Abel W. Lin

University of California, San Diego, San Diego, California, United States

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Publications (18)16.78 Total impact

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    Nucleic Acids Research. 01/2011; 39:546-551.
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    ABSTRACT: The Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA, http://camera.calit2.net/) is a database and associated computational infrastructure that provides a single system for depositing, locating, analyzing, visualizing and sharing data about microbial biology through an advanced web-based analysis portal. CAMERA collects and links metadata relevant to environmental metagenome data sets with annotation in a semantically-aware environment allowing users to write expressive semantic queries against the database. To meet the needs of the research community, users are able to query metadata categories such as habitat, sample type, time, location and other environmental physicochemical parameters. CAMERA is compliant with the standards promulgated by the Genomic Standards Consortium (GSC), and sustains a role within the GSC in extending standards for content and format of the metagenomic data and metadata and its submission to the CAMERA repository. To ensure wide, ready access to data and annotation, CAMERA also provides data submission tools to allow researchers to share and forward data to other metagenomics sites and community data archives such as GenBank. It has multiple interfaces for easy submission of large or complex data sets, and supports pre-registration of samples for sequencing. CAMERA integrates a growing list of tools and viewers for querying, analyzing, annotating and comparing metagenome and genome data.
    Nucleic Acids Research 11/2010; 39(Database issue):D546-51. · 8.81 Impact Factor
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    ABSTRACT: The objective of the CAMERA project is to provide a facility to enable researchers to achieve revolutionary advances in the understanding of marine microbial ecology.
    LPI Contributions. 04/2010;
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    ABSTRACT: Over the last decade, workflows have been established as a mechanism for scientific developers to create simplified views of complex scientific processes. However, there is a need for a comprehensive system architecture to link scientific developers creating workflows with researchers launching workflows in large scale computing environments. We present the architecture for the CAMERA 2.0 Cyber infrastructure platform that provides a scaffold where workflows can be uploaded into the system, and user interface components for launching and viewing results are automatically generated. In CAMERA 2.0, scientific developers and metagenomics researchers seamlessly collaborate to (i) wrap data-analysis software applications and heterogeneous tools as Resource Oriented Architecture (ROA) components integrating them using scientific workflows; (ii) publish and run scientific workflows via dynamically generated uniform portal interfaces; (iii) map heterogeneous workflow products to provenance and CAMERA semantic database through a transformation component, to save output data resulting from workflow runs based on this mapping; (iv) record and visualize the provenance of all workflow run-related data and processes; and (v) conduct queries across multiple workflow executions and link these workflow executions to each other through data and provenance related to these runs. Furthermore, workflows added to CAMERA also have access to a variety of physical resources for computation and data management. Here, we demonstrate the usability of this framework with some of the developed metagenomics workflows.
    Services (SERVICES-1), 2010 6th World Congress on; 01/2010
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    ABSTRACT: Community Cyber infrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA) is an eScience project to enable the microbial ecology community in managing the challenges of metagenomics analysis. CAMERA supports extensive metadata based data acquisition and access, as well as execution of metagenomics experiments through standard and customized scientific workflows. Users can use a wide range of community analysis tools to select and invoke integrated annotation of genomic datasets. Users can also search and sort information based on selected metadata over the underlying semantic database. We present the semantic data model of CAMERA and its integration with scientific workflow execution information. We also describe how this model is used to interlink related workflows, where outputs of previous workflow executions can be used as inputs by subsequent workflow executions. We demonstrate the effectiveness of our model and approach through scenarios built on currently supported CAMERA workflows and analysis.
    2010 Sixth IEEE International Conference on e-Science Workshops. 01/2010;
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    ABSTRACT: Two devastating hurricanes ripped across the Gulf Coast of the United States during 2005. The effects of Hurricane Katrina were especially severe: the human and environmental health impacts on New Orleans, Louisiana, and other Gulf Coast communities will be felt for decades to come. The Federal Emergency Management Agency (FEMA) estimates that Katrina's destruction disrupted the lives of roughly 650,000 Americans. Over 1,300 people died. The projected economic costs for recovery and reconstruction are likely to exceed $125 billion. The NIEHS (National Institute of Environmental Health Sciences) Portal aims to provide decision makers with the data, information, and the tools they need to a) monitor human and environmental health impacts of disasters; b) assess and reduce human exposures to contaminants; and c) develop science-based remediation, rebuilding, and repopulation strategies. The NIEHS Portal combines advances in geographic information systems (GIS), data mining/integration, and visualization technologies through new forms of grid-based (distributed, web-accessible) cyberinfrastructure. The scale and complexity of the problems presented by Hurricane Katrina made it evident that no stