Proceedings of the 2014 6th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation : the CHIC Project Workshop (IARWISOCI) : Athens, Greece, 3-4 November 2014. International Advanced Research Workshop on...最新文献
Pub Date : 2014-11-01DOI: 10.1109/IARWISOCI.2014.7034636
I. Stura, D. Gabriele, C. Guiot
Cancer is not a homogenous tissue, but a very complex mix of different cell populations; moreover, a delicate equilibrium exists between these components of a tumour mass. In this work we address prostate cancer although the methods presented can be generalized to most tumour types. The aim of our work is to model the behaviour of the different cell populations within the tumour and simulate changes which occur during natural evolution and treatments.
{"title":"A two population model of cancer growth with fixed capacity","authors":"I. Stura, D. Gabriele, C. Guiot","doi":"10.1109/IARWISOCI.2014.7034636","DOIUrl":"https://doi.org/10.1109/IARWISOCI.2014.7034636","url":null,"abstract":"Cancer is not a homogenous tissue, but a very complex mix of different cell populations; moreover, a delicate equilibrium exists between these components of a tumour mass. In this work we address prostate cancer although the methods presented can be generalized to most tumour types. The aim of our work is to model the behaviour of the different cell populations within the tumour and simulate changes which occur during natural evolution and treatments.","PeriodicalId":93358,"journal":{"name":"Proceedings of the 2014 6th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation : the CHIC Project Workshop (IARWISOCI) : Athens, Greece, 3-4 November 2014. International Advanced Research Workshop on...","volume":"248 1","pages":"1-4"},"PeriodicalIF":0.0,"publicationDate":"2014-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77712946","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-11-01DOI: 10.1109/iarwisoci.2014.7034630
G Stamatakos, Dimitra Dionysiou, Fay Misichroni, Norbert Graf, Stefaan van Gool, Rainar Bohle, Feng Dong, Marco Viceconti, Kostas Marias, Vangelis Sakkalis, Nikolaus Forgo, Ravi Radhakrishnan, Helen Byrne, Caterina Guiot, Philippe Buechler, Elias Neri, Anca Bucur, Bernard de Bono, Debora Testi, Manolis Tsiknakis
This paper briefly outlines the aim, the objectives, the architecture and the main building blocks of the ongoing large scale integrating transatlantic research project CHIC (http://chic-vph.eu/).
{"title":"Computational Horizons In Cancer (CHIC): Developing Meta- and Hyper-Multiscale Models and Repositories for <i>In Silico</i> Oncology - a Brief Technical Outline of the Project.","authors":"G Stamatakos, Dimitra Dionysiou, Fay Misichroni, Norbert Graf, Stefaan van Gool, Rainar Bohle, Feng Dong, Marco Viceconti, Kostas Marias, Vangelis Sakkalis, Nikolaus Forgo, Ravi Radhakrishnan, Helen Byrne, Caterina Guiot, Philippe Buechler, Elias Neri, Anca Bucur, Bernard de Bono, Debora Testi, Manolis Tsiknakis","doi":"10.1109/iarwisoci.2014.7034630","DOIUrl":"https://doi.org/10.1109/iarwisoci.2014.7034630","url":null,"abstract":"<p><p>This paper briefly outlines the aim, the objectives, the architecture and the main building blocks of the ongoing large scale integrating transatlantic research project CHIC (http://chic-vph.eu/).</p>","PeriodicalId":93358,"journal":{"name":"Proceedings of the 2014 6th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation : the CHIC Project Workshop (IARWISOCI) : Athens, Greece, 3-4 November 2014. International Advanced Research Workshop on...","volume":"2014 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2014-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/iarwisoci.2014.7034630","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39432680","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-11-01DOI: 10.1109/IARWISOCI.2014.7034633
J. Grogan, P. Maini, J. Pitt-Francis, H. Byrne
The vasculature plays an important role in tumour development and treatment, acting as a conduit for nutrients, waste products and therapeutics. Simulating transport and network structure evolution in malformed tumour networks is a challenging multi-scale problem. Current approaches for modelling the vasculature at distinct size scales are described here, followed by a discussion of current efforts in developing integrated multi-scale modelling approaches for simulating the growth and treatment of vascular tumours.
