text:
in Modelica}},
year = {2008}
}
@article{Saliba2012,
abstract = {PURPOSE: Innovative technologies to deliver health care across borders have attracted both evangelists and sceptics. Our aim was to systematically identify factors that hinder or support implementation of cross-border telemedicine services worldwide in the last two decades. METHODS: Two reviewers independently searched ten databases including MEDLINE and EMBASE, in June 2011 including citations from 1990 onwards when at least an abstract was available in English. We also searched ELDIS and INTUTE databases and Internet search engines to identify grey literature. We included studies which (a) described the use of telemedicine to deliver cross-border healthcare and, or (b) described the factors that hinder or support implementation of cross-border telemedicine services. All study designs were included. Two reviewers independently assessed titles and abstracts of articles identified. Papers were allocated to one of four reviewers who extracted relevant data and validated it. We took a qualitative approach to the analysis, conducting a narrative synthesis of the evidence. RESULTS: 6026 records were identified of which 5806 were excluded following screening of titles and abstracts. We assessed 227 full text articles, excluding 133 because they were fatally flawed or did not meet the inclusion criteria, producing a final sample of 94. They involved 76 countries worldwide, most involving collaborations between high and low or middle income countries. Most described services delivering a combination of types of telemedicine but specialties most represented were telepathology, telesurgery, Emergency and trauma telemedicine and teleradiology. Most link health professionals, with only a few linking professionals directly to patients. A main driver for the development of cross-border telemedicine is the need to improve access to specialist services in low and middle income countries and in underserved rural areas in high income countries. Factors that hinder or support implementation clustered into four main themes: (1) legal factors; (2) sustainability factors; (3) cultural factors; and (4) contextual factors. CONCLUSIONS: National telemedicine programmes may build infrastructure and change mindsets, laying the foundations for successful engagement in cross-border services. Regional networks can also help with sharing of expertise and innovative ways of overcoming barriers to the implementation of services. Strong team leadership, training, flexible and locally responsive services delivered at low cost, using simple technologies, and within a clear legal and regulatory framework, are all important factors for the successful implementation of cross-border telemedicine services.},
author = {Saliba, Vanessa and Legido-Quigley, Helena and Hallik, Riina and Aaviksoo, Ain and Car, Josip and McKee, Martin},
doi = {10.1016/j.ijmedinf.2012.08.003},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Saliba et al. - 2012 - Telemedicine across borders a systematic review of factors that hinder or support implementation.pdf:pdf},
issn = {1872-8243},
journal = {International journal of medical informatics},
keywords = {Culture,Humans,International Cooperation,Leadership,Neoplasms,Neoplasms: prevention \& control,Telemedicine,Telemedicine: legislation \& jurisprudence,Telemedicine: utilization},
month = dec,
number = {12},
pages = {793--809},
pmid = {22975018},
title = {{Telemedicine across borders: a systematic review of factors that hinder or support implementation.}},
volume = {81},
year = {2012}
}
@article{Sarkar2010,
abstract = {Biomedical informatics involves a core set of methodologies that can provide a foundation for crossing the "translational barriers" associated with translational medicine. To this end, the fundamental aspects of biomedical informatics (e.g., bioinformatics, imaging informatics, clinical informatics, and public health informatics) may be essential in helping improve the ability to bring basic research findings to the bedside, evaluate the efficacy of interventions across communities, and enable the assessment of the eventual impact of translational medicine innovations on health policies. Here, a brief description is provided for a selection of key biomedical informatics topics (Decision Support, Natural Language Processing, Standards, Information Retrieval, and Electronic Health Records) and their relevance to translational medicine. Based on contributions and advancements in each of these topic areas, the article proposes that biomedical informatics practitioners ("biomedical informaticians") can be essential members of translational medicine teams.},
author = {Sarkar, Indra Neil},
doi = {10.1186/1479-5876-8-22},
file = {:home/tomaton/Downloads/1479-5876-8-22.pdf:pdf},
isbn = {1479-5876 (Electronic)$\backslash$r1479-5876 (Linking)},
issn = {1479-5876},
journal = {Journal of translational medicine},
pages = {22},
pmid = {20187952},
title = {{Biomedical informatics and translational medicine.}},
volume = {8},
year = {2010}
}
@inproceedings{fritzson2002,
author = {Fritzson, Peter and Bunus, Peter},
booktitle = {Simulation Symposium, 2002. Proceedings. 35th Annual},
organization = {IEEE},
pages = {365--380},
title = {{Modelica-a general object-oriented language for continuous and discrete-event system modeling and simulation}},
year = {2002}
}
@article{Curcin2008,
abstract = {The past decade has witnessed a growing trend in designing and using workflow systems with a focus on supporting the scientific research process in bioinformatics and other areas of life sciences. The aim of these systems is mainly to simplify access, control and orchestration of remote distributed scientific data sets using remote computational resources, such as EBI web services. In this paper we present the state of the art in the field by reviewing six such systems: Discovery Net, Taverna, Triana, Kepler, Yawl and BPEL. We provide a high-level framework for comparing the systems based on their control flow and data flow properties with a view of both informing future research in the area by academic researchers and facilitating the selection of the most appropriate system for a specific application task by practitioners.},
author = {Curcin, V. and Ghanem, M.},
doi = {10.1109/CIBEC.2008.4786077},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Curcin, Ghanem - 2008 - Scientific workflow systems - can one size fit all.pdf:pdf},
isbn = {978-1-4244-2694-2},
journal = {2008 Cairo International Biomedical Engineering Conference},
title = {{Scientific workflow systems - can one size fit all?}},
year = {2008}
}
@article{Palladino1997,
abstract = {Myocardial contractile properties form the cornerstone of the heart's ability to pump blood. Efforts have been made to characterize these properties via classic elasticity theory concepts, which can lead to spurious results, as demonstrated by experiments measuring intramyocardial pressure. Two ways out of these difficulties are identified. One is to start at the cellular level, the other at the chamber level. The latter allows separation of ventricle (source) and arterial (load) effects on measured pressure and flow, distinct from previous definitions of ventricular contractility which tended to lump the two.},
author = {Palladino, Joseph L and Rabbany, Sina Y and Mulier, Jan P and Noordergraaf, Abraham},
journal = {Technology and Health Care},
month = jan,
number = {1},
pages = {135--144},
title = {{A perspective on myocardial contractility}},
url = {http://iospress.metapress.com/content/5REMNVKBRLKGHHJN},
volume = {5},
year = {1997}
}
@book{Foster1995,
abstract = {From the Publisher: At last, a practitioner's guide to parallel programming! Students and professionals who use parallel or distributed computer systems will be able to solve real problems with Designing and Building Parallel Programs. This book provides a comprehensive introduction to parallel algorithm design, performance analysis, and program construction. It describes the tools needed to write parallel programs and provides numerous examples. A unique feature is the companion on-line version, accessible via the World Wide Web using browsers such as Mosaic. This provides a convenient hypertext version of the text with pointers to programming tools, example programs, and other resources on parallel and distributed computing.},
author = {Foster, Ian},
booktitle = {Interface},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Foster - 1995 - Designing and Building Parallel Programs.pdf:pdf},
isbn = {0201575949},
publisher = {Addison-Wesley Publishing Company},
title = {{Designing and Building Parallel Programs}},
year = {1995}
}
@inproceedings{Cobham1964,
author = {Cobham, Alan},
booktitle = {Proc. 1964 Congress for Logic,Methodology and Philosophy of Science.},
pages = {24--30},
title = {{The intrinsic computational difficulty of functions}},
year = {1964}
}
@article{Kacsuk2012,
abstract = {The WS-PGRADE/gUSE generic DCI gateway framework has been developed to support a large variety of user communities. It provides a generic purpose, workflow-oriented graphical user interface to create and run workflows on various DCIs including clusters, Grids, desktop Grids and clouds. The framework can be used by NGIs to support small user communities who cannot afford to develop their own customized science gateway. The WS-PGRADE/gUSE framework also provides two API interfaces (Application Specific Module API and Remote API) to create application-specific science gateways according to the needs of different user communities. The paper describes in detail the workflow concept of WS-PGRADE, the DCI Bridge service that enables access to most of the popular European DCIs and the Application Specific Module and Remote API concepts to generate application-specific science gateways.},
author = {Kacsuk, Peter and Farkas, Zoltan and Kozlovszky, Miklos and Hermann, Gabor and Balasko, Akos and Karoczkai, Krisztian and Marton, Istvan},
doi = {10.1007/s10723-012-9240-5},
file = {:home/tomaton/Downloads/art\%3A10.1007\%2Fs10723-012-9240-5.pdf:pdf},
isbn = {1570-7873},
issn = {15707873},
journal = {Journal of Grid Computing},
keywords = {Customized interface,Distributed computing infrastructures,Science gateway,Workflow},
pages = {601--630},
title = {{WS-PGRADE/gUSE Generic DCI Gateway Framework for a Large Variety of User Communities}},
volume = {10},
year = {2012}
}
@book{Erl2008,
author = {Erl, Thomas},
publisher = {Prentice Hall},
title = {{SOA Principles of Service Design}},
year = {2008}
}
@article{Marosi2013,
abstract = {The paper completes the work started in the EU FP7 EDGI project for extending service grids with volunteer (global) and institutional (local) desktop grids. The Generic BOINC Application Client (GBAC) concept described in the paper enables the transparent and automatic forwarding of parameter sweep application (parametric) jobs from service grid VOs (Virtual Organizations) into connected desktop grids without any porting effort. GBAC that introduces virtualization for the volunteer BOINC (Berkeley Open Infrastructure for Network Computing) clients can also be considered as a first step towards establishing volunteer cloud systems since it provides solutions for several problems of creating such a volunteer cloud system. © 2012 Elsevier B.V. All rights reserved.},
author = {Marosi, Attila and Kov\'{a}cs, J\'{o}zsef and Kacsuk, Peter},
doi = {10.1016/j.future.2012.03.013},
file = {:home/tomaton/Downloads/toward\_a\_volunteer\_cloud(1).pdf:pdf},
issn = {0167739X},
journal = {Future Generation Computer Systems},
keywords = {Cloud,Desktop grid,Virtualization,Volunteer computing},
number = {6},
pages = {1442--1451},
publisher = {Elsevier B.V.},
title = {{Towards a volunteer cloud system}},
url = {http://dx.doi.org/10.1016/j.future.2012.03.013},
volume = {29},
year = {2013}
}
@article{Guyton1972,
author = {Guyton, A C and Coleman, T G and Granger, H J},
doi = {10.1146/annurev.ph.34.030172.000305},
issn = {0066-4278},
journal = {Annual review of physiology},
keywords = {Aldosterone,Aldosterone: physiology,Angiotensin II,Angiotensin II: physiology,Biological,Blood Circulation,Blood Pressure,Body Fluids,Body Fluids: physiology,Cardiac Output,Heart Failure,Heart Failure: physiopathology,Homeostasis,Hypertension,Hypertension: physiopathology,Kidney,Kidney: physiology,Models,Natriuresis,Nephrosis,Nephrosis: physiopathology,Oxygen,Oxygen: blood,Physical Exertion,Pressoreceptors,Pressoreceptors: physiology,Reflex,Renal,Renal: physiopathology,Renin,Renin: physiology,Systems Analysis},
pages = {13--46},
pmid = {4334846},
title = {{Circulation: overall regulation.}},
volume = {34},
year = {1972}
}
@inproceedings{Cook1971,
abstract = {It is shown that any recognition problem solved by a polynomial time-bounded nondeterministic Turing machine can be “reduced” to the problem of determining whether a given propositional formula is a tautology. Here “reduced” means, roughly speaking, that the first problem can be solved deterministically in polynomial time provided an oracle is available for solving the second. From this notion of reducible, polynomial degrees of difficulty are defined, and it is shown that the problem of determining tautologyhood has the same polynomial degree as the problem of determining whether the first of two given graphs is isomorphic to a subgraph of the second. Other examples are discussed. A method of measuring the complexity of proof procedures for the predicate calculus is introduced and discussed.},
author = {Cook, Stephen A.},
booktitle = {STOC '71 Proceedings of the third annual ACM symposium on Theory of computing},
doi = {10.1145/800157.805047},
issn = {08985626},
pages = {151--158},
title = {{The Complexity of Theorem-Proving Procedures}},
year = {1971}
}
@article{Avanzolini1988,
abstract = {A pulsatile simulator of the closed-loop cardiovascular system, designed to solve simulation, identification and control problems in a research and education context, is presented. Its implimentation makes use of a command-driven interactive program for simulation of non-linear ordinary differential equations. The flexibility of the simulator is demonstrated by the results presented which refer to a basal steady-state circulatory condition as well as a transient induced by an abrupt change in peripheral resistance.},
