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@article{Itu2013,
abstract = {We propose a CFD-based approach for the non-invasive hemodynamic assessment of pre- and post-operative coarctation of aorta (CoA) patients. Under our approach, the pressure gradient across the coarctation is determined from computational modeling based on physiological principles, medical imaging data, and routine non-invasive clinical measurements. The main constituents of our approach are a reduced-order model for computing blood flow in patient-specific aortic geometries, a parameter estimation procedure for determining patient-specific boundary conditions and vessel wall parameters from non-invasive measurements, and a comprehensive pressure-drop formulation coupled with the overall reduced-order model. The proposed CFD-based algorithm is fully automatic, requiring no iterative tuning procedures for matching the computed results to observed patient data, and requires approximately 6-8 min of computation time on a standard personal computer (Intel Core2 Duo CPU, 3.06 GHz), thus making it feasible for use in a clinical setting. The initial validation studies for the pressure-drop computations have been performed on four patient datasets with native or recurrent coarctation, by comparing the results with the invasively measured peak pressure gradients recorded during routine cardiac catheterization procedure. The preliminary results are promising, with a mean absolute error of less than 2 mmHg in all the patients.},
author = {Itu, Lucian and Sharma, Puneet and Ralovich, Krist\'{o}f and Mihalef, Viorel and Ionasec, Razvan and Everett, Allen and Ringel, Richard and Kamen, Ali and Comaniciu, Dorin},
doi = {10.1007/s10439-012-0715-0},
file = {:home/tomaton/Downloads/ralovich2013abme.pdf:pdf},
issn = {00906964},
journal = {Annals of Biomedical Engineering},
keywords = {CFD,Coarctation of aorta,Non-invasive,PC-MRI,Pressure gradient,Reduced-order models},
number = {4},
pages = {669--681},
pmid = {23232558},
title = {{Non-invasive hemodynamic assessment of aortic coarctation: Validation with in vivo measurements}},
volume = {41},
year = {2013}
}
@article{Gupta1993,
abstract = {Parallel computers have demonstrated a remarkable potential for achieving high performance at a reasonable cost for many computer vision and image processing (CVIP) applications. A major obstacle to the use of parallel computers is the lack of a universally accepted metric to study the scalability of parallel algorithms and architectures. The authors apply different scalability measures to various 2-D FFT algorithms and target architectures and compare the expected performance to the measured results. A number of algorithms in computer vision and image processing exhibit regular communication patterns similar to the 2-D FFT. The authors can therefore extrapolate the observations to determine which aspects of these measures are relevant to the scalability analysis of other similar image processing algorithms},
author = {Gupta, Anshul and Kumar, Vipin},
doi = {10.1109/CAMP.1993.622464},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Gupta, Kumar - 1993 - The Scalability of FFT on Parallel Computers.pdf:pdf},
isbn = {0-8186-5420-1},
journal = {IEEE Transactions on Parallel and Distributed Systems},
number = {8},
pages = {1--27},
title = {{The Scalability of FFT on Parallel Computers}},
volume = {4},
year = {1993}
}
@article{Suga1980,
author = {Suga, H and Sagawa, K and Demer, L},
doi = {10.1161/01.RES.46.2.256},
file = {:home/tomaton/Downloads/Circulation Research-1980-Suga-256-63.pdf:pdf},
issn = {0009-7330},
journal = {Circulation research},
pages = {256--263},
pmid = {7351043},
title = {{Determinants of instantaneous pressure in canine left ventricle. Time and volume specification.}},
volume = {46},
year = {1980}
}
@article{Hartmanis1965,
author = {Hartmanis, J and Stearns, RE},
file = {:home/tomaton/Downloads/HartmanisStearns1965.pdf:pdf},
journal = {Transactions of the American Mathematical \ldots},
pages = {285--306},
title = {{On the computational complexity of algorithms}},
url = {http://www.jstor.org/stable/1994208},
volume = {117},
year = {1965}
}
@article{Vines2014,
abstract = {Policies ensuring that research data are available on public archives are increasingly being implemented at the government [1], funding agency [2-4], and journal [5, 6] level. These policies are predicated on the idea that authors are poor stewards of their data, particularly over the long term [7], and indeed many studies have found that authors are often unable or unwilling to share their data [8-11]. However, there are no systematic estimates of how the availability of research data changes with time since publication. We therefore requested data sets from a relatively homogenous set of 516 articles published between 2 and 22 years ago, and found that availability of the data was strongly affected by article age. For papers where the authors gave the status of their data, the odds of a data set being extant fell by 17\% per year. In addition, the odds that we could find a working e-mail address for the first, last, or corresponding author fell by 7\% per year. Our results reinforce the notion that, in the long term, research data cannot be reliably preserved by individual researchers, and further demonstrate the urgent need for policies mandating data sharing via public archives. © 2014 Elsevier Ltd.},
archivePrefix = {arXiv},
arxivId = {1312.5670},
author = {Vines, Timothy H. and Albert, Arianne Y K and Andrew, Rose L. and D\'{e}barre, Florence and Bock, Dan G. and Franklin, Michelle T. and Gilbert, Kimberly J. and Moore, Jean S\'{e}bastien and Renaut, S\'{e}bastien and Rennison, Diana J.},
doi = {10.1016/j.cub.2013.11.014},
eprint = {1312.5670},
file = {:home/tomaton/Downloads/1-s2.0-S0960982213014000-main.pdf:pdf},
isbn = {0960-9822},
issn = {09609822},
journal = {Current Biology},
pages = {94--97},
pmid = {24361065},
title = {{The availability of research data declines rapidly with article age}},
volume = {24},
year = {2014}
}
@misc{harvi2013,
title = {{Harvi - interactive simulation-based digital textbook of cardiovascular physiology and hemodynamics}},
url = {http://www.pvloops.com}
}
@article{Youseff2006,
author = {Youseff, Lamia and Wolski, Rich and Gorda, Brent and Krintz, Chandra},
doi = {10.1007/11942634\_49},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Youseff et al. - 2006 - Paravirtualization for HPC Systems(2).pdf:pdf},
journal = {Frontiers of High Performance Computing and Networking \^{a}€“ ISPA 2006 Workshops},
pages = {474--486},
title = {{Paravirtualization for HPC Systems}},
year = {2006}
}
@article{Diaz2012,
abstract = {In this work, we present a survey of the different parallel programming models and tools available today with special consideration to their suitability for high-performance computing. Thus, we review the shared and distributed memory approaches, as well as the current heterogeneous parallel programming model. In addition, we analyze how the partitioned global address space (PGAS) and hybrid parallel programming models are used to combine the advantages of shared and distributed memory systems. The work is completed by considering languages with specific parallel support and the distributed programming paradigm. In all cases, we present characteristics, strengths, and weaknesses. The study shows that the availability of multi-core CPUs has given new impulse to the shared memory parallel programming approach. In addition, we find that hybrid parallel programming is the current way of harnessing the capabilities of computer clusters with multi-core nodes. On the other hand, heterogeneous programming is found to be an increasingly popular paradigm, as a consequence of the availability of multi-core CPUs+GPUs systems. The use of open industry standards like OpenMP, MPI, or OpenCL, as opposed to proprietary solutions, seems to be the way to uniformize and extend the use of parallel programming models.},
author = {Diaz, Javier and Mu\~{n}oz-Caro, Camelia and Ni\~{n}o, Alfonso},
doi = {10.1109/TPDS.2011.308},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Diaz, Mu\~{n}oz-Caro, Ni\~{n}o - 2012 - A survey of parallel programming models and tools in the multi and many-core era.pdf:pdf},
isbn = {1045-9219},
issn = {10459219},
journal = {IEEE Transactions on Parallel and Distributed Systems},
keywords = {Distributed programming,Heterogeneous (hybrid) systems,Parallelism and concurrency},
number = {8},
pages = {1369--1386},
title = {{A survey of parallel programming models and tools in the multi and many-core era}},
volume = {23},
year = {2012}
}
@inproceedings{Kofranek2012,
author = {Kofr\'{a}nek, Jiř\'{\i} and Pecinovsk\'{y}, Rudolf and Nov\'{a}k, Petr},
booktitle = {International Conference Foundations of Computer Science},
file = {:home/tomaton/Downloads/Kopenograms\_Graphical\_Language\_for\_Structured\_Algorithms.pdf:pdf},
keywords = {algorithmic,algorithms,education,for writing data structures,graphical language,on describing how those,programmiong methodology,therefore in our contribution,uml,we shall focus only},
pages = {90--96},
title = {{Kopenograms – Graphical Language for Structured Algorithms}},
year = {2012}
}
@article{Chervenak2000,
author = {Chervenak, A and Foster, I and Kesselman, C and Salisbury, C and Tuecke, S},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Chervenak et al. - 2000 - The data grid Towards an architecture for the distributed management and analysis of large scientific datasets.pdf:pdf},
journal = {Journal of network and computer applications},
number = {3},
pages = {187--200},
publisher = {Elsevier},
title = {{The data grid: Towards an architecture for the distributed management and analysis of large scientific datasets}},
volume = {23},
year = {2000}
}
@inproceedings{Kulhanek2009Mefanet,
author = {Kulh\'{a}nek, Tom\'{a}\v{s} and Fri\v{c}, Marek and \v{S}\'{a}rek, Milan},
booktitle = {Mefanet 2009},
editor = {Schwarz, Daniel and Majern\'{\i}k, Jaroslav and Du\v{s}ek, Ladislav and \v{S}t\'{\i}pek, Stanislav and Mih\'{a}l, Vladim\'{\i}r},
file = {:home/tomaton/Downloads/kulhanek\_full.pdf:pdf},
keywords = {phoniatric application,remote desktop,virtualization},
publisher = {MSD Brno},
title = {{Vzd\'{a}len\'{y} př\'{\i}stup k virtu\'{a}ln\'{\i}m v\'{y}ukov\'{y}m a v\'{y}zkumn\'{y}m aplikac\'{\i}m - podpora foniatrick\'{y}ch vy\v{s}etřen\'{\i}}},
url = {http://www.mefanet.cz/res/file/mefanet2009/prispevky/kulhanek\_full.pdf},
year = {2009}
}
@article{Bayer1972Sym,
author = {Bayer, Rudolf},
doi = {10.1007/BF00289509},
issn = {0001-5903},
journal = {Acta Informatica},
number = {4},
pages = {290--306},
title = {{Symmetric binary B-Trees: Data structure and maintenance algorithms}},
volume = {1},
year = {1972}
}
@article{Barham2003,
abstract = {Numerous systems have been designed which use virtualization to subdivide the ample resources of a modern computer. Some require specialized hardware, or cannot support commodity operating systems. Some target 100\% binary compatibility at the expense of performance. Others sacrifice security or functionality for speed. Few offer resource isolation or performance guarantees; most provide only best-effort provisioning, risking denial of service.This paper presents Xen, an x86 virtual machine monitor which allows multiple commodity operating systems to share conventional hardware in a safe and resource managed fashion, but without sacrificing either performance or functionality. This is achieved by providing an idealized virtual machine abstraction to which operating systems such as Linux, BSD and Windows XP, can be ported with minimal effort.Our design is targeted at hosting up to 100 virtual machine instances simultaneously on a modern server. The virtualization approach taken by Xen is extremely efficient: we allow operating systems such as Linux and Windows XP to be hosted simultaneously for a negligible performance overhead --- at most a few percent compared with the unvirtualized case. We considerably outperform competing commercial and freely available solutions in a range of microbenchmarks and system-wide tests.},
author = {Barham, Paul and Dragovic, Boris and Fraser, Keir and Hand, Steven and Harris, Tim and Ho, Alex and Neugebauer, Rolf and Pratt, Ian and Warfield, Andrew},
doi = {10.1145/1165389.945462},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Barham et al. - 2003 - Xen and the art of virtualization.pdf:pdf},
isbn = {1-58113-757-5},
issn = {01635980},
journal = {ACM SIGOPS Operating Systems Review},
keywords = {hypervisors,paravirtualization,virtual machine monitors},
pages = {164},
pmid = {685953},
title = {{Xen and the art of virtualization}},
volume = {37},
year = {2003}
}
@article{Urbah2009,
author = {Urbah, Etienne and Kacsuk, Peter and Farkas, Zoltan and Fedak, Gilles and Kecskemeti, Gabor and Lodygensky, Oleg and Marosi, Attila and Balaton, Zoltan and Caillat, Gabriel and Gombas, Gabor and Kornafeld, Adam and Kovacs, Jozsef and He, Haiwu and Lovas, Robert},
doi = {10.1007/s10723-009-9137-0},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Urbah et al. - 2009 - EDGeS Bridging EGEE to BOINC and XtremWeb.pdf:pdf},
issn = {1570-7873},
journal = {Journal of Grid Computing},
month = sep,
number = {3},
pages = {335--354},
title = {{EDGeS: Bridging EGEE to BOINC and XtremWeb}},
volume = {7},
year = {2009}
}
@misc{Fric2007,
address = {Praha},
author = {Fri\v{c}, Marek},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Fri\v{c} - 2007 - Parametrizovan\'{y} fonetogram obecn\'{y}ch ře\v{c}ov\'{y}ch a hlasov\'{y}ch projevů - ParVRP.pdf:pdf},
publisher = {V\'{y}zkumn\'{e} centrum hudebn\'{\i} akustiky HAMU},
title = {{Parametrizovan\'{y} fonetogram obecn\'{y}ch ře\v{c}ov\'{y}ch a hlasov\'{y}ch projevů - ParVRP}},
url = {http://zvuk.hamu.cz/vyzkum/dokumenty/TL12x.pdf},
year = {2007}
}
@article{Perrey2003,
abstract = {This paper attempts a definition of service derived by unifying its usage in practice. In doing so it identifies participant's perspective as separate from actual different usages. Using this as an aid, the paper analyses the criteria applied in the use of service and considers how these can be aligned to derive commonality underlying the usage. Also included is a brief outline of the way in which a service-oriented architecture following such a model would affect the practice and process of developing large-scale, distributed software systems.},
author = {Perrey, R. and Lycett, M.},
