Shayan Shahand

Shayan Shahand
Academisch Medisch Centrum Universiteit van Amsterdam | AMC · Department of Clinical Epidemiology and Biostatistics

PhD

About

21
Publications
2,032
Reads
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145
Citations
Additional affiliations
March 2010 - June 2016
Academisch Medisch Centrum Universiteit van Amsterdam
Position
  • Researcher, PhD candidate, Scientific Programmer

Publications

Publications (21)
Article
Full-text available
The lessons learned during six years of experience in design, development, and operation of four Science Gateway (SG) generations motivated us to develop yet another generation of platforms coined “Rosemary”. At the core of Rosemary the three fundamental SG functions, namely related to data, computing, and collaboration management, are integrated t...
Article
Full-text available
The lessons learned during six years of experience in design, development, and operation of four Science Gateway (SG) generations motivated us to develop yet another generation of platforms coined “Rosemary”. At the core of Rosemary the three fundamental SG functions, namely related to data, computing, and collaboration management, are integrated t...
Conference Paper
Science Gateways (SGs) have emerged as systems that facilitate access to cyberinfrastructures. There is a growing interest in the exploitation and development of SGs. However, it remains challenging to understand and design SG with the required properties because of the complex nature of SGs. Additionally, it is difficult to decide upon frameworks...
Article
The sustainability of science gateways has been a topic of active discussion because they have been created and supported in the context of temporary research and infrastructure projects. As successful projects come to an end, it is necessary to find (new) models to secure continuous exploitation of products generated by these projects. Taking this...
Chapter
Computational neuroscientists face challenges to manage ever-increasing large volume of data and to process them with applications that require great computational power. The Brain Imaging Centre of the Academic Medical Centre of the University of Amsterdam is a community of neuroscientists who are involved in various computational neuroscience res...
Article
Science gateways provide UIs and high-level services to access and manage applications and data collections on distributed resources. They facilitate users to perform data analysis on distributed computing infrastructures without getting involved into the technical details. The e-BioInfra Gateway is a science gateway for biomedical data analysis on...
Article
Grid computing and workflow management systems emerged as solutions to the challenges arising from the processing and storage of shear volumes of data generated by modern simulations and data acquisition devices. Workflow management systems usually document the process of the workflow execution either as structured provenance information or as log...
Conference Paper
Full-text available
Current workflow abstractions in general lack: (a) an adequate approach to handle distributed data and (b) proper separation between logical tasks and data-flow from their mapping onto physical locations. As the complexity and dynamism of data and processing distribution have increased, optimized mapping of logical tasks to physical resources have...
Conference Paper
Full-text available
Science gateways provide user interfaces and highlevel services to access and manage applications and data collections on distributed resources. They facilitate users to perform data analysis on distributed computing infrastructures (DCIs) without getting involved into the technical details. The e-BioInfra Gateway is a science gateway for biomedica...
Article
Biomedical researchers can leverage Grid computing technology to address their increasing demands for data- and compute-intensive data analysis. However, usage of existing Grid infrastructures remains difficult for them. The e-infrastructure for biomedical science (e-BioInfra) is a platform with services that shield middleware complexities, in part...
Article
Analyzing Diffusion Tensor Image data of the human brain of large study groups is complex and demands new, sophisticated and computationally intensive pipelines that can efficiently be executed. We present our progress over the past five years in the development and porting of the DTI analysis pipeline to a grid infrastructure. Starting with simple...
Article
Full-text available
Scientific research has become very data and compute intensive because of the progress in data acquisition and measurement devices, which is particularly true in Life Sciences. To cope with this deluge of data, scientists use distributed computing and storage infrastructures. The use of such infrastructures introduces by itself new challenges to th...
Article
Computational neuroscience is a new field of research in which neurodegenerative diseases are studied with the aid of new imaging techniques and computation facilities. Researchers with different expertise collaborate in these studies. A study requires scalable computational and storage capacity and information management facilities to succeed. Man...
Conference Paper
As the focus of e-Science is moving toward the forth paradigm and data intensive science, data access remains dependent on the architecture of the used e-Science infrastructure. Such architecture is in general job-driven, i.e., a (grid) job is a sequence of commands that run on the same worker node. Making use of the infrastructure involves having...
Article
Full-text available
The e-infrastructure for bioscience (e-BioInfra) is a platform integrating various services and middleware to facilitate access to grid resources for biomedical re-searchers at the Academic Medical Center of the University of Amsterdam. In the past six years the user interfaces with the e-BioInfra have evolved from command-line interfaces to a Java...
Article
Full-text available
Grid computing boosts productivity by maximizing resource utilization and simplifying access to resources which are shared among virtual organizations. Recently, the Grid and Web Service communities have established a set of common interests and requirements. The latest version of the Globus Toolkit implements the Web Service Resource Framework (WS...
Article
Full-text available
Many mathematical and computational models have been developed to investigate the complexity of HIV dynamics, immune response and drug therapy. However, there are not many models which consider the dynamics of virus intracellular replication at a single level. We propose a model of HIV intracellular replication where infected cells undergo a single...
Conference Paper
Full-text available
Grid computing is a fundamental technology for large scale distributed resource sharing. Workflow management is becoming one of the most important grid services. A lot of research work has been done on different issues involved in workflow management systems. The focus of this paper is on three areas: workflow partitioning, enactment and data movem...