author = {Avanzolini, Guido and Barbini, Paolo and Cappello, Angelo and Cevenini, Gabriele},
doi = {10.1016/0020-7101(88)90006-2},
issn = {00207101},
journal = {International Journal of Bio-Medical Computing},
keywords = {Cardiac assist devices,Cardiovascular system,Interactive simulation,Pulsatile model,Simulation language},
month = jan,
number = {1},
pages = {39--49},
title = {{CADCS simulation of the closed-loop cardiovascular system}},
url = {http://www.sciencedirect.com/science/article/pii/0020710188900062},
volume = {22},
year = {1988}
}
@article{Westerhof1971,
author = {Westerhof, N and Elzinga, G and Sipkema, P},
journal = {Journal of Applied Physiology},
month = nov,
number = {5},
pages = {776--781},
title = {{An artificial arterial system for pumping hearts.}},
url = {http://jap.physiology.org/content/31/5/776.abstract},
volume = {31},
year = {1971}
}
@article{Morley2007,
abstract = {OBJECTIVE: Current left ventricular assist devices are designed to provide full hemodynamic support for patients with end-stage failing hearts, but their use has been limited by operative risks, low reliability, and device-related morbidity. Such concerns have resulted in minimum use of left ventricular assist devices for destination therapy. We hypothesize that partial circulatory support, which could be achieved with small pumps implanted with less-invasive procedures, might expand the role of circulatory support devices for treatment of heart failure. METHODS: We examine the hemodynamic effects of partial left ventricular support using a previously described computational model of the cardiovascular system. Results from simulations were validated by comparison with an in vivo hemodynamic study. RESULTS: Simulations demonstrated that partial support (2-3 L/min) increased total cardiac output (left ventricular assist device output plus native heart output) by more than 1 L/min and decreased left ventricular end-diastolic pressure by 7 to 10 mm Hg with moderate-to-severe heart failure. Analyses showed that the hemodynamic benefits of increased cardiac output and decreased left ventricular end-diastolic pressure are greater in less-dilated and less-dysfunctional hearts. Both the relationships between ventricular assist device flow and cardiac output and ventricular assist device flow and left atrial pressure predicted by the model closely approximated the same relationships obtained during hemodynamic study in a bovine heart failure model. CONCLUSIONS: Results suggest that a pump with a flow rate of 2 to 3 L/min could meaningfully affect cardiac output and blood pressure in patients with advanced compensated heart failure. The development of small devices capable of high reliability and minimal complications that can be implanted with less-invasive techniques is supported by these findings.},
author = {Morley, Deborah and Litwak, Kenneth and Ferber, Paul and Spence, Paul and Dowling, Robert and Meyns, Bart and Griffith, Bartley and Burkhoff, Daniel},
doi = {10.1016/j.jtcvs.2006.07.037},
issn = {1097-685X},
journal = {The Journal of thoracic and cardiovascular surgery},
keywords = {Animals,Blood Pressure,Cardiac Output,Cardiovascular,Cardiovascular Physiological Phenomena,Cattle,Computer Simulation,Heart Failure,Heart Failure: physiopathology,Heart Failure: therapy,Heart-Assist Devices,Humans,Male,Models,Ventricular Pressure},
number = {1},
pages = {21--28},
pmid = {17198776},
title = {{Hemodynamic effects of partial ventricular support in chronic heart failure: results of simulation validated with in vivo data.}},
volume = {133},
year = {2007}
}
@article{Cooling2008,
author = {Cooling, M T and Hunter, P and Crampin, E J},
doi = {10.1049/iet-syb},
journal = {Systems Biology, IET},
number = {April 2007},
pages = {73--79},
title = {{Modelling biological modularity with CellML}},
url = {http://ieeexplore.ieee.org/xpls/abs\_all.jsp?arnumber=4483541},
year = {2008}
}
@article{Gyenge2003,
abstract = {This study is concerned with the formulation of a 'kidney module' linked to the plasma compartment of a larger mathematical model previously developed. Combined, these models can be used to predict, amongst other things, fluid and small ion excretion rates by the kidney; information that should prove useful in evaluating values and trends related to whole-body fluid balance for different clinical conditions to establish fluid administration protocols and for educational purposes. The renal module assumes first-order, negative-feedback responses of the kidney to changes in plasma volume and/or plasma sodium content from their normal physiological set points. Direct hormonal influences are not explicitly formulated in this empiric model. The model also considers that the renal excretion rates of small ions other than sodium are proportional to the excretion rate of sodium. As part of the model development two aspects are emphasized (1): the estimation of parameters related to the renal elimination of fluid and small ions, and (2) model validation via comparisons between the model predictions and selected experimental data. For validation, model predictions of the renal dynamics are compared with new experimental data for two cases: plasma overload resulting from external fluid infusion (e.g. infusions of iso-osmolar solutions and/or hypertonic/hyperoncotic saline solutions), and untreated hypo volemic conditions that result from the external loss of blood. The present study demonstrates that the empiric kidney module presented above can provide good short-term predictions with respect to all renal outputs considered here. Physiological implications of the model are also presented.},
author = {Gyenge, Christina C and Bowen, Bruce D and Reed, Rolf K and Bert, Joel L},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Gyenge et al. - 2003 - Mathematical model of renal elimination of fluid and small ions during hyper- and hypovolemic conditions.pdf:pdf},
issn = {0001-5172},
journal = {Acta anaesthesiologica Scandinavica},
keywords = {Algorithms,Animals,Blood Volume,Blood Volume: physiology,Chlorides,Chlorides: urine,Hemorrhage,Hemorrhage: physiopathology,Hypovolemia,Hypovolemia: physiopathology,Ions,Ions: urine,Kidney,Kidney: metabolism,Kidney: physiology,Least-Squares Analysis,Models, Biological,Models, Statistical,Osmolar Concentration,Potassium,Potassium: urine,Reproducibility of Results,Saline Solution, Hypertonic,Sodium,Sodium: urine,Swine,Urodynamics,Urodynamics: physiology},
month = feb,
number = {2},
pages = {122--37},
pmid = {12631040},
title = {{Mathematical model of renal elimination of fluid and small ions during hyper- and hypovolemic conditions.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12631040},
volume = {47},
year = {2003}
}
@article{Ross2010,
abstract = {Teleradiology aims to even radiologists' workload, ensure on-call services, reduce waiting lists, consult other specialists and cut costs. Cross-border teleradiology widens this scope beyond the country borders. However, the new service should not reduce the quality of radiology. Quality and trust are key factors in establishment of teleradiology. Additionally there are organizational, technical, legal, security and linguistic issues influencing the service. Herein, we have used experiences from two partially European Union funded telemedicine projects to evaluate factors affecting cross-border teleradiology. Clinical partners from Czech Republic, Denmark, Estonia, Finland, Lithuania and the Netherlands went through 649 radiology test cases in two different teleradiology projects to build trust and agree about the report structure. Technical set-up was established using secure Internet data transfer, streaming technology, integration of workflows and creating structured reporting tool to overcome language barriers. The biggest barrier to overcome in cross-border teleradiology was the language issue. Establishment of the service was technically and semantically successful but limited to knee and hip X-ray examinations only because the structured reporting tool did not cover any other anatomical regions yet. Special attention has to be paid to clinical quality and trust between partners in cross-border teleradiology. Our experience shows that it is achievable. Legal, security and financial aspects are not covered in this paper because today they differ country by country. There is however an European Union level harmonization process started to enable cross-border eHealth in general.},
author = {Ross, Peeter and Sepper, Ruth and Pohjonen, Hanna},
doi = {10.1016/j.ejrad.2009.10.016},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Ross, Sepper, Pohjonen - 2010 - Cross-border teleradiology-experience from two international teleradiology projects.pdf:pdf},
issn = {1872-7727},
journal = {European journal of radiology},
keywords = {Europe,Interinstitutional Relations,Internationality,Internet,Internet: trends,Medical Informatics,Medical Informatics: trends,Radiology Information Systems,Radiology Information Systems: trends,Telemedicine,Telemedicine: trends},
month = jan,
number = {1},
pages = {20--5},
pmid = {19914019},
title = {{Cross-border teleradiology-experience from two international teleradiology projects.}},
volume = {73},
year = {2010}
}
@book{foster2004,
author = {Foster, I and Kesselman, C},
publisher = {Morgan Kaufmann},
title = {{The grid 2: blueprint for a new computing infrastructure}},
year = {2004}
}
@article{Butterworth2014,
author = {Butterworth, Erik and Jardine, Bartholomew E. and Raymond, Gary M. and Neal, Maxwell L. and Bassingthwaighte, James B.},
doi = {10.12688/f1000research.2-288.v2},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Butterworth et al. - 2014 - JSim, an open-source modeling system for data analysis.pdf:pdf},
issn = {2046-1402},
journal = {F1000Research},
month = may,
title = {{JSim, an open-source modeling system for data analysis}},
volume = {2},
year = {2014}
}
@book{suetens2009,
author = {Suetens, Paul},
publisher = {Cambridge University Press},
title = {{Fundamentals of medical imaging}},
year = {2009}
}
@article{Yu2005a,
abstract = {With the advent of Grid and application technologies, scientists and engineers are building more and more complex applications to manage and process large data sets, and execute scientific experiments on distributed resources. Such application scenarios require means for composing and executing complex workflows. Therefore, many efforts have been made towards the development of workflow management systems for Grid computing. In this paper, we propose a taxonomy that characterizes and classifies various approaches for building and executing workflows on Grids. The taxonomy not only highlights the design and engineering similarities and differences of state-of-the-art in Grid workflow systems, but also identifies the areas that need further research.},
author = {Yu, Jia and Buyya, Rajkumar},
doi = {10.1145/1084805.1084814},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Yu, Buyya - 2005 - A taxonomy of scientific workflow systems for grid computing.pdf:pdf},
isbn = {1084805108},
issn = {01635808},
journal = {ACM SIGMOD Record},
keywords = {grid computing,scientific workflows,taxonomy},
number = {3},
pages = {44},
title = {{A taxonomy of scientific workflow systems for grid computing}},
volume = {34},
year = {2005}
}
@inproceedings{Reddy2014,
abstract = {In recent years Medical Informatics related apps, combine information technology with raw and clinical Medical data to improve the standards in health care diagnosis and Medical Research. This paper mainly deals with how the environment for storing, analysis and processing of Image Databases will be created and operated over the networks. In addition to that different considerable elements like network protocols, Grid based distributed computing systems and accessible elements are explained in this paper. Cloud computing brings radical changes in Medical Image Database management systems operating over the wide area of networks across the Globe. In a holistic way this frame work enables researchers and doctors to design and operate Image Processing Application in a simple, economy manner. It also enables them to make best use of Cloud and other network resources as they are available at real time situations.},
author = {Reddy, A Nanda Gopal and Bhatnagar, Roheet},
booktitle = {2014 International Conference on Advances in Energy Conversion Technologies (ICAECT)},
doi = {10.1109/ICAECT.2014.6757071},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Reddy, Bhatnagar - 2014 - Distributed Medical Image Management A platform for storing, analysis and processing of Image Database over th.pdf:pdf},
isbn = {978-1-4799-2206-2},
keywords = {Cloud Computing,Conferences,DSL,Decision support systems,Energy conversion,Grid,High definition video,Medical Image,Networks,Protocols,clinical medical data,cloud computing,distributed medical image management,grid based distributed computing systems,health care,health care diagnosis,image processing application,information technology,medical image database management systems,medical image processing,medical informatics,medical research,network protocols,network resources,storing,visual databases},
month = jan,
pages = {108--112},
publisher = {IEEE},
shorttitle = {Advances in Energy Conversion Technologies (ICAECT},
title = {{Distributed Medical Image Management: A platform for storing, analysis and processing of Image Database over the cloud}},
url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=6757071},
year = {2014}
}
@article{Kulhanek2014c,
abstract = {This letter introduces an alternative approach to modeling the cardiovascular system with a short-term control mechanism published in Computers in Biology and Medicine, Vol. 47 (2014), pp. 104-112. We recommend using abstract components on a distinct physical level, separating the model into hydraulic components, subsystems of the cardiovascular system and individual subsystems of the control mechanism and scenario. We recommend utilizing an acausal modeling feature of Modelica language, which allows model variables to be expressed declaratively. Furthermore, the Modelica tool identifies which are the dependent and independent variables upon compilation. An example of our approach is introduced on several elementary components representing the hydraulic resistance to fluid flow and the elastic response of the vessel, among others. The introduced model implementation can be more reusable and understandable for the general scientific community.},