doi = {10.1109/SAINTW.2003.1210138},
file = {:home/tomaton/Downloads/01210138.pdf:pdf},
isbn = {0-7695-1873-7},
journal = {2003 Symposium on Applications and the Internet Workshops, 2003. Proceedings.},
keywords = {Business,Computer architecture,Contracts,Creep,Information systems,Internet,Large-scale systems,Ontologies,Service oriented architecture,Software systems,Web services,business data processing,business services,large-scale distributed systems,organisation,service-oriented architecture,software engineering},
pages = {116--119},
title = {{Service-oriented architecture}},
url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=1210138},
year = {2003}
}
@article{Bernstein2009,
abstract = {Cloud computing is a term applied to large, hosted datacenters, usually geographically distributed, which offer various computational services on a ldquoutilityrdquo basis. Most typically the configuration and provisioning of these datacenters, as far as the services for the subscribers go, is highly automated, to the point of the service being delivered within seconds of the subscriber request. Additionally, the datacenters typically use hypervisor based virtualization as a technique to deliver these services. The concept of a cloud operated by one service provider or enterprise interoperating with a clouds operated by another is a powerful idea. So far that is limited to use cases where code running on one cloud explicitly references a service on another cloud. There is no implicit and transparent interoperability. Use cases for interoperability, as well as work-in-progress around inter-cloud protocols and formats for enabling those use cases, are discussed in this paper.},
author = {Bernstein, David and Ludvigson, Erik and Sankar, Krishna and Diamond, Steve and Morrow, Monique},
doi = {10.1109/ICIW.2009.55},
file = {:home/tomaton/Downloads/05072540(1).pdf:pdf},
isbn = {9780769536132},
journal = {Proceedings of the 2009 4th International Conference on Internet and Web Applications and Services, ICIW 2009},
pages = {328--336},
title = {{Blueprint for the intercloud - Protocols and formats for cloud computing interoperability}},
year = {2009}
}
@article{Shi1996,
author = {Shi, Yuan},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Shi - 1996 - Reevaluating Amdahl's Law and Gustafson's Law.pdf:pdf},
journal = {Computer Science Department, Temple University},
pages = {1--9},
title = {{Reevaluating Amdahl's Law and Gustafson's Law}},
year = {1996}
}
@article{Hoimyr2012,
author = {H\o imyr, N and Blomer, J and Buncic, P and Giovannozzi, M and Gonzalez, A and Harutyunyan, A and Jones, P L and Karneyeu, A and Marquina, M a and Mcintosh, E and Segal, B and Skands, P and Grey, F and {Lombra\~{n}a Gonz\'{a}lez}, D and Zacharov, I},
doi = {10.1088/1742-6596/396/3/032057},
file = {:home/tomaton/Downloads/1742-6596\_396\_3\_032057.pdf:pdf},
issn = {1742-6588},
journal = {Journal of Physics: Conference Series},
month = dec,
number = {3},
pages = {032057},
title = {{BOINC service for volunteer cloud computing}},
volume = {396},
year = {2012}
}
@inproceedings{Kofranek2011f,
author = {Kofr\'{a}nek, Jiř\'{\i} and Matej\'{a}k, Marek and Je\v{z}ek, Filip and Privitzer, Pavol and \v{S}ilar, Jan},
booktitle = {sborn\'{\i}k př\'{\i}sp\v{e}vků MEDSOFT},
file = {:home/tomaton/Downloads/Medsoft\_2011\_Kofranek\_Jan\_2.pdf:pdf},
pages = {106--121},
title = {{V\'{Y}UKOV\'{Y} WEBOV\'{Y} SIMUL\'{A}TOR KREVN\'{I}HO OB\v{E}HU}},
year = {2011}
}
@article{Plankensteiner2013,
abstract = {Today there exist a wide variety of scientific workflow management systems, each designed to fulfill the needs of a certain scientific community. Unfortunately, once a workflow application has been designed in one particular system it becomes very hard to share it with users working with different systems. Portability of workflows and interoperability between current systems barely exists. In this work, we present the fine-grained interoperability solution proposed in the SHIWA European project that brings together four representative European workflow systems: ASKALON, MOTEUR, WS-PGRADE, and Triana. The proposed interoperability is realised at two levels of abstraction: abstract and concrete. At the abstract level, we propose a generic Interoperable Workflow Intermediate Representation (IWIR) that can be used as a common bridge for translating workflows between different languages independent of the underlying distributed computing infrastructure. At the concrete level, we propose a bundling technique that aggregates the abstract IWIR representation and concrete task representations to enable workflow instantiation, execution and scheduling. We illustrate case studies using two real-workflow applications designed in a native environment and then translated and executed by a foreign workflow system in a foreign distributed computing infrastructure.},
author = {Plankensteiner, Kassian and Prodan, Radu and Janetschek, Matthias and Fahringer, Thomas and Montagnat, Johan and Rogers, David and Harvey, Ian and Taylor, Ian and Balask\'{o}, \'{A}kos and Kacsuk, P\'{e}ter},
doi = {10.1007/s10723-013-9261-8},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Plankensteiner et al. - 2013 - Fine-Grain Interoperability of Scientific Workflows in Distributed Computing Infrastructures.pdf:pdf},
issn = {15707873},
journal = {Journal of Grid Computing},
keywords = {Distributed computing,Grid computing,Intermediate representation,Interoperability,Portability,Scientific workflow},
pages = {429--455},
title = {{Fine-Grain Interoperability of Scientific Workflows in Distributed Computing Infrastructures}},
volume = {11},
year = {2013}
}
@incollection{Riedel2009,
author = {Riedel, M and Laure, E and Field, L and Navarro, J P and Casey, J and Litmaath, M and Koblitz, B and Catlett, C and Skow, D and Zheng, C and Papadopoulos, P M and Katz, M and Sharma, N and Smirnova, O and Arzberger, P and Rana, A S and Martin, T and Wan, M and Welch, V and Rimovsky, T and Newhouse, S and Vanni, A and Tanaka, Y and Tanimura, Y and Ikegami, T and Abramson, D and Enticott, C and Jenkins, G and Pordes, R and Timm, S and Moont, G and Aggarwal, M and Colling, D and Aa, O Van Der and Sim, A and Natarajan, V and Shoshani, A and Gu, J and Chen, S and Galang, G and Zappi, R and Magnoni, L and Ciaschini, V and Pace, M and Venturi, V and Marzolla, M and Andreetto, P and Cowles, B and Wang, S and Saeki, Y and Sato, H and Matsuoka, S and Uthayopas, P and Sriprayoonsakul, S and Koeroo, O and Viljoen, M and Pearlman, L and Pickles, S and Wallom, David and Moloney, G and Lauret, J and Marsteller, J and Sheldon, P and Pathak, S and Witt, S De and Jensen, J and Hodges, M and Ross, D and Phatanapherom, S and Netzer, G and Gregersen, A R and Jones, M and Kacsuk, P and Streit, A and Mallmann, D and Wolf, F and Huedo, E and Geddes, N},
booktitle = {Concurrency and Computation: Practice and Experience 21.8},
doi = {10.1002/cpe},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Riedel et al. - 2009 - Interoperation of world-wide production e-Science infrastructures.pdf:pdf},
number = {March},
pages = {961--990},
title = {{Interoperation of world-wide production e-Science infrastructures}},
year = {2009}
}
@book{Meurs2011,
author = {van Meurs, W},
publisher = {McGraw-Hill Professional},
title = {{Modeling and Simulation in Biomedical Engineering: Applications in Cardiorespiratory Physiology}},
year = {2011}
}
@article{Zhao2008,
abstract = {With the advances in e-Sciences and the growing complexity of scientific analyses, more and more scientists and researchers are relying on workflow systems for process coordination, derivation automation, provenance tracking, and bookkeeping. While workflow systems have been in use for decades, it is unclear whether scientific workflows can or even should build on existing workflow technologies, or they require fundamentally new approaches. In this paper, we analyze the status and challenges of scientific workflows, investigate both existing technologies and emerging languages, platforms and systems, and identify the key challenges that must be addressed by workflow systems for e-science in the 21st century.},
archivePrefix = {arXiv},
arxivId = {0808.3545},
author = {Zhao, Yong and Raicu, Ioan and Foster, Ian},
eprint = {0808.3545},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Zhao, Raicu, Foster - 2008 - Scientific workflow systems for 21st century, new bottle or new wine.pdf:pdf},
journal = {IEEE Congress on Services - Part I, 2008.},
pages = {467 -- 471},
title = {{Scientific Workflow Systems for 21st Century e-Science, New Bottle or New Wine?}},
year = {2008}
}
@book{Berman2003,
abstract = {From the Summary of the Book: This book, Grid Computing: Making the Global Infrastructure a Reality, [1] brings together many of the major projects that are driving and shaping an emerging global Grid. In the chapters of this book you will find the perspectives of a pioneering group of Grid developers, researchers and application scientists whose vision forms the present and provides a view into the future of Grid computing. Many of the chapters in this book provide definitions and characterizations of the Grid – peruse these and you will form your own view. Common to all perspectives is the notion that the Grid supports the integration of resources (computers, networks, data archives, instruments etc.). To build an integrated system, individuals and communities are working in coordination to ensure that the large and complex system of Grid software will be robust, useful, and provide an interoperable collection of services that support large-scale distributed computing and data management. Grids are intrinsically distributed and heterogeneous but must be viewed by the user (whether an individual or another computer) as a virtual environment with uniform access to resources. Much of Grid software technology addresses the issues of resource schedul- ing, quality of service, fault tolerance, decentralized control and security and so on, which enable the Grid to be perceived as a single virtual platform by the user. For example, Grid security technologies must ensure that a single sign-on will generate security credentials that can be used for the many different actions (potentially on multiple resources) that may be needed in a Grid session. For some researchers and developers, the Grid is viewed as the future of the Web or Internet computing. The Web largely consists of individuals talking independently to servers; the Grid provides a collection of servers and clients often work- ing collectively together to solve a problem. Computer-to-computer traffic is characteristic of Grids and both exploits and drives the increasing network backbone bandwidth. The term Grid was originally used in analogy to other infrastructure (such as electrical power) grids.We will see in this book that the analogy correctly characterizes some aspects of Grid Computing (ubiquity, for example), but not others (the performance variability of different resources that can support the same code, for example).},
doi = {10.1002/0470867167.ch21},
editor = {Berman, Fran and Fox, G and Hey, AJG},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Unknown - 2003 - Grid computing making the global infrastructure a reality.pdf:pdf},
isbn = {0471495166},
publisher = {Wiley},
title = {{Grid Computing - Making the Global Infrastructure a Reality}},
url = {http://eprints.soton.ac.uk/257695/},
year = {2003}
}
@article{Burkhoff1993,
abstract = {One of the most important consequences of acute left ventricular dysfunction (LVD) is pulmonary edema resulting from a rise in pulmonary venous pressure (PVP). It is generally believed that the PVP rise is a direct hemodynamic consequence of LVD. While this paradigm seems plausible, especially if the LV is viewed as a sump pump, there is no specific evidence to support this simple explanation. A theoretical analysis was performed to assess the hemodynamic mechanisms responsible for the dramatic rise in PVP after acute LVD. The ventricles were modeled as time-varying elastances; pulmonary and systemic vascular systems were modeled as series of resistive and capacitive elements. In response to a 50\% decrease in LV contractile strength [end-systolic elastance (Ees)], cardiac output (CO) and mean arterial pressure (MAP) dropped substantially, while PVP increased minimally from its baseline of 12 to approximately 15 mmHg. With LV Ees set at 50\% of normal, the effects of sympathetic activation were tested. When heart rate and total peripheral resistance were increased, CO and MAP improved, yet PVP still did not rise. The only intervention that caused a substantial increase in PVP was to simulate the decrease in unstressed volume (VU) of the venous system known to occur with sympathetic activation. When VU was decreased by about 15-20\% (comparable to experimentally observed shifts with acute heart failure), PVP increased above 25 mmHg. The effects of pericardial constraints were investigated, and the results suggest a major role of this organ in determining the overall hemodynamic response to acute LVD, sympathetic activation, and explaining the responses to therapy. Thus this analysis suggests that elevations of PVP do not occur simply as a direct hemodynamic consequence of acute LVD. Rather, changes in PVP may be dictated more by sympathetic control on venous capacity. If confirmed, recognition of this as a primary mechanism may prove important in directing development of new therapies and in understanding the mechanisms of disease progression in heart failure.},
author = {Burkhoff, D and Tyberg, J V},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Burkhoff, Tyberg - 1993 - Why does pulmonary venous pressure rise after onset of LV dysfunction a theoretical analysis.pdf:pdf},
institution = {Department of Medicine, Columbia Presbyterian Hospital, New York, New York 10032.},
isbn = {0002-9513 (Print)$\backslash$r0002-9513 (Linking)},
issn = {0002-9513},
journal = {The American journal of physiology},
number = {5 Pt 2},
pages = {H1819--H1828},
pmid = {8238596},
title = {{Why does pulmonary venous pressure rise after onset of LV dysfunction: a theoretical analysis.}},
volume = {265},
year = {1993}
}
@misc{epacs2014,
title = {{ePACS}},
url = {http://www.epacs.cz}
}
@inproceedings{Kulhanek2008Mefanet,
author = {Kulh\'{a}nek, Tom\'{a}\v{s} and \v{S}\'{a}rek, Milan},
booktitle = {Mefanet 2008},
file = {:home/tomaton/Downloads/25\_kulhanek.pdf:pdf},
publisher = {MSD Brno},
title = {{Virtualizace a integrace v gridov\'{e}m pacs syst\'{e}mu (cze) virtualization and integration in grid pacs system (eng)}},
url = {http://www.mefanet.cz/res/file/mefanet2008/prispevky/25\_kulhanek.pdf},
year = {2008}
}
@article{Kulhanek2014Modeling,
author = {Kulh\'{a}nek, Tom\'{a}\v{s} and Kofr\'{a}nek, Jiř\'{\i} and Matej\'{a}k, Marek},
doi = {10.1016/j.compbiomed.2014.08.025},
journal = {Computers in Biology and Medicine},
number = {1},
pages = {137--144},
title = {{Modeling of short-term mechanism of arterial pressure control in the cardiovascular system: Object oriented and acausal approach}},
volume = {54},
year = {2014}
}
@article{Takahashi2003,
abstract = {In this paper, we propose a high-performance parallel three-dimensional fast Fourier transform (FFT) algorithm on clusters of PCs. The three-dimensional FFT algorithm can be altered into a block three-dimensional FFT algorithm to reduce the number of cache misses. We show that the block three-dimensional FFT algorithm improves performance by utilizing the cache memory effectively. We use the block three-dimensional FFT algorithm to implement the parallel three-dimensional FFT algorithm. We succeeded in obtaining performance of over 1.3 GFLOPS on an 8-node dual Pentium III 1 GHz PC SMP cluster. ?? 2002 Elsevier Science B.V. All rights reserved.},
author = {Takahashi, Daisuke},
doi = {10.1016/S0010-4655(02)00818-4},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Takahashi - 2003 - Efficient implementation of parallel three-dimensional FFT on clusters of PCs.pdf:pdf},
issn = {00104655},
journal = {Computer Physics Communications},
keywords = {All-to-all communication,Cache memory,Clusters of PCs,Cyclic distribution,Fast Fourier transform},
pages = {144--150},
title = {{Efficient implementation of parallel three-dimensional FFT on clusters of PCs}},
volume = {152},
year = {2003}
}
@book{Sipser2012,
author = {Sipser, Michael},
file = {:home/tomaton/Downloads/Introduction\_to\_the\_theory\_of\_computation.pdf:pdf},
title = {{Introduction to the Theory of Computation}},
year = {2012}
}
@article{Kacsuk2009,
author = {Kacsuk, Peter and Kovacs, Jozsef and Farkas, Zoltan and Marosi, Attila Csaba and Gombas, Gabor and Balaton, Zoltan},
doi = {10.1007/s10723-009-9139-y},
file = {:home/tomaton/Downloads/art\%3A10.1007\%2Fs10723-009-9139-y.pdf:pdf},
issn = {1570-7873},
journal = {Journal of Grid Computing},
keywords = {boinc,desktop,grid,is partly supported by,parameter sweep,portal,published in this paper,the european commission,the research and development,volunteer},
month = sep,
number = {4},
pages = {439--461},
title = {{SZTAKI Desktop Grid (SZDG): A Flexible and Scalable Desktop Grid System}},
volume = {7},
year = {2009}
}
@article{Zatloukal2012,
author = {Zatloukal, Vladim\'{\i}r and Ro\v{c}ek, Ale\v{s}},
file = {:home/tomaton/Downloads/DNMAT-15.pdf:pdf},
isbn = {9781618041180},
journal = {Advances in Data Networks, Communications, Computers and Materials},
pages = {104--108},
title = {{Secure medical multimedia DICOM data transfers over Internet 1}},
year = {2012}
}
@article{Raman1998,
abstract = {Conventional resource management systems use a system model to describe resources and a centralized scheduler to control their allocation. We argue that this paradigm does not adapt well to distributed systems, particularly those built to support high throughput computing. Obstacles include heterogeneity of resources, which make uniform allocation algorithms difficult to formulate, and distributed ownership, leading to widely varying allocation policies. Faced with these problems, we developed and implemented the classified advertisement (classad) matchmaking framework, a flexible and general approach to resource management in distributed environment with decentralized ownership of resources. Novel aspects of the framework include a semi structured data model that combines schema, data, and query in a simple but powerful specification language, and a clean separation of the matching and claiming phases of resource allocation. The representation and protocols result in a robust, scalable and flexible framework that can evolve with changing resources. The framework was designed to solve real problems encountered in the deployment of Condor, a high throughput computing system developed at the University of Wisconsin-Madison. Condor is heavily used by scientists at numerous sites around the world. It derives much of its robustness and efficiency from the matchmaking architecture},
author = {Raman, Rajesh and Livny, M. and Solomon, Marvin},
doi = {10.1109/HPDC.1998.709966},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Raman, Livny, Solomon - 1998 - Matchmaking distributed resource management for high throughput computing.pdf:pdf},
isbn = {0-8186-8579-4},
journal = {Proceedings. The Seventh International Symposium on High Performance Distributed Computing (Cat. No.98TB100244)},
pages = {140--146},
title = {{Matchmaking: distributed resource management for high throughput computing}},
url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=709966},
year = {1998}
}
@misc{Tiller2014,
annote = {Web accessed: April 2014},
author = {Tiller, Michael},
title = {{Modelica by Example}},
url = {http://book.xogeny.com},
year = {2014}
}
@article{Krefting2009,
abstract = {Many scenarios in medical research are predestined for grid computing. Large amounts of data in complex medical image, biosignal and genome processing demand large computing power and data storage. Integration of distributed, heterogeneous data, e.g. correlation between phenotype and genotype data are playing an essential part in life sciences. Sharing of specialized software, data and processing results for collaborative work are further tasks which would strongly benefit from the use of grid infrastructures. However, two major barriers are identified in existing grid environments that prevent extensive use within the life sciences community: Extended security requirements and appropriate usability. To meet these requirements, the MediGRID project is enhancing the basic D-Grid infrastructure along with the implementation of prototype applications from different fields of biomedical research. In this paper, we focus on the developments for ease-of-use under consideration of different aspects of security. They encompass not only security within the grid infrastructure, but also the boundary conditions of network security on the site of the research institutions. For medical grids, we propose a strictly web-portal-based access to grid resources for end-users, with user-guiding, application specific, graphical interfaces. Different levels of authorization are implemented, from fully authorized users to guests without certificate authentication in order to allow hands-on experience for potential grid users. © 2008 Elsevier B.V. All rights reserved.},
author = {Krefting, Dagmar and Bart, Julian and Beronov, Kamen and Dzhimova, Olga and Falkner, J\"{u}rgen and Hartung, Michael and Hoheisel, Andreas and Knoch, Tobias a. and Lingner, Thomas and Mohammed, Yassene and Peter, Kathrin and Rahm, Erhard and Sax, Ulrich and Sommerfeld, Dietmar and Steinke, Thomas and Tolxdorff, Thomas and Vossberg, Michal and Viezens, Fred and Weisbecker, Anette},
doi = {10.1016/j.future.2008.05.005},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Krefting et al. - 2009 - MediGRID Towards a user friendly secured grid infrastructure.pdf:pdf},
issn = {0167739X},
journal = {Future Generation Computer Systems},
keywords = {Grid computing,Healthgrids,Security,Usability},
number = {3},
pages = {326--336},
publisher = {Elsevier B.V.},
title = {{MediGRID: Towards a user friendly secured grid infrastructure}},
volume = {25},
year = {2009}
}
@article{Titze1992,
author = {Titze, Ingo R.},
doi = {10.1044/jshr.3501.21},
issn = {1092-4388},
journal = {Journal of Speech Language and Hearing Research},
number = {1},
pages = {21},
publisher = {American Speech-Language-Hearing Association},
title = {{Acoustic Interpretation of the Voice Range Profile (Phonetogram)}},
url = {http://jslhr.pubs.asha.org/article.aspx?articleid=1779116},
volume = {35},
year = {1992}
}
@article{matejakmedsoft2011,
author = {Matej\'{a}k, M and Kofr\'{a}nek, J},
journal = {sborn\'{\i}k př\'{\i}sp\v{e}vků Medsoft 2011},
title = {{Hummod - Golem edition - rozs\'{a}hl\'{y} model fyziologick\'{y}ch syst\'{e}mů}}
}
@book{Pacheco1997,
abstract = {A hands-on introduction to parallel programming based on the Message-Passing Interface (MPI) standard, the de-facto industry standard adopted by major vendors of commercial parallel systems. This textbook/tutorial, based on the C language, contains many fully-developed examples and exercises. The complete source code for the examples is available in both C and Fortran 77. Students and professionals will find that the portability of MPI, combined with a thorough grounding in parallel programming principles, will allow them to program any parallel system, from a network of workstations to a parallel supercomputer.* Proceeds from basic blocking sends and receives to the most esoteric aspects of MPI.* Includes extensive coverage of performance and debugging.* Discusses a variety of approaches to the problem of basic I/O on parallel machines.* Provides exercises and programming assignments.},
author = {Pacheco, Peter S.},
isbn = {1558603395},
pages = {418},
publisher = {Morgan Kaufmann},
title = {{Parallel Programming with MPI}},
year = {1997}
}
@inproceedings{Sarek2009,
author = {\v{S}\'{a}rek, Milan and Kulh\'{a}nek, Tom\'{a}\v{s}},
booktitle = {sborn\'{\i}k př\'{\i}sp\v{e}vků MEDSOFT},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/\v{S}\'{a}rek, Kulh\'{a}nek - 2009 - Nov\'{e} sm\v{e}ry medic\'{\i}nsk\'{y}ch aplikac\'{\i} sdru\v{z}en\'{\i} CESNET(2).pdf:pdf},
pages = {145--148},
title = {{Nov\'{e} sm\v{e}ry medic\'{\i}nsk\'{y}ch aplikac\'{\i} sdru\v{z}en\'{\i} CESNET}},
url = {http://www.creativeconnections.cz/medsoft/2009/Medsoft\_2009\_\%C5\%A0\%C3\%A1rek\_Milan.pdf},
year = {2009}
}
@inproceedings{Blockwitz2012,
author = {Blockwitz, Torsten and Otter, Martin and Akesson, Johan and Arnold, Martin and Clau�, Christoph and Elmqvist, Hilding and Friedrich, Markus and Junghanns, Andreas and Mauss, Jakob and Neumerkel, Dietmar and Olsson, Hans and Viel, Antoine},
booktitle = {Proceedings of the 9 th International Modelica Conference},
doi = {10.3384/ecp12076173},
file = {:home/tomaton/Downloads/dymola/dymola-2014.2.orig/opt/dymola/documentation/Functional Mockup Interface 2.0 The Standard for Tool independent Exchange of Simulation Models - Modelica 2012.pdf:pdf},
keywords = {change,co-simulation,fmi,fmu,func-,functional mockup interface,model ex-,simulation,tional mockup unit},
month = nov,
pages = {173--184},
title = {{Functional Mockup Interface 2.0: The Standard for Tool independent Exchange of Simulation Models}},
url = {http://www.ep.liu.se/ecp\_article/index.en.aspx?issue=76;article=17},
year = {2012}
}
@book{Tanenbaum2007,
abstract = {Virtually every computing system today is part of a distributed system. Programmers, developers, and engineers need to understand the underlying principles and paradigms as well as the real-world application of those principles. Now, internationally renowned expert Andrew S. Tanenbaum with colleague Martin van Steen presents a complete introduction that identifies the seven key principles of distributed systems, with extensive examples of each. Adds a completely new chapter on architecture to address the principle of organizing distributed systems. Provides extensive new material on peer-to-peer systems, grid computing and Web services, virtualization, and application-level multicasting. Updates material on clock synchronization, data-centric consistency, object-based distributed systems, and file systems and Web systems coordination. For all developers, software engineers, and architects who need an in-depth understanding of distributed systems.},
author = {Tanenbaum, Andrew S and {Van Steen}, Maarten},
booktitle = {Communication},
file = {:home/tomaton/Downloads/TU\_Wien-Verteilte\_Systeme\_VO\_(G\"{o}schka)\_-\_Tannenbaum-distributed\_systems\_principles\_and\_paradigms\_2nd\_edition.pdf:pdf},
isbn = {9780132392273},
title = {{Distributed Systems: Principles and Paradigms, 2/E}},
year = {2007}
}
@article{Abbass2012,
author = {Abbass, Mohamed a. and ElSamahy, Emad and Genedy, Ahmed},
doi = {10.1109/iCBEB.2012.62},
file = {:home/tomaton/Downloads/06245052.pdf:pdf},
isbn = {9780769547060},
journal = {Proceedings - 2012 International Conference on Biomedical Engineering and Biotechnology, iCBEB 2012},
keywords = {Luczak model,cardiovascular system,coefficient of determination,parameter estimation,pattern search method,sensitivity analysis},
pages = {45--48},
title = {{An optimized cardiovascular model: A pattern search approach}},
volume = {1},
year = {2012}
}
@inproceedings{Kulhanek2010Mefanet,
author = {Kulh\'{a}nek, Tom\'{a}\v{s} and \v{S}ilar, Jan and Kofr\'{a}nek, Jiř\'{\i} and Matej\'{a}k, Marek and Privitzer, Pavol and Tribula, Martin},
booktitle = {Mefanet 2010},
editor = {Schwarz, Daniel and Komenda, Martin and Majern\'{\i}k, Jaroslav and \v{S}t\'{\i}pek, Stanislav and Mih\'{a}l, Vladim\'{\i}r and Du\v{s}ek, Ladislav},
file = {:home/tomaton/Downloads/kulhanekmefanet2010.pdf:pdf},
keywords = {desktop grid,grid,identification of physiological systems},
publisher = {MSD Brno},
title = {{Od v\'{y}ukov\'{e}ho modelu k identifikaci fyziologick\'{e}ho syst\'{e}mu}},
url = {http://www.mefanet.cz/res/file/mefanet2010/prispevky/kulhanek-full.pdf},
year = {2010}
}
@article{Wassink2009,
abstract = {Life science workflow systems are developed to help life scientists to conveniently connect various programs and Web services. In practice however, much time is spent on data conversion, because Web services provided by different organisations use different data formats. We have analysed all the Taverna workflows available at the my Experiment Web site on December 11, 2008. Our analysis of the tasks in these workflows shows several noticeable aspects: their number ranges from 1 to 70 tasks per workflow; 18\% of the workflows consist of a single task.Of the tasks used are 22\% Web services; local services, i.e. tasks executed by the workflow system itself, are very popular and cover 57\% of tasks; tasks implemented by the workflow designer, scripting tasks, are is also used often (14\%). Our analysis shows that over 30\% of tasks are related to data conversion.},
