Citation Relationships

Gewaltig MO, Cannon R (2014) Current practice in software development for computational neuroscience and how to improve it. PLoS Comput Biol 10:e1003376 [PubMed]

References and models cited by this paper

References and models that cite this paper

Baxter SM, Day SW, Fetrow JS, Reisinger SJ (2006) Scientific software development is not an oxymoron. PLoS Comput Biol 2:e87 [Journal] [PubMed]

Bednar JA (2009) Topographica: Building and Analyzing Map-Level Simulations from Python, C/C++, MATLAB, NEST, or NEURON Components. Front Neuroinform 3:8 [Journal] [PubMed]

Bhalla US, Bilitch DH, Bower JM (1992) Rallpacks: a set of benchmarks for neuronal simulators. Trends Neurosci 15:453-8 [PubMed]

Bower JM, Beeman D (1998) The Book Of Genesis: Exploring Realistic Neural Models With The General Neural Simulation System

Brooks F (1995) The mythical man-month: essays on software engineering

Cannon RC, Gewaltig MO, Gleeson P, Bhalla US, Cornelis H, Hines ML, Howell FW, Muller E, Stiles JR, Wils S, De Schutter E (2007) Interoperability of neuroscience modeling software: current status and future directions. Neuroinformatics 5:127-38 [Journal] [PubMed]

Cannon RC, O'Donnell C, Nolan MF (2010) Stochastic ion channel gating in dendritic neurons: morphology dependence and probabilistic synaptic activation of dendritic spikes. PLoS Comput Biol [Journal] [PubMed]

   Stochastic ion channels and neuronal morphology (Cannon et al. 2010) [Model]

Davison AP, BrĂ¼derle D, Eppler J, Kremkow J, Muller E, Pecevski D, Perrinet L, Yger P (2008) PyNN: A Common Interface for Neuronal Network Simulators. Front Neuroinform 2:11 [Journal] [PubMed]

De Schutter E (2008) Why are computational neuroscience and systems biology so separate? PLoS Comput Biol 4:e1000078 [Journal] [PubMed]

De Schutter E (2013) Collaborative modeling in neuroscience: time to go open model? Neuroinformatics 11:135-6 [Journal] [PubMed]

Diesmann M, Gewaltig MO, Aertsen A (1995) SYNOD: An environment forneural systems simulations: Language interface and tutorial Tel Aviv:Weizmann Institute of Science

Djurfeldt M, Hjorth J, Eppler JM, Dudani N, Helias M, Potjans TC, Bhalla US, Diesmann M, Kotaleski JH, Ekeberg O (2010) Run-time interoperability between neuronal network simulators based on the MUSIC framework. Neuroinformatics 8:43-60 [Journal] [PubMed]

Donoho DL, Maleki A, Ur_rahman I , Shahram M, Stodden V (2009) Fifteen years of reproducible research in computational harmonic analysis Ieee Computing In Science And Engineering 11:8-18

Gewaltig M-O, Diesmann M (2007) NEST (Neural Simulation Tool) Scholarpedia 2:1430

Gillespie DT (1977) Exact stochastic simulation of coupled chemical reactions. Journal Of Physical Chemistry 81:2340-2361

Gleeson P, Crook S, Cannon RC, Hines ML, Billings GO, Farinella M, Morse TM, Davison AP, Ray S, Bhalla US, Barnes SR, Dimitrova YD, Silver RA (2010) NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. PLoS Comput Biol 6:e1000815 [Journal] [PubMed]

Gleeson P, Steuber V, Silver RA (2007) neuroConstruct: a tool for modeling networks of neurons in 3D space. Neuron 54:219-35 [Journal] [PubMed]

Goddard N, Hood G, Howell F, Hines M, De_Schutter E (2001) NEOSIM: Portable largescaleplug and play modelling Neurocomputing 38-40:1657-1661

Goodman D, Brette R (2008) Brian: a simulator for spiking neural networks in python. Front Neuroinform 2:5 [Journal] [PubMed]

Heroux M, Bartlett R, Howle V, Hoekstra R, Hu J, Et_al (2003) An overview of Trilinos. Sandina National Laboratories Report 2003-2927

Hines ML, Carnevale NT (2003) NEURON simulation environment The Handbook of Brain Theory and Neural Networks (2nd Ed)

House_of_Commons_Science_and_Technology_Committee (2010) The disclosure of climate data from the Climatic Research Unit at the University of East Anglia Eighth Report of Session 2009-10

Ince DC, Hatton L, Graham-Cumming J (2012) The case for open computer programs. Nature 482:485-8 [Journal] [PubMed]

Interagency_modeling , Analysis_group (2009) Futures Meeting: the impact of modeling on biomedical research, final report;-9-99-IFM2009_Final_Report.doc

Izhikevich EM (2003) Simple model of spiking neurons. IEEE Trans Neural Netw 14:1569-72 [Journal] [PubMed]

   Artificial neuron model (Izhikevich 2003, 2004, 2007) [Model]

Izhikevich EM (2010) Hybrid spiking models. Philos Trans A Math Phys Eng Sci 368:5061-70 [Journal] [PubMed]

Kennedy D (2006) Where's the beef ? Missing data in the information age. Neuroinformatics 4:271-3 [Journal] [PubMed]

Markram H (2006) The blue brain project. Nat Rev Neurosci 7:153-60 [Journal] [PubMed]

Matsumoto M, Nishimura T (1998) Marsenne Twister: A 623-dimensionally equidistributed uniform pseudorandom number generator ACM Trans On Modelling And Computer Simulation 8:3-30

Miller G (2006) Scientific publishing. A scientist's nightmare: software problem leads to five retractions. Science 314:1856-7 [Journal] [PubMed]

National_Science_Foundation (2010) Dear Colleague Letter: Software Infrastructure for Sustained Innovation (SI2) NSF 10-029

Nelson B (2009) Data sharing: Empty archives. Nature 461:160-3 [Journal] [PubMed]

Neylon C, Aerts J, Brown CT, Coles SJ, Hatton L, Lemire D, Millman KJ, Murray-Rust P, Perez F, Saunders N, Shah N, Smith A, Varoquaux G, Willighagen E (2012) Changing computational research. The challenges ahead. Source Code Biol Med 7:2 [Journal] [PubMed]

Perlewitz J (2013)

Post DE, Votta LG (2005) Computational science demands a new paradigm Phys Today 58:35-41

Wilson G (2006) Where's the real bottleneck in scientific computing Am Sci 94:15-16

Jedrzejewski-Szmek Z, Abrahao KP, Jedrzejewska-Szmek J, Lovinger DM, Blackwell KT (2018) Parameter Optimization Using Covariance Matrix Adaptation-Evolutionary Strategy (CMA-ES), an Approach to Investigate Differences in Channel Properties Between Neuron Subtypes. Front Neuroinform 12:47 [Journal] [PubMed]

   Parameter optimization using CMA-ES (Jedrzejewski-Szmek et al 2018) [Model]

Stockton DB, Santamaria F (2015) NeuroManager: a workflow analysis based simulation management engine for computational neuroscience. Front Neuroinform 9:24 [Journal] [PubMed]

   NeuroManager: a workflow analysis based simulation management engine (Stockton & Santamaria 2015) [Model]

(38 refs)