taking courses in computational neuroscience and developing theories at the circuit level; the rest of the PhD will be with Professor Hausser testing those theories using advanced experimental tools for linking neural circuit function with behavior (most notably targeted optogenetics and fast 2-photon imaging). The applicant should have a strong analytical background and a keen interest in neuroscience. Experience in an experimental lab is desirable but not absolutely necessary. The applicant will be fully funded for four years. Start date is flexible (but ideally by 1 October 2014). Closing date is May 15! Applicants should apply directly to Professor Latham (pel(a)gatsby.ucl.ac.uk) Please send, in PDF or plain text format where possible, the following: - CV - statement of research interests, - transcript(s) for previous degrees, and arrange for three academic letters of recommendation, also to pel(a)gatsby.ucl.ac.uk . For further details of research interests please visit our websites: Latham: http://www.gatsby.ucl.ac.uk/~pel/ Hausser: http://www.dendrites.org/

April 16, 2014

Second Call for Papers: LDAB@CIBB2014

by Andrea Bracciali

[We apologize if you have received multiple copies of this message] ==================================================== Second Call for Papers Large-scale and HPC data analysis in bioinformatics: Intelligent methods for computational, systems and synthetic biology. 26-28 June 2014 University of Cambridge, UK http://www.cussb.unisr.it/cibb2014/ss.html#LSAHDAIB Special Session of CIBB 2014: Eleventh International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics http://www.cussb.unisr.it/cibb2014/index.html *** Submission deadline: 5th May 2014 *** ==================================================== AIMS and SCOPE Biomedical research is currently facing the Big Data wave created by the huge amount of experiments performed every day in omics sciences. This new situation demands appropriate IT-infrastructures and scalable software to analyse data within an acceptable timespan. Massive parallel clusters, distributed technologies, on-Chip solutions such as GPGPU and Xeon Phi must be exploited with adequate algorithmic solutions to reach their full potential. The aim of this special session is to bring together researchers interested in cutting-edge methods to address the challenges posed by the huge amount of data produced in omics science. The idea is to present the latest advancements concerning High Performance Computing solutions required to treat multi-omics data and the related Big Data paradigms that are needed to manage the large-scale challenges of current computational biology. Examples of relevant areas of interest within this context include - but are not limited to - - Next-Generation Sequencing data analysis and interpretation, - Genomics patterns identification and mining, - Transcriptomics and Proteomics data integration, - Systems Biology models simulation and optimization, - Structural Biology and Molecular Dynamics, - Synthetic Biology circuits design and simulation. SUBMISSION GUIDELINES http://www.cussb.unisr.it/cibb2014/calls.html#submissions Papers should be submitted in PDF format on the Easy Chair conference system. Paper length should be at least 4 pages and should not exceed 6 pages. Papers are required to be structured according to the following five sections: • 1. Scientific background • 2. Material and methods • 3. Results • 4. Conclusion • 5. References (no more than 10) (Please refer to the latex template on the web page for more accurate instructions). Please note that only PDF versions of papers can be accepted, as the proceedings of CIBB will be produced starting from them. A correct submission requires selecting this special session in the submission system. PUBLICATION Each paper will be peer-reviewed and the resulting scores used to determine invitations for oral or poster presentations. Following the conference, an extended version of the presented contributions (12 page format) will be considered for publication in the Springer’s Lecture Notes in Bioinformatics (LNBI) series. Moreover, a selection of the best papers will be considered for pu blication in a special issue of BMC Bioinformatics dedicated to CIBB2014. IMPORTANT DATES Paper submission: 5th May 2014 Acceptance notification: 10th May 2014 Camera ready due: 30th May 2014 Conference: 26th - 28th June 2014 ORGANISERS Andrea Bracciali, University of Stirling, UK Ivan Merelli, CNR-ITB, Italy CONTACTS Andrea Bracciali, University of Stirling, UK Computing Science and Mathematics School of Natural Sciences Stirling University abb(a)cs.stir.ac.uk +44 (0)1786 467446 Ivan Merelli, CNR-ITB, Italy Institute for Biomedical Technologies Consiglio Nazionale delle Ricerche ivan.merelli(a)itb.cnr.it +39 02 26422600

April 16, 2014

Post-doctoral position - Boston University

by Michael Hasselmo

Post-doctoral position – Boston University The Hasselmo laboratory in the Center for Memory and Brain at Boston University is looking for a post-doctoral fellow to work on a multi-disciplinary university research initiative (MURI) project in collaboration with the Leonard and Roy labs at MIT and the Milford lab at QUT. Applicants should have experience in the area of robotics with an emphasis on spatial navigation and computational neuroscience. This background should include a degree in electrical engineering, computer science, computational neuroscience or mechanical engineering. The successful candidate will extend current research on goal directed spatial behavior, including work on modeling navigation in robots guided by models of neurophysiological circuits. He/she will also implement previously developed computational models in 3D simulation environments and robotic hardware. The ideal candidate will have experience in path planning, autonomous navigation, computational modeling, neural networks, AI and/or computer vision. Excellent programming skills in MATLAB, Python and/or C++ are a must. Experience in implementing computational models on hardware platforms is a plus. Requirements: - A degree in one of the following areas: electrical engineering, computer science, computational neuroscience, mechanical engineering. - Experience in robotics, mathematical modeling, autonomous navigation, and/or neural networks. - Excellent coding skills in MATLAB, C++ and/or Python. -- Prof. Michael Hasselmo Center for Memory and Brain, Department of Psychological and Brain Sciences, Graduate Program for Neuroscience, Principal Investigator, ONR Multi-disciplinary University Research Initiative on Grid cells and Autonomous Systems, Boston University, 2 Cummington St., Boston, MA, 02215, USA Tel: (617) 353-1397, e-mail: hasselmo(a)bu.edu, http://www.bu.edu/hasselmo

