How to cite the Neuroscience Gateway

If you used resources available from the NSG for your research, please cite us as follows:
S Sivagnanam, A Majumdar, K Yoshimoto, V Astakhov, A Bandrowski, M. E. Martone, and N. T. Carnevale. Introducing the Neuroscience Gateway, IWSG, volume 993 of CEUR Workshop Proceedings, CEUR-WS.org, 2013.

Neuroscience publications, posters enabled by NSG:

  1. Pelot NA, Behrend C, Grill W. Modeling the response of small myelinated axons in a compound nerve to kilohertz frequency signals, J. Neural Engineering, 2017 Mar 31, doi: 10.1088/1741-2552/aa6a5f
  2. Bielczyk, N., Piskała, K., Płomecka, M., Todorova, L., Poleszczuk, J., Foryś, U. (2017). A Switch Between Cooperation and Competition: Hopf Bifurcation as a Mechanism for Decision Making in Presence of Ambivalent Stimuli. Front Comp Neurosci. (under review)
  3. Karunamuni, Roshan A., Tyler M. Seibert, Nathan S. White, Linda McEvoy, Nikdokht Farid, James Brewer, Anders M. Dale, Carrie R. McDonald, and Jona A. Hattangadi-Gluth. "Abnormalities in hippocampal volume of glioma patients prior to radiotherapy." Acta Oncologica (2017): 1-4.
  4. Krishnan, Giri P., Sylvain Chauvette, Isaac Shamie, Sara Soltani, Igor Timofeev, Sydney S. Cash, Eric Halgren, and Maxim Bazhenov. "Cellular and neurochemical basis of sleep stages in the thalamocortical network." eLife 5 (2016): e18607.
  5. Short SM, Morse TM, McTavish TS, Shepherd GM, and Verhagen, "Respiration Gates Sensory Input Resonses in the Mitral Cell Layer of the Olfactory Bulb," PLoS One, 2016 Dec 22; 11(12);e0168356. doi:10.1371/journal.pone.0168356. eCollection 2016.
  6. Marianne J Bezaire, Ivan Raikov, Kelly Burk, Dhrumil Vyas, Ivan Soltesz, "Interneuronal mechanisms of hippocampal theta oscillation in a full-scale model of the rodent CA1 circuit," eLife December 2016; 10.7554/eLife.18566; DOI: http://dx.doi.org/10.7554/eLife.18566.
  7. Samuel A Neymotin, Benjamin A Suter, Salvador Dura-Bernal, Gordon M. G. Shepherd, Michele Migliore, William W. Lytton, "Optimizing computer models of corticospinal neurons to replicatae in vitro dynamics," Journal of Neurophysiology Oct 2016, Vol. 117, pages 148--162, Jn. 00570.2016; DOI: 10.1152/jn.00570.2016
  8. Evans, Benjamin D., and Konstantin Nikolic. "From bytes to insights with modelling as a service a new paradigm for computational modelling illustrated with PyRhO." In Biomedical Circuits and Systems Conference (BioCAS), 2016 IEEE, pp. 316-319. IEEE, 2016.
  9. William W. Lytton, Alexandra H. Seidenstein, Salvador Dura-Bernal, Robert A. McDougal, Felix Schurmann and Michael L. Hines , "Simulation Neurotechnologies for Advancing Brain Research: Parallelizing Large Networks in NEURON," Neural Computation 2016 28:10, 2063-2090 .
  10. G. P. Krishnan, M. Komarov, S. Skorheim, M. Bazhenov, "Slow-wave sleep improves learning through spike sequence replay", Poster, Society for Neuroscience Annual Meeting, San Diego, Nov 12-16, 2016.
  11. P. Sanda, P. Malerba, G. P. Krishnan, M. Bazhenov, "Precise Ripple Timing affects Spatio-Temporal pattern of sleep slow oscillations in a Model of Memory Consolidation", Poster, Society for Neuroscience Annual Meeting, San Diego, Nov 12-16, 2016.