author = {Wassink, Ingo and {Van Der Vet}, Paul E. and Wolstencroft, Katy and Neerincx, Pieter B T and Roos, Marco and Rauwerda, Han and Breit, Timo M.},
doi = {10.1109/SERVICES-I.2009.48},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Wassink et al. - 2009 - Analysing scientific workflows Why workflows not only connect web services.pdf:pdf},
isbn = {9780769538129},
journal = {SERVICES 2009 - 5th 2009 World Congress on Services},
keywords = {Data conversion,Scientific workflow,Scripting,Sub-workflow,Web services},
pages = {314--321},
title = {{Analysing scientific workflows: Why workflows not only connect web services}},
year = {2009}
}
@article{Vinoski2007,
abstract = {This paper discusses the representational state transfer (REST) and service-oriented architecture (SOA) debate. The author tries to explain REST from the viewpoint of someone steeped in SOA, with the intention of helping SOA people understand the value the REST camp so rightfully touts},
author = {Vinoski, Steve},
doi = {10.1109/MIC.2007.22},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Vinoski - 2007 - REST eye for the SOA guy.pdf:pdf},
isbn = {1089-7801 VO  - 11},
issn = {10897801},
journal = {IEEE Internet Computing},
keywords = {Representational State Transfer,Service-oriented architecture},
pages = {82--84},
title = {{REST eye for the SOA guy}},
volume = {11},
year = {2007}
}
@article{VanHoudt2012,
abstract = {Nicolaides Baraitser syndrome heterozygous SMARCA2 ...},
author = {{Van Houdt}, Jeroen K J and Nowakowska, Beata Anna and Sousa, S\'{e}rgio B and van Schaik, Barbera D C and Seuntjens, Eve and Avonce, Nelson and Sifrim, Alejandro and Abdul-Rahman, Omar a and van den Boogaard, Marie-Jos\'{e} H and Bottani, Armand and Castori, Marco and Cormier-Daire, Val\'{e}rie and Deardorff, Matthew a and Filges, Isabel and Fryer, Alan and Fryns, Jean-Pierre and Gana, Simone and Garavelli, Livia and Gillessen-Kaesbach, Gabriele and Hall, Bryan D and Horn, Denise and Huylebroeck, Danny and Klapecki, Jakub and Krajewska-Walasek, Malgorzata and Kuechler, Alma and Lines, Matthew a and Maas, Saskia and MacDermot, Kay D and McKee, Shane and Magee, Alex and de Man, Stella a and Moreau, Yves and Morice-Picard, Fanny and Obersztyn, Ewa and Pilch, Jacek and Rosser, Elizabeth and Shannon, Nora and Stolte-Dijkstra, Irene and {Van Dijck}, Patrick and Vilain, Catheline and Vogels, Annick and Wakeling, Emma and Wieczorek, Dagmar and Wilson, Louise and Zuffardi, Orsetta and van Kampen, Antoine H C and Devriendt, Koenraad and Hennekam, Raoul and Vermeesch, Joris Robert},
doi = {10.1038/ng.1105},
file = {:home/tomaton/Downloads/document.pdf:pdf},
isbn = {1546-1718 (Electronic)$\backslash$n1061-4036 (Linking)},
issn = {1061-4036},
journal = {Nature Genetics},
number = {4},
pages = {445--449},
pmid = {22366787},
title = {{Heterozygous missense mutations in SMARCA2 cause Nicolaides-Baraitser syndrome}},
volume = {44},
year = {2012}
}
@article{Kofranek2011d,
author = {Kofr\'{a}nek, Jiř\'{\i} and Matej\'{a}k, Marek and Privitzer, Pavol},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Kofr\'{a}nek, Matej\'{a}k, Privitzer - 2011 - Complex Model of Integrated Physiological System - A Theoretical Basis For Medical Training Simu.pdf:pdf},
isbn = {9788021055391},
journal = {Mefanet Report 04},
pages = {32--59},
title = {{Complex Model of Integrated Physiological System - A Theoretical Basis For Medical Training Simulators}},
url = {http://www.mefanet.cz/res/file/reporty/mefanet-report-2011.pdf},
year = {2011}
}
@article{Kulhanek2014mefanet,
author = {Kulh\'{a}nek, Tom\'{a}\v{s} and Tribula, Martin and Kofr\'{a}nek, Jiř\'{\i} and Matej\'{a}k, Marek},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Kulh\'{a}nek et al. - 2014 - Simple models of the cardiovascular system for educational and research purposes.pdf:pdf},
isbn = {1805-9171},
journal = {MEFANET Journal},
number = {2},
pages = {56--63},
title = {{Simple models of the cardiovascular system for educational and research purposes}},
volume = {2},
year = {2014}
}
@article{Hucka2004,
author = {Hucka, Michael and Finney, ABBJ and Bornstein, Benjamin J and Keating, Sarah M and Shapiro, Bruce E and Matthews, Joanne and Kovitz, Ben L and Schilstra, Maria J and Funahashi, Akira and Doyle, John C},
file = {::;:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Hucka et al. - 2004 - Evolving a lingua franca and associated software infrastructure for computational systems biology the Systems Biol.pdf:pdf},
isbn = {1741-248X},
journal = {Systems biology},
number = {1},
pages = {41--53},
title = {{Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project}},
volume = {1},
year = {2004}
}
@inproceedings{kulhanek2009,
author = {Kulh\'{a}nek, Tom\'{a}\v{s} and \v{S}\'{a}rek, Milan},
booktitle = {Proceedings of the 2009 Euro American Conference on Telematics and Information Systems: New Opportunities to increase Digital Citizenship},
doi = {10.1145/1551722.1551732},
organization = {ACM},
pages = {10},
title = {{Processing of medical images in virtual distributed environment}},
year = {2009}
}
@article{Cunsolo2009,
abstract = {Only commercial cloud solutions have been implemented so far, offering computing resources and services for renting. Some interesting projects, such as Nimbus, OpenNEbula, Reservoir, work on cloud. One of their aims is to provide a cloud infrastructure able to provide and share resources and services for scientific purposes. The encouraging results of volunteer computing projects in this context and the flexibility of the cloud, suggested to address our research efforts towards a combined new computing paradigm we named Cloud@Home.On one hand it can be considered as a generalization of the @homephilosophy, knocking down the barriers of volunteer computing, and also allowing to share more general services. On the other hand, Cloud@Home can be considered as the enhancement of the grid-utility vision of cloud computing. In this new paradigm, userspsila hosts are not passive interface to cloud services anymore, but they can interact (free or by charge) with other clouds. In this paper we present the Cloud@Home paradigm, highlighting its contribution to the actual state of the art on the topic of distributed and cloud computing. We detail the functional architecture and the core structure implementing such paradigm, demonstrating how it is really possible to build up a Cloud@Home infrastructure.},
author = {Cunsolo, Vincenzo D. and Distefano, Salvatore and Puliafito, Antonio and Scarpa, Marco},
doi = {10.1109/NCA.2009.41},
file = {:home/tomaton/Downloads/05190364.pdf:pdf},
isbn = {9780769536989},
journal = {Proceedings - 2009 8th IEEE International Symposium on Network Computing and Applications, NCA 2009},
pages = {134--139},
title = {{Volunteer computing and desktop cloud: The cloud @ home paradigm}},
year = {2009}
}
@article{Sneddon2011,
abstract = {Managing the overwhelming numbers of molecular states and interactions is a fundamental obstacle to building predictive models of biological systems. Here we introduce the Network-Free Stochastic Simulator (NFsim), a general-purpose modeling platform that overcomes the combinatorial nature of molecular interactions. Unlike standard simulators that represent molecular species as variables in equations, NFsim uses a biologically intuitive representation: objects with binding and modification sites acted on by reaction rules. During simulations, rules operate directly on molecular objects to produce exact stochastic results with performance that scales independently of the reaction network size. Reaction rates can be defined as arbitrary functions of molecular states to provide powerful coarse-graining capabilities, for example to merge Boolean and kinetic representations of biological networks. NFsim enables researchers to simulate many biological systems that were previously inaccessible to general-purpose software, as we illustrate with models of immune system signaling, microbial signaling, cytoskeletal assembly and oscillating gene expression.},
author = {Sneddon, Michael W and Faeder, James R and Emonet, Thierry},
doi = {10.1038/nmeth.1546},
file = {:home/tomaton/Downloads/document(1).pdf:pdf},
isbn = {1548-7105 (Electronic)$\backslash$n1548-7091 (Linking)},
issn = {1548-7091},
journal = {Nature methods},
number = {2},
pages = {177--183},
pmid = {21186362},
title = {{Efficient modeling, simulation and coarse-graining of biological complexity with NFsim.}},
volume = {8},
year = {2011}
}
@inproceedings{Kulhanek2012,
author = {Kulh\'{a}nek, Tom\'{a}\v{s} and Fri\v{c}, Marek and Hrb, Jaroslav},
booktitle = {sborn\'{\i}k př\'{\i}sp\v{e}vků MEDSOFT},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Kulh\'{a}nek, Fri\v{c}, Hrb - 2012 - VZD\'{A}LEN\'{A} ANAL\'{Y}ZA LIDSK\'{E}HO HLASU V RE\'{A}LN\'{E}M \v{C}ASE .pdf:pdf},
pages = {180--184},
title = {{Vzd\'{a}len\'{a} anal\'{y}za lidsk\'{e}ho hlasu v re\'{a}ln\'{e}m \v{c}ase}},
url = {http://www.creativeconnections.cz/medsoft/2012/Medsoft\_Kulh\'{a}nek\_Tom\'{a}\v{s}.pdf},
year = {2012}
}
@article{hester2011,
abstract = {Mathematical models and simulations are important tools in discovering key causal relationships governing physiological processes. Simulations guide and improve outcomes of medical interventions involving complex physiology. We developed HumMod, a Windows-based model of integrative human physiology. HumMod consists of 5000 variables describing cardiovascular, respiratory, renal, neural, endocrine, skeletal muscle, and metabolic physiology. The model is constructed from empirical data obtained from peer-reviewed physiological literature. All model details, including variables, parameters, and quantitative relationships, are described in Extensible Markup Language (XML) files. The executable (HumMod.exe) parses the XML and displays the results of the physiological simulations. The XML description of physiology in HumMod's modeling environment allows investigators to add detailed descriptions of human physiology to test new concepts. Additional or revised XML content is parsed and incorporated into the model. The model accurately predicts both qualitative and quantitative changes in clinical and experimental responses. The model is useful in understanding proposed physiological mechanisms and physiological interactions that are not evident, allowing one to observe higher level emergent properties of the complex physiological systems. HumMod has many uses, for instance, analysis of renal control of blood pressure, central role of the liver in creating and maintaining insulin resistance, and mechanisms causing orthostatic hypotension in astronauts. Users simulate different physiological and pathophysiological situations by interactively altering numerical parameters and viewing time-dependent responses. HumMod provides a modeling environment to understand the complex interactions of integrative physiology. HumMod can be downloaded at http://hummod.org.},
author = {Hester, Robert L and Brown, Alison J and Husband, Leland and Iliescu, Radu and Pruett, Drew and Summers, Richard and Coleman, Thomas G},
doi = {10.3389/fphys.2011.00012},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Hester et al. - 2011 - HumMod A Modeling Environment for the Simulation of Integrative Human Physiology(2).pdf:pdf},
issn = {1664-042X},
journal = {Frontiers in physiology},
keywords = {hummod,integrative physiology,model,physiome},
month = jan,
number = {April},
pages = {12},
pmid = {21647209},
publisher = {Frontiers Media SA},
title = {{HumMod: a modeling environment for the simulation of integrative human physiology}},
volume = {2},
year = {2011}
}
@article{P.BryanHeidorn2008,
abstract = {One of the primary outputs of the scientific enterprise is data, but many institutions such as libraries that are charged with preserving and disseminating scholarly output have largely ignored this form of documentation of scholarly activity. This paper focuses on a particularly troublesome class of data, termed dark data. “Dark data” is not carefully indexed and stored so it becomes nearly invisible to scientists and other potential users and therefore is more likely to remain underutilized and eventually lost. The article discusses how the concepts from long-tail economics can be used to understand potential solutions for better curation of this data. The paper describes why this data is critical to scientific progress, some of the properties of this data, as well as some social and technical barriers to proper management of this class of data. Many potentially useful institutional, social, and technical solutions are under development and are introduced in the last sections of the paper, but these solutions are largely unproven and require additional research and development.},
author = {{P. Bryan Heidorn}},
doi = {10.1353/lib.0.0036},
file = {:home/tomaton/Downloads/heidorn.pdf:pdf},
isbn = {1559-0682},
issn = {1559-0682},
journal = {Library Trends},
number = {2},
pages = {280--299},
title = {{Shedding Light on the Dark Data in the Long Tail of Science}},
volume = {57},
year = {2008}
}
@article{LeNovere2006,
abstract = {BioModels Database (http://www.ebi.ac.uk/biomodels/), part of the international initiative BioModels.net, provides access to published, peer-reviewed, quantitative models of biochemical and cellular systems. Each model is carefully curated to verify that it corresponds to the reference publication and gives the proper numerical results. Curators also annotate the components of the models with terms from controlled vocabularies and links to other relevant data resources. This allows the users to search accurately for the models they need. The models can currently be retrieved in the SBML format, and import/export facilities are being developed to extend the spectrum of formats supported by the resource.},
author = {{Le Nov\`{e}re}, Nicolas and Bornstein, Benjamin and Broicher, Alexander and Courtot, M\'{e}lanie and Donizelli, Marco and Dharuri, Harish and Li, Lu and Sauro, Herbert and Schilstra, Maria and Shapiro, Bruce and Snoep, Jacky L and Hucka, Michael},
doi = {10.1093/nar/gkj092},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Le Nov\`{e}re et al. - 2006 - BioModels Database a free, centralized database of curated, published, quantitative kinetic models of biochem.pdf:pdf},
isbn = {1362-4962 (Electronic)$\backslash$r0305-1048 (Linking)},
issn = {1362-4962},
journal = {Nucleic acids research},
