Exploració per autor "Ponce De Leon, Miguel"Més informació

Ara es mostren els items 1-14 de 14

    • A flux balance approach to integrate cell metabolism into multicelluar agent-based simulations 

      Ponce De Leon, Miguel (Barcelona Supercomputing Center, 2020)
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      The study of multicellular systems such as tumors, tissues, or organoids is critical to improve our understanding of the complex dynamics exhibited by these systems. For instance, the emergence of resistant cancer cells ...

    • BioFVM-X: an MPI+OpenMP 3-D simulator for biological systems 

      Saxena, Gaurav; Ponce De Leon, Miguel; Montagud, Arnau; Vicente Dorca, David; Valencia, Alfonso (Springer, 2021)
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      Multi-scale simulations require parallelization to address large-scale problems, such as real-sized tumor simulations. BioFVM is a software package that solves diffusive transport Partial Differential Equations for 3-D ...

    • COVID-19 Flow-Maps an open geographic information system on COVID-19 and human mobility for Spain 

      Ponce De Leon, Miguel; Valle, Javier del; Fernández González, Jose María; Bernardo, Marc; Cirillo, Davide; Sanchez Valle, Jon; Smith, Matthew; Capella Gutiérrez, Salvador; Gullón, Tania; Valencia, Alfonso (Nature Research, 2021)
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      COVID-19 is an infectious disease caused by the SARS-CoV-2 virus, which has spread all over the world leading to a global pandemic. The fast progression of COVID-19 has been mainly related to the high contagion rate of the ...

    • COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms 

      Ostaszewski, Marek; Niarakis, Anna; Mazein, Alexander; Kuperstein, Inna; Phair, Robert; Montagud, Arnau; Ponce De Leon, Miguel; Vazquez, Miguel; Valencia, Alfonso (Wiley Open Access, 2021-10-21)
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      We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. ...

    • Drug-Target identification in COVID-19 disease mechanisms using computational systems biology approaches 

      Niarakis, Anna; Ostaszewski, Marek; Mazein, Alexander; Kuperstein, Inna; Kutmon, Martina; Montagud, Arnau; Ponce De Leon, Miguel; Valencia, Alfonso (Frontiers Media, 2023)
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      The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop ...

    • Evaluating the policy of closing bars and restaurants in Cataluña and its effects on mobility and COVID19 incidence 

      Smith, Matthew; Ponce De Leon, Miguel; Valencia, Alfonso (Nature Research, 2022-06)
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      The world has gone through unprecedented changes since the global pandemic hit. During the early phase of the pandemic, the absence of known drugs or pharmaceutical treatments forced governments to introduce different ...

    • Implementation of cellular transport models within a multiscale simulation software 

      Hayoun-Mya, Othmane; Ponce De Leon, Miguel; Montagud, Arnau; Valencia, Alfonso (Barcelona Supercomputing Center, 2022-05)
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      Agent-based models (ABM) have been increasingly employed to study dynamics of biological systems. However, these mostly lack transport mechanisms that interface between the agents and their microenvironment. We considered ...

    • INforE: Interactive cross-platform analytics for everyone 

      Giatrakos, Nikos; Arnu, David; Bitsakis, Theodoros; Deligiannakis, Antonios; Garofalakis, Minos; Klinkenberg, Ralf; Konidaris, Aris; Kontaxakis, Antonis; Kotidis Kotidis, Yannis; Samoladas, Vasilis; Simitsis, Alkis; Stamatakis, George; Temme, Fabian; Torok, Mate; Yaqub, Edwin; Montagud, Arnau; Ponce De Leon, Miguel; Arndt, Holger; Burkard, Stefan (Association for Computing Machinery (ACM), 2020-10)
      Comunicació de congrés
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      We present INforE, a prototype supporting non-expert programmers in performing optimized, cross-platform, streaming analytics at scale. INforE offers: a) a new extension to the RapidMiner Studio for graphical design of Big ...

    • Optimizing dosage-specific treatments in a multi-Scale model of a tumor growth 

      Ponce De Leon, Miguel; Montagud, Arnau; Akasiadis, Charilaos; Schreiber, Janina; Ntiniakou, Thaleia; Valencia, Alfonso (Frontiers Media, 2022-04)
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      The emergence of cell resistance in cancer treatment is a complex phenomenon that emerges from the interplay of processes that occur at different scales. For instance, molecular mechanisms and population-level dynamics ...

    • Optimizing Resource Allocation for Tumor Simulations over HPC Infrastructures 

      Streviniotis, Errikos; Giatrakos, Nikos; Kotidis, Yannis; Ntiniakou, Thaleia; Ponce De Leon, Miguel (Institute of Electrical and Electronics Engineers (IEEE), 2023)
      Comunicació de congrés
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      We introduce RATS (Resource Allocator for Tumor Simulations), the first optimizer for the execution of tumor simulations over HPC infrastructures. The optimization framework of RATS incorporates 3 vital performance criteria ...

    • Parallel model exploration for tumor treatment simulations 

      Akasiadis, Charilaos; Ponce De Leon, Miguel; Montagud, Arnau; Michelioudakis, Evangelos; Atsidakou, Alexia; Alevizos, Elias; Artikis, Alexander; Valencia, Alfonso; Paliouras, Georgios (Parallel model exploration for tumor treatment simulations, 2022-03)
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      Abstract Computational systems and methods are often being used in biological research, including the understanding of cancer and the development of treatments. Simulations of tumor growth and its response to different ...

    • PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks 

      Ponce De Leon, Miguel; Montagud, Arnau; Noël, Vincent; Meert, Annika; Pradas, Gerard; Barillot, Emmanuel; Calzone, Laurence; Valencia, Alfonso (Nature Research, 2023)
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      In systems biology, mathematical models and simulations play a crucial role in understanding complex biological systems. Different modelling frameworks are employed depending on the nature and scales of the system under ...

    • Simulating SARS-CoV-2 epidemics by region-specific variables and modeling contact tracing app containment 

      Ferrari, Alberto; Santus, Enrico; Cirillo, Davide; Ponce De Leon, Miguel; Marino, Nicola; Ferreti, Maria Teresa; Santuccione Chadha, Antonella; Mavridis, Nikolaos; Valencia, Alfonso (Springer Nature, 2021)
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      Targeted contact-tracing through mobile phone apps has been proposed as an instrument to help contain the spread of COVID-19 and manage the lifting of nation-wide lock-downs currently in place in USA and Europe. However, ...

    • Systems Biology at the giga-scale: large multi-scale models of complex, heterogeneous multicellular systems 

      Montagud, Arnau; Ponce De Leon, Miguel; Valencia, Alfonso (Elsevier, 2021)
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      Agent-based modelling has proven its usefulness in several biomedical projects by explaining and uncovering mechanisms in diseases. Nevertheless, the scenarios addressed in these models usually consider a small number of ...