  12. P. Malerba, A. L. Fodder, M. W. Jones, M. Bazhenov, "Modeling of coordinated sequence replay in ca3 and ca1 during sharp wave-ripples", Poster, Society for Neuroscience Annual Meeting, San Diego, Nov 12-16, 2016.
  13. Y. Wei, G. P. Krishnan, M. Bazhenov, "Effect of learning cues on sleep-related memory consolidation depends on the phase of sleep slow oscillation," Poster, Society for Neuroscience Annual Meeting, San Diego, Nov 12-16, 2016.
  14. Y. Wei, G. P. Krishnan, M. Bazhenov, "Synaptic mechanisms of memory consolidation during NREM sleep", Poster, Society for Neuroscience Annual Meeting, San Diego, Nov 12-16, 2016.
  15. Short SM, Morse TM, McTavish TS, Shepherd GM, Verhagen JV, "Respiration Gates Sensory Input Responses in the Mitral Cell Layer of the Olfactory Bulb," poster 524. 38th Annual AChemS Meeting, 2016.
  16. McDougal, Robert A. and Morse, Thomas M. and Carnevale, Ted and Marenco, Luis and Wang, Rixin and Migliore, Michele and Miller, Perry L. and Shepherd, Gordon M. and Hines, Michael L., "Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience", journal="Journal of Computational Neuroscience", year="2016", pages="1--10",issn="1573-6873", doi="10.1007/s10827-016-0623-7", url="http://dx.doi.org/10.1007/s10827-016-0623-7"
  17. Dura-Bernal S, Neymotin S.A., Kerr C.C., Sivagnanam S., Majumdar A., Francis J.T., Lytton W.W., Evolutionary algorithm optimization of biological parameters in a biomimetic neuroprosthesis, IBM Journal of Research and Development . Computational Neuroscience Special Issue, 2016 (in press).
  18. Rumbell, Timothy H., Danel Dragulji., Aniruddha Yadav, Patrick R. Hof, Jennifer I. Luebke, and Christina M. Weaver. "Automated evolutionary optimization of ion channel conductances and kinetics in models of young and aged rhesus monkey pyramidal neurons." Journal of computational neuroscience (2016): 1-26. http://www.ncbi.nlm.nih.gov/pubmed/27106692
  19. Van Geit W, Gevaert M, Chindemi G, Rssert C, Courcol J, Muller EB, Schrmann F, Segev I and Markram H (2016). BluePyOpt: Leveraging open source software and cloud infrastructure to optimise model parameters in neuroscience. Front. Neuroinform. 10:17. doi: 10.3389/fninf.2016.00017
  20. R. McDougal; A. Bulanova; W. Lytton, "Reproducibility in Computational Neuroscience Models and Simulations," in IEEE Transactions on Biomedical Engineering , vol. 63, pages. 2021--2035, doi: 10.1109/TBME.2016.2539602
  21. Hodge, Victoria; Jessop, Mark; Fletcher, Martyn; Weeks, Michael; Turner, Aaron; Jackson, Tom; Ingram, Colin; Smith, Leslie and Austin, Jim", "A Digital Repository and Execution Platform for Interactive Scholarly Publications in Neuroscience", journal="Neuroinformatics", vol. 14, no. 1, pp 23-40, year 2016.
  22. Dura-Bernal S, Suter BA, Neymotin SA, Kerr CC, Quintana A, Gleeson P, Shepherd GMG, Lytton WW. NetPyNE: a Python package for NEURON to facilitate development and parallel simulation of biological neuronal networks. Computational Neuroscience (CNS), 2016.
  23. Guet-McCreight A, Camire. O, Topolnik L, Skinner FK. Using A Semi-Automated Strategy To Develop Multi-Compartment Models That Predict Biophysical Properties Of Interneuron Specific 3 (IS3) Cells In Hippocampus. eNeuro. 3(4). 2016, pii: ENEURO.00877-16.2016 .