{"title":"Simulating tumour vasculature at multiple scales","authors":"J. Grogan, P. Maini, J. Pitt-Francis, H. Byrne","doi":"10.1109/IARWISOCI.2014.7034633","DOIUrl":"https://doi.org/10.1109/IARWISOCI.2014.7034633","url":null,"abstract":"The vasculature plays an important role in tumour development and treatment, acting as a conduit for nutrients, waste products and therapeutics. Simulating transport and network structure evolution in malformed tumour networks is a challenging multi-scale problem. Current approaches for modelling the vasculature at distinct size scales are described here, followed by a discussion of current efforts in developing integrated multi-scale modelling approaches for simulating the growth and treatment of vascular tumours.","PeriodicalId":93358,"journal":{"name":"Proceedings of the 2014 6th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation : the CHIC Project Workshop (IARWISOCI) : Athens, Greece, 3-4 November 2014. International Advanced Research Workshop on...","volume":"286 1","pages":"1-4"},"PeriodicalIF":0.0,"publicationDate":"2014-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75631038","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-11-01DOI: 10.1109/IARWISOCI.2014.7034641
Marek Blazewicz, E. Georgiadi, Juliusz Pukacki, G. Stamatakos
The purpose of this research was the parallelization of the Wilms' Oncosimulator, an integrated cancer treatment support system modeling the growth of nephroblastoma tumors and their in vivo response to chemotherapeutic modalities. In this concept, the Oncosimulator has been optimized in order to perform efficient computations on the newest heterogeneous parallel architectures: the CPU and GPU based computing architectures. The simulator has been implemented using a novel solution for distributed computing on heterogeneous architectures - the Cactus computational toolkit with CaKernel as the module for the computations performed on computing accelerators. In this publication the challenges faced during the process of porting the Oncosimulator onto the aforementioned architectures (within CaKernel framework) are addressed, and the performance benefits of such approaches are analyzed. The successful parallelization of the Oncosimulator advances its computational efficiency and enhances its reusability as well as its eventual translation into clinical practice. The research was performed in the context of the p-medicine project*.
{"title":"Development of the p-medicine oncosimulator as a parallel treatment support system","authors":"Marek Blazewicz, E. Georgiadi, Juliusz Pukacki, G. Stamatakos","doi":"10.1109/IARWISOCI.2014.7034641","DOIUrl":"https://doi.org/10.1109/IARWISOCI.2014.7034641","url":null,"abstract":"The purpose of this research was the parallelization of the Wilms' Oncosimulator, an integrated cancer treatment support system modeling the growth of nephroblastoma tumors and their in vivo response to chemotherapeutic modalities. In this concept, the Oncosimulator has been optimized in order to perform efficient computations on the newest heterogeneous parallel architectures: the CPU and GPU based computing architectures. The simulator has been implemented using a novel solution for distributed computing on heterogeneous architectures - the Cactus computational toolkit with CaKernel as the module for the computations performed on computing accelerators. In this publication the challenges faced during the process of porting the Oncosimulator onto the aforementioned architectures (within CaKernel framework) are addressed, and the performance benefits of such approaches are analyzed. The successful parallelization of the Oncosimulator advances its computational efficiency and enhances its reusability as well as its eventual translation into clinical practice. The research was performed in the context of the p-medicine project*.","PeriodicalId":93358,"journal":{"name":"Proceedings of the 2014 6th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation : the CHIC Project Workshop (IARWISOCI) : Athens, Greece, 3-4 November 2014. International Advanced Research Workshop on...","volume":"32 1","pages":"1-5"},"PeriodicalIF":0.0,"publicationDate":"2014-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88282026","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-11-01DOI: 10.1109/IARWISOCI.2014.7034645
Georgios C. Manikis, Evaggelia Maniadi, M. Tsiknakis, K. Marias
This paper presents a user-friendly web-based collaborative environment for analyzing, assessing the quality of large multi-level clinical datasets and deriving predictive models. The Multi-Modal Medical Data Analysis Platform (3MDAP) follows two main objectives: a) to empower the user to analyze with ease clinic-genomic data in order to get simple statistics on selected parameters, perform survival analyses, compare regiments in selected cohort of patient and obtain genomic analysis results, and b) to perform heterogeneous clinical data modeling for deriving and cross-validating in multiple datasets predictive clinic-genomic models of patient response, and assessing the value of candidate biomarkers. 3MDAP's enhanced functionality is coupled with a security framework for enabling user authentication and authorization, a set of services that facilitate the process of loading and retrieving data from a data-warehouse (either locally based or in a cloud), and a widget-based front-end environment for assisting users in interacting with the platform's functionality in a user friendly manner. For each running analysis, 3MDAP supports an engine to create dynamically analysis reports. Last, the framework provides an internal database where a full analysis record of an executed analysis is stored, including metadata information (i.e. timestamp information, the examined data, any memory constraints, the dynamically generated reports in both .pdf and .html format, and etc.) in order to be used for future reference.