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},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Kulh\'{a}nek, Kofr\'{a}nek, Matej\'{a}k - 2014 - Modeling of short-term mechanism of arterial pressure control in the cardiovascular system Objec.pdf:pdf},
issn = {1879-0534},
journal = {Computers in biology and medicine},
month = sep,
pages = {137--144},
pmid = {25240104},
title = {{Modeling of short-term mechanism of arterial pressure control in the cardiovascular system: Object-oriented and acausal approach.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25240104},
volume = {54C},
year = {2014}
}
@book{Rich2008,
author = {Rich, Elaine},
isbn = {9780132288064},
publisher = {Prentice-Hal},
title = {{Automata, Computability and Complexity}},
year = {2008}
}
@article{openmodelica2005,
author = {Fritzson, Peter and Aronsson, Peter and Lundvall, H\aa kan and Nystr\"{o}m, Kaj and Pop, Adrian and Saldamli, Levon and Broman, David},
journal = {Simulation News Europe},
number = {45},
title = {{The OpenModelica Modeling, Simulation, and Software Development Environment}},
volume = {44},
year = {2005}
}
@misc{Maojo2003,
abstract = {In this report, the authors compare and contrast medical informatics (MI) and bioinformatics (BI) and provide a viewpoint on their complementarities and potential for collaboration in various subfields. The authors compare MI and BI along several dimensions, including: (1) historical development of the disciplines, (2) their scientific foundations, (3) data quality and analysis, (4) integration of knowledge and databases, (5) informatics tools to support practice, (6) informatics methods to support research (signal processing, imaging and vision, and computational modeling, (7) professional and patient continuing education, and (8) education and training. It is pointed out that, while the two disciplines differ in their histories, scientific foundations, and methodologic approaches to research in various areas, they nevertheless share methods and tools, which provides a basis for exchange of experience in their different applications. MI expertise in developing health care applications and the strength of BI in biological "discovery science" complement each other well. The new field of biomedical informatics (BMI) holds great promise for developing informatics methods that will be crucial in the development of genomic medicine. The future of BMI will be influenced strongly by whether significant advances in clinical practice and biomedical research come about from separate efforts in MI and BI, or from emerging, hybrid informatics subdisciplines at their interface.},
author = {Maojo, Victor and Kulikowski, Casimir A.},
booktitle = {Journal of the American Medical Informatics Association},
doi = {10.1197/jamia.M1305},
file = {:home/tomaton/Downloads/515.pdf:pdf},
isbn = {1067-5027},
issn = {10675027},
number = {6},
pages = {515--522},
pmid = {12925552},
title = {{Bioinformatics and Medical Informatics: Collaborations on the Road to Genomic Medicine?}},
volume = {10},
year = {2003}
}
@article{Frey2001,
abstract = {In recent years, there has been a dramatic increase in the amount
of available computing and storage resources, yet few have been able to
exploit these resources in an aggregated form. We present the Condor-G
system, which leverages software from Globus and Condor to allow users
to harness multi-domain resources as if they all belong to one personal
domain. We describe the structure of Condor-G and how it handles job
management, resource selection, security and fault tolerance},
author = {Frey, J. and Tannenbaum, T. and Livny, M. and Foster, I. and Tuecke, S.},
doi = {10.1109/HPDC.2001.945176},
isbn = {0-7695-1296-8},
issn = {1082-8907},
journal = {Proceedings 10th IEEE International Symposium on High Performance Distributed Computing},
title = {{Condor-G: a computation management agent for multi-institutional
grids}},
year = {2001}
}
@article{Pearl1987,
author = {Pearl, J and Korf, R E},
doi = {10.1146/annurev.cs.02.060187.002315},
file = {:home/tomaton/Downloads/annurev\%2Ecs\%2E02\%2E060187\%2E002315.pdf:pdf},
issn = {8756-7016},
journal = {Annual Review of Computer Science},
pages = {451--467},
title = {{Search Techniques}},
volume = {2},
year = {1987}
}
@article{Litzkow1990,
abstract = {Condor is a distributed batch system designed to provide
convenient access to unutilized workstations while preserving the rights
of their owners and to meet the needs of users who are frustrated by the
limitations of computing on a single workstation. Several principles
have driven the design of Condor. The first is that workstation owners
should always have the resources of the workstation they own at their
disposal. The second is that access to remote capacity must be easy and
should approximate the local execution environment as closely as
possible. The third is portability, which is essential because of rapid
developments in the workstations on which Condor operates. Mechanisms
basic to the operation of Condor, working experience, and software
support requirements are outlined},
author = {Litzkow, M. and Livny, M.},
doi = {10.1109/EDS.1990.138057},
isbn = {0818620927},
journal = {IEEE Workshop on Experimental Distributed Systems},
title = {{Experience with the Condor distributed batch system}},
year = {1990}
}
@article{Yu2011,
abstract = {MOTIVATION: The Physiome Model Repository 2 (PMR2) software was created as part of the IUPS Physiome Project (Hunter and Borg, 2003), and today it serves as the foundation for the CellML model repository. Key advantages brought to the end user by PMR2 include: facilities for model exchange, enhanced collaboration and a detailed change history for each model. AVAILABILITY: PMR2 is available under an open source license at http://www.cellml.org/tools/pmr/; a fully functional instance of this software can be accessed at http://models.physiomeproject.org/.},
author = {Yu, Tommy and Lloyd, Catherine M and Nickerson, David P and Cooling, Michael T and Miller, Andrew K and Garny, Alan and Terkildsen, Jonna R and Lawson, James and Britten, Randall D and Hunter, Peter J and Nielsen, Poul M F},
doi = {10.1093/bioinformatics/btq723},
issn = {1367-4811},
journal = {Bioinformatics (Oxford, England)},
keywords = {Biological,Computational Biology,Computational Biology: methods,Databases,Factual,Internet,Models,Software},
number = {5},
pages = {743--744},
pmid = {21216774},
title = {{The Physiome Model Repository 2.}},
volume = {27},
year = {2011}
}
@article{Tudor2008,
abstract = {Despite the continuous advances of the last years in grid computing, the grid computing programming paradigms are dominated by the message passing concept. There is little support for other paradigms such as shared data or associative programming. In this paper we analyze why previous attempts did not have a significant impact in the grid computing community. We start by assessing the landscape of grid programming solutions with a focus on shared data concepts. Next, we introduce an original idea to attack shared data programming on the grid by making use of both relaxed consistency models and user specified type consistency in an object oriented model.},
author = {Tudor, Dacian and Cretu, Vladimir},
doi = {10.1109/CISIS.2008.118},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Tudor, Cretu - 2008 - Experiences on grid shared data programming.pdf:pdf},
isbn = {0769531091},
issn = {1741-847X},
journal = {Proceedings - CISIS 2008: 2nd International Conference on Complex, Intelligent and Software Intensive Systems},
number = {2},
pages = {387--393},
title = {{Experiences on grid shared data programming}},
year = {2008}
}
@inproceedings{maffioletti2012computational,
author = {Maffioletti, Sergio and Murri, Riccardo and Jonen, B and Scheuring, S},
booktitle = {Proceedings of the EGI Community Forum},
file = {:home/tomaton/Downloads/EGICF12-EMITC2\_063.pdf:pdf},
title = {{Computational workflows with GC3Pie}},
year = {2012}
}
@book{Butenhof1997,
abstract = {With this practical book, you will attain a solid understanding of threads and will discover how to put this powerful mode of programming to work in real-world applications. The primary advantage of threaded programming is that it enables your applications to accomplish more than one task at the same time by using the number-crunching power of multiprocessor parallelism and by automatically exploiting I/O concurrency in your code, even on a single processor machine. The result: applications that are faster, more responsive to users, and often easier to maintain. Threaded programming is particularly well suited to network programming where it helps alleviate the bottleneck of slow network I/O. This book offers an in-depth description of the IEEE operating system interface standard, POSIXAE (Portable Operating System Interface) threads, commonly called Pthreads. Written for experienced C programmers, but assuming no previous knowledge of threads, the book explains basic concepts such as asynchronous programming, the lifecycle of a thread, and synchronization. You then move to more advanced topics such as attributes objects, thread-specific data, and realtime scheduling. An entire chapter is devoted to "real code," with a look at barriers, read/write locks, the work queue manager, and how to utilize existing libraries. In addition, the book tackles one of the thorniest problems faced by thread programmers-debugging-with valuable suggestions on how to avoid code errors and performance problems from the outset. Numerous annotated examples are used to illustrate real-world concepts. A Pthreads mini-reference and a look at future standardization are also included.},
author = {Butenhof, David R.},
isbn = {0201633922},
title = {{Programming with POSIX Threads}},
year = {1997}
}
@article{Pasley2005,
abstract = { As the use of Web services grows, organizations are increasingly choosing the Business Process Execution Language for modeling business processes within the Web services architecture. In addition to orchestrating organizations' Web services, BPEL's strengths include asynchronous message handling, reliability, and recovery. By developing Web services with BPEL in mind, organizations can implement aspects of the service-oriented architecture that might previously have been difficult to achieve.},
author = {Pasley, James},
doi = {10.1109/MIC.2005.56},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Pasley - 2005 - How BPEL and SOA are changing web services development.pdf:pdf},
isbn = {1089-7801},
issn = {10897801},
journal = {IEEE Internet Computing},
number = {June},
pages = {60--67},
title = {{How BPEL and SOA are changing web services development}},
volume = {9},
year = {2005}
}
@inproceedings{Pierce2014,
abstract = {We present an overview of the Apache Airavata Application Programming Interface (API), describe the design choices and implementation details, and describe how API methods map to the UltraScan Science Gateway use case. The Airavata API is designed to standardize access to Airavata services that provide gateways with scientific application metadata and execution management. The API also represents an important milestone in the development of Science Gateway Platform as a Service (SciGaP), a hosted, multi-tenanted gateway service based on open source Airavata software. The UltraScan gateway is a production XSEDE gateway that has been using Airavata services for over three years through customized interfaces and represents a stringent test of the API design and implementation.},
author = {Pierce, Marlon and Marru, Suresh and Demeler, Borries and Singh, Raminderjeet and Gorbet, Gary},
booktitle = {2014 9th Gateway Computing Environments Workshop},
doi = {10.1109/GCE.2014.15},
file = {:home/tomaton/Downloads/p25-pierce.pdf:pdf},
isbn = {978-1-4799-7030-8},
keywords = {Catalogs,Communities,Data models,Educational institutions,Logic gates,Science gateways,Servers,Software,application programming interfac,application programming interface design,cloud computing,cyberinfrastructure},
month = nov,
pages = {25--29},
publisher = {IEEE},
shorttitle = {Gateway Computing Environments Workshop (GCE), 201},
title = {{The Apache Airavata Application Programming Interface: Overview and Evaluation with the UltraScan Science Gateway}},
url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=7021845},
year = {2014}
}
@article{Tolson2007,
abstract = {A new global optimization algorithm, dynamically dimensioned search (DDS), is introduced for automatic calibration of watershed simulation models. DDS is designed for calibration problems with many parameters, requires no algorithm parameter tuning, and automatically scales the search to find good solutions within the maximum number of user-specified function (or model) evaluations. As a result, DDS is ideally suited for computationally expensive optimization problems such as distributed watershed model calibration. DDS performance is compared to the shuffled complex evolution (SCE) algorithm for multiple optimization test functions as well as real and synthetic SWAT2000 model automatic calibration formulations. Algorithms are compared for optimization problems ranging from 6 to 30 dimensions, and each problem is solved in 1000 to 10,000 total function evaluations per optimization trial. Results are presented so that future modelers can assess algorithm performance at a computational scale relevant to their modeling case study. In all four of the computationally expensive real SWAT2000 calibration formulations considered here (14, 14, 26, and 30 calibration parameters), results show DDS to be more efficient and effective than SCE. In two cases, DDS requires only 15–20\% of the number of model evaluations used by SCE in order to find equally good values of the objective function. Overall, the results also show that DDS rapidly converges to good calibration solutions and easily avoids poor local optima. The simplicity of the DDS algorithm allows for easy recoding and subsequent adoption into any watershed modeling application framework.},
author = {Tolson, Bryan a. and Shoemaker, Christine a.},
doi = {10.1029/2005WR004723},
file = {:home/tomaton/Downloads/wrcr10694.pdf:pdf},
isbn = {0043-1397},
issn = {00431397},
journal = {Water Resources Research},
keywords = {http://dx.doi.org/10.1029/2005WR004723, doi:10.102},