  24. Short SM, McTavish TS, Morse TM, Shepherd GM, Verhagen JV," Circuit models identify mechanisms of respiration driven lateral inhibition underlying mitral activity", SfN Nanosymposium 561.08, 2015.
  25. Shahand, S. (2015). Science gateways for biomedical big data analysis.
  26. Dura-Bernal S, Majumdar A, Neymotin SA, Sivagnanam S, Francis JT, Lytton WW. A dynamic data-driven approach to closed-loop neuroprosthetics based on multiscale biomimetic brain models. IEEE Conference on High Performance Computing 2015 Workshop: Dynamic Data Driven Applications Systems (DDDAS), 2015.
  27. Stockton DB, Santamaria F. NeuroManager: a workflow analysis based simulation management engine for computational neuroscience. Frontiers in Neuroinformatics. 2015;9:24. doi:10.3389/fninf.2015.00024.
  28. S.A Neymotin, B.A. Suter, M. Migliore, S. Dura-Bernal, G.M.G. Shepard, W.W. Lytton, .Optimizing computer models of layer 5 motor cortex pyramidal neurons using somatic whole cell recordings,. Society for Neuroscience Annual Meeting (poster), Chicago, IL, October, 2015.
  29. Dura-Bernal S, Suter BA, Neymotin SA, Quintana AJ, Gleeson P, Shepherd GMG, Lytton WW. .Normalized cortical depth (NCD) as a primary coordinate system for cell connectivity in cortex: experiment and model.. Society for Neuroscience (SFN), Chicago, IL, October 2015.
  30. A. Seidenstein, S.A. Neymotin, A. Fesharaki, M.L. Hines, R.A., McDougal, A.S. Bulanova, W.W. Lytton, .Neuronal network bump attractors augmented by calcium up-regulation of lh in multiscale computer model of prefrontal cortex,. Society for Neuroscience Annual Meeting (poster), Chicago, IL, October, 2015.
  31. C. Mitelut, S. L. Gratiy, D. Denman, J. H. Siegle, S. Durand, K. Godfrey, C. Lee, R.C. Reid, M. Hawrylycz, C. Koch, N.V. Swindle, C. Anastassiou, .Standardizing spike sorting: an In vitro, in silico and In vivo study to develop quantitative metrics for sorting extracellularly recorded spiking activity,. Society for Neuroscience Annual Meeting (poster), Chicago, IL, October, 2015.
  32. A.H. Seidenstein, R.A. McDougal, M.L. Hines, A.Fesharaki, W.W. Lytton, .Parallelizing large networks using NEURON-python,. Computational Neuroscience (CNS) Annual Meeting (poster), Prague, July, 2015.
  33. Pelot, Nicole A., Christina E. Behrend, and Warren M. Grill. "Modeling the response of small myelinated and unmyelinated axons to kilohertz frequency signals." In 2015 7th International IEEE/EMBS Conference on Neural Engineering (NER), pp. 406-409. IEEE, 2015.
  34. Shahand, Shayan, Ammar Benabdelkader, Mohammad Mahdi Jaghoori, Mostapha al Mourabit, Jordi Huguet, Matthan WA Caan, Antoine HC Kampen, and Sílvia D. Olabarriaga. "A data‐centric neuroscience gateway: design, implementation, and experiences." Concurrency and Computation: Practice and Experience 27, no. 2 (2015): 489-506.
  35. Neymotin SA, Suter BA, Migliore M, Dura-Bernal S, Shepherd GMG, Lytton WW. Optimizing computer models of layer 5 motor cortex pyramidal neurons using somatic whole-cell recordings. Society for Neuroscience (SFN), 2015.
