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Interoperability Of Neuroscience Modeling Software: Current Status And Future Directions

R C Cannon, M O Gwealtig, P Gleeson, H Cornelis, M L Hines, F W Howell, J R Stiles, S Wills, E de Schutter
2007 Zenodo  
We assess the current state of interoperability of neural simulation software and explore the future directions that will enable the field to advance.  ...  Neuroscience increasingly uses computational models to assist in the exploration and interpretation of complex phenomena.  ...  Robert Cannon was supported by NIH NIDA grant DA16454 as part of the CRCNS program. Michael Hines is funded by grants NINDS NS11613 (NEURON) and NIH DC04732 (ModelDB).  ... 
doi:10.5281/zenodo.810888 fatcat:5ruhjgbxsrhqngdmbscjirb4yi

Interoperability of Neuroscience Modeling Software: Current Status and Future Directions

Robert C. Cannon, Marc-Oliver Gewaltig, Padraig Gleeson, Upinder S. Bhalla, Hugo Cornelis, Michael L. Hines, Fredrick W. Howell, Eilif Muller, Joel R. Stiles, Stefan Wils, Erik De Schutter
2007 Neuroinformatics  
We assess the current state of interoperability of neural simulation software and explore the future directions that will enable the field to advance.  ...  Neuroscience increasingly uses computational models to assist in the exploration and interpretation of complex phenomena.  ...  The aim of the workshop was to assess the current state of interoperability of neural simulation software and to explore the future directions that will enable the field to advance.  ... 
doi:10.1007/s12021-007-0004-5 pmid:17873374 pmcid:PMC2658651 fatcat:b4dvutgqpba4vdb5d65dmewmfi

Innovation in biological microscopy: Current status and future directions

Jason R. Swedlow
2012 Bioessays  
The current revolution in biological microscopy stems from the realisation that advances in optics and computational tools and automation make the modern microscope an instrument that can access all scales  ...  As these and more new technologies appear, the challenges of delivering them to the community grows as well.  ...  In this overview, I summarise the current state of the field of biological microscopy and highlight some challenges for the future.  ... 
doi:10.1002/bies.201100168 pmid:22408015 pmcid:PMC3427900 fatcat:ybxzbxidpratnm5djbykylw3ym

Biological imaging software tools

Kevin W Eliceiri, Michael R Berthold, Ilya G Goldberg, Luis Ibáñez, B S Manjunath, Maryann E Martone, Robert F Murphy, Hanchuan Peng, Anne L Plant, Badrinath Roysam, Nico Stuurman, Jason R Swedlow (+2 others)
2012 Nature Methods  
Narayanswamy of the Roysam lab for their assistance in preparing figures, and L. Kamentsky and M. Bray of the Carpenter lab for useful input and edits on the manuscript.  ...  A.E.C. and K.W.E. were supported by US National Institutes of  ...  of image data representation, which will in the future substantially improve their interoperability.  ... 
doi:10.1038/nmeth.2084 pmid:22743775 pmcid:PMC3659807 fatcat:6wnzuhdrdfd67o72cmcgwwpgka

MPScope: A versatile software suite for multiphoton microscopy

Quoc-Thang Nguyen, Philbert S. Tsai, David Kleinfeld
2006 Journal of Neuroscience Methods  
The combination of optimized code, multithreading and COM (Common Object Model) technologies enables MPScope to fully take advantage of custom-built two-photon microscopes and to simplify their realization  ...  The analysis program MPView allows viewing of stored frames, projections, automatic detection of cells and plotting of their average intensity across frames, direct frame transfer to Matlab, AVI movie  ...  P.S.T. and D.K. are supported by the National Institute of Health (RR021907 and EB003832) and the National Science Foundation (DBI0455027).  ... 
doi:10.1016/j.jneumeth.2006.03.001 pmid:16621010 fatcat:kwziev625jhjjfdmq5nlovgozm

A Survey of Fuzzy Systems Software: Taxonomy, Current Research Trends, and Prospects

Jesus Alcala-Fdez, Jose M. Alonso
2016 IEEE transactions on fuzzy systems  
and to develop well founded future work.  ...  Moreover, we provide a snapshot of the status of the publications in this field according to the ISI Web of Knowledge.  ...  TIC-6858 and P11-TIC-7765, and the GENIL program of the CEI BioTIC GRANADA under Grant PYR-2014-2.  ... 
doi:10.1109/tfuzz.2015.2426212 fatcat:dwnvwkek35emhnjwb3etcmb3ry

Statistical Software for Psychology: Comparing Development Practices Between CRAN and Other Communities [article]

Spencer Smith, Yue Sun, Jacques Carette
2018 arXiv   pre-print
We also recommend close coupling of source code and documentation, to improve verifiability.  ...  Method: We compared and ranked 30 software tools with respect to adherence to best software engineering practices on items that could be measured by end-users.  ...  Categories and Status The development models of each package fell into three categories: 1.  ... 
arXiv:1802.07362v1 fatcat:vwxdthekdbalphjv3gxxfvqb4y

M2.15 Assessment report on 'FAIRness of software'

