From 40a3bf9481c43e6cc756c5a9225766a513fce3d9 Mon Sep 17 00:00:00 2001 From: Michael Hanke Date: Sat, 1 Jun 2013 10:56:57 +0200 Subject: [PATCH] Attempt to collect literature on and around NeuroDebian --- bib/references.bib | 140 ++++++++++++++++++++++++++++++++++++++++ sphinx/whoisusingit.rst | 82 +++++++++++++++++++++++ 2 files changed, 222 insertions(+) create mode 100644 bib/references.bib create mode 100644 sphinx/whoisusingit.rst diff --git a/bib/references.bib b/bib/references.bib new file mode 100644 index 0000000..5b160ab --- /dev/null +++ b/bib/references.bib @@ -0,0 +1,140 @@ +@inproceedings{GBC+2010, + title={Nipype: opensource platform for unified and replicable interaction with existing neuroimaging tools}, + author={Ghosh, S and Burns, C and Clark, D and Gorgolewski, K and Halchenko, Y and Madison, C and Tungaraza, R and Millman, KJ}, + booktitle={16th Annual Meeting of the Organization for Human Brain Mapping}, + pages={106}, + year={2010} +} + +@article{NDR+2011, + title={Lin4Neuro: a customized Linux distribution ready for neuroimaging analysis}, + author={Nemoto, Kiyotaka and Dan, Ippeita and Rorden, Christopher and Ohnishi, Takashi and Tsuzuki, Daisuke and Okamoto, Masako and Yamashita, Fumio and Asada, Takashi}, + journal={BMC medical imaging}, + volume={11}, + number={1}, + pages={3}, + year={2011}, + publisher={BioMed Central Ltd} +} + +@article{YIO+2012, + title={Simulation Platform: A cloud-based online simulation environment}, + author={Yamazaki, Tadashi and Ikeno, Hidetoshi and Okumura, Yoshihiro and Satoh, Shunji and Kamiyama, Yoshimi and Hirata, Yutaka and Inagaki, Keiichiro and Ishihara, Akito and Kannon, Takayuki and Usui, Shiro}, + journal={Neural networks}, + volume={24}, + number={7}, + pages={693--698}, + year={2011}, + publisher={Elsevier} +} + +@article{GDL+2011, + title={The connectome viewer toolkit: an open source framework to manage, analyze, and visualize connectomes}, + author={Gerhard, Stephan and Daducci, Alessandro and Lemkaddem, Alia and Meuli, Reto and Thiran, Jean-Philippe and Hagmann, Patric}, + journal={Frontiers in neuroinformatics}, + volume={5}, + year={2011}, + publisher={Frontiers Media SA} +} + +@article{Agu2012, + title={FIASCO, VoxBo, and MEDx: Behind the code}, + author={Aguirre, Geoffrey K}, + journal={NeuroImage}, + volume={62}, + number={2}, + pages={765--767}, + year={2012}, + publisher={Elsevier} +} + +@article{MST2012, + author={Mathôt, S. and Schreij, D. and Theeuwes, J.}, + year={2012}, + title={OpenSesame: An open-source, graphical experiment builder for the social sciences}, + journal={Behavior Research Methods}, + volume={44}, + pages={314--324}, + doi={10.3758/s13428-011-0168-7} +} + +@inproceedings{SLZ+2011, + title={A cloud-based data-sharing and analysis cyberinfrastructure for neuroinformatics}, + author={Stoner, R and Larson, S and Zaslavsky, I and Hill, S and Ellisman, M and Courchesne, E}, + booktitle={Front. Neuroinform. Conference Abstract: 4th INCF Congress of Neuroinformatics. doi: 10.3389/conf. fninf}, + volume={34}, + year={2011} +} + +@article{SMT+2011, + title={Integrative visualization of temporally varying medical image patterns}, + author={Soh, Jung and Mei Xiao, Thao Do and Meruvia-Pastor, Oscar and Sensen, Christoph W}, + journal={Journal of integrative bioinformatics}, + volume={8}, + number={2}, + pages={161}, + year={2011} +} + +@inproceedings{MDT+2012, + title={Mouse neuroimaging phenotyping in the cloud}, + author={Minervini, Massimo and Damiano, Mario and Tucci, Valter and Bifone, Angelo and Gozzi, Alessandro and Tsaftaris, Sotirios A}, + booktitle={Image Processing Theory, Tools and Applications (IPTA), 2012 3rd International Conference on}, + pages={55--60}, + year={2012}, + organization={IEEE} +} + +@inproceedings{GDS+2012, + title={A hierachical configuration system for a massively parallel neural hardware platform}, + author={Galluppi, Francesco and Davies, Sergio and Rast, Alexander and Sharp, Thomas and Plana, Luis A and Furber, Steve}, + booktitle={Proceedings of the 9th conference on Computing Frontiers}, + pages={183--192}, + year={2012}, + organization={ACM} +} + +@article{CCT+2012, + title={Meta-analytic clustering of the insular cortex Characterizing the meta-analytic connectivity of the insula when involved in active tasks}, + author={Cauda, Franco and Costa, Tommaso and Torta, Diana ME and Sacco, Katiuscia and D'Agata, Federico and Duca, Sergio and Geminiani, Giuliano and Fox, Peter T and Vercelli, Alessandro}, + journal={Neuroimage}, + year={2012}, + publisher={Elsevier} +} + +@article{GEF+2012, + title={Oral contraceptive