  36. M. Schirner, S. Rothmeier, V. K. Jirsa, A. R. McIntosh, P. Ritter, An Automated Pipeline for Constructing Personalized Virtual Brains from Multimodal Neuroimaging Data, NeuroImage, March 2015; doi:10.1016/j.neuroimage.2015.03.055
  37. Rumbell, Timothy, Danel Dragulj., Jennifer Luebke, Patrick Hof, and Christina M. Weaver. "Prediction of ion channel parameter differences between groups of young and aged pyramidal neurons using multi-stage compartmental model optimization." BMC Neuroscience 16, no. 1 (2015): 1.
  38. Forrest MD, .Simulation of Alcohol Action upon a Detailed Purkinje Neuron Model and a Simpler Surrogate Model that runs >400 times faster.. BMC Neuroscience 2015, 16:27.
  39. Guet-McCreight A, Camire. O, Topolnik L, Skinner FK. (2016). Poster Presentation: Developing Multi-Compartment Models of Interneuron Specific 3 (IS3) Cells in Hippocampus Using a Semi-Automated Approach. 2-B-17 CAN2016, Canadian Association for Neuroscience, May, 2016.
  40. T. Rumbell, D. Draguljic, J. I. Luebke, P. R. Hof, C. M. Weaver, .Compartmental model optimization predicts altered channel densities and kinetics in aged versus young pyramidal neurons of rhesus monkey prefrontal cortex., Society for Neuroscience Annual Meeting, Washington D.C., Nov. 15-19, 2014.
  41. Rumbell, Timothy, Danel Dragulji., Jennifer Luebke, Patrick Hof, and Christina M. Weaver., "Automatic fitness function selection for compartment model optimization." BMC Neuroscience 15, no. Suppl 1 (2014): O5.
  42. Lee S, Marchionni I, Bezaire MJ, Danielson N, Lovett-Barron M, Losonczy A, Soltesz I. (2014) .GABAergic Basket Cells Differentiate Among Hippocampal Pyramidal Cells. Neuron., 1129-1144, June 4, 2014.
  43. Ingber L, Pappalepore M, and Stesiak R, .Electroencephalographic fiend influence on calcium momentum waves,. Journal of Theoretical Biology, Volume 343, pp 138-153, February 2014.

Cyberinfrastructure related NSG publications, posters:

  1. A. Majumdar, S. Sivagnanam, T. Carnevale, K. Yoshimoto, "The Neuroscience Gateway - Enabling Large-Scale Neuroscience Simulations and Data Processing Using Supercomputers, " Poster, Third Annual BREAIN Initiative PI Meeting, Bethesda, MD, Dec 12-14, 2016.
  2. S. Sivagnanam, A. Majumdar, P. Kumbhar, M. Hines, K. Yoshomoto, T. Carnevale, "Neuroscience Gateway - Understanding the scaling behavior of NEURON application, " Poster, SC16, Salt Lake City, Utah, November, 2016.
  3. A. Majumdar, S. Sivagnanam, K. Yoshimoto, T. Carnecvale, "Understanding Collaborative Cyberinfrastructure Need of Neuroscientists - Survey Results", White Paper, September, 2016.
  4. S. Sivagnanam, A. Majumdar, K. Yoshimoto, T. Carnevale, "NSG-R: Programmatic Access to Neuroscience Applications on HPC," Poster XSEDE16, Miami, July 17-21, 2016.
  5. N. T. Carnevale, P. Gleeson, R. A. Silver, A. Majumdar, S. Sivagnanam, K. Yoshimoto, "Seamless Integration of Neuroscience Models and Tools with High Performance Computing, " Poster, Society for Neuroscience Annual Meeting, San Diego, Nov 12-16, 2016.
  6. Majumdar, A., Sivagnanam, S., Yoshimoto, K., Carnevale, N. T., Quintana, A., Gleeson, P. and Silver, R. A., "NSG-R Programmatic access to neuroscience applications", poster, Workshop Collaborative Development of Data-Driven Models of Neural Systems, HHMI Janelia Research Campus, Virginia, USA, Sept 18-21, 2016.