pages = {D689--D691},
pmid = {16381960},
title = {{BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems.}},
volume = {34},
year = {2006}
}
@article{Takahashi2013,
abstract = {This paper describes the application of Model Based approach for constructing the simulator for the cardiovascular system. Each organ composing the cardiovascular system is modeled based on the previously suggested electrical circuit approach and the entire simulator is implemented by using MATLAB / Simulink. This simulator makes it possible to estimate parameters of the cardiovascular system as an inverse-problem solving approach. The experimental results showed that the parameters were precisely estimated. These results also indicate the possibility of the application of Model Based approach to the coupled simulation in the medical engineering filed.},
author = {Takahashi, Shuji and Sakawa, Kenta and Shiraishi, Yoichi and Miyashita, Hiroshi and Technology, Science},
file = {:home/tomaton/Downloads/06736195.pdf:pdf},
keywords = {Arterial System,Blood,Blood flow,Cardiovascular System,Heart,Integrated circuit modeling,Inverse-problem,Mathematical model,Medical Engineering,Model,Simulation,arterial system,cardiovascular system,inverse-problem,medical engineering,model,simulation},
pages = {493--500},
shorttitle = {SICE Annual Conference (SICE), 2013 Proceedings of},
title = {{Modeling, simulation and parameter estimation of the cardiovascular system by using Model Based approach}},
year = {2013}
}
@inproceedings{Kulhanek2012a,
address = {Prague},
author = {Kulh\'{a}nek, Tom\'{a}\v{s} and Fri\v{c}, Marek},
booktitle = {EGI Technical Forum, Prague},
file = {:home/tomaton/Downloads/Remote analysis of human voice - environment for voice training and ORL medicine - Contribution.pdf:pdf},
title = {{Remote analysis of human voice - environment for voice training and ORL medicine}},
year = {2012}
}
@article{Xin2011,
abstract = {Cloud computing has been considered as a significant change, especially to the so-called \&\#x201C;long tail\&\#x201D; in the Internet industry, which targets at a niche market. This paper focuses on the innovation of Internet long tail in the cloud environment. For this purpose, it systematically analyzes and summarizes the influence of cloud computing on innovation and how to seize these opportunities for Internet long tail. The result reveals that Cloud computing has brought unprecedented innovative opportunities for Internet long tail to access to the markets monopolized by big corporations, making the long tail more valuable to meet the various demand.},
author = {Xin, Liu and Song, Chen},
doi = {10.1109/ICPIM.2011.5983735},
file = {:home/tomaton/Downloads/05983735.pdf:pdf},
isbn = {9781457703584},
journal = {Proceedings of 2011 International Conference on Product Innovation Management, ICPIM 2011},
keywords = {Cloud computing,innovation,the Internet long tail},
pages = {603--607},
title = {{Cloud-based innovation of Internet long tail}},
year = {2011}
}
@article{Sa2006,
abstract = {Full-body patient simulators provide a technological basis for clinical education without risk to real patients. In a previous study, we described a model for educational simulation of infant cardiovascular physiology. Using essentially the same methodology, we derive a mathematical model for the cardiovascular system of a healthy 1-week-old neonate. Computer simulations of this model result in vital signs that are close to target hemodynamic variables. Simulated systemic arterial pressure waveform and left ventricular pressure-volume loop are realistic, and the system reacts appropriately to blood loss. We also adapt the model structure and change its parameters to reflect the congenital heart defects: patent ductus arteriosus, tetralogy of Fallot, complex coarctation of the aorta with patent foramen ovale, and transposition of the great arteries. Simulated vital signs are again close to target hemodynamic variables. The resulting model for neonatal cardiovascular pathophysiology is an essential step in attaining a full-body, model-driven neonatal acute care simulator.},
author = {{S\'{a} Couto}, Carla D and van Meurs, Willem L and Goodwin, Jane A and Andriessen, Peter},
journal = {Simulation in Healthcare},
keywords = {1,1 in a previous,12,4,cardiovascular physiology,congenital heart defect,mathematical model,medical education,neonate,simul healthcare 2006,simulation,study,ulator technology,we described a model},
number = {Inaugural},
pages = {4--12},
title = {{A Model for Educational Simulation of Neonatal Cardiovascular Pathophysiology}},
volume = {1},
year = {2006}
}
@misc{Foster1997,
abstract = {Emerging high-performance applications require the ability to exploit diverse, geographically distributed resources. These applications use high-speed networks to integrate supercomputers, large databases, archival storage devices, advanced visualization devices, and/or scientific instruments to form networked virtual supercomputers or metacomputers. While the physical infrastructure to build such systems is becoming widespread, the heterogeneous and dynamic nature of the metacomputing environment poses new challenges for developers of system software, parallel tools, and applications. In this article, we introduce Globus, a system that we are developing to address these challenges. The Globus system is intended to achieve a vertically integrated treatment of application, middleware, and network. A low-level toolkit provides basic mechanisms such as communication, authentication, network information, and data access. These mechanisms are used to construct various higher-level metacomputing services, such as parallel programming tools and schedulers. Our long-term goal is to build an Adaptive Wide Area Resource Environment (AWARE), an integrated set of higher-level services that enable applications to adapt to heterogeneous and dynamically changing metacomputing environments. Preliminary versions of Globus components were deployed successfully as part of the I-WAY networking experiment. 1},
author = {Foster, I. and Kesselman, C.},
booktitle = {International Journal of High Performance Computing Applications},
doi = {10.1177/109434209701100205},
issn = {1094-3420},
pages = {115--128},
title = {{Globus: a Metacomputing Infrastructure Toolkit}},
volume = {11},
year = {1997}
}
@book{Nilsson2006,
author = {Nilsson, Jimmy},
publisher = {Pearson Education, Inc.},
title = {{Applying Domain-Driven Design and Patterns}},
year = {2006}
}
@article{Santamore1991,
abstract = {Because of close anatomic association, the pressure and volume in one ventricle can directly influence the pressure and volume in the opposite ventricle. To examine the importance of ventricular interdependence in controlling the circulation, we developed a computer model in which ventricular interdependence could be turned on and off. Left ventricular chamber contractility, as judged by maximal elastance (Emax), was enhanced on the order of 10\% as a result of ventricular interaction, whereas right ventricular Emax was affected by as much as 60\% under physiological conditions. With increases in systemic vascular resistance, ventricular interaction caused a smaller stroke volume (SV) decrease than with no interaction. For canine data (SV = 21.4 ml), doubling systemic vascular resistance decreased SV by 3.7 without ventricular interdependence, 3.5 with diastolic ventricular interdependence, and 3.3 ml with diastolic and systolic ventricular interdependence. In contrast, with increases in pulmonary vascular resistance, ventricular interaction caused a greater decrease in SV than with no interaction present. Decreasing left ventricular free wall elastance or right ventricular free wall elastance decreased SV. Diastolic ventricular interdependence reduced the SV changes, whereas systolic ventricular interdependence accentuated the SV changes with alterations in right and left ventricular free-wall elastance. The results of the present simulation demonstrate the importance of ventricular interdependence in the observed responses of the right ventricle to volume overload, pressure overload, and ischemia.},
author = {Santamore, W P and Burkhoff, D},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Santamore, Burkhoff - 1991 - Hemodynamic consequences of ventricular interaction as assessed by model analysis.pdf:pdf},
institution = {Philadelphia Heart Institute, Presbyterian Medical Center, Pennsylvania 19104.},
journal = {The American journal of physiology},
number = {1 Pt 2},
pages = {H146--H157},
pmid = {1992793},
title = {{Hemodynamic consequences of ventricular interaction as assessed by model analysis.}},
volume = {260},
year = {1991}
}
@article{Gunarathne2010,
abstract = {Cloud computing offers exciting new approaches for scientific computing that leverage major commercial players’ hardware and software investments in large-scale data centers. Loosely coupled problems are very important in many scientific fields, and with the ongoing move towards data-intensive computing, they are on the rise. There exist several different approaches to leveraging clouds and cloud-oriented data processing frameworks to perform pleasingly parallel (also called embarrassingly parallel) computations. In this paper, we present three pleasingly parallel biomedical applications: (i) assembly of genome fragments; (ii) sequence alignment and similarity search; and (iii) dimension reduction in the analysis of chemical structures, which are implemented utilizing a cloud infrastructure service-based utility computing models of Amazon Web Services (http://Amazon.com Inc., Seattle, WA, USA) and Microsoft Windows Azure (Microsoft Corp., Redmond, WA, USA) as well as utilizing MapReduce-based data processing frameworks Apache Hadoop (Apache Software Foundation, Los Angeles, CA, USA) and Microsoft DryadLINQ. We review and compare each of these frameworks, performing a comparative study among them based on performance, cost, and usability. High latency, eventually consistent cloud infrastructure service-based frameworks that rely on off-the-node cloud storage were able to exhibit performance efficiencies and scalability comparable to the MapReduce-based frameworks with local disk-based storage for the applications considered. In this paper, we also analyze variations in cost among the different platform choices (e.g., Elastic Compute Cloud instance types), highlighting the importance of selecting an appropriate platform based on the nature of the computation. Copyright © 2011 John Wiley \& Sons, Ltd.},
author = {Gunarathne, Thilina and Wu, Tak Lon and Choi, Jong Youl and Bae, Seung Hee and Qiu, Judy},
doi = {10.1002/cpe.1780},
file = {:home/tomaton/Downloads/cpe1780.pdf:pdf},
isbn = {9781605589428},
issn = {15320626},
journal = {Concurrency Computation Practice and Experience},
keywords = {bioinformatics,cloud technology,map reduce},
number = {June},
pages = {2338--2354},
title = {{Cloud computing paradigms for pleasingly parallel biomedical applications}},
volume = {23},
year = {2011}
}
@phdthesis{Raicu2009,
author = {Raicu, Ioan},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Raicu - 2009 - Many-task computing bridging the gap between high-throughput computing and high-performance computing.pdf:pdf},
number = {March},
title = {{Many-task computing: bridging the gap between high-throughput computing and high-performance computing}},
year = {2009}
}
@article{Slavicek2010,
abstract = {Masaryk University in Brno is operating a regional PACS archive serving to mostly all hospitals in Brno metropolis and a lot of remote medicine institutions. The communication between modalities (i.e. CT, ultrasound, X-ray, etc.) PACS archive and viewing stations is based on DICOM standard. This paper describes current state of the art of this medicine images storage system.},
author = {Slavicek, K. and Dostal, O. and Javornik, M. and Drdla, M.},
doi = {10.1109/WKDD.2010.133},
file = {:home/tomaton/Downloads/05432612.pdf:pdf},
isbn = {978-1-4244-5397-9},
journal = {2010 Third International Conference on Knowledge Discovery and Data Mining},
keywords = {-pacs,Biomedical imaging,Brno metropolis,DICOM,Data processing,Data security,Hospitals,MEDIMED,Masaryk University,Medical diagnostic imaging,Network servers,PACS,PACS archive,Picture archiving and communication systems,Ultrasonic imaging,X-ray imaging,dicom,medical image processing,medicine image data processing,medicine images storage system,regional centre,remote medicine institutions,visual databases},
month = jan,
pages = {310--313},
publisher = {Ieee},
shorttitle = {Knowledge Discovery and Data Mining, 2010. WKDD '1},
title = {{MEDIMED - Regional Centre for Medicine Image Data Processing}},
year = {2010}
}
@book{Holland1975,
abstract = {Genetic algorithms were developed initially by Holland et al. in the 1960s and 1970s!!! Genetic algorithms are playing an increasingly important role in studies of complex adaptive systems, ranging from adaptive agents in economic theory to the use of machine learning techniques in the design of complex devices such as aircraft turbines and integrated circuits. Adaptation in Natural and Artificial Systems is the book that initiated this field of study, presenting the theoretical foundations and exploring applications. In its most familiar form, adaptation is a biological process, whereby organisms evolve by rearranging genetic material to survive in environments confronting them. In this now classic work, Holland presents a mathematical model that allows for the nonlinearity of such complex interactions. He demonstrates the model's universality by applying it to economics, physiological psychology, game theory, and artificial intelligence and then outlines the way in which this approach modifies the traditional views of mathematical genetics. Initially applying his concepts to simply defined artificial systems with limited numbers of parameters, Holland goes on to explore their use in the study of a wide range of complex, naturally occuring processes, concentrating on systems having multiple factors that interact in nonlinear ways. Along the way he accounts for major effects of coadaptation and coevolution: the emergence of building blocks, or schemata, that are recombined and passed on to succeeding generations to provide, innovations and improvements. John H. Holland is Professor of Psychology and Professor of Electrical Engineering and Computer Science at the University of Michigan. He is also Maxwell Professor at the Santa Fe Institute and is Director of the University of Michigan/Santa Fe Institute Advanced Research Program.},