use changes brain activity and mood in women with previous negative affect on the pill—A double-blinded, placebo-controlled randomized trial of a levonorgestrel-containing combined oral contraceptive}, + author={Gingnell, Malin and Engman, Jonas and Frick, Andreas and Moby, Lena and Wikstr{\"o}m, Johan and Fredrikson, Mats and Sundstr{\"o}m-Poromaa, Inger}, + journal={Psychoneuroendocrinology}, + year={2012}, + publisher={Elsevier} +} + +@article{GMB+2012, + title={Menstrual cycle effects on amygdala reactivity to emotional stimulation in premenstrual dysphoric disorder}, + author={Gingnell, Malin and Morell, Arvid and Bannbers, Elin and Wikstr{\"o}m, Johan and Poromaa, Inger Sundstr{\"o}m}, + journal={Hormones and behavior}, + year={2012}, + publisher={Elsevier} +} + +@article{Mil2012, +title = "Open Neuroscience Solutions for the Connectome-wide Association Era", +journal = "Neuron", +volume = "73", +number = "2", +pages = "214--218", +year = "2012", +doi = "10.1016/j.neuron.2011.11.004", +url = "http://www.sciencedirect.com/science/article/pii/S0896627311010038", +author = "Michael Peter Milham" +} + +@article{Vis2012, + author={Vişan, Ana-Maria}, + title={Temporal meta-programming: treating time as a spatial dimension}, + year={2012}, + journal={Computer Science Dissertations}, + volume={27}, + url={http://hdl.handle.net/2047/d20002935} +} diff --git a/sphinx/whoisusingit.rst b/sphinx/whoisusingit.rst new file mode 100644 index 0000000..2601699 --- /dev/null +++ b/sphinx/whoisusingit.rst @@ -0,0 +1,82 @@ +.. -*- mode: rst; fill-column: 78; indent-tabs-mode: nil -*- +.. vi: set ft=rst sts=4 ts=4 sw=4 et tw=79: + ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### + # + # See COPYING file distributed along with the NeuroDebian package for the + # copyright and license terms. + # + ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### + + +.. index:: Who is using it?, Publications +.. _chap_whoisusingit: + +**************** +Who Is Using It? +**************** + + +.. only:: html + + If you are using NeuroDebian or have published a study employing it, please + leave a comment at the bottom of this page, if you want to be listed here as + well. + + +Tools and systems built atop NeuroDebian +======================================== + +* ref:`Nemoto et al., BMC Medical Imaging (2011) `: Lin4Neuro: a + customized Linux distribution ready for neuroimaging analysis. + +* ref:`Stoner et al., Frontiers in Neuroinformatics (2012) `: + A cloud-based data-sharing and analysis cyberinfrastructure for + neuroinformatics. + +Articles referring to NeuroDebian +================================= + +* :ref:`Yamazaki et al., NeuralNetworks (2011) `: Simulation platform: + A cloud-based online simulation environment. + +* ref:`Aguirre, NeuroImage (2012) `: FIASCO, VoxBo, and MEDx: Behind + the code. + +* ref:`Mathôt et al., Behavioral Research Methods (2012) `: OpenSesame: + An open-source, graphical experiment builder for the social sciences. + +* ref:`Minervini et al., Image Processing Theory, Tools and Applications (2012) + `: Mouse neuroimaging phenotyping in the cloud. + +* ref:`Galluppi et al., Computing Frontiers (2012) `: A hierachical + configuration system for a massively parallel neural hardware platform. + +* ref:`Cauda et al., NeuroImage (2012) `: Meta-analytic clustering of + the insular cortex Characterizing the meta-analytic connectivity of the insula + when involved in active tasks. + +* ref:`Gingnell et al., Psychoneuroendocrinology (2012) `: Oral + contraceptive use changes brain activity and mood in women with previous + negative affect on the pill—A double-blinded, placebo-controlled randomized + trial of a levonorgestrel-containing combined oral contraceptive. + +* ref:`Gingnell et al., Hormones and Behavior (2012) `: Menstrual + cycle effects on amygdala reactivity to emotional stimulation in premenstrual + dysphoric disorder. + +* ref:`Milham, Neuron, (2012) `: Open Neuroscience Solutions for the + Connectome-wide Association Era. + +* ref:`Visan, Computer Science Dissertations (2012) `: Temporal + meta-programming: treating time as a spatial dimension. + +* ref:`Gerhard et al., Frontiers in Neuroinformatics (2011) `: The + connectome viewer toolkit: an open source framework to manage, analyze, and + visualize connectomes. + +* ref:`Soh et al., Journal of Integrative Bioinformatics (2011) `: + Integrative visualization of temporally varying medical image patterns. + +* ref:`Gosh et al., HBM (2010) `: Nipype: opensource platform for + unified and replicable interaction with existing neuroimaging tools. + -- 2.39.2