  7. Majumdar A, Sivagnanam S, Carnevale NT, Yoshimoto K, Gleeson P, Quintana A and Silver RA (2016), "Neuroscience Gateway - Cyberinfrastructure Providing Supercomputing Resources for Large Scale Computational Neuroscience Research," Front. Neuroinform. Conference Abstract: Neuroinformatics 2016. Neuroinformatics 2016, Reading, United Kingdom, 3 Sep - 4 Sep, 2016. doi: 10.3389/conf.fninf.2016.20.00008
  8. A. Majumdar, S. Sivagnanam, K. Yoshimoto, T. Carnevale, "Understanding the Evolving Cyberinfrastructure Needs of the Neuroscience Community," Proceedings of the XSEDE16 Conference on Diversity, Big Data, and Science at Scale (XSEDE16). ACM, New York, NY, USA, , Article 45 , 7 pages. DOI: http://dx.doi.org/10.1145/2949550.2949657
  9. S. Sivagnanam, A. Majumdar, K. Yoshimoto, T. Carnevale, "NSG-R: Programmatic Access to Neuroscience Applications," (poster) Proceedings XSEDE16, Miami, July 17-21, 2016.
  10. S. Dura-Bernal, S. A. Neymotin, W. L. Lytton, A. Majumdar, and S. Sivagnanam, " A Dynamic Data-Driven Approach to Closed-loop Neuroprosthetics Based on Multiscale Biomimetic Brain Models," Dynamic data Driven Application Systems Workshop, IEEE International Conference on High Performance Computing, Dec. 16-19, 2015, Bengaluru, India.
  11. S. Sivagnanam, A. Majumdar, P. Kumbhar, M. Hines, K. Yoshimoto, T. Carnevale, .Neuroscience Gateway . Enabling HPC for Computational Neuroscience,. Supercomputing 2015 (poster), Austin, TX, November, 2015.
  12. T. Carnevale, A. Majumdar, S. Sivagnanam, K. Yoshimoto, P. Gleeson, R.A. Silver. Seamless integration of neuroscience models and tools with high performance computing. Poster, Society for Neuroscience Annual Meeting, Chicago, IL, Oct. 17 - 21, 2015.
  13. B. Lytton, M. Hines, .NEURON and the Neuroscience Gateway Portal,. HPC Workshop, 2015 Computational Neuroscience Annual Meeting, Prague, July, 2015.
  14. M. Miller, T. Schwartz, P. Hoover, K. Yoshimoto, S. Sivagnanam, A. Majumdar, "The CIPRES Workbench: A Flexible Framework for Creating Science Gateways", Proceedings XSEDE15, St. Louis, MO, July 26-30, 2015.
  15. 7. A. Majumdar, S. Sivagnanam, K. Yoshimoto, T. Carnevale, .Neuroscience Gateway . Seamless Access to XSEDE High Performance Computing Resources for the Computational Neuroscience Community,. XSEDE 15 Conference (poster), St. Louis, MO, July 26-30, 2015.
  16. Ted Carnevale, Amit Majumdar, Subhashini Sivagnanam, Kenneth Yoshimoto, Vadim Astakhov, Anita Bandrowski, Maryann Martone, “The Neuroscience Gateway Portal - High Performance Computing Made Easy,” Poster, Computational Neuroscience (CNS) 2014 Annual Meeting, Quebec City, Canada, July 26-31, 2014.
  17. S. Sivagnanam, A. Majumdar, K. Yoshimoto, V. Astakhov, A. Bandrowski, M. Martone, and N. T. Carnevale, "Early experiences in developing and managing the neuroscience gateway," Journal of Concurrency and Computation: Practice and Experience,Vol 27, Issue 2, pages 473-488, 2015 UR: http://dx.doi.org/10.1002/cpe.3283.