number = {August 2006},
pages = {1--16},
title = {{Dynamically dimensioned search algorithm for computationally efficient watershed model calibration}},
volume = {43},
year = {2007}
}
@article{Hunter2013,
abstract = {Peter Hunter1,3⇓, Tara Chapman4,5, Peter V. Coveney6, Bernard de Bono3,8, Vanessa Diaz7, John Fenner9, Alejandro F. Frangi11,12, Peter Harris13, Rod Hose9, Peter Kohl2,14, Pat Lawford9, Keith McCormack9, Miriam Mendes6, Stig Omholt15, Alfio Quarteroni16,17, Nour Shublaq6, John Sk\aa r18, Karl Stroetmann20, Jesper Tegner19, S. Randall Thomas21,22, Ioannis Tollis23,25, Ioannis Tsamardinos24,25, Johannes H. G. M. van Beek26 and Marco Viceconti10,271Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK2Department of Computer Science, University of Oxford, Oxford, UK3Auckland Bioengineering Institute (ABI), University of Auckland, New Zealand4Laboratory of Anatomy, Biomechanics and Organogenesis, Faculty of Medicine, Universit\'{e} Libre de Bruxelles, Belgium5Laboratory of Anthropology and Prehistory, Royal Belgian Institute of Natural Sciences, Brussels, Belgium6Centre for Computational Science, University College London, London, UK7Department of Mechanical Engineering, University College London, London, UK8CHIME Institute, Archway Campus, University College London, London, UK9Department of Cardiovascular Science (Medical Physics Group), Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, UK10INSIGNEO Institute for in silico medicine, University of Sheffield, Sheffield, UK11Networking Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain12Center for Computational Imaging and Simulation Technologies in Biomedicine (CISTIB), Department of Mechanical Engineering, University of Sheffield, Sheffield, UK13Department of Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Australia14National Heart and Lung Institute, Imperial College London, London, UK15Cardiac Exercise Research Group, Department of Circulation and Medical Imaging, NTNU Norwegian University of Science and Technology, Trondheim, Norway16Ecole Polytechnique F\'{e}d\'{e}rale de Lausanne, Switzerland17Politecnico di Milano, Milan, Italy18Department of LIME, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden19Department of Medicine, Unit for Computational Medicine, Center for Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden20Empirica Communication and Technology Research, Bonn, Germany21IR4M CNRS UMR8081, Institut Gustave-Roussy, Dept Imagerie/Echographie, Orsay, France22Universit\'{e} Paris-Sud, CNRS, Orsay, France23Computational Medicine Laboratory, Foundation for Research and Technology Hellas (FORTH), Heraklion, Crete, Greece24Bioinformatics Laboratory, Institute of Computer Science, Foundation for Research and Technology Hellas (FORTH), Heraklion, Crete, Greece25Computer Science Department, University of Crete, Heraklion, Crete, Greece26Section Medical Genomics, Department of Clinical Genetics, VU University Medical Centre, Amsterdam, The Netherlands27Laboratorio di Tecnologia Medica, Istituto Ortopedico Rizzoli, Bologna, Italye-mail: p.hunter\{at\}auckland.ac.nzAbstract European funding under Framework 7 (FP7) for the virtual physiological human (VPH) project has been in place now for 5 years. The VPH Network of Excellence (NoE) has been set up to help develop common standards, open source software, freely accessible data and model repositories, and various training and dissemination activities for the project. It is also working to coordinate the many clinically targeted projects that have been funded under the FP7 calls. An initial vision for the VPH was defined by the FP6 STEP project in 2006. In 2010, we wrote an assessment of the accomplishments of the first two years of the VPH in which we considered the biomedical science, healthcare and information and communications technology challenges facing the project (Hunter et al. 2010 Phil. Trans. R. Soc. A 368, 2595–2614 (doi:10.1098/rsta.2010.0048)). We proposed that a not-for-profit professional umbrella organization, the VPH Institute, should be established as a means of sustaining the VPH vision beyond the time-frame of the NoE. Here, we update and extend this assessment and in particular address the following issues raised in response to Hunter et al.: (i) a vision for the VPH updated in the light of progress made so far, (ii) biomedical science and healthcare challenges that the VPH initiative can address while also providing innovation opportunities for the European industry, and (iii) external changes needed in regulatory policy and business models to realize the full potential that the VPH has to offer to industry, clinics and society generally. virtual physiological humanphysiomecomputational physiologysystems biologymultiscale modellingFootnotesOne contribution of 25 to a Theme Issue ‘The virtual physiological human: integrative approaches to computational biomedicine’.© 2013 The Author(s) Published by the Royal Society. All rights reserved.},
author = {Hunter, Peter and Chapman, Tara and Coveney, Peter V and de Bono, Bernard and Diaz, Vanessa and Fenner, John and Frangi, Alejandro F and Harris, Peter and Hose, Rod and Kohl, Peter and Lawford, Pat and McCormack, Keith and Mendes, Miriam and Omholt, Stig and Quarteroni, Alfio and Shublaq, Nour and Sk\aa r, John and Stroetmann, Karl and Tegner, Jesper and Thomas, S Randall and Tollis, Ioannis and Tsamardinos, Ioannis and van Beek, Johannes H G M and Viceconti, Marco},
file = {:home/tomaton/Downloads/20130004.full.pdf:pdf},
journal = {Interface Focus},
month = feb,
number = {2},
title = {{A vision and strategy for the virtual physiological human: 2012 update}},
url = {http://rsfs.royalsocietypublishing.org/content/3/2/20130004.abstract},
volume = {3},
year = {2013}
}
@misc{Fric2012,
address = {Praha},
author = {Fri\v{c}, Marek and Kulh\'{a}nek, Tom\'{a}\v{s} and Hrb, Jaroslav},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Fri\v{c}, Kulh\'{a}nek, Hrb - 2012 - Syst\'{e}m pro vzd\'{a}len\v{e} př\'{\i}stupnou anal\'{y}zu hlasu RealVoiceLab.pdf:pdf},
publisher = {V\'{y}zkumn\'{e} centrum hudebn\'{\i} akustiky HAMU},
title = {{Syst\'{e}m pro vzd\'{a}len\v{e} př\'{\i}stupnou anal\'{y}zu hlasu RealVoiceLab}},
url = {http://zvuk.hamu.cz/vyzkum/dokumenty/TL46x.pdf},
year = {2012}
}
@article{Kacsuk2011,
abstract = {P-GRADE portal is one of the most widely used general-purpose grid portal in Europe. The paper summarizes the most advanced features of P-GRADE, such as parameter sweep workflow execution, multi-grid workflow execution and integration with the DSpace workflow repository. It also shows the NGS P-GRADE portal that extends P-GRADE with the GEMLCA legacy code execution support in Grid systems, as well as with coarse-grain workflow interoperability services. Next, the paper introduces the second generation P-GRADE portal called WS-PGRADE that merges the advanced features of the first generation P-GRADE portals and extends them with new workflow and architecture concepts. Finally, the application-specific science gateway of the CancerGrid project is briefly described to demonstrate that application-specific portals can easily be developed on top of the general-purpose WS-PGRADE portal.},
author = {Kacsuk, Peter},
doi = {10.1002/cpe.1654},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Kacsuk - 2011 - P-GRADE portal family for grid infrastructures.pdf:pdf},
issn = {15320626},
journal = {Concurrency Computation Practice and Experience},
keywords = {grid,interoperability,portal,portal framework,repository,science gateway,workflow},
pages = {235--245},
title = {{P-GRADE portal family for grid infrastructures}},
volume = {23},
year = {2011}
}
@article{Memon2014,
author = {Memon, Shahbaz and Riedel, Morris and Janetzko, Florian and Demeler, Borries and Gorbet, Gary and Marru, Suresh and Grimshaw, Andrew and Gunathilake, Lahiru and Singh, Raminder and Attig, Norbert and Lippert, Thomas},
doi = {10.1002/cpe.3251},
file = {:home/tomaton/Downloads/cpe3251.pdf:pdf},
issn = {15320626},
journal = {Concurrency and Computation: Practice and Experience},
month = sep,
number = {13},
pages = {2280--2291},
title = {{Advancements of the UltraScan scientific gateway for open standards-based cyberinfrastructures}},
volume = {26},
year = {2014}
}
@inproceedings{kulhanek2009dd,
author = {Kulh\'{a}nek, Tom\'{a}\v{s}},
booktitle = {Proceeding of PhD. Conference 2009 was published as: Doktorandsk\'{e} dny '09},
editor = {Ku\v{z}elov\'{a}, D},
pages = {62--64},
publisher = {Institute of Computer Science/MatfyzPress},
title = {{Virtual Distributed Environment for Exchange of Medical Images}},
url = {http://www.cs.cas.cz/hakl/doktorandsky-den/files/2009/sbornik-dd-2009.pdf},
year = {2009}
}
@book{Hohpe2002,
author = {Hohpe, Gregor and Woolf, Bobby},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Hohpe - 2002 - Enterprise Integration Patterns.pdf:pdf},
publisher = {Pearson Education, Inc.},
title = {{Enterprise Integration Patterns}},
year = {2002}
}
@inproceedings{Fedak2001,
author = {Fedak, Gilles and Cappello, Franck and Sud, Universitc Paris},
booktitle = {Proceedings of First IEEE/ACM International Symposium on Cluster Computing and the Grid},
doi = {10.1109/CCGRID.2001.923246},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Fedak, Cappello, Sud - 2001 - XtremWeb A Generic Global Computing System.pdf:pdf},
isbn = {0769510108},
pages = {582--587},
title = {{XtremWeb : A Generic Global Computing System}},
year = {2001}
}
@article{Westerhof2009,
abstract = {Frank's Windkessel model described the hemodynamics of the arterial system in terms of resistance and compliance. It explained aortic pressure decay in diastole, but fell short in systole. Therefore characteristic impedance was introduced as a third element of the Windkessel model. Characteristic impedance links the lumped Windkessel to transmission phenomena (e.g., wave travel). Windkessels are used as hydraulic load for isolated hearts and in studies of the entire circulation. Furthermore, they are used to estimate total arterial compliance from pressure and flow; several of these methods are reviewed. Windkessels describe the general features of the input impedance, with physiologically interpretable parameters. Since it is a lumped model it is not suitable for the assessment of spatially distributed phenomena and aspects of wave travel, but it is a simple and fairly accurate approximation of ventricular afterload.},
author = {Westerhof, Nico and Lankhaar, Jan-Willem and Westerhof, Berend E},
doi = {10.1007/s11517-008-0359-2},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Westerhof, Lankhaar, Westerhof - 2009 - The arterial Windkessel.pdf:pdf},
issn = {1741-0444},
journal = {Medical \& biological engineering \& computing},
keywords = {Aorta,Aorta: physiology,Arteries,Arteries: physiology,Cardiovascular,Hemodynamics,Hemodynamics: physiology,Humans,Models,Vascular Resistance,Vascular Resistance: physiology},
month = feb,
number = {2},
pages = {131--41},
pmid = {18543011},
title = {{The arterial Windkessel.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18543011},
volume = {47},
year = {2009}
}
@book{Fowler2003,
abstract = {The practice of enterprise application development has benefited from the emergence of many new enabling technologies. Multi-tiered object-oriented platforms, such as Java and .NET, have become commonplace. These new tools and technologies are capable of building powerful applications, but they are not easily implemented. Common failures in enterprise applications often occur because their developers do not understand the architectural lessons that experienced object developers have learned. Patterns of Enterprise Application Architecture is written in direct response to the stiff challenges that face enterprise application developers. The author, noted object-oriented designer Martin Fowler, noticed that despite changes in technology-from Smalltalk to CORBA to Java to .NET-the same basic design ideas can be adapted and applied to solve common problems. With the help of an expert group of contributors, Martin distills over forty recurring solutions into patterns. The result is an indispensable handbook of solutions that are applicable to any enterprise application platform. This book is actually two books in one. The first section is a short tutorial on developing enterprise applications, which you can read from start to finish to understand the scope of the book's lessons. The next section, the bulk of the book, is a detailed reference to the patterns themselves. Each pattern provides usage and implementation information, as well as detailed code examples in Java or C. The entire book is also richly illustrated with UML diagrams to further explain the concepts. Armed with this book, you will have the knowledge necessary to make important architectural decisions about building an enterprise application and the proven patterns for use when building them.},
author = {Fowler, Martin},
booktitle = {Trial},
isbn = {0321127420},
pages = {560},
publisher = {Pearson Education, Inc.},
title = {{Patterns of Enterprise Application Architecture}},
year = {2003}
}
@article{Leung2014,
author = {Leung, Kai Yan Eugene and van der Lijn, Fedde and Vrooman, Henri a. and Sturkenboom, Miriam C. J. M. and Niessen, Wiro J.},
doi = {10.1007/s12021-014-9240-7},
file = {:home/tomaton/Downloads/art\%3A10.1007\%2Fs12021-014-9240-7.pdf:pdf},
issn = {1539-2791},
journal = {Neuroinformatics},
keywords = {imaging,magnetic resonance,medical informatics,neuroimaging,radiology information systems},
pages = {65--81},
title = {{IT Infrastructure to Support the Secondary Use of Routinely Acquired Clinical Imaging Data for Research}},
url = {http://link.springer.com/10.1007/s12021-014-9240-7},
volume = {13},
year = {2014}
}
@misc{Kofranek2014a,
author = {Kofr\'{a}nek, Jiř\'{\i} and Privitzer, Pavol and Tribula, Martin and \v{S}ilar, Jan and Kulh\'{a}nek, Tom\'{a}\v{s} and Matej\'{a}k, Marek and Je\v{z}ek, Filip},
publisher = {Charles University in Prague, Com-Sys Trade s.r.o., Creative Connections s.r.o.},
title = {{Virtual patient simulator, CZ Utility model. Application number: 2014-30329. Issue number: 27613}},
url = {http://isdv.upv.cz/portal/pls/portal/portlets.pts.det?xprim=10082946},
year = {2014}
}
@book{Russell2009,