author = {Holland, John H},
booktitle = {Ann Arbor MI University of Michigan Press},
isbn = {0262581116},
issn = {10834419},
pages = {211},
pmid = {15369078},
title = {{Adaptation in Natural and Artificial Systems}},
url = {http://www.citeulike.org/group/664/article/400721},
volume = {Ann Arbor},
year = {1975}
}
@article{Benkner2010,
abstract = {The increasing volume of data describing human disease processes and the growing complexity of understanding, managing, and sharing such data presents a huge challenge for clinicians and medical researchers. This paper presents the @neurIST system, which provides an infrastructure for biomedical research while aiding clinical care, by bringing together heterogeneous data and complex processing and computing services. Although @neurIST targets the investigation and treatment of cerebral aneurysms, the system's architecture is generic enough that it could be adapted to the treatment of other diseases. Innovations in @neurIST include confining the patient data pertaining to aneurysms inside a single environment that offers clinicians the tools to analyze and interpret patient data and make use of knowledge-based guidance in planning their treatment. Medical researchers gain access to a critical mass of aneurysm related data due to the system's ability to federate distributed information sources. A semantically mediated grid infrastructure ensures that both clinicians and researchers are able to seamlessly access and work on data that is distributed across multiple sites in a secure way in addition to providing computing resources on demand for performing computationally intensive simulations for treatment planning and research.},
author = {Benkner, Siegfried and Arbona, Antonio and Berti, Guntram and Chiarini, Alessandro and Dunlop, Robert and Engelbrecht, Gerhard and Frangi, Alejandro F. and Friedrich, Christoph M. and Hanser, Susanne and Hasselmeyer, Peer and Hose, Rod D. and Iavindrasana, Jimison and Khler, Martin and Iacono, Luigi Lo and Lonsdale, Guy and Meyer, Rodolphe and Moore, Bob and Rajasekaran, Hariharan and Summers, Paul E. and Whrer, Alexander and Wood, Steven},
doi = {10.1109/TITB.2010.2049268},
file = {:home/tomaton/Downloads/05456192.pdf:pdf},
isbn = {1558-0032 (Electronic)$\backslash$r1089-7771 (Linking)},
issn = {10897771},
journal = {IEEE Transactions on Information Technology in Biomedicine},
keywords = {Aneurysms,architecture,biomechanical simulation,biomedical grid,ontology},
number = {6},
pages = {1365--1377},
pmid = {20435543},
title = {{@neurIST: Infrastructure for advanced disease management through integration of heterogeneous data, computing, and complex processing services}},
volume = {14},
year = {2010}
}
@article{Feron2013,
author = {Feron, Hwa and Lehmann, Axel and Hofmann, Marko},
doi = {10.1109/WSC.2013.6721651},
file = {:home/tomaton/Downloads/p2807-feron.pdf:pdf},
isbn = {978-1-4799-3950-3},
journal = {2013 Winter Simulations Conference (WSC)},
keywords = {WSC 2012},
month = dec,
pages = {2807--2818},
publisher = {Ieee},
title = {{Challenges of and criteria for validating a physiology model within a TCCC serious game}},
url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=6721651},
year = {2013}
}
@article{Wu2014,
abstract = {Big Data concern large-volume, complex, growing data sets with multiple, autonomous sources. With the fast development of networking, data storage, and the data collection capacity, Big Data are now rapidly expanding in all science and engineering domains, including physical, biological and biomedical sciences. This paper presents a HACE theorem that characterizes the features of the Big Data revolution, and proposes a Big Data processing model, from the data mining perspective. This data-driven model involves demand-driven aggregation of information sources, mining and analysis, user interest modeling, and security and privacy considerations. We analyze the challenging issues in the data-driven model and also in the Big Data revolution.},
author = {Wu, Xindong and Zhu, Xingquan and Wu, Gong-Qing and Ding, Wei},
doi = {10.1109/TKDE.2013.109},
file = {:home/tomaton/Downloads/06547630.pdf:pdf},
isbn = {1041-4347},
issn = {1041-4347},
journal = {IEEE Transactions on Knowledge and Data Engineering},
keywords = {Big Data,Big Data processing model,Big Data revolution,HACE theorem,autonomous sources,complex and evolving associations,data collection capacity,data driven model,data mining,data storage,demand driven aggregation,growing data sets,heterogeneity,information sources,networking,user interest modeling,user modelling},
number = {1},
pages = {97--107},
title = {{Data mining with big data}},
url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=6547630},
volume = {26},
year = {2014}
}
@article{mitamura1987,
author = {Mitamura, Y},
journal = {IFAC Control Aspects of Biomedical Engineering},
pages = {37--51},
title = {{Control aspects of the circulatory system}},
year = {1987}
}
@article{Wilkins-Diehr2007,
author = {Wilkins-Diehr, Nancy},
doi = {10.1002/cpe.1098},
file = {:home/tomaton/Downloads/1098\_ftp.pdf:pdf},
issn = {15320626},
journal = {Concurrency and Computation: Practice and Experience},
month = apr,
number = {6},
pages = {743--749},
title = {{Special Issue: Science Gateways—Common Community Interfaces to Grid Resources}},
url = {http://doi.wiley.com/10.1002/cpe.1098},
volume = {19},
year = {2007}
}
@article{Tondel2011,
abstract = {Deterministic dynamic models of complex biological systems contain a large number of parameters and state variables, related through nonlinear differential equations with various types of feedback. A metamodel of such a dynamic model is a statistical approximation model that maps variation in parameters and initial conditions (inputs) to variation in features of the trajectories of the state variables (outputs) throughout the entire biologically relevant input space. A sufficiently accurate mapping can be exploited both instrumentally and epistemically. Multivariate regression methodology is a commonly used approach for emulating dynamic models. However, when the input-output relations are highly nonlinear or non-monotone, a standard linear regression approach is prone to give suboptimal results. We therefore hypothesised that a more accurate mapping can be obtained by locally linear or locally polynomial regression. We present here a new method for local regression modelling, Hierarchical Cluster-based PLS regression (HC-PLSR), where fuzzy C-means clustering is used to separate the data set into parts according to the structure of the response surface. We compare the metamodelling performance of HC-PLSR with polynomial partial least squares regression (PLSR) and ordinary least squares (OLS) regression on various systems: six different gene regulatory network models with various types of feedback, a deterministic mathematical model of the mammalian circadian clock and a model of the mouse ventricular myocyte function.},
author = {T\o ndel, Kristin and Indahl, Ulf G and Gjuvsland, Arne B and Vik, Jon Olav and Hunter, Peter and Omholt, Stig W and Martens, Harald},
doi = {10.1186/1752-0509-5-90},
file = {:home/tomaton/Downloads/1752-0509-5-90.pdf:pdf},
isbn = {1752-0509},
issn = {1752-0509},
journal = {BMC systems biology},
number = {1},
pages = {90},
pmid = {21627852},
publisher = {BioMed Central Ltd},
title = {{Hierarchical cluster-based partial least squares regression (HC-PLSR) is an efficient tool for metamodelling of nonlinear dynamic models.}},
url = {http://www.biomedcentral.com/1752-0509/5/90},
volume = {5},
year = {2011}
}
@article{Goodwin2004,
abstract = {Full-body patient simulators provide the technology and the environment necessary for excellent clinical education while eliminating risk to the patient. The extension of simulator-based training into management of basic and critical situations in complex patient populations is natural. We describe the derivation of an infant cardiovascular model through the redefinition of a complete set of parameters for an existing adult model. Specifically, we document a stepwise parameter estimation process, explicit simplifying assumptions, and sources for these parameters. The simulated vital signs are within the target hemodynamic variables, and the simulated systemic arterial pressure wave form and left ventricular pressure volume loop are realistic. The system reacts appropriately to blood loss, and incorporation of aortic stenosis is straightforward. This infant cardiovascular model can form the basis for screen-based educational simulations. The model is also an essential step in attaining a full-body, model-driven infant simulator.},
author = {Goodwin, Jane A and van Meurs, Willem L and {S\'{a} Couto}, Carla D and Beneken, Jan E W and Graves, Shirley A},
doi = {10.1213/01.ANE.0000134797.52793.AF},
institution = {Nemours Children's Clinic-Jacksonville, 807 Children's Way, Jacksonville, FL 32207, USA. jgoodwin@nemours.org},
isbn = {0003-2999},
issn = {0003-2999},
journal = {Anesthesia and analgesia},
number = {6},
pages = {1655--1664},
pmid = {15562049},
title = {{A model for educational simulation of infant cardiovascular physiology.}},
volume = {99},
year = {2004}
}
@article{Saritas2013,
abstract = {Magnetic Particle Imaging (MPI) is a new tracer imaging modality that is gaining significant interest from NMR and MRI researchers. While the physics of MPI differ substantially from MRI, it employs hardware and imaging concepts that are familiar to MRI researchers, such as magnetic excitation and detection, pulse sequences, and relaxation effects. Furthermore, MPI employs the same superparamagnetic iron oxide (SPIO) contrast agents that are sometimes used for MR angiography and are often used for MRI cell tracking studies. These SPIOs are much safer for humans than iodine or gadolinium, especially for Chronic Kidney Disease (CKD) patients. The weak kidneys of CKD patients cannot safely excrete iodine or gadolinium, leading to increased morbidity and mortality after iodinated X-ray or CT angiograms, or after gadolinium-MRA studies. Iron oxides, on the other hand, are processed in the liver, and have been shown to be safe even for CKD patients. Unlike the "black blood" contrast generated by SPIOs in MRI due to increased T2 dephasing, SPIOs in MPI generate positive, "bright blood" contrast. With this ideal contrast, even prototype MPI scanners can already achieve fast, high-sensitivity, and high-contrast angiograms with millimeter-scale resolutions in phantoms and in animals. Moreover, MPI shows great potential for an exciting array of applications, including stem cell tracking in vivo, first-pass contrast studies to diagnose or stage cancer, and inflammation imaging in vivo. So far, only a handful of prototype small-animal MPI scanners have been constructed worldwide. Hence, MPI is open to great advances, especially in hardware, pulse sequence, and nanoparticle improvements, with the potential to revolutionize the biomedical imaging field. © 2012 Elsevier Inc. All rights reserved.},
author = {Saritas, Emine U. and Goodwill, Patrick W. and Croft, Laura R. and Konkle, Justin J. and Lu, Kuan and Zheng, Bo and Conolly, Steven M.},
doi = {10.1016/j.jmr.2012.11.029},
file = {:home/tomaton/Downloads/1-s2.0-S1090780712003734-main.pdf:pdf},
isbn = {10907807 (ISSN)},
issn = {10907807},
journal = {Journal of Magnetic Resonance},
keywords = {Angiography,MPI,Magnetic Particle Imaging,Magnetic nanoparticles,SPIO,Stem cell tracking,Superparamagnetic iron oxide},
pages = {116--126},
pmid = {23305842},
title = {{Magnetic particle imaging (MPI) for NMR and MRI researchers}},
url = {http://dx.doi.org/10.1016/j.jmr.2012.11.029},
volume = {229},
year = {2013}
}
@misc{Modelica,
title = {{Modelica and the Modelica Association}},
url = {http://www.modelica.org}
}
@article{novak2007deployment,
author = {Nov\'{a}k, V\'{a}clav and Vojt\v{e}ch, Josef},
journal = {Networking Studies},
pages = {27},
title = {{Deployment of a DWDM System with CLA Optical Amplifiers in the CESNET2 Network}},
year = {2007}
}
@article{Matejak2014sj,
author = {Matej\'{a}k, Marek and Kulh\'{a}nek, Tom\'{a}\v{s} and Matou\v{s}ek, Stanislav},
doi = {10.3109/00365513.2014.984320},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Matej\'{a}k, Kulh\'{a}nek, Matou\v{s}ek - 2014 - Adair-Based Hemoglobin Equilibrium with Oxygen, Carbon Dioxide and Hydrogen Ion Activity.pdf:pdf},
journal = {Scandinavian journal of clinical and laboratory investigation},
keywords = {acid-base equilibrium,blood gas analysis,carboxyhemoglobin,hemoglobin a},
title = {{Adair-Based Hemoglobin Equilibrium with Oxygen, Carbon Dioxide and Hydrogen Ion Activity}},
year = {2014}
}
@article{Iosup2010,
author = {Iosup, Alexandru and Ostermann, Simon and Yigitbasi, Nezih and Prodan, Radu and Fahringer, Thomas and Epema, D},
file = {:home/tomaton/Downloads/05719609.pdf:pdf},
journal = {IEEE Transactions on Parallel and Distributed Systems},
number = {6},
pages = {931--945},
title = {{Performance Analysis of Cloud Computing Services for Many-Tasks Scientific Computing}},
volume = {22},
year = {2010}
}
@article{Camarasu-Pop2010,
abstract = {Medical imaging research deals with large, heterogeneous and fragmented amounts of medical images. The need for secure, federated and functional medical image databases is very strong within these research communities. This paper provides an overview of the different projects concerned with building medical image databases for medical imaging research. It also discusses the characteristics and requirements of this community and tries to determine to what extent existing solutions can answer these specific requirements.},
author = {Camarasu-Pop, Sorina and Cervenansky, Frederic and Cardenas, Yonny and Nief, Jean Yves and Benoit-Cattin, Hugues},
doi = {10.1109/CCGRID.2010.55},
file = {:home/tomaton/Downloads/05493396.pdf:pdf},
isbn = {9781424469871},
journal = {CCGrid 2010 - 10th IEEE/ACM International Conference on Cluster, Cloud, and Grid Computing},
pages = {739--744},
title = {{Overview of medical data management solutions for research communities}},
year = {2010}
}
@article{Olabarriaga2010,