{"title":"Multi-Modal Medical Data Analysis Platform (3MDAP) for analysis and predictive modelling of cancer trial data","authors":"Georgios C. Manikis, Evaggelia Maniadi, M. Tsiknakis, K. Marias","doi":"10.1109/IARWISOCI.2014.7034645","DOIUrl":"https://doi.org/10.1109/IARWISOCI.2014.7034645","url":null,"abstract":"This paper presents a user-friendly web-based collaborative environment for analyzing, assessing the quality of large multi-level clinical datasets and deriving predictive models. The Multi-Modal Medical Data Analysis Platform (3MDAP) follows two main objectives: a) to empower the user to analyze with ease clinic-genomic data in order to get simple statistics on selected parameters, perform survival analyses, compare regiments in selected cohort of patient and obtain genomic analysis results, and b) to perform heterogeneous clinical data modeling for deriving and cross-validating in multiple datasets predictive clinic-genomic models of patient response, and assessing the value of candidate biomarkers. 3MDAP's enhanced functionality is coupled with a security framework for enabling user authentication and authorization, a set of services that facilitate the process of loading and retrieving data from a data-warehouse (either locally based or in a cloud), and a widget-based front-end environment for assisting users in interacting with the platform's functionality in a user friendly manner. For each running analysis, 3MDAP supports an engine to create dynamically analysis reports. Last, the framework provides an internal database where a full analysis record of an executed analysis is stored, including metadata information (i.e. timestamp information, the examined data, any memory constraints, the dynamically generated reports in both .pdf and .html format, and etc.) in order to be used for future reference.","PeriodicalId":93358,"journal":{"name":"Proceedings of the 2014 6th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation : the CHIC Project Workshop (IARWISOCI) : Athens, Greece, 3-4 November 2014. International Advanced Research Workshop on...","volume":"59 1","pages":"1-4"},"PeriodicalIF":0.0,"publicationDate":"2014-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85336747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-11-01DOI: 10.1109/IARWISOCI.2014.7034637
Christos A. Kyroudis, D. Dionysiou, E. Kolokotroni, Jesper F. Kallehague, K. Tanderup, G. Stamatakos
The goal of this article is to present basic scientific principles and core algorithms of the simulation module of the CERvical cancer ONCOsimulator (CERONCO) developed within the context of the DrTherapat project (FP7-ICT-600852). CERONCO simulates the response of cervical tumours to radiotherapy treatment (external beam radiotherapy followed by brachytherapy) with concomitant weekly cisplatin, in the patient-individualized context. Results from a preliminary clinical adaptation study based on the MR imaging data of a clinical case are presented as well.