abstract = {The long-anticipated revision of this \#1 selling book offers the most comprehensive, state of the art introduction to the theory and practice of artificial intelligence for modern applications. Intelligent Agents. Solving Problems by Searching. Informed},
author = {Russell, Stuart and Norvig, Peter},
booktitle = {Prentice Hall},
doi = {10.1017/S0269888900007724},
file = {:home/tomaton/Downloads/Artificial-Intelligence-A-Modern-Approach-3rd-Edition.pdf:pdf},
isbn = {0136042597},
issn = {0269-8889},
title = {{Artificial Intelligence: A Modern Approach, 3rd edition}},
url = {http://portal.acm.org/citation.cfm?id=1671238\&coll=DL\&dl=GUIDE\&CFID=190864501\&CFTOKEN=29051579$\backslash$npapers2://publication/uuid/4B787E16-89F6-4FF7-A5E5-E59F3CFEFE88},
year = {2009}
}
@article{Erberich2007,
abstract = {The Digital Imaging and Communications in Medicine (DICOM) standard defines Radiology medical device interoperability and image data exchange between modalities, image databases - Picture Archiving and Communication Systems (PACS) - and image review end-points. However the scope of DICOM and PACS technology is currently limited to the trusted and static environment of the hospital. In order to meet the demand for ad-hoc tele-radiology and image guided medical procedures within the global healthcare enterprise, a new technology must provide mobility, security, flexible scale of operations, and rapid responsiveness for DICOM medical devices and subsequently medical image data. Grid technology, an informatics approach to securely federate independently operated computing, storage, and data management resources at the global scale over public networks, meets these core requirements. Here we present an approach to federate DICOM and PACS devices for large-scale medical image workflows within a global healthcare enterprise. The Globus MEDICUS (Medical Imaging and Computing for Unified Information Sharing) project uses the standards-based Globus Toolkit Grid infrastructure to vertically integrate a new service for DICOM devices - the DICOM Grid Interface Service (DGIS). This new service translates between DICOM and Grid operations and thus transparently extends DICOM to Globus based Grid infrastructure. This Grid image workflow paradigm has been designed to provide not only solutions for global image communication, but fault-tolerance and disaster recovery using Grid data replication technology. Actual use-case of 40 MEDICUS Grid connected international hospitals of the Childerns Oncology Group and the Neuroblastoma Cancer Foundation and further clinical applications are discussed. The open-source Globus MEDICU http://dev.globus.org/wiki/Incubator/MEDICUS.},
author = {Erberich, Stephan G and Silverstein, Jonathan C and Chervenak, Ann and Schuler, Robert and Nelson, Marvin D and Kesselman, Carl},
file = {:home/tomaton/Downloads/00b495256f029e3f31000000.pdf:pdf},
isbn = {0926-9630 (Print)$\backslash$r0926-9630 (Linking)},
issn = {0926-9630},
journal = {Studies in health technology and informatics},
pages = {269--278},
pmid = {17476069},
title = {{Globus MEDICUS - federation of DICOM medical imaging devices into healthcare Grids.}},
volume = {126},
year = {2007}
}
@article{Pruett2013,
author = {Pruett, William A and Husband, Leland D and Husband, Graham and Dakhlalla, Muhammad and Bellamy, Kyle and Coleman, Thomas G and Hester, Robert L},
file = {:home/tomaton/Downloads/journal.pone.0074329.pdf:pdf},
isbn = {1932-6203},
journal = {PloS one},
number = {9},
pages = {e74329},
title = {{A Population Model of Integrative Cardiovascular Physiology}},
volume = {8},
year = {2013}
}
@article{Smith2004,
author = {Smith, Bram W and Chase, J Geoffrey and Nokes, Roger I and Shaw, Geoffrey M and Wake, Graeme},
doi = {10.1016/j.medengphy.2003.10.001},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Smith et al. - 2004 - Minimal haemodynamic system model including ventricular interaction and valve dynamics.pdf:pdf},
issn = {1350-4533},
journal = {Medical engineering \& physics},
keywords = {Blood Flow Velocity,Blood Pressure,Blood Pressure: physiology,Cardiac Output,Cardiac Output: physiology,Cardiovascular,Cardiovascular Physiological Phenomena,Computer Simulation,Heart Valves,Heart Valves: physiology,Hemorheology,Hemorheology: methods,Humans,Models,Ventricular Function},
number = {2},
pages = {131--139},
pmid = {15036180},
title = {{Minimal haemodynamic system model including ventricular interaction and valve dynamics.}},
volume = {26},
year = {2004}
}
@article{Anderson2002,
author = {Anderson, David P. and Cobb, Jeff and Korpela, Eric and Lebofsky, Matt and Werthimer, Dan},
doi = {10.1145/581571.581573},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Anderson et al. - 2002 - SETI@home an experiment in public-resource computing.pdf:pdf},
issn = {00010782},
journal = {Communications of the ACM},
month = nov,
number = {11},
pages = {56--61},
title = {{SETI@home: an experiment in public-resource computing}},
volume = {45},
year = {2002}
}
@article{Skaburskas2008,
author = {Skaburskas, K and Estrella, F and Shade, J and Manset, D and Revillard, J and Rios, a and Anjum, a and Branson, a and Bloodsworth, P and Hauer, T and McClatchey, R and Rogulin, D},
doi = {10.1088/1742-6596/119/8/082011},
file = {:home/tomaton/Downloads/1742-6596\_119\_8\_082011.pdf:pdf},
isbn = {1742-6596},
issn = {17426588},
journal = {Journal of Physics: Conference Series},
pages = {082011},
title = {{Health-e-Child: a grid platform for european paediatrics}},
volume = {119},
year = {2008}
}
@book{Mattson2004,
abstract = {The Parallel Programming Guide for Every Software Developer From grids and clusters to next-generation game consoles, parallel computing is going mainstream. Innovations such as Hyper-Threading Technology, HyperTransport Technology, and multicore microprocessors from IBM, Intel, and Sun are accelerating the movement's growth. Only one thing is missing: programmers with the skills to meet the soaring demand for parallel software. That's where Patterns for Parallel Programming comes in. It's the first parallel programming guide written specifically to serve working software developers, not just computer scientists. The authors introduce a complete, highly accessible pattern language that will help any experienced developer "think parallel"-and start writing effective parallel code almost immediately. Instead of formal theory, they deliver proven solutions to the challenges faced by parallel programmers, and pragmatic guidance for using today's parallel APIs in the real world. Coverage includes: Understanding the parallel computing landscape and the challenges faced by parallel developers Finding the concurrency in a software design problem and decomposing it into concurrent tasks Managing the use of data across tasks Creating an algorithm structure that effectively exploits the concurrency you've identified Connecting your algorithmic structures to the APIs needed to implement them Specific software constructs for implementing parallel programs Working with today's leading parallel programming environments: OpenMP, MPI, and Java Patterns have helped thousands of programmers master object-oriented development and other complex programming technologies. With this book, you will learn that they're the best way to master parallel programming too.},
author = {Mattson, Timothy G. and Sanders, Beverly A. and Massingill, Berna L.},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Unknown - Unknown - No Title(4).pdf:pdf},
isbn = {0321630033},
pages = {384},
publisher = {Pearson Education},
title = {{Patterns for Parallel Programming}},
volume = {5},
year = {2004}
}
@article{Svec2007,
abstract = {OBJECTIVES: Kymographic imaging through videokymography has been recognized as a convenient, novel way to display laryngeal behavior, yet little systematic research has been done to map the relevant features displayed in such images. Here we have aimed at specification of these features to enable systematic visual characterization and categorization of vocal fold vibratory patterns in voice disorders.

METHODS: A cross-sectional, descriptive design was used. We selected 45 subjects and extracted 100 videokymographic images from the archive of more than 7,000 videokymographic examinations of subjects with a wide range of voice disorders. The images showed a large variety of vocal fold vibratory behaviors during sustained phonations. We visually identified the prominent features that distinguished the vibration patterns across the images.

RESULTS: We divided the findings into 10 feature categories. They included refined traditional features (eg, mucosal waves), as well as additional features that are obscured in strobolaryngoscopy (eg, different types of irregularities, left-right frequency differences, shapes of lateral and medial peaks, cycle aberrations).

CONCLUSIONS: The variations in the identified features reveal different behavioral origins of voice disorders. The findings open new possibilities for objective documentation and for monitoring vocal fold behavior in clinical practice through kymographic imaging.},
author = {Svec, Jan G and Sram, Frantisek and Schutte, Harm K},
issn = {0003-4894},
journal = {The Annals of otology, rhinology, and laryngology},
keywords = {Cross-Sectional Studies,Female,Humans,Image Processing, Computer-Assisted,Kymography,Kymography: methods,Laryngoscopy,Male,Mucous Membrane,Mucous Membrane: physiopathology,Retrospective Studies,Vibration,Video Recording,Video Recording: methods,Vocal Cords,Vocal Cords: physiopathology,Voice Disorders,Voice Disorders: diagnosis},
language = {en},
month = mar,
number = {3},
pages = {172--80},
pmid = {17419520},
title = {{Videokymography in voice disorders: what to look for?}},
url = {http://europepmc.org/abstract/MED/17419520},
volume = {116},
year = {2007}
}
@phdthesis{Proß2013a,
author = {Pro\ss, Sabrina},
file = {:home/tomaton/Downloads/Ver\"{o}ffentlichungsreihe-IuM-Pross(1).pdf:pdf},
title = {{Hybrid modeling and optimization of biological processes}},
url = {http://pub.uni-bielefeld.de/download/2562185/2562188},
year = {2013}
}
@article{Humphrey2012,
author = {Humphrey, Marty and Beekwilder, Norm and Goodall, Jonathan L. and Ercan, Mehmet B.},
doi = {10.1109/eScience.2012.6404420},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Humphrey, Beekwilder - 2012 - Calibration of watershed models using cloud computing.pdf:pdf},
isbn = {9781467344661},
journal = {2012 IEEE 8th International Conference on E-Science},
keywords = {-cloud computing,Biological system modeling,Calibration,Cloud computing,Clouds,Computational modeling,Data models,Microsoft Windows Azure,SWAT,Water resources,Windows Azure,calibration,cloud computing,cloud cores,cloud-based system,computational model parameters,hydrologic systems,hydrology,laptop computer,model calibration,physically-observed phenomena,real-time interactive model,river basins,rivers,search algorithm,search problems,water quality,watershed model calibration,watershed modeling},
language = {English},
month = oct,
number = {1048222},
pages = {1--8},
publisher = {IEEE},
title = {{Calibration of watershed models using cloud computing}},
year = {2012}
}
@article{Matejak2014mj,
author = {Matej\'{a}k, Marek},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Matej\'{a}k - 2014 - Physiology in modelica.pdf:pdf},
journal = {MEFANET Journal},
number = {1},
pages = {10--14},
title = {{Physiology in modelica}},
url = {http://mj.mefanet.cz/mj-03140307},
volume = {2},
year = {2014}
}
@book{Chapman2008,
abstract = {Programming languages evolve just as natural languages do, driven by human desires to express thoughts more cleverly, succinctly, or elegantly than in the past. A big difference is the fact that one key receiver of programs is nonhuman. These nonhumans evolve faster than humans do, helping drive language mutation after mutation, andtogether with the human program writers and readersnaturally selecting among the mutations. In the 1970s, vector and parallel computer evolution was on the move. Programming assistance was provided by language extensionsfirst to Fortran and then to Cin the form of directives and pragmas, respectively. Vendors differentiated themselves by providing better extensions than did their competitors; and by the mid-1980s things had gotten out of hand for software vendors. At Kuck and Associates (KAI), we had the problem of dealing with the whole industry, so Bruce Leasure and I set out to fix things by forming an industrywide committee, the Parallel Computing Forum (PCF). PCF struck a nerve and became very active. In a few years we had a draft standard that we took through ANSI, and after a few more years it became the ANSI X3.H5 draft. Our stamina gave out before it became an official ANSI standard, but the industry paid attention, and extensions evolved more uniformly. This situation lasted for a few years, but the 1980s were a golden era for parallel architectural evolution, with many people writing parallel programs, so extensions again diverged, and programming needs grew. KAI took on the challenge of rethinking things and defining parallel profiling and correctness-checking tools at the same time, with the goal of innovative software development products. By the mid-1990s we had made a lot of progress and had discussed it a bit with some hardware vendors. When SGI bought Cray in April 1996, they had an immediate directive problem (two distinct extensions) and approached us about working with them. Together we refined what we had, opened up to the industry, and formed the Architecture Review Board (ARB). OpenMP was born 18 months later, as the New York Times reported:},
author = {Chapman, B and Jost, G and {Van Der Pas}, Ruud},
file = {:home/tomaton/Downloads/9780262533027\_sch\_0001.pdf:pdf},
isbn = {0262533022},
publisher = {MIT press},
title = {{Using OpenMP}},
volume = {10},
year = {2008}
}
@article{Kacsuk2008a,
abstract = {Grid interoperability has recently become a major issue at Grid forums. Most of the current ideas try to solve the problem at the middleware level where unfortunately too many components (information system, broker, etc.) should be made interoperable. As an alternative concept the P-GRADE portal is the first Grid portal that tries to solve the problem at the level of workflows. It means that the components of a workflow can be executed simultaneously in several Grids. In this way the user can exploit more parallelism than inside one Grid. More than that the workflow level completely hides the low level Grid details for the end-user who does not have to learn the low level Grid commands of different Grids. In this way porting workflow application between different Grids can be done with minimal user efforts. The paper describes those features and techniques that are provided and used by the P-GRADE portal to solve the Grid interoperability problem. ?? 2008 Elsevier B.V. All rights reserved.},