abstract = {This paper presents the design, implementation, and usage of a virtual laboratory for medical image analysis. It is fully based on the Dutch grid, which is part of the Enabling Grids for E-sciencE (EGEE) production infrastructure and driven by the gLite middleware. The adopted service-oriented architecture enables decoupling the user-friendly clients running on the user's workstation from the complexity of the grid applications and infrastructure. Data are stored on grid resources and can be browsed/viewed interactively by the user with the Virtual Resource Browser (VBrowser). Data analysis pipelines are described as Scufl workflows and enacted on the grid infrastructure transparently using the MOTEUR workflow management system. VBrowser plug-ins allow for easy experiment monitoring and error detection. Because of the strict compliance to the grid authentication model, all operations are performed on behalf of the user, ensuring basic security and facilitating collaboration across organizations. The system has been operational and in daily use for eight months (December 2008), with six users, leading to the submission of 9000 jobs/month in average and the production of several terabytes of data.},
author = {Olabarriaga, S\'{\i}lvia D and Glatard, Tristan and de Boer, Piter T},
doi = {10.1109/TITB.2010.2046742},
file = {:home/tomaton/Downloads/05443468.pdf:pdf},
issn = {1558-0032},
journal = {IEEE transactions on information technology in biomedicine : a publication of the IEEE Engineering in Medicine and Biology Society},
number = {4},
pages = {979--985},
pmid = {20371412},
title = {{A virtual laboratory for medical image analysis.}},
volume = {14},
year = {2010}
}
@incollection{zhao2014migrating,
author = {Zhao, Yong and Li, Youfu and Raicu, Ioan and Lin, Cui and Tian, Wenhong and Xue, Ruini},
booktitle = {Cloud Computing for Data-Intensive Applications},
pages = {231--256},
publisher = {Springer},
title = {{Migrating Scientific Workflow Management Systems from the Grid to the Cloud}},
year = {2014}
}
@article{Brunberg2009,
author = {Brunberg, A and Abel, D and Autschbach, R},
journal = {4th European Conference of the International Federation for Medical and Biological Engineering IFMBE Proceedings},
keywords = {a,cardiovascular system,ii,m aterials and methods,model requirements,modeling,physiological control loops,simulation},
pages = {2600--2603},
title = {{An Object-oriented Model of the Cardiovascular System with a Focus on Physiological Control Loops}},
volume = {22},
year = {2009}
}
@incollection{Brunberg2010,
author = {Brunberg, A and Maschuw, J and Autschbach, R and Abel, D},
booktitle = {World Congress on Medical Physics and Biomedical Engineering, September 7 - 12, 2009, Munich, Germany SE  - 48},
doi = {10.1007/978-3-642-03895-2\_48},
editor = {D\"{o}ssel, Olaf and Schlegel, WolfgangC.},
isbn = {978-3-642-03894-5},
keywords = {Modeling,cardiovascular system,graphical user interface,physiological control loops,simulation},
pages = {166--169},
publisher = {Springer Berlin Heidelberg},
series = {IFMBE Proceedings},
title = {{Object-oriented Model Library of the Cardiovascular System Including Physiological Control Loops}},
url = {http://dx.doi.org/10.1007/978-3-642-03895-2\_48},
volume = {25/13},
year = {2010}
}
@book{Saltelli2004,
abstract = {This book is a ‘primer’ in global sensitivity analysis (SA). Its am- bition is to enable the reader to apply global SA to a mathematical or computational model. It offers a description of a few selected techniques for sensitivity analysis, used for assessing the relative importance of model input factors. These techniques will answer questions of the type ‘which of the uncertain input factors is more important in determining the uncertainty in the output of interest?’ or ‘if we could eliminate the uncertainty in one of the input factors, which factor should we choose to reduce the most the variance of the output?’ Throughout this primer, the input factors of interest will be those that are uncertain, i.e. whose value lie within a finite interval of non-zero width. As a result, the reader will not find sensitivity analysis methods here that look at the local property of the input–output relationships, such as derivative-based analysis1. Special attention is paid to the selection of the method, to the fram- ing of the analysis and to the interpretation and presentation of the results. The examples will help the reader to apply the methods in a way that is unambiguous and justifiable, so as to make the sensitiv- ity analysis an added value to model-based studies or assessments. Both diagnostic and prognostic uses of models will be considered (a description of these is in Chapter 2), and Bayesian tools of anal- ysis will be applied in conjunction with sensitivity analysis. When discussing sensitivity with respect to factors, we shall interpret the term ‘factor’ in a very broad sense: a factor is anything that can be changed in a model prior to its execution. This also includes struc- tural or epistemic sources of uncertainty. To make an example, factors will be presented in applications that are in fact ‘triggers’, used to select one model structure versus another, one mesh size ver- sus another, or altogether different conceptualisations of a system.},
author = {Saltelli, Andrea and Tarantola, Stefano and Campolongo, Francesca and Ratto, Marco},
doi = {10.1002/0470870958},
file = {:home/tomaton/Downloads/SALTELLI2004.pdf:pdf},
isbn = {0470870931},
pages = {219},
title = {{Sensitivity Analysis in Practice}},
year = {2004}
}
@article{fielding2000chapter,
author = {Fielding, Roy Thomas},
institution = {University of California},
journal = {Architectural Styles and the Design of Network-based Software Architectures, Dissertation},
title = {{Chapter 5: Representational State Transfer (REST)}},
year = {2000}
}
@book{khoo2000,
author = {Khoo, Michael C K},
publisher = {IEEE press},
title = {{Physiological control systems}},
year = {2000}
}
@article{Kulhanek2010,
author = {Kulh\'{a}nek, Tom\'{a}\v{s} and \v{S}ilar, J and Matej\'{a}k, Marek and Privitzer, Pavol and Kofranek, Jiř\'{\i} and Tribula, Martin},
journal = {VPH conference},
title = {{Distributed computation and parameter estimation in identification of physiological systems}},
year = {2010}
}
@article{Moles2003,
author = {Moles, Carmen G and Mendes, Pedro and Banga, Julio R},
doi = {10.1101/gr.1262503.},
file = {:home/tomaton/Downloads/0132467.pdf:pdf},
journal = {Genome Research},
pages = {2467--2474},
title = {{Parameter Estimation in Biochemical Pathways: A Comparison of Global Optimization Methods}},
year = {2003}
}
@article{Mell2011,
author = {Mell, Peter and Grance, Timothy},
file = {:home/tomaton/Downloads/SP800-145.pdf:pdf},
title = {{The NIST definition of cloud computing}},
url = {http://csrc.nist.gov/publications/nistpubs/800-145/SP800-145.pdf},
year = {2011}
}
@article{Korf1985,
author = {Korf, Richard E},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Korf - 1985 - Depth -First Iterativ e-Deepening An Optimal Admissible Tree Search.pdf:pdf},
journal = {Artificial Intelligence},
pages = {97--109},
title = {{Depth-First Iterative-Deepening: An Optimal Admissible Tree Search}},
volume = {27},
year = {1985}
}
@article{Zimmermann1980,
author = {Zimmermann, Hubert},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Unknown - Unknown - OSI(1).pdf.pdf:pdf},
journal = {IEEE Transactions om Communications},
title = {{OSI Reference Model - The ISO Model of Architecture for Open Systems Interconnection}},
year = {1980}
}
@article{Anjum2012,
author = {Anjum, Ashiq and Hill, Richard and McClatchey, Richard and Bessis, Nik and Branson, Andrew},
doi = {10.1504/IJWGS.2012.049169},
file = {:home/tomaton/Downloads/Glueing\%20Grids\%20and\%20Clouds\%20Together.pdf:pdf},
journal = {International Journal of Web and Grid Services},
number = {3},
pages = {248--265},
title = {{Glueing grids and clouds together: a service-oriented approach}},
volume = {8},
year = {2012}
}
@article{Kofranek2011,
abstract = {The paper is a presentation of the current state of development for the Atlas of Physiology and Pathophysiology (Atlas). Our main aim is to provide a novel interactive multimedia application that can be used for biomedical education where (a) simulations are combined with tutorials and (b) the presentation layer is simplified while the underlying complexity of the model is retained. The development of the Atlas required the cooperation of many professionals including teachers, system analysts, artists, and programmers. During the design of the Atlas, tools were developed that allow for component-based creation of simulation models, creation of interactive multimedia and their final coordination into a compact unit based on the given design. The Atlas is a freely available online application, which can help to explain the function of individual physiological systems and the causes and symptoms of their disorders.},
author = {Kofranek, Jiri and Matousek, Stanislav and Rusz, Jan and Stodulka, Petr and Privitzer, Pavol and Matejak, Marek and Tribula, Martin},
doi = {10.1016/j.cmpb.2010.12.007},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Kofranek et al. - 2011 - The Atlas of Physiology and Pathophysiology Web-based multimedia enabled interactive simulations.pdf:pdf},
issn = {1872-7565},
journal = {Computer methods and programs in biomedicine},
keywords = {Atlases as Topic,Computer Simulation,Internet,Physiology},
month = nov,
number = {2},
pages = {143--53},
pmid = {21232813},
title = {{The Atlas of Physiology and Pathophysiology: Web-based multimedia enabled interactive simulations.}},
volume = {104},
year = {2011}
}
@article{Kumar2014,
author = {Kumar, R and Gupta, N and Charu, S and Jain, K and Jangir, SK},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Kumar et al. - 2014 - Open Source Solution for Cloud Computing Platform Using OpenStack.pdf:pdf},
keywords = {cloud computing,eucalyptus,icehouse,open nebula,openstack},
number = {5},
pages = {89--98},
title = {{Open Source Solution for Cloud Computing Platform Using OpenStack}},
url = {http://www.ijcsmc.com/docs/papers/May2014/V3I5201427.pdf},
volume = {3},
year = {2014}
}
@inproceedings{Raicu2008,
abstract = {Many-task computing aims to bridge the gap between two computing paradigms, high throughput computing and high performance computing. Many task computing differs from high throughput computing in the emphasis of using large number of computing resources over short periods of time to accomplish many computational tasks (i.e. including both dependent and independent tasks), where primary metrics are measured in seconds (e.g. FLOPS, tasks/sec, MB/s I/O rates), as opposed to operations (e.g. jobs) per month. Many task computing denotes high-performance computations comprising multiple distinct activities, coupled via file system operations. Tasks may be small or large, uniprocessor or multiprocessor, compute-intensive or data-intensive. The set of tasks may be static or dynamic, homogeneous or heterogeneous, loosely coupled or tightly coupled. The aggregate number of tasks, quantity of computing, and volumes of data may be extremely large. Many task computing includes loosely coupled applications that are generally communication-intensive but not naturally expressed using standard message passing interface commonly found in high performance computing, drawing attention to the many computations that are heterogeneous but not ldquohappilyrdquo parallel.},
author = {Raicu, Ioan and Foster, Ian T. and Zhaoyo, Yong},
booktitle = {2008 Workshop on Many-Task Computing on Grids and Supercomputers, MTAGS 2008},
doi = {10.1109/MTAGS.2008.4777912},
isbn = {9781424428724},
keywords = {HPC,HTC,High Performance Computing,High Throughput Computing,MTC,Many-task Computing},
title = {{Many-task computing for grids and supercomputers}},
year = {2008}
}
@article{Kroon1996,
author = {Kroon, F. W.},
doi = {10.1007/BF00372775},
issn = {0039-3215},
journal = {Studia Logica},
month = may,
number = {3},
pages = {427--454},
title = {{The intrinsic difficulty of recursive functions}},
url = {http://link.springer.com/10.1007/BF00372775},
volume = {56},
year = {1996}
}
@book{Rauber2013,
author = {Rauber, Thomas and R\"{u}nger, Gudula},
file = {:home/tomaton/Documents/Studium-Dokumenty/Articles/Theory Of Computation/Parallel Programming - T Rauber.G Runger.PDF:PDF},
isbn = {9783642048173},
publisher = {Springer},
title = {{Parallel programming: For multicore and cluster systems}},
year = {2013}
}
@article{Beard2005,
author = {Beard, Daniel a and Bassingthwaighte, James B and Greene, Andrew S},
doi = {10.1152/physiolgenomics.00117.2005},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Beard, Bassingthwaighte, Greene - 2005 - Computational modeling of physiological systems.pdf:pdf},
issn = {1531-2267},
journal = {Physiological genomics},
pages = {1--3},
pmid = {16179418},
title = {{Computational modeling of physiological systems.}},
volume = {23},
year = {2005}
}
@article{Chervenak2012,
abstract = {Progress in our understanding of brain disorders increasingly relies on the costly collection of large standardized brain magnetic resonance imaging (MRI) data sets. Moreover, the clinical interpretation of brain scans benefits from compare and contrast analyses of scans from patients with similar, and sometimes rare, demographic, diagnostic, and treatment status. A solution to both needs is to acquire standardized, research-ready clinical brain scans and to build the information technology infrastructure to share such scans, along with other pertinent information, across hospitals. This paper describes the design, deployment, and operation of a federated imaging system that captures and shares standardized, de-identified clinical brain images in a federation across multiple institutions. In addition to describing innovative aspects of the system architecture and our initial testing of the deployed infrastructure, we also describe the Standardized Imaging Protocol (SIP) developed for the project and our interactions with the Institutional Review Board (IRB) regarding handling patient data in the federated environment.},
author = {Chervenak, Ann L. and {Van Erp}, Theo G M and Kesselman, Carl and D'Arcy, Mike and Sobell, Janet and Keator, David and Dahm, Lisa and Murry, Jim and Law, Meng and Hasso, Anton and Ames, Joseph and MacCiardi, Fabio and Potkin, Steven G.},
doi = {10.3233/978-1-61499-054-3-19},
file = {:home/tomaton/Downloads/HealthGrid2012-BIRN.pdf:pdf},
isbn = {9781614990536},
issn = {09269630},
journal = {Studies in Health Technology and Informatics},