April 16, 2014

Recruitment for Post-doctoral Position: Sinapse, Singapore

by Wong Kian Foong

Postdoctoral Research in Neuroimaging Data Processing and Analysis National University of Singapore – Singapore Institute for Neurotechnology (Cognitive Engineering Group) A postdoctoral appointment is available in the Singapore Institute for Neurotechnology (SINAPSE) (http://sinapseinstitute.org/) at National University of Singapore. The post-holder will be a member Professor Anastasios Bezerianos’s group focused on Neuroimaging data processing and analysis. Professor Bezerianos’s group makes use of concurrent EEG and fMRI recording to study the mechanisms of brain under various mental states. We are looking for a research fellow who is interested in developing and employing advanced signal processing techniques for analysis of neuroimaging data and developing pattern recognition approaches to classify different brain states. The candidate has to have expertise in design and running of fMRI experiments, management of fMRI data and knwoledge of existing tools for fMRI image analaysis The ideal candidate should have a strong background in Neuroimaging data processing and (or) machine learning techniques. Previous experience on multimodal neuroimaging signal processing techniques is preferable but not necessary. Previous research experience with concurrent EEG/fMRI techniques would be an advantage. You will have the ability to manage the day-to-day running of research project including assisting junior researchers, and good communication and writing skills. You will have to and should be able to work independently as well as in a team. You will have the ability to deliver results to the required standard and schedule. The position is full-time fixed-term for minimum 1 year in the first instance with potential 2 year extension. Competitive salaries according to the NUS standards. Interested applicants will be required to send you CV and supporting documents to: Prof. Anastasios Bezerianos Singapore Institute for Neurotechnology National University of Singapore Email: tassos.bezerianos(a)nus.edu.sg

April 16, 2014

Applications open for INCF two-day course "Introduction to neuroinformatics"

by Malin Sandström

Dear all, Application is now open for our two-day course "Introduction to Neuroinformatics" in Leiden in August. The course aim is to give researchers and advanced students an introduction to the field, with lectures given by carefully selected world experts. The content is suitable for both neuroscience and informatics backgrounds. Please help us spread the word to fellow researchers and students in your department! There is no course fee, and we have some travel support available. The application deadline is May 20th. More info: http://www.incf.org/community/events/incf-short-course-2014 Download course poster: http://www.incf.org/community/events/incf-short-course-2014/at_download/eve… In case of questions, please contact Mathew Abrams on course-admin(a)incf.org Best regards, Malin -- Malin Sandström, PhD Community Engagement Officer malin.sandstrom(a)incf.org International Neuroinformatics Coordinating Facility Karolinska Institutet Nobels väg 15 A SE-171 77 Stockholm Sweden http://www.incf.org

April 16, 2014

BCF/NWG course "Analysis and Models in Neurophysiology" 2014 at the Bernstein Center Freiburg, Germany

by Birgit Ahrens

BCF/NWG-Course "Analysis and Models in Neurophysiology" /Sunday, October 5 - Friday, October 10, 2014 / /Bernstein Center Freiburg, Hansastraße 9a, 79104 Freiburg, Germany/ *Aim of the course:* The course is intended to provide advanced Diploma/Masters and PhD students, as well as young researchers from the neurosciences with approaches for the analysis of electrophysiological data and the theoretical concepts behind them. *The course includes various topics such as*: * Neuron models and spike train statistics * Point processes and correlation measures * Systems and signals * Local field potentials The course will consist of lectures in the morning and and matching exercises using Matlab and Mathematica in the afternoon. Experience with these software packages will be helpful but is not required for registration. The participants should have a basic understanding of scientific programming. This course is designated especially for advanced diploma/master-students and PhD-students (preferentially in their first year). *Application:* Please apply by sending one pdf document containing your CV and a meaningful letter of motivation to nwg-course(a)bcf.uni-freiburg.de. The letter of motivation should refer to the following points: * Reasons for wanting to take this course * Background in mathematics * Experience using Matlab/Python/Mathematika * Background in neuroscience The course is limited to 20 participants. *Course fees:* NWG members - 50EUR, others - 125EUR *Application deadline: *June 30, 2014 *More information: *http://www.bcf.uni-freiburg.de/events/conferences-workshops/20141005-nwgcourse *-- Dr. Birgit Ahrens --* Teaching & Training Coordinator Bernstein Center Freiburg University of Freiburg Hansastr. 9a D - 79104 Freiburg Germany Phone: +49 (0) 761 203-9575 Fax: +49 (0) 761 203-9559

April 16, 2014