{"title":"Simulation of cervical cancer response to radiotherapy","authors":"Christos A. Kyroudis, D. Dionysiou, E. Kolokotroni, Jesper F. Kallehague, K. Tanderup, G. Stamatakos","doi":"10.1109/IARWISOCI.2014.7034637","DOIUrl":"https://doi.org/10.1109/IARWISOCI.2014.7034637","url":null,"abstract":"The goal of this article is to present basic scientific principles and core algorithms of the simulation module of the CERvical cancer ONCOsimulator (CERONCO) developed within the context of the DrTherapat project (FP7-ICT-600852). CERONCO simulates the response of cervical tumours to radiotherapy treatment (external beam radiotherapy followed by brachytherapy) with concomitant weekly cisplatin, in the patient-individualized context. Results from a preliminary clinical adaptation study based on the MR imaging data of a clinical case are presented as well.","PeriodicalId":93358,"journal":{"name":"Proceedings of the 2014 6th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation : the CHIC Project Workshop (IARWISOCI) : Athens, Greece, 3-4 November 2014. International Advanced Research Workshop on...","volume":"53 1","pages":"1-4"},"PeriodicalIF":0.0,"publicationDate":"2014-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82283712","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-11-01DOI: 10.1109/IARWISOCI.2014.7034644
R. David, F. Dong, Yvonne Braun, N. Graf
The MyHealthAvatar (MHA) is an EC FP7 project aimed to focus on research and demonstration actions, through which the achievability of an innovative representation of the health status of citizens is explored. The aim of MHA survey was to enhance our understanding of patient and public views about the MHA platform. First, we investigated the background (sociodemographic characteristics) of our respondents, their understating of the basic terms like EHR and PHR. Second, we addressed complex questions about the expected and proposed for implementation MHA platform's functionalities and of special interest were the questions about the security and privacy concerns the end users might have. In general terms the survey allowed us to examine individuals' specific hopes and concerns about MHA platform and now we have a deeper understanding of patient and public views about further MHA platform's functionalities.
{"title":"MyHealthAvatar survey: Scenario based user needs and requirements","authors":"R. David, F. Dong, Yvonne Braun, N. Graf","doi":"10.1109/IARWISOCI.2014.7034644","DOIUrl":"https://doi.org/10.1109/IARWISOCI.2014.7034644","url":null,"abstract":"The MyHealthAvatar (MHA) is an EC FP7 project aimed to focus on research and demonstration actions, through which the achievability of an innovative representation of the health status of citizens is explored. The aim of MHA survey was to enhance our understanding of patient and public views about the MHA platform. First, we investigated the background (sociodemographic characteristics) of our respondents, their understating of the basic terms like EHR and PHR. Second, we addressed complex questions about the expected and proposed for implementation MHA platform's functionalities and of special interest were the questions about the security and privacy concerns the end users might have. In general terms the survey allowed us to examine individuals' specific hopes and concerns about MHA platform and now we have a deeper understanding of patient and public views about further MHA platform's functionalities.","PeriodicalId":93358,"journal":{"name":"Proceedings of the 2014 6th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation : the CHIC Project Workshop (IARWISOCI) : Athens, Greece, 3-4 November 2014. International Advanced Research Workshop on...","volume":"1 1","pages":"1-5"},"PeriodicalIF":0.0,"publicationDate":"2014-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83096008","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-02-05DOI: 10.1109/IARWISOCI.2014.7034642
D. Tartarini, Kewei Duan, N. Gruel, D. Testi, Dawn Walker, M. Viceconti
The VPH Hypermodelling framework is a collaborative computational platform providing a complete Problem Solving Environment to execute, on distributed computational architectures, sophisticated predictive models involving patient medical data or specialized repositories. In the CHIC1 project, it will be enhanced to support clinicians in providing prompt personalised cancer treatments. It supports several computational architectures with strict security policies.
{"title":"The VPH Hypermodelling framework for cancer multiscale models in the clinical practice","authors":"D. Tartarini, Kewei Duan, N. Gruel, D. Testi, Dawn Walker, M. Viceconti","doi":"10.1109/IARWISOCI.2014.7034642","DOIUrl":"https://doi.org/10.1109/IARWISOCI.2014.7034642","url":null,"abstract":"The VPH Hypermodelling framework is a collaborative computational platform providing a complete Problem Solving Environment to execute, on distributed computational architectures, sophisticated predictive models involving patient medical data or specialized repositories. In the CHIC1 project, it will be enhanced to support clinicians in providing prompt personalised cancer treatments. It supports several computational architectures with strict security policies.","PeriodicalId":93358,"journal":{"name":"Proceedings of the 2014 6th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation : the CHIC Project Workshop (IARWISOCI) : Athens, Greece, 3-4 November 2014. International Advanced Research Workshop on...","volume":"17 1","pages":"1-4"},"PeriodicalIF":0.0,"publicationDate":"2014-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81962104","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Proceedings of the 2014 6th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation : the CHIC Project Workshop (IARWISOCI) : Athens, Greece, 3-4 November 2014. International Advanced Research Workshop on...
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