author = {Kacsuk, Peter and Kiss, Tamas and Sipos, Gergely},
doi = {10.1016/j.future.2008.02.008},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Kacsuk, Kiss, Sipos - 2008 - Solving the grid interoperability problem by P-GRADE portal at workflow level.pdf:pdf},
issn = {0167739X},
journal = {Future Generation Computer Systems},
keywords = {Grid,Interoperability,Legacy code,Portal,Workflow},
pages = {744--751},
title = {{Solving the grid interoperability problem by P-GRADE portal at workflow level}},
volume = {24},
year = {2008}
}
@book{Hager2010,
abstract = {Written by high performance computing (HPC) experts, Introduction to High Performance Computing for Scientists and Engineers provides a solid introduction to current mainstream computer architecture, dominant parallel programming models, and useful optimization strategies for scientific HPC. From working in a scientific computing center, the authors gained a unique perspective on the requirements and attitudes of users as well as manufacturers of parallel computers. The text first introduces the architecture of modern cache-based microprocessors and discusses their inherent performance limitations, before describing general optimization strategies for serial code on cache-based architectures. It next covers shared- and distributed-memory parallel computer architectures and the most relevant network topologies. After discussing parallel computing on a theoretical level, the authors show how to avoid or ameliorate typical performance problems connected with OpenMP. They then present cache-coherent nonuniform memory access (ccNUMA) optimization techniques, examine distributed-memory parallel programming with message passing interface (MPI), and explain how to write efficient MPI code. The final chapter focuses on hybrid programming with MPI and OpenMP. Users of high performance computers often have no idea what factors limit time to solution and whether it makes sense to think about optimization at all. This book facilitates an intuitive understanding of performance limitations without relying on heavy computer science knowledge. It also prepares readers for studying more advanced literature.},
author = {Hager, Georg and Wellein, Gerhard},
doi = {10.1201/EBK1439811924},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Hager, Wellein - 2010 - Introduction to High Performance Computing for Scientists and Engineers.pdf:pdf},
isbn = {9781439811924},
pages = {356},
title = {{Introduction to High Performance Computing for Scientists and Engineers}},
year = {2010}
}
@article{Letchford2012,
author = {Letchford, Adam},
doi = {10.1007/978-3-642-16729-4},
file = {:home/tomaton/Downloads/9783642167287-c1.pdf:pdf},
isbn = {978-3-642-16728-7},
keywords = {HB Economic Theory},
pages = {17--41},
title = {{Review of “The Linear Ordering Problem: Exact and Heuristic Methods in Combinatorial Optimization”}},
url = {http://eprints.lancs.ac.uk/55579/},
year = {2012}
}
@article{Cook1983,
abstract = {An historical overview of computational complexity is presented. Emphasis is on the fundamental issues of defining the intrinsic computational complexity of a problem and proving upper and lower bounds on the complexity of problems. Probabilistic and parallel computation are discussed.},
author = {Cook, Stephen A.},
doi = {10.1145/358141.358144},
file = {:home/tomaton/Downloads/p400-cook.pdf:pdf},
isbn = {0001-0782},
issn = {00010782},
journal = {Communications of the ACM},
month = jun,
number = {6},
pages = {400--408},
title = {{An overview of computational complexity}},
volume = {26},
year = {1983}
}
@book{Eykhoff1981,
address = {Oxford},
annote = {Monograph},
author = {Eykhoff, P},
isbn = {008025683X},
keywords = {estimation,mathematical models,operationeel onderzoek,operations research,schatting,systeemanalyse,systems analysis,testen,testing,wiskundige modellen},
publisher = {Pergamon},
series = {IFAC series for graduates, research workers and practising engineers;vol. 1},
title = {{Trends and progress in system identification}},
year = {1981}
}
@book{Greenlaw1995,
address = {Oxford},
author = {Greenlaw, Raymond and Hoover, H James and Ruzzo, Walter L},
file = {:home/tomaton/Downloads/limits-to-parallel-computation-p-completeness-theory.9780195085914.35897.pdf:pdf},
publisher = {Oxford university press},
title = {{Limits to Parallel Computation}},
year = {1995}
}
@article{Moler1986,
author = {Moler, Cleve},
journal = {Hypercube multiprocessors},
pages = {181--195},
title = {{Matrix computation on distributed memory multiprocessors}},
year = {1986}
}
@inproceedings{Brugard2009,
author = {Brug\aa rd, Jan and Hedberg, Daniel and Cascante, Marta and Cedersund, Gunnar and G\'{o}mez-Garrido, \`{A}lex and Maier, Dieter and Nyman, Elin and Selivanov, Vitaly and Str\aa lfors, Peter and {Biomax Informatics}, A G},
booktitle = {7th International Modelica Conference, Como, Italy},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Brug\aa rd et al. - 2009 - Creating a Bridge between Modelica and the Systems Biology Community.pdf:pdf},
title = {{Creating a Bridge between Modelica and the Systems Biology Community}},
year = {2009}
}
@inproceedings{Kulhanek2014,
author = {Kulh\'{a}nek, Tom\'{a}\v{s} and Matej\'{a}k, Marek and \v{S}ilar, Jan and Kofr\'{a}nek, Jiř\'{\i}},
booktitle = {sborn\'{\i}k př\'{\i}sp\v{e}vků MEDSOFT},
pages = {148--153},
title = {{IDENTIFIKACE FYZIOLOGICK\'{Y}CH SYST\'{E}MŮ}},
url = {http://www.creativeconnections.cz/medsoft/2014/Medsoft\_2014\_Kulhanek.pdf},
year = {2014}
}
@book{Papadimitriou1995,
author = {Papadimitriou, CH},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Papadimitriou - 1995 - Computational complexity.pdf:pdf},
publisher = {Addison-WesleyPublishing Company},
title = {{Computational complexity}},
year = {1995}
}
@article{Campbell1990,
abstract = {Elastance-resistance [E(t)-R] representations of the left ventricle (LV) were evaluated for their ability to reproduce instantaneous pressure [P(t)] and outflow [Q(t)]. Experiments were performed in open-chest rats. P(t) and Q(t) were measured during steady-state ejecting beats and during a beat in which the aorta was suddenly clamped. The degree of clamping varied from partial to total occlusion. The total occlusion beat was considered an isovolumic beat that generated an isovolumic pressure [Piso(t)] with a characteristic time to maximal Piso(t) [Tpisomax]. In ejecting beats, 34\% of stroke volume was delivered after Tpisomax. P(t) and Q(t) from the steady-state ejecting beats and Piso(t) from the clamped beat were then used to estimate parameters of an E(t)-R model. Components of P(t) and Q(t) not accounted for by E(t)-R were identified and termed extra-pressure [Pext(t)] and extra-outflow [Qext(t)]. Pext(t) and Qext(t) were near-zero valued until Tpisomax; then they became systematically positive and finally negative valued after end ejection. During partial aortic occlusion, P(t) was elevated and Q(t) was reduced. However, the time of ejection was extended, and the fraction of stroke volume delivered after Tpisomax increased as P(t) was made higher. Partial occlusion also prolonged the positive phase of Pext(t) and Qext(t). Elements possessing "active" and "deactive" properties were added to the E(t)-R model in an attempt to account for Pext(t) and Qext(t) during partial occlusion. Optional forms of these elements were considered. These expanded E(t)-R models were fitted to basal ejecting data and then asked to predict data from a partial occlusion beat. All expanded models failed to adequately predict the partial occlusion pressure and/or outflow. It was concluded that 1) late ejection was quantitatively important to LV pumping, 2) behavior during late ejection was inconsistent with E(t)-R, and 3) ad hoc modification of E(t)-R models was not likely to yield LV pumping models that could satisfactorily reproduce instantaneous P(t) and Q(t) behavior over the entire ejection period.},
author = {Campbell, K B and Kirkpatrick, R D and Knowlen, G G and Ringo, J a},
doi = {10.1161/01.RES.66.1.218},
file = {:home/tomaton/Downloads/Circulation Research-1990-Campbell-218-33.pdf:pdf},
issn = {0009-7330},
journal = {Circulation research},
pages = {218--233},
pmid = {2295140},
title = {{Late-systolic pumping properties of the left ventricle. Deviation from elastance-resistance behavior.}},
volume = {66},
year = {1990}
}
@article{Livny1997,
abstract = {Little attention has been devoted to high throughput computing (HTC)$\backslash$nenvironments that can deliver large amounts of processing capacity$\backslash$nover long time periods. For almost a decade, we have been developing,$\backslash$nimplementing, and deploying, HTC tools that harness the capacity$\backslash$nof hundreds of distributively owned workstations. Using our software,$\backslash$nthe Condor HTC environment, scientists may simultaneously and transparently$\backslash$nexploit resources they are not even aware exist. We outline the architecture$\backslash$nof Condor and discuss the principles that have been guiding us and$\backslash$nthe lessons we have learned},
author = {Livny, Miron and Basney, Jim and Raman, Rajesh and Tannenbaum, Todd},
issn = {1421-6337},
journal = {SPEEDUP Journal},
pages = {36--40},
title = {{Mechanisms for High Throughput Computing}},
volume = {11},
year = {1997}
}
@book{fritzson2010,
author = {Fritzson, Peter},
publisher = {Wiley. com},
title = {{Principles of object-oriented modeling and simulation with Modelica 2.1}},
year = {2010}
}
@article{Hucka2003,
author = {Hucka, M. and Finney, A. and Sauro, H. M. and Bolouri, H. and Doyle, J. C. and Kitano, H. and Arkin, a. P. and Bornstein, B. J. and Bray, D. and Cornish-Bowden, A. and Cuellar, a. a. and Dronov, S. and Gilles, E. D. and Ginkel, M. and Gor, V. and Goryanin, I. I. and Hedley, W. J. and Hodgman, T. C. and Hofmeyr, J.-H. and Hunter, P. J. and Juty, N. S. and Kasberger, J. L. and Kremling, A. and Kummer, U. and {Le Novere}, N. and Loew, L. M. and Lucio, D. and Mendes, P. and Minch, E. and Mjolsness, E. D. and Nakayama, Y. and Nelson, M. R. and Nielsen, P. F. and Sakurada, T. and Schaff, J. C. and Shapiro, B. E. and Shimizu, T. S. and Spence, H. D. and Stelling, J. and Takahashi, K. and Tomita, M. and Wagner, J. and Wang, J.},
doi = {10.1093/bioinformatics/btg015},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Hucka et al. - 2003 - The systems biology markup language (SBML) a medium for representation and exchange of biochemical network models.pdf:pdf},
issn = {1367-4803},
journal = {Bioinformatics},
month = mar,
number = {4},
pages = {524--531},
title = {{The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models}},
volume = {19},
year = {2003}
}
@article{Cooley1965,
author = {Cooley, JW and Tukey, JW},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Cooley, Tukey - 1965 - An algorithm for the machine calculation of complex Fourier series.pdf:pdf},
journal = {Mathematics of computation},
pages = {297--301},
title = {{An algorithm for the machine calculation of complex Fourier series}},
url = {http://www.jstor.org/stable/2003354},
year = {1965}
}
@inproceedings{Matejak2014,
author = {Matej\'{a}k, Marek and Kulh\'{a}nek, Tom\'{a}\v{s} and \v{S}ilar, Jan and Privitzer, Pavol and Je\v{z}ek, Filip and Kofr\'{a}nek, Jiř\'{\i}},
booktitle = {Proceedings of the 10th International Modelica Conference, March 10-12, 2014, Lund, Sweden},
doi = {10.3384/ecp14096499},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Matej\'{a}k et al. - 2014 - Physiolibrary - Modelica library for Physiology.pdf:pdf},
keywords = {HumMod,Integrative physiology,Modelica library,Physiolibrary,Physiology,System biology},
pages = {499--505},
publisher = {Link\"{o}ping University Electronic Press},
title = {{Physiolibrary - Modelica library for Physiology}},
year = {2014}
}
@article{Foster2008,
author = {Foster, Ian and Zhao, Yong and Raicu, Ioan and Lu, Shiyong},
doi = {10.1109/GCE.2008.4738445},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Foster et al. - 2008 - Cloud computing and grid computing 360-degree compared.pdf:pdf},
journal = {Grid Computing Environments \ldots},
title = {{Cloud computing and grid computing 360-degree compared}},
year = {2008}
}
@article{kulhanek2010b,
author = {Kulh\'{a}nek, Tom\'{a}\v{s} and Fri\v{c}, Marek and \v{S}\'{a}rek, Milan},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Kulh\'{a}nek, Fri\v{c}, \v{S}\'{a}rek - 2010 - Remote Analysis of Human Voice--Lossless Sound Recording Redirection.pdf:pdf},
journal = {Analysis of Biomedical Signals and Images. Proceedings of 20th International EURASIP Conference (BIOSIGNAL)},
pages = {394--397},
title = {{Remote Analysis of Human Voice--Lossless Sound Recording Redirection}},
url = {http://bs2010.biosignal.cz/papers/1092.pdf},
year = {2010}
}
@article{Gustafson1988,
author = {Gustafson, John L.},
doi = {10.1145/42411.42415},
file = {:home/tomaton/Downloads/p532-gustafson.pdf:pdf},
issn = {00010782},
journal = {Communications of the ACM},
month = may,
number = {5},
pages = {532--533},
title = {{Reevaluating Amdahl's law}},
volume = {31},
year = {1988}
}
@article{Bird2009,
author = {Bird, I. and Jones, B. and Kee, K.F.},
doi = {10.1109/MC.2009.28},
file = {:home/tomaton/Downloads/04755154.pdf:pdf},
issn = {0018-9162},
journal = {Computer},
month = jan,
number = {1},
pages = {36--46},
title = {{The Organization and Management of Grid Infrastructures}},
volume = {42},
year = {2009}
}
@inproceedings{Kulhanek2014Parameters,
author = {Kulh\'{a}nek, Tom\'{a}\v{s} and Matej\'{a}k, Marek and \v{S}ilar, Jan and Kofr\'{a}nek, Jiř\'{\i}},
booktitle = {Biomedical and Health Informatics (BHI), 2014 IEEE-EMBS International Conference on},
doi = {10.1109/BHI.2014.6864463},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Kulhanek et al. - 2014 - Parameter estimation of complex mathematical models of human physiology using remote simulation distributed in.pdf:pdf},
isbn = {9781479921317},
keywords = {cloud computing,information services,parallel proc},
pages = {712--715},