  18. Ted Carnevale, Amit Majumdar, Subhashini Sivagnanam, Kenneth Yoshimoto, Vadim Astakhov, Anita Bandrowski, Maryann Martone, " High performance computing in neuroscience via the Neuroscience Gateway Portal", Poster, Society for Neuroscience Annual Meeting, Washington D.C, Nov. 15 - 19, 2014.
  19. Ted Carnevale, Amit Majumdar, Subhashini Sivagnanam, Kenneth Yoshimoto, Vadim Astakhov, Anita Bandrowski, Maryann Martone, .The Neuroscience Gateway Portal - High Performance Computing Made Easy,. BMC Neuroscience, Vol 15, No 1, 2014, doi="10.1186/1471-2202-15-S1-P101", url="http://dx.doi.org/10.1186/1471-2202-15-S1-P101.
  20. N.T. Carnevale, A. Majumdar, S. Sivagnanam, K. Yoshimoto, V. Astakhov, A. Bandrowski, M. Martone, "The Neuroscience Gateway Portal: facilitating access to high performance computing resources," Poster, Society for Neuroscience Annual Meeting, San Diego, Nov. 9-13, 2013.
  21. S. Sivagnanam, K. Yoshimoto, A. Majumdar, N. T. Carnevale, V. Astakhov, M. Martone, A. Bandrowski, "A Neuroscience Gateway: Software and Implementation," Proceedings XSEDE13 Gateway to Discovery, San Diego, CA, July 22-25, 2013.
  22. S. Sivagnanam, A. Majumdar, K. Yoshimoto, N. T. Carnevale, V. Astakhov, A. Bandrowski, M. Martone, "Introducing The Neuroscience Gateway," Proceedings International Workshop on Science Gateways , Zurich, Switzerland, June 3-5, 2013.
  23. N.T. Carnevale, S. Sivagnanam, K. K. Yoshimoto, V. Astakhov, A. E. Bandrowski, M. E. Martone, A. Majumdar, "A Neuroscience Gateway for High Performance Computing," Poster,Society for Neuroscience Annual Meeting, New Orleans, October 13-17, 2012.

Educational projects/publications:

  1. NSG webinar tutorial was given for the .NIH BRAIN Initiative Summer Course on Models and Neurobiology. at University of Missouri, Columbia, MO, June 13, 2016. 24 pre- and post-docs and faculties attended this workshop which was funded by NIH R25 Research and Training grant http://engineering.missouri.edu/neuro/outreach/nih-neuroscience-course/
  2. S. Sahand, .Science Gateways for biomedical big data analysis,. Ph. D Thesis, 2015, University of Amsterdam, http://hdl.handle.net/11245/1.490613
  3. Alexandre Guet McCreight, .Predicting Cell-Type Specific Active Properties by Developing Multi-Compartment Models Using Databases and Electrophysiological Feature Constraints: Application to Interneuron Specific 3 (IS3) Cells in the Hippocampus., Master.s Thesis, University of Toronto, August, 2015.
  4. Kait Folweiler, .Computational Model of the Dentate Gyrus,. Ph.D qualifying research, 2015, University of Pennsylvania.
  5. Another research project, titled, .Dendritic Excitation Dependence on Synaptic Democracy in CA1 Pyramidal Neurons,. Chung, P, George, V, and Hermiz, J used the NSG for their research. Ref. http://www.isn.ucsd.edu/courses/bggn260/2013/reports/Chung_George_Hermiz.pdf (2014)i
  6. NSG was used in a class project by graduate student Nikki Pelot, Biomedical Engineering, Duke University, 2014.
  7. The NSG was used by attendees of the Open Source Brain Hackathon in London in November, 2013 (http://www.opensourcebrain.org/projects/osb/wiki/Hackathon2013), where users tested large scale models of cortical networks on the NSG provided resources during the meeting. This was reported by Padraig Gleeson who ran the workshop and is from the Department of Neuroscience, Physiology and Pharmacology, University College of London.