biblio.bib

@inproceedings{pieper20043d,
  title={3D Slicer},
  author={Pieper, Steve and Halle, Michael and Kikinis, Ron},
  booktitle={IEEE International Symposium on Biomedical Imaging: Nano to Macro},
  pages={632--635},
  year={2004},
  organization={IEEE}
}

@book{penny2011statistical,
  title={Statistical parametric mapping: the analysis of functional brain images},
  author={Penny, William D and Friston, Karl J and Ashburner, John T and Kiebel, Stefan J and Nichols, Thomas E},
  year={2011},
  publisher={Academic press}
}


@article{gorgolewski2011nipype,
  title={Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in {P}ython},
  author={Gorgolewski, Krzysztof and Burns, Christopher D and Madison, Cindee and Clark, Dav and Halchenko, Yaroslav O and Waskom, Michael L and Ghosh, Satrajit S},
  journal={Frontiers in Neuroinformatics},
  volume={5},
  number={3},
  year={2011}
}

@article{SHER-14,
  title={{CBRAIN}: a web-based, distributed computing platform for collaborative neuroimaging research},
  author={Sherif, Tarek and Rioux, Pierre and Rousseau, Marc-Etienne and Kassis, Nicolas and Beck, Natacha and Adalat, Reza and Das, Samir and Glatard, Tristan and Evans, Alan C},
  journal={Frontiers in Neuroinformatics},
  volume=8,
  number=54,
  year=2014
}

@article{das2016mni,
  title={The MNI data-sharing and processing ecosystem},
  author={Das, Samir and Glatard, Tristan and MacIntyre, Leigh C and Madjar, Cecile and Rogers, Christine and Rousseau, Marc-Etienne and Rioux, Pierre and MacFarlane, Dave and Mohades, Zia and Gnanasekaran, Rathi and others},
  journal={NeuroImage},
  volume={124},
  pages={1188--1195},
  year={2016},
  publisher={Elsevier}
}

@inproceedings{hull2004treating,
  title={Treating “shimantic web” syndrome with ontologies},
    author={Hull, Duncan and Stevens, Robert and Lord, Phillip and Wroe, Chris and Goble, Carole},
      year={2004}
}


 @Misc{cwl,
  author =    {Amstutz, Peter and Crusoe, Michael R.  and Tijanić, Nebojša  and Chapman, Brad and Chilton, John  and Heuer, Michael  and Kartashov, Andrey  and Leehr, Dan  and Ménager, Hervé  and Nedeljkovich, Maya and Scales, Matt and Soiland-Reyes, Stian  and Stojanovic, Luka },
  title =     {Common Workflow Language, v2.0},
  month =     Jul,
  year =      2016,
  doi = {https://dx.doi.org/10.6084/m9.figshare.3115156.v2}
}

@inproceedings{plankensteiner2011iwir,
  title={IWIR: a language enabling portability across grid workflow systems},
  author={Plankensteiner, Kassian and Montagnat, Johan and Prodan, Radu},
  booktitle={Proceedings of the 6th workshop on Workflows in support of large-scale science},
  pages={97--106},
  year={2011},
  organization={ACM}
}


, Geneva, Switzerland, 2016.

@InProceedings{GLAT-16,
  author =       {Glatard, Tristan and Quirion, Pierre-Olivier  and Adalat, Reza  and Beck, Natacha and Bernard, Remi and Caron, Bryan L. and Nguyen, Quan  and Rioux, Pierre  and Rousseau, Marc-Étienne and Evans, Alan C. and Bellec, Pierre},
  title =        {Integration between PSOM and CBRAIN for distributed execution of neuroimaging pipelines},
  booktitle = {Meeting of the Organization for Human Brain Mapping},
  year =      {2016},
  address =   {Geneva, Switzerlad}
}

@article{bellec2012pipeline,
  title={{The Pipeline System for Octave and Matlab (PSOM): a lightweight scripting framework and execution engine for scientific workflows}},
  author={Bellec, Pierre and Lavoie-Courchesne, S{\'e}bastien and Dickinson, Phil and Lerch, Jason and Zijdenbos, Alex and Evans, Alan C},
  journal={Frontiers in neuroinformatics},
  volume={6},
  number = 7,
  year={2012}
  }

@Article{glatard2016fgcs,
  author =       {Glatard, Tristan and Rousseau, Marc-\'Etienne and Camarasu-Pop, Sorina and Adalat, Reza and Beck, Natacha and Das, Samir and Ferreira da Silva, Rafael and Khalili-Mahani, Najmeh and Korkhov, Vladimir and Quirion, Pierre-Olivier and Rioux, Pierre and Olabarriaga, S\'ilvia D. and Bellec, Pierre and Evans, Alan C.},
  title =        {Software architectures to integrate workflow engines in science gateways},
  journal =      {Future Generation Computer Systems (under revisions)},
  year =         {2017}
}