title = {{Parameter estimation of complex mathematical models of human physiology using remote simulation distributed in scientific cloud}},
year = {2014}
}
@article{Matsunaga2008,
author = {Matsunaga, Andr\'{e}a and Tsugawa, Maur\'{\i}cio and Fortes, Jos\'{e}},
doi = {10.1109/eScience.2008.62},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Matsunaga, Tsugawa, Fortes - 2008 - CloudBLAST Combining MapReduce and Virtualization on Distributed Resources for Bioinformatics Applic.pdf:pdf},
isbn = {978-1-4244-3380-3},
journal = {2008 IEEE Fourth International Conference on eScience},
keywords = {-cloud},
month = dec,
pages = {222--229},
publisher = {Ieee},
title = {{CloudBLAST: Combining MapReduce and Virtualization on Distributed Resources for Bioinformatics Applications}},
url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=4736761},
year = {2008}
}
@article{Thain2005,
abstract = {Since 1984, the Condor project has enabled ordinary users to do extraordinary computing. Today, the project continues to explore the social and technical problems of cooperative computing on scales ranging from the desktop to the world-wide computational grid. In this chapter, we provide the history and philosophy of the Condor project and describe how it has interacted with other projects and evolved along with the field of distributed computing. We outline the core components of the Condor system and describe how the technology of computing must correspond to social structures. Throughout, we reflect on the lessons of experience and chart the course traveled by research ideas as they grow into production systems.},
author = {Thain, Douglas and Tannenbaum, Todd and Livny, Miron},
doi = {10.1002/cpe.938},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Thain, Tannenbaum, Livny - 2005 - Distributed computing in practice The Condor experience.pdf:pdf},
isbn = {1532-0626},
issn = {15320626},
journal = {Concurrency Computation Practice and Experience},
keywords = {Community,Condor,Grid,History,Planning,Scheduling,Split execution},
pages = {323--356},
title = {{Distributed computing in practice: The Condor experience}},
volume = {17},
year = {2005}
}
@inproceedings{Kulhanek2010d,
author = {Kulh\'{a}nek, Tom\'{a}\v{s} and Fri\v{c}, Marek and \v{S}\'{a}rek, Milan},
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{s}, \v{S}\'{a}rek - 2010 - VZD\'{A}LEN\'{A} ANAL\'{Y}ZA LIDSK\'{E}HO HLASU - BEZEZTR\'{A}TOV\'{E} NAHR\'{A}-.pdf:pdf},
pages = {96--101},
title = {{Vzd\'{a}len\'{a} anal\'{y}za lidsk\'{e}ho hlasu - bezeztr\'{a}tov\'{e} nahr\'{a}v\'{a}n\'{\i} zvuku přes ip s\'{\i}t\v{e}}},
year = {2010}
}
@article{Foster2006,
author = {Foster, I},
file = {:home/tomaton/Downloads/GT4.pdf:pdf},
journal = {Journal of Computer Science and Technology},
pages = {513--520},
title = {{Globus toolkit version 4:Software for service-oriented systems}},
volume = {21(4)},
year = {2006}
}
@article{Hui2007,
abstract = {Published models of excitable cells can be used to fit to a range of action potential experimental data. CellML is a well-defined standard for publishing and exchanging such models, but currently there is a lack of software that utilizes CellML for parameter analysis. In this paper, we introduce a Java-based utility capable of performing model simulation, identifiability analysis, and parameter optimization of ionic cardiac cell models written in CellML. Identifiability analysis was performed in seven CellML models. Parameter identifiability was consistently improved by using the compensatory membrane current as opposed to the membrane voltage as the residual. as well as through the introduction of an additional stimulus set used in the fitting process.},
author = {Hui, Ben B B and Dokos, Socrates and Lovell, Nigel H},
doi = {10.1109/IEMBS.2007.4353539},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Hui, Dokos, Lovell - 2007 - Parameter identifiability of cardiac ionic models using a novel CellML least squares optimization tool.pdf:pdf},
issn = {1557-170X},
journal = {Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference},
keywords = {Action Potentials,Action Potentials: physiology,Animals,Cardiac,Cardiac: physiology,Cardiovascular,Computer Graphics,Computer Simulation,Heart Conduction System,Heart Conduction System: physiology,Humans,Ion Channel Gating,Ion Channel Gating: physiology,Ion Channels,Ion Channels: physiology,Least-Squares Analysis,Models,Myocytes,Programming Languages,User-Computer Interface},
month = jan,
pages = {5307--10},
pmid = {18003205},
shorttitle = {Engineering in Medicine and Biology Society, 2007.},
title = {{Parameter identifiability of cardiac ionic models using a novel CellML least squares optimization tool.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18003205},
volume = {2007},
year = {2007}
}
@inproceedings{kulhanek2011dd,
author = {Kulh\'{a}nek, Tom\'{a}\v{s}},
booktitle = {Proceeding of PhD. Conference 2011 was published as: Doktorandsk\'{e} dny '11},
editor = {Ku\v{z}elov\'{a}, D},
pages = {90--94},
publisher = {Institute of Computer Science/MatfyzPress},
title = {{Infrastructure for Data Storage and Computation in Biomedical Research}},
url = {http://www.cs.cas.cz/hakl/doktorandsky-den/files/2011/sbornik-dd-2011.pdf},
year = {2011}
}
@article{Foster2003,
author = {Foster, Ian and Kesselman, Carl and Nick, Jeffrey M and Tuecke, Steven},
file = {:home/tomaton/Downloads/ogsa.pdf:pdf},
journal = {Grid computing: making the global infrastructure a reality},
pages = {217--249},
title = {{The Physiology of the Grid: An Open Grid Service Architecture for Distributed Systems Integration}},
year = {2003}
}
@phdthesis{Fielding2000,
author = {Fielding, RT},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Fielding - 2000 - Architectural styles and the design of network-based software architectures.pdf:pdf},
school = {University of California},
title = {{Architectural styles and the design of network-based software architectures}},
url = {http://jpkc.fudan.edu.cn/picture/article/216/35/4b/22598d594e3d93239700ce79bce1/7ed3ec2a-03c2-49cb-8bf8-5a90ea42f523.pdf},
year = {2000}
}
@article{Svec2010,
abstract = {This tutorial addresses fundamental characteristics of microphones (frequency response, frequency range, dynamic range, and directionality), which are important for accurate measurements of voice and speech.},
author = {\v{S}vec, Jan G. and Granqvist, Svante},
doi = {10.1044/1058-0360(2010/09-0091)},
file = {:home/tomaton/Downloads/document(3).pdf:pdf},
issn = {10580360},
journal = {American Journal of Speech-Language Pathology},
keywords = {Measurement,Microphones,Requirements,Voice},
number = {November},
pages = {356--368},
pmid = {20601621},
title = {{Guidelines for selecting microphones for human voice production research}},
volume = {19},
year = {2010}
}
@article{Hunter2009,
abstract = {<para> The revolution in molecular biology over the past 50 years has given us an extraordinarily detailed parts list for life, but little understanding of how the parts integrate into the physiological function of the healthy and diseased human body. In contrast, the engineering sciences, from a detailed knowledge of its components, have successfully explained how a plane actually flies. The key difference is the use of mathematical models based on physical principles and a systematic approach to knowledge management. In this review, we describe the efforts of the Virtual Physiological Human (VPH) Physiome Project to address the challenge of integrating molecular, cellular and tissue/organ structure and function through the use of multiscale modeling based on the development of community standards, open source tools and web-accessible databases. We illustrate two applications of the framework, one to cardiology and one to bone fracture prediction in the elderly. </para>},
author = {Hunter, P. J. and Viceconti, M.},
doi = {10.1109/RBME.2009.2036204},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Hunter, Viceconti - 2009 - The VPH-Physiome Project Standards and Tools for Multiscale Modeling in Clinical Applications.pdf:pdf},
isbn = {1937-3333},
issn = {1937-3333},
journal = {IEEE Reviews in Biomedical Engineering},
keywords = {Bioengineering,VPH,computational physiology,multiscale modeling,physiome},
pages = {40--53},
title = {{The VPH-Physiome Project: Standards and Tools for Multiscale Modeling in Clinical Applications}},
volume = {2},
year = {2009}
}
@inproceedings{Tribula2013,
author = {Tribula, Martin and Je\v{z}ek, Filip and Privitzer, Pavol and Kofr\'{a}nek, Jiř\'{\i} and Kolman, Josef},
booktitle = {sborn\'{\i}k př\'{\i}sp\v{e}vků MEDSOFT},
file = {:home/tomaton/Downloads/Medsoft\_2013\_Tribula.pdf:pdf},
pages = {197--204},
title = {{Webov\'{y} v\'{y}ukov\'{y} simul\'{a}tor krevn\'{\i}ho ob\v{e}hu}},
year = {2013}
}
@inproceedings{Duque,
address = {Tokyo, Japan},
author = {Duque, H and Montagnat, J and Pierson, J and Brunie, L and Magnin, I E},
booktitle = {Biogrid'03 workshop},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Duque et al. - Unknown - DM 2 A Distributed Medical Data Manager for Grids ∗.pdf:pdf},
pages = {138--147},
title = {{DM 2 : A Distributed Medical Data Manager for Grids}}
}
@article{kulhanek2010c,
author = {Kulh\'{a}nek, Tom\'{a}\v{s}},
issn = {1801-5603},
journal = {European Journal for Biomedical Informatics (EJBI)},
number = {1},
pages = {55--58},
title = {{Infrastructure for data storage and computation in biomedical research}},
url = {http://www.ejbi.org/img/ejbi/ejbi2010-1.pdf},
volume = {6},
year = {2010}
}
@article{Belgacem2015,
author = {Belgacem, Mohamed Ben and Chopard, Bastien},
doi = {10.1016/j.future.2014.08.003},
file = {:home/tomaton/Downloads/1-s2.0-S0167739X14001514-main.pdf:pdf},
issn = {0167-739X},
journal = {Future Generation Computer Systems},
keywords = {distributed computation},
pages = {11--21},
publisher = {Elsevier B.V.},
title = {{A hybrid HPC/cloud distributed infrastructure: Coupling EC2 cloud resources with HPC clusters to run large tightly coupled multiscale applications}},
url = {http://dx.doi.org/10.1016/j.future.2014.08.003},
volume = {42},
year = {2015}
}
@techreport{EGICompendium2013,
file = {:home/tomaton/Downloads/EGI-Compendium-2012.pdf:pdf},
institution = {EGI.eu},
number = {December 2012},
pages = {65--67},
title = {{The EGI Compendium of National Grid Infrastructures in Europe 2012 Edition}},
year = {2013}
}
@article{Hofmann2005,
author = {Hofmann, M.},
doi = {10.1177/154851290500200405},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Hofmann - 2005 - On the Complexity of Parameter Calibration in Simulation Models.pdf:pdf},
issn = {1548-5129},
journal = {The Journal of Defense Modeling and Simulation: Applications, Methodology, Technology},
keywords = {1,already,complexity theory,computer science,existing model to a,if system data,introduction,military applications,model calibration,model calibration is the,or,reference system,task of adjusting an,validation methodology},
month = oct,
number = {4},
pages = {217--226},
title = {{On the Complexity of Parameter Calibration in Simulation Models}},
volume = {2},
year = {2005}
}
@article{Laure2006,
abstract = {The past few years have seen the creation of the first producti on level Grid infrastructures that offer their users a dependab le service at an unprecedented scale. Depending on the flavor of middleware services these infrastructures deploy (for instance Condor, gLite, Globus, UNICORE, to name only a few) different interfaces to program the Grid infrastructures are provided. Despite ongoing efforts to standardize Grid service interfaces, there are still si gnificant differences in how applications can interface to a Grid infrastructure. In this paper we describe the middleware (gLite) and services deployed on the EGEE Grid infrastructure and explain how applications can interface to them.},
author = {Laure, E and Fisher, S and Frohner, A and Grandi, C and Kunszt, P and Krenek, A and Mulmo, O and Pacini, F and Prelz, F and White, J and Others},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Laure et al. - 2006 - Programming the Grid with gLite.pdf:pdf},
journal = {Computational Methods in Science and Technology},
pages = {33--45},
title = {{Programming the Grid with gLite}},
volume = {12},
year = {2006}
}
@inproceedings{Blochwitza,
author = {Blochwitz, T and Otter, M and Arnold, M and Bausch, C},
booktitle = {Proceeding of 8th Modelica Conference, Dresden},
file = {:home/tomaton/Downloads/otter2011-FMI-ecp11063013.pdf:pdf},
title = {{The functional mockup interface for tool independent exchange of simulation models}},
year = {2011}
}
@article{Kohl2010,
abstract = {In just over a decade, Systems Biology has moved from being an idea, or rather a disparate set of ideas, to a mainstream feature of research and funding priorities. Institutes, departments, and centers of various flavors of Systems Biology have sprung up all over the world. An Internet search now produces more than 2 million hits. Of the 2,800 entries in PubMed with "Systems Biology" in either the title or the abstract, only two papers were published before 2000, and >90\% were published in the past five years. In this article, we interpret Systems Biology as an approach rather than as a field or a destination of research. We illustrate that this approach is productive for the exploration of systems behavior, or "phenotypes," at all levels of structural and functional complexity, explicitly including the supracellular domain, and suggest how this may be related conceptually to genomes and biochemical networks. We discuss the role of models in Systems Biology and conclude with a consideration of their utility in biomedical research and development.},
author = {Kohl, P and Crampin, E J and Quinn, T A and Noble, D},
doi = {10.1038/clpt.2010.92},
isbn = {1532-6535 (Electronic)$\backslash$n0009-9236 (Linking)},
issn = {1532-6535},
journal = {Clinical pharmacology and therapeutics},
pages = {25--33},
pmid = {20531468},
title = {{Systems biology: an approach.}},
volume = {88},
year = {2010}
}
@article{Garey1979,