keywords = {Architecture,Brain,De-identification,Federation,Health,Hospitals,Imaging,Infrastructure,MRI,Open source,Pilot,Protocol,Sharing,Standardization},
pages = {19--28},
pmid = {22941984},
title = {{A system architecture for sharing de-identified, research-ready brain scans and health information across clinical imaging centers}},
volume = {175},
year = {2012}
}
@article{Armbrust2010,
author = {Armbrust, Michael and Stoica, Ion and Zaharia, Matei and Fox, Armando and Griffith, Rean and Joseph, Anthony D. and Katz, Randy and Konwinski, Andy and Lee, Gunho and Patterson, David and Rabkin, Ariel},
doi = {10.1145/1721654.1721672},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Armbrust et al. - 2010 - A view of cloud computing.pdf:pdf},
issn = {00010782},
journal = {Communications of the ACM},
month = apr,
number = {4},
pages = {50--58},
title = {{A view of cloud computing}},
volume = {53},
year = {2010}
}
@inproceedings{Kulhanek2013b,
author = {Kulh\'{a}nek, Tom\'{a}\v{s} and Matej\'{a}k, Marek and \v{S}ilar, Jan and Privitzer, Pavol and Tribula, Martin and Je\v{z}ek, Filip and Kofr\'{a}nek, Jiř\'{\i}},
booktitle = {sborn\'{\i}k př\'{\i}sp\v{e}vků MEDSOFT},
pages = {115--121},
title = {{HYBRIDN\'{I} ARCHITEKTURA PRO WEBOV\'{E} SIMUL\'{A}TORY}},
url = {http://www.creativeconnections.cz/medsoft/2013/Medsoft\_2013\_Kulhanek.pdf},
year = {2013}
}
@article{Madden2012,
author = {Madden, PH},
doi = {10.1109/MDT.2012.2230391},
file = {:home/tomaton/Downloads/06363528.pdf:pdf},
journal = {IEEE Design \& Test of Computers},
number = {April},
pages = {58--64},
title = {{Dispelling the myths of parallel computing}},
year = {2012}
}
@phdthesis{Cantu-Paz1999,
author = {Cantu-Paz, Erick},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Cantu-Paz - 1999 - Designing efficient and accurate parallel genetic algorithms.pdf:pdf},
school = {University of Illinois at Urbana-Champaign},
title = {{Designing efficient and accurate parallel genetic algorithms}},
year = {1999}
}
@book{Li2014,
address = {New York, NY},
doi = {10.1007/978-1-4939-1905-5},
editor = {Li, Xiaolin and Qiu, Judy},
isbn = {978-1-4939-1904-8},
publisher = {Springer New York},
title = {{Cloud Computing for Data-Intensive Applications}},
url = {http://link.springer.com/10.1007/978-1-4939-1905-5},
year = {2014}
}
@inproceedings{Kofranek2011hummod,
author = {Kofranek, J and Matejak, M and Privitzer, P},
booktitle = {Proceedings 8th Modelica Conference, Dresden, Germany},
pages = {713--724},
title = {{Hummod-large scale physiological models in modelica}},
year = {2011}
}
@book{Ashlock2005,
author = {Ashlock, D. and Ashlock, D.},
booktitle = {Guelph, Ontario: Springer},
file = {:home/tomaton/Downloads/Evolutionary computation for modeling and optimization.pdf:pdf},
isbn = {9780387221960},
pages = {571},
title = {{Evolutionary Computation for Modeling and Optimization}},
year = {2005}
}
@book{Karp1972,
author = {Karp, Richard M.},
doi = {10.1007/978-1-4684-2001-2\_9},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Karp - 1972 - Reducibility among combinatorial problems.pdf:pdf},
publisher = {Springer US},
title = {{Reducibility among combinatorial problems}},
year = {1972}
}
@article{Barker2008,
abstract = {Workflow technologies are emerging as the dominant approach to coordinate groups of distributed services. However with a space filled with competing specifications, standards and frameworks from multiple domains, choosing the right tool for the job is not always a straightforward task. Researchers are often unaware of the range of technology that already exists and focus on implementing yet another proprietary workflow system. As an antidote to this common problem, this paper presents a concise survey of existing workflow technology from the business and scientific domain and makes a number of key suggestions towards the future development of scientific workflow systems.},
author = {Barker, Adam and {Van Hemert}, Jano},
doi = {10.1145/2213836.2213899},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Barker, Van Hemert - 2008 - Scientific Workflow A Survey and Research Directions.pdf:pdf},
isbn = {3-540-68105-1, 978-3-540-68105-2},
journal = {Proceedings of the 7th International Conference on Parallel Processing and Applied Mathematics},
pages = {746--753},
title = {{Scientific Workflow: A Survey and Research Directions}},
url = {http://dl.acm.org/citation.cfm?id=1786194.1786281},
year = {2008}
}
@article{Pruett2014,
abstract = {The acute response of parathyroid hormone to perturbations in serum ionized calcium ([Ca(2+)]) is physiologically complex, and poorly understood. The literature provides numerous observations of quantitative and qualitative descriptions of parathyroid hormone (PTH) dynamics. We present a physiologically based mathematical model of PTH secretion constructed from mechanisms suggested in the literature, and validated against complex [Ca(2+)] clamping protocols from human data. The model is based on two assumptions. The first is that secretion is a fraction of cellular reserves, with the fraction being determined by the kinetics of [Ca(2+)] with its receptor. The second is that there are multiple distinct populations of parathyroid cells, with different secretory parameters. The steady state and transient PTH secretion responses of the model are in agreement with human experimental PTH responses to different hypocalcemia and hypercalcemia stimuli. This mathematical model suggests that a population of secreting cells is responsible for the PTH secretory dynamics observed experimentally.},
author = {Pruett, William a and Hester, Robert L},
doi = {10.1002/phy2.231},
file = {:home/tomaton/Downloads/e00231.full.pdf:pdf},
isbn = {6019841820},
issn = {2051-817X},
journal = {Physiological reports},
keywords = {calcium,hysteresis,parathyroid hormone},
month = feb,
number = {2},
pages = {e00231},
pmid = {24744900},
title = {{Parathyroid hormone secretion by multiple distinct cell populations, a time dynamic mathematical model.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3966243\&tool=pmcentrez\&rendertype=abstract},
volume = {2},
year = {2014}
}
@inproceedings{Amdahl1967,
author = {Amdahl},
booktitle = {Proceedings of AFIPS Conference},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Amdahl - 1967 - Validity of the single processor approach to achieving large scale computing capabilities.pdf:pdf},
pages = {483--485},
title = {{Validity of the single processor approach to achieving large scale computing capabilities}},
year = {1967}
}
@book{Hall2010a,
abstract = {The 12th edition of Guyton and Hall Textbook of Medical Physiology continues this bestselling title's long tradition as one of the world's favorite physiology textbooks. The immense success of this book is due to its description of complex physiologic principles in language that is easy to read and understand. Now with an improved color art program, thorough updates reflecting today's medicine and science, and accessible online at studentconsult.com, this textbook is an excellent source for mastering essential human physiology knowledge. Learn and remember vital concepts easily thanks to short, easy-to-read, masterfully edited chapters and a user-friendly full-color design. See core concepts applied to real-life situations with clinical vignettes throughout the text. Discover the newest in physiology with updates that reflect the latest advances in molecular biology, cardiovascular, neurophysiology and gastrointestinal topics. Visualize physiologic principles clearly with over 1000 bold, full-color drawings and diagrams. Distinguish core concepts from more in-depth material with a layout that uses gray shading to clearly differentiate between "need-to-know" and "nice-to-know" information. Access the complete contents online at studentconsult.com along with bonus resources such as image banks, self-assessment questions, physiology animations and more! This new edition continues the long tradition of "Guyton" as one of the world's favorite physiology textbooks},
author = {Hall, John E},
booktitle = {Physiology},
isbn = {0721602401},
pages = {1091},
pmid = {15882912},
title = {{Guyton and Hall Textbook of Medical Physiology}},
year = {2010}
}
@article{Kofranek2008,
author = {Kofr\'{a}nek, J and Matej\'{a}k, M and Privitzer, P and Tribula, M},
journal = {Technical Computing Prague},
pages = {1--16},
title = {{Causal or acausal modeling: labour for humans or labour for machines}},
year = {2008}
}
@article{Shroff1985,
author = {Shroff, S. G. and Janicki, J. S. and Weber, K. T.},
journal = {Am J Physiol Heart Circ Physiol},
month = aug,
number = {2},
pages = {H358--370},
title = {{Evidence and quantitation of left ventricular systolic resistance}},
url = {http://ajpheart.physiology.org/content/249/2/H358},
volume = {249},
year = {1985}
}
@incollection{Raicu2012,
abstract = {Many-task computing aims to bridge the gap between two computing paradigms, high throughput computing and high performance computing. Many task computing denotes high-performance computations comprising multiple distinct activities, coupled via file system operations. The aggregate number of tasks, quantity of computing, and volumes of data may be extremely large. Traditional techniques to support many-task computing commonly found in scientific computing (i.e. the reliance on parallel file systems with static configurations) do not scale to today’s largest systems for data intensive application, as the rate of increase in the number of processors per system is outgrowing the rate of performance increase of parallel file systems. We argue that in such circumstances, data locality is critical to the successful and efficient use of large distributed systems for data-intensive applications. We propose a “data diffusion” approach to enable data- intensive many-task computing. Data diffusion acquires compute and storage resources dynamically, replicates data in response to demand, and schedules computations close to data, effectively harnessing data locality in application data access patterns. As demand increases, more resources are acquired, thus allowing faster response to subsequent requests that refer to the same data; when demand drops, resources are released. To explore the feasibility of data diffusion, we offer both a theoretical and empirical analysis. We define an abstract model for data diffusion, define and implement scheduling policies with heuristics that optimize real world performance, and develop a competitive online caching eviction policy. We also offer many empirical experiments to explore the benefits of data diffusion, both under static and dynamic resource provisioning. We show performance improvements of one to two orders of magnitude across three diverse workloads when compared to the performance of parallel file systems with throughputs approaching 80Gb/s on a modest cluster of 200 processors. We also compare data diffusion with a best model for active storage, contrasting the difference between a pull-model found in data diffusion and a push-model found in active storage, on up to 5832 processors. We conclude the chapter with performance results from a large scale astronomy application demonstrating that our approach improves both its performance and scalability.},
author = {Raicu, Ioan and Foster, Ian and Zhao, Yong and Al., Et},
booktitle = {Data intensive distributed computing / challenges and solutions for large scale information management},
pages = {28--73},
title = {{Towards Data Intensive Many-Task Computing}},
year = {2012}
}
@article{Allcock2005,
abstract = { The GridFTP extensions to the File Transfer Protocol define a general-purpose mechanism for secure, reliable, high-performance data movement. We report here on the Globus striped GridFTP framework, a set of client and server libraries designed to support the construction of data-intensive tools and applications. We describe the design of both this framework and a striped GridFTP server constructed within the framework. We show that this server is faster than other FTP servers in both single-process and striped configurations, achieving, for example, speeds of 27.3 Gbit/s memory-to-memory and 17 Gbit/s disk-to-disk over a 60 millisecond round trip time, 30 Gbit/s network. In another experiment, we show that the server can support 1800 concurrent clients without excessive load. We argue that this combination of performance and modular structure make the Globus GridFTP framework both a good foundation on which to build tools and applications, and a unique testbed for the study of innovative data management techniques and network protocols.},
author = {Allcock, William and Bresnahan, John and Kettimuthu, Rajkumar and Link, Michael and Dumitrescu, Catalin and Raicu, Ioan and Foster, Ian},
doi = {10.1109/SC.2005.72},
file = {:home/tomaton/Documents/27580054.pdf:pdf},
isbn = {1595930612},
journal = {Proceedings of the ACM/IEEE 2005 Supercomputing Conference, SC'05},
number = {c},
pages = {1--11},
title = {{The Globus striped GridFTP framework and server}},
volume = {2005},
year = {2005}
}
@inproceedings{fritzson2006openmodelica,
author = {Fritzson, Peter and Aronsson, Peter and Pop, Adrian and Lundvall, Hakan and Nystrom, Kaj and Saldamli, Levon and Broman, David and Sandholm, Anders},
booktitle = {Computer Aided Control System Design, 2006 IEEE International Conference on Control Applications, 2006 IEEE International Symposium on Intelligent Control},
organization = {IEEE},
pages = {1588--1595},
title = {{OpenModelica-A free open-source environment for system modeling, simulation, and teaching}},
year = {2006}
}
@article{Anjum,
author = {Anjum, Ashiq and Bloodsworth, Peter and Branson, Andrew and Hauer, Tam\'{a}s and Munir, Kamran and Rogulin, Dmitry and Shamdasani, Jetendr and Lane, Coldharbour and Bs, Bristol and Anjum, Email Ashiq and Hauer, Tamas and Mcclatchey, Richard},
file = {:home/tomaton/Downloads/0707.0763v1.pdf:pdf},
keywords = {biomedical application,data modelling,ontologies,user requirements},
title = {{The Requirements for Ontologies in Medical Data Integration : A Case Study}}
}
@misc{dicom2011,
title = {{DICOM Standard 2011}},
url = {https://dabsoft.ch/dicom/index.html},
year = {2011}
}
@article{Tiller2008,
author = {Tiller, Michael M},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Tiller - 2008 - Patterns and Anti-Patterns in Modelica.pdf:pdf},
journal = {Proceedings Modelica 2008 Conference},
keywords = {anti-patterns,patterns},
pages = {647--655},
title = {{Patterns and Anti-Patterns