@Article{Craddock2016,
author="Craddock, R. Cameron
and Bellec, Pierre
and Margules, Daniel S.
and Nichols, B. Nolan
and Pfannm{\"o}ller, J{\"o}rg P.
and Badhwar, AmanPreet
and Kennedy, David
and Poline, Jean-Baptiste
and Toro, Roberto
and Cipollini, Ben
and Rokem, Ariel
and Clark, Daniel
and Gorgolewski, Krzysztof J.
and Craddock, R. Cameron
and Craddock, R. Cameron
and Clark, Daniel J.
and Das, Samir
and Madjar, C{\'e}cile
and Sengupta, Ayan
and Mohades, Zia
and Dery, Sebastien
and Deng, Weiran
and Earl, Eric
and Demeter, Damion V.
and Mills, Kate
and Mihai, Glad
and Ruzic, Luka
and Ketz, Nick
and Reineberg, Andrew
and Reddan, Marianne C.
and Goddings, Anne-Lise
and Gonzalez-Castillo, Javier
and Gorgolewski, Krzysztof J.
and Froehlich, Caroline
and Dekel, Gil
and Margulies, Daniel S.
and Craddock, R. Cameron
and Fulcher, Ben D.
and Glatard, Tristan
and Das, Samir
and Adalat, Reza
and Beck, Natacha
and Bernard, R{\'e}mi
and Khalili-Mahani, Najmeh
and Rioux, Pierre
and Rousseau, Marc-{\'E}tienne
and Evans, Alan C.
and Halchenko, Yaroslav O.
and Castello, Matteo Visconti di Oleggio
and Hern{\'a}ndez-P{\'e}rez, Ra{\'u}l
and Morales, Edgar A.
and Cuaya, Laura V.
and Ito, Kaori L.
and Liew, Sook-Lei
and Johnson, Hans J.
and Kan, Erik
and Anglin, Julia
and Borich, Michael
and Jahanshad, Neda
and Thompson, Paul
and Liew, Sook-Lei
and Margulies, Daniel S.
and Falkiewicz, Marcel
and Huntenburg, Julia M.
and O'Connor, David
and Clark, Daniel J.
and Milham, Michael P.
and Craddock, R. Cameron
and Pereira, Ramon Fraga
and Heinsfeld, Anibal S{\'o}lon
and Franco, Alexandre Rosa
and Buchweitz, Augusto
and Meneguzzi, Felipe
and Pfannm{\"o}ller, J{\"o}rg P.
and Mesquita, Rickson
and Herrera, Luis C. T.
and Dentico, Daniela
and Sochat, Vanessa
and Nichols, B. Nolan
and Heinsfeld, Anibal S{\'o}lon
and Franco, Alexandre Rosa
and Buchweitz, Augusto
and Meneguzzi, Felipe
and Villalon-Reina, Julio E.
and Garyfallidis, Eleftherios",
title="2015 Brainhack Proceedings",
journal="GigaScience",
year="2016",
volume="5",
number="1",
pages="1--26",
abstract="I1 Introduction to the 2015 Brainhack Proceedings",
issn="2047-217X",
doi="10.1186/s13742-016-0147-0",
url="http://dx.doi.org/10.1186/s13742-016-0147-0"
}
@inproceedings{larrabide2009gimias,
  title={GIMIAS: an open source framework for efficient development of research tools and clinical prototypes},
  author={Larrabide, Ignacio and Omedas, Pedro and Martelli, Yves and Planes, Xavier and Nieber, Maarten and Moya, Juan A and Butakoff, Constantine and Sebasti{\'a}n, Rafael and Camara, Oscar and De Craene, Mathieu and others},
  booktitle={International Conference on Functional Imaging and Modeling of the Heart},
  pages={417--426},
  year={2009},
  organization={Springer}
}

@inproceedings{toussaint2007medinria,
  title={MedINRIA: medical image navigation and research tool by INRIA},
  author={Toussaint, Nicolas and Souplet, Jean-Christophe and Fillard, Pierre and others},
  booktitle={Proc. of MICCAI},
  volume={7},
  pages={280},
  year={2007},
  organization={Citeseer}
}

@inproceedings{heckel2009object,
  title={Object-oriented application development with MeVisLab and Python.},
  author={Heckel, Frank and Schwier, Michael and Peitgen, Heinz-Otto},
  booktitle={GI Jahrestagung},
  pages={1338--1351},
  year={2009}
}

@article{nolden2013medical,
  title={The medical imaging interaction toolkit: challenges and advances},
  author={Nolden, Marco and Zelzer, Sascha and Seitel, Alexander and Wald, Diana and M{\"u}ller, Michael and Franz, Alfred M and Maleike, Daniel and Fangerau, Markus and Baumhauer, Matthias and Maier-Hein, Lena and others},
  journal={International journal of computer assisted radiology and surgery},
  volume={8},
  number={4},
  pages={607--620},
  year={2013},
  publisher={Springer}
}

@article{delaitre2005gemlca,
  title={GEMLCA: Running legacy code applications as grid services},
  author={Delaitre, Thierry and Kiss, Tamas and Goyeneche, Ariel and Terstyanszky, Gabor and Winter, Stephen and Kacsuk, Peter},
  journal={Journal of Grid Computing},
  volume={3},
  number={1-2},
  pages={75--90},
  year={2005},
  publisher={Springer}
}

@article{terstyanszky2014enabling,
  title={Enabling scientific workflow sharing through coarse-grained interoperability},
  author={Terstyanszky, Gabor and Kukla, Tamas and Kiss, Tamas and Kacsuk, Peter and Balask{\'o}, {\'A}kos and Farkas, Zoltan},
  journal={Future Generation Computer Systems},
  volume={37},
  pages={46--59},
  year={2014},
  publisher={Elsevier}
}