abstract = {This book's introduction features a humorous story of a man with a line of people behind him, who explains to his boss, "I can't find an efficient algorithm, but neither can all these famous people." This man illustrates an important quality of a class of problems, namely, the NP-complete problems: if you can prove that a problem is in this class, then it has no known polynomial-time solution that is guaranteed to work in general. This quality implies that the problem is difficult to deal with in practice. The focus of this book is to teach the reader how to identify, deal with, and understand the essence of NP-complete problems; Computers and Intractability does all of those things effectively. In a readable yet mathematically rigorous manner, the book covers topics such as how to prove that a given problem is NP-complete and how to cope with NP-complete problems. (There is even a chapter on advanced topics, with numerous references.) Computers and Intractability also contains a list of more than 300 problems-most of which are known to be NP-complete-with comments and references.},
author = {Garey, M R and Johnson, D S},
file = {:home/tomaton/Downloads/Theory Of Computation/Computers And Intractability A Guide To The Theory Of Np-Completeness - Michael Garey.djvu:djvu;:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Garey, Johnson - 1979 - Computers and Intractability A Guide to the Theory of NP-Completeness (Series of Books in the Mathematical Sc(2).pdf:pdf},
isbn = {0716710455},
journal = {Computers and Intractability},
pages = {340},
title = {{Computers and Intractability: A Guide to the Theory of NP-Completeness (Series of Books in the Mathematical Sciences)}},
year = {1979}
}
@inproceedings{Balaton2007,
author = {Balaton, Zoltan and Gombas, Gabor and Kacsuk, Peter and Kornafeld, Adam and Kovacs, Jozsef and Marosi, Attila Csaba and Vida, Gabor and Podhorszki, Norbert and Kiss, Tamas},
booktitle = {Parallel and Distributed Processing Symposium},
doi = {10.1109/IPDPS.2007.370665},
publisher = {IEEE},
title = {{SZTAKI desktop grid: a modular and scalable way of building large computing grids}},
year = {2007}
}
@article{Ralovich2012,
abstract = {Coarctation of the aorta (CoA), is a congenital defect characterized by a severe narrowing of the aorta, usually distal to the aortic arch. The treatment options include surgical repair, stent implantation, and balloon angioplasty. In order to evaluate the physiological significance of the pre-operative coarctation and to assess the post-operative results, the hemodynamic analysis is usually performed by measuring the pressure gradient (deltaP) across the coarctation site via invasive cardiac catheterization. The measure of success is reduction of the (deltaP > 20 mmHg) systolic blood pressure gradient. In this paper, we propose a non-invasive method based on Computational Fluid Dynamics and MR imaging to estimate the pre- and post-operative hemodynamics for both native and recurrent coarctation patients. High correlation of our results and catheter measurements is shown on corresponding pre- and post-operative examination of 5 CoA patients.},
author = {Ralovich, Krist\'{o}f and Itu, Lucian and Mihalef, Viorel and Sharma, Puneet and Ionasec, Razvan and Vitanovski, Dime and Krawtschuk, Waldemar and Everett, Allen and Ringel, Richard and Navab, Nassir and Comaniciu, Dorin},
file = {:home/tomaton/Documents/chp\%3A10.1007\%2F978-3-642-33418-4\_60.pdf:pdf},
isbn = {978-3-642-33417-7},
journal = {Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention},
keywords = {Aorta,Aorta: pathology,Aorta: physiopathology,Aortic Coarctation,Aortic Coarctation: pathology,Aortic Coarctation: physiopathology,Blood Flow Velocity,Computer-Assisted,Computer-Assisted: methods,Humans,Image Enhancement,Image Enhancement: methods,Image Interpretation,Magnetic Resonance Angiography,Magnetic Resonance Angiography: methods,Myocardial Perfusion Imaging,Myocardial Perfusion Imaging: methods,Reproducibility of Results,Sensitivity and Specificity},
pages = {486--93},
pmid = {23286084},
title = {{Hemodynamic assessment of pre- and post-operative aortic coarctation from MRI.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23286084},
volume = {15},
year = {2012}
}
@article{FernandezDeCanete2013,
abstract = {The modeling of physiological systems via mathematical equations reflects the calculation procedure more than the structure of the real system modeled, with the simulation environment SIMULINK™ being one of the best suited to this strategy. Nevertheless, object-oriented modeling is spreading in current simulation environments through the use of the individual components of the model and its interconnections to define the underlying dynamic equations. In this paper we describe the use of the SIMSCAPE™ simulation environment in the object-oriented modeling of the closed loop cardiovascular system. The described approach represents a valuable tool in the teaching of physiology for graduate medical students.},
author = {{Fernandez de Canete}, Javier and del Saz-Orozco, P and Moreno-Boza, D and Duran-Venegas, E},
doi = {10.1016/j.compbiomed.2013.01.007},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Ferandez de Canete et al. - 2013 - Object-oriented modeling and simulation of the closed loop cardiovascular system by using SIMSCAPE.pdf:pdf},
issn = {1879-0534},
journal = {Computers in biology and medicine},
keywords = {Algorithms,Cardiology,Cardiology: instrumentation,Cardiology: methods,Cardiovascular System,Computer Simulation,Computer-Assisted,Humans,Left,Left: physiology,Models,Respiration,Right,Right: physiology,Signal Processing,Theoretical,User-Computer Interface,Ventricular Function},
month = may,
number = {4},
pages = {323--33},
title = {{Object-oriented modeling and simulation of the closed loop cardiovascular system by using SIMSCAPE.}},
volume = {43},
year = {2013}
}
@misc{jsim,
title = {{JSim: Java-based Simulation Platform for Data Analysis}},
url = {http://www.physiome.org/jsim}
}
@article{hunter2002,
author = {Hunter, Peter and Robbins, Peter and Noble, Denis},
journal = {European journal of physiology},
number = {1},
pages = {1--9},
publisher = {Springer},
title = {{The IUPS human physiome project}},
volume = {445},
year = {2002}
}
@inproceedings{Adamova2014,
author = {Adamova, Dagmar},
booktitle = {52 International Winter Meeting on Nuclear Physics, Bormio,Italy},
file = {:home/tomaton/Downloads/Bormio2014\_021.pdf:pdf},
number = {January},
title = {{Computing framework for the LHC: current status and challenges of the High Luminosity LHC future}},
url = {http://pos.sissa.it/archive/conferences/212/021/Bormio2014\_021.pdf},
year = {2014}
}
@article{Barga2011,
abstract = {Extending the capabilities of desktop and mobile applications through on-demand cloud, data-driven services will significantly broaden the research community's capabilities, accelerating the pace of engineering and scientific discovery. The net effect will be the democratization of research capabilities that are now available only to the most elite scientists.},
author = {Barga, Roger and Gannon, Dennis and Reed, Daniel},
doi = {10.1109/MIC.2011.20},
file = {:home/tomaton/Downloads/05676168.pdf:pdf},
isbn = {1089-7801},
issn = {10897801},
journal = {IEEE Internet Computing},
keywords = {Internet,MapReduce,cloud computing,data analytics,datacenters,scientific research},
pages = {72--75},
title = {{The client and the cloud: Democratizing research computing}},
volume = {15},
year = {2011}
}
@article{Kulhanek2013c,
author = {Kulh\'{a}nek, Tom\'{a}\v{s} and Je\v{z}ek, Filip and Matej\'{a}k, Marek and \v{S}ilar, Jan and Privitzer, Pavol and Tribula, Martin and Kofr\'{a}nek, Jiř\'{\i}},
doi = {10.11239/jsmbe.51.R-32},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Kulh\'{a}nek et al. - 2013 - RESTful web service to build loosely coupled web based simulation of human physiology a s.pdf:pdf},
journal = {Transactions of Japanese Society for Medical and Biological Engineering},
number = {Supplement},
pages = {R--32},
title = {{RESTful web service to build loosely coupled web based simulation of human physiology}},
volume = {51},
year = {2013}
}
@article{Ortiz2011,
abstract = {Cloud-computing standards haven't yet gained traction, and industry observers say this could limit future adoption of the technology.},
author = {Ortiz, Sixto},
doi = {10.1109/MC.2011.220},
file = {:home/tomaton/Downloads/05958700.pdf:pdf},
issn = {00189162},
journal = {Computer},
keywords = {Cloud computing,Hypervisor,IEEE P2301,IEEE P2302,Standards,Virtualization},
number = {July},
pages = {13--16},
title = {{The problem with cloud-computing standardization}},
volume = {44},
year = {2011}
}
@book{Bankman2000,
booktitle = {Book},
editor = {Bankman, Issac N.},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Bankman - 2000 - Handbook of Medical Imaging.pdf:pdf},
isbn = {0120777908},
title = {{Handbook of Medical Imaging; Processing and Analysis}},
year = {2000}
}
@article{Beberg2009,
abstract = {Accurate simulation of biophysical processes requires vast computing resources. Folding@home is a distributed computing system first released in 2000 to provide such resources needed to simulate protein folding and other biomolecular phenomena. Now operating in the range of 5 PetaFLOPS sustained, it provides more computing power than can typically be gathered and operated locally due to cost, physical space, and electrical/cooling load. This paper describes the architecture and operation of Folding@home, along with some lessons learned over the lifetime of the project.},
author = {Beberg, Adam L. and Ensign, Daniel L. and Jayachandran, Guha and Khaliq, Siraj and Pande, Vijay S.},
doi = {10.1109/IPDPS.2009.5160922},
file = {:home/tomaton/Downloads/05160922.pdf:pdf},
isbn = {9781424437504},
issn = {1530-2075},
journal = {IPDPS 2009 - Proceedings of the 2009 IEEE International Parallel and Distributed Processing Symposium},
title = {{Folding@home: Lessons from eight years of volunteer distributed computing}},
year = {2009}
}
@article{Helton2006,
abstract = {Sampling-based methods for uncertainty and sensitivity analysis are reviewed. The following topics are considered: (i) definition of probability distributions to characterize epistemic uncertainty in analysis inputs, (ii) generation of samples from uncertain analysis inputs, (iii) propagation of sampled inputs through an analysis, (iv) presentation of uncertainty analysis results, and (v) determination of sensitivity analysis results. Special attention is given to the determination of sensitivity analysis results, with brief descriptions and illustrations given for the following procedures/techniques: examination of scatterplots, correlation analysis, regression analysis, partial correlation analysis, rank transformations, statistical tests for patterns based on gridding, entropy tests for patterns based on gridding, nonparametric regression analysis, squared rank differences/rank correlation coefficient test, two-dimensional Kolmogorov-Smirnov test, tests for patterns based on distance measures, top down coefficient of concordance, and variance decomposition. ?? 2005 Elsevier Ltd. All rights reserved.},
author = {Helton, J. C. and Johnson, J. D. and Sallaberry, C. J. and Storlie, C. B.},
doi = {10.1016/j.ress.2005.11.017},
file = {:home/tomaton/Downloads/1-s2.0-S0951832005002292-main.pdf:pdf},
isbn = {0951-8320},
issn = {09518320},
journal = {Reliability Engineering and System Safety},
keywords = {Aleatory uncertainty,Epistemic uncertainty,Latin hypercube sampling,Monte Carlo,Sensitivity analysis,Uncertainty analysis},
pages = {1175--1209},
title = {{Survey of sampling-based methods for uncertainty and sensitivity analysis}},
volume = {91},
year = {2006}
}
@article{Hester2011systems,
abstract = {Over the last 10 years, 'Systems Biology' has focused on the integration of biology and medicine with information technology and computation. The current challenge is to use the discoveries of the last 20 years, such as genomics and proteomics, to develop targeted therapeutical strategies. These strategies are the result of understanding the aetiologies of complex diseases. Scientists predict the data will make personalized medicine rapidly available. However, the data need to be considered as a highly complex system comprising multiple inputs and feedback mechanisms. Translational medicine requires the functional and conceptual linkage of genetics to proteins, proteins to cells, cells to organs, organs to systems and systems to the organism. To help understand the complex integration of these systems, a mathematical model of the entire human body, which accurately links the functioning of all organs and systems together, could provide a framework for the development and testing of new hypotheses that will be important in clinical outcomes. There are several efforts to develop a 'Human Physiome', with the strengths and weaknesses of each being presented here. The development of a 'Human Model', with verification, documentation and validation of the underlying and integrative responses, is essential to provide a usable environment. Future development of a 'Human Model' requires integrative physiologists working in collaboration with other scientists, who have expertise in all areas of human biology, to develop the most accurate and usable human model.},
author = {Hester, Robert L and Iliescu, Radu and Summers, Richard and Coleman, Thomas G},
doi = {10.1113/jphysiol.2010.201558},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Hester et al. - 2011 - Systems biology and integrative physiological modelling.pdf:pdf},
issn = {1469-7793},
journal = {The Journal of physiology},
keywords = {Biological,Genomics,Humans,Models,Proteomics,Systems Biology},
month = mar,
number = {Pt 5},
pages = {1053--60},
pmid = {21135044},
publisher = {Physiological Soc},
title = {{Systems biology and integrative physiological modelling.}},
volume = {589},
year = {2011}
}
@article{Montagnat2007,
author = {Montagnat, Johan and Frohner, \'{A}kos and Jouvenot, Daniel and Pera, Christophe and Kunszt, Peter and Koblitz, Birger and Santos, Nuno and Loomis, Charles and Texier, Romain and Lingrand, Diane and Guio, Patrick and {Brito Da Rocha}, Ricardo and {Sobreira de Almeida}, Antonio and Farkas, Zolt\'{a}n},
doi = {10.1007/s10723-007-9088-2},
file = {:home/tomaton/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Montagnat et al. - 2007 - A Secure Grid Medical Data Manager Interfaced to the gLite Middleware.pdf:pdf},
issn = {1570-7873},
journal = {Journal of Grid Computing},
month = jul,
number = {1},
pages = {45--59},
title = {{A Secure Grid Medical Data Manager Interfaced to the gLite Middleware}},
volume = {6},

license_type: permissive

branch_name: refs/heads/master

extension: bib