Morane Gruenpeter, Roberto Di Cosmo, Hylke Koers, Patricia Herterich, Rob Hooft, Jessica Parland-von Essen, Jonas Tana, Tero Aalto, Sarah Jones
2020 Zenodo  
Furthermore, we present an analysis of nine resources that call for the recognition of software in academia and that present guidelines or recommendations to improve its status - either by becoming more  ...  We identify the challenges of different stakeholders when it comes to finding and reusing software.  ...  We have also analyzed nine current resources that call for the recognition of software in academia and present guidelines or recommendations to improve software status, by becoming FAIR or by improving  ... 
doi:10.5281/zenodo.5472911 fatcat:wscidegolfbdvmpiowhh6ipn7y

Grids and Grid technologies for wide-area distributed computing

Mark Baker, Rajkumar Buyya, Domenico Laforenza
2002 Software, Practice & Experience  
The last decade has seen a substantial increase in commodity computer and network performance, mainly as a result of faster hardware and more sophisticated software.  ...  Nevertheless, there are still problems, in the fields of science, engineering, and business, which cannot be effectively dealt with using the current generation of supercomputers.  ...  ACKNOWLEDGEMENTS The authors would like to acknowledge all developers of the systems or projects described in this article.  ... 
doi:10.1002/spe.488 fatcat:qcgblfolg5aori5m4fncgqdhsy

Strategic Plan for a Scientific Software Innovation Institute (S2I2) for High Energy Physics [article]

Peter Elmer, Mark Neubauer, Michael D. Sokoloff
2018 arXiv   pre-print
The discovery of the Higgs boson, the observation of exceedingly rare decays of B mesons, and stringent constraints on many viable theories of physics beyond the Standard Model (SM) demonstrate the great  ...  The quest to understand the fundamental building blocks of nature and their interactions is one of the oldest and most ambitious of human scientific endeavors.  ...  The workshop focused both on the current status and the 5-10 year time scale covered by the CWP.  ... 
arXiv:1712.06592v2 fatcat:gm6v2suqj5dkphccrp4bcsymau

TractoR: Magnetic Resonance Imaging and Tractography withR

Jonathan D. Clayden, Susana Muñoz Maniega, Amos J. Storkey, Martin D. King, Mark E. Bastin, Chris A. Clark
2011 Journal of Statistical Software  
In this manuscript we describe a software tool called TractoR (for "Tractography with R"), a collection of packages for the R language and environment, along with additional infrastructure for straightforwardly  ...  Applications for these techniques cover a broad spectrum of research, including many preclinical and clinical studies, and in some cases these methods are working their way into widespread routine use.  ...  Note that since this is an abstraction, the layout of session directories may change in a future version of the software.  ... 
doi:10.18637/jss.v044.i08 fatcat:tqxtxfxzpja3xkv6fhg46t6jxi

A separation-based UI architecture with a DSL for role specialization

Ivan Gibbs, Sergiu Dascalu, Frederick C. Harris, Jr.
2015 Journal of Systems and Software  
A climate science application was created to verify the validity of the methodology using modern practices of UX, DSLs, code generation, and model-driven engineering.  ...  Analyzing related work provides an overview of other methods similar to our method. Subsequently we evaluate the climate science application, conclude, and detail future work.  ...  Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.  ... 
doi:10.1016/j.jss.2014.11.039 fatcat:26w427j3mjf63i44iepwpwci7q

Reconfiguring film studies through software cinema and procedural spectatorship

Marina Hassapopoulou, Mediarep.Org
2018 NECSUS : European journal of media studies  
The increasing use of software and database aesthetics in film and video production has created hybrid modes of spectatorship by altering the dynamic between media production and reception.  ...  Just as early cinema prepared audiences and worked as a buffer for shocks of technological and industrial modernity, software cinema trains the viewer in new modes of film spectatorship and new modes of  ...  Acknowledgements The author would like to thank professors Terry Harpold, Barbara Mennel, Roger Beebe, and the anonymous NECSUS peer reviewers for their feedback and editing suggestions. Notes  ... 
doi:10.25969/mediarep/15146 fatcat:mqzrliynsjdj7jh6nen7e2paae

The NIF LinkOut Broker: A Web Resource to Facilitate Federated Data Integration using NCBI Identifiers

Luis Marenco, Giorgio A. Ascoli, Maryann E. Martone, Gordon M. Shepherd, Perry L. Miller
2008 Neuroinformatics  
The NLB is designed to coordinate the assembly of links to neuroscience information items (e.g., experimental data, knowledge bases, and software tools) that are (1) accessible via the Web, and (2) related  ...  The paper describes the current NLB system and discusses certain design issues that arose during its implementation.  ...  Health, Department of Health and Human Services, under Contract No.  ... 
doi:10.1007/s12021-008-9025-y pmid:18975149 pmcid:PMC2704600 fatcat:7amfwzpe3fhszjjslcd4o76hxu

BlenderPhotonics: an integrated open-source software environment for three-dimensional meshing and photon simulations in complex tissues

Yuxuang Zhang, Qianqian Fang
2022 Journal of Biomedical Optics  
We responded to the above challenge by combining the powerful, open-source three-dimensional (3D) modeling software, Blender, with state-of-the-art 3D mesh generation and MC simulation tools, utilizing  ...  The lack of efficient tools to accurately model tissue structures and subsequently perform quantitative multiphysics modeling greatly impedes the clinical translation of these modalities.  ...  Code, Data, and Materials Availability The latest BlenderPhotonics software can be downloaded at http://mcx.space/bp.  ... 
doi:10.1117/1.jbo.27.8.083014 pmid:35429155 pmcid:PMC9010662 fatcat:pr7dktilw5cf7jmt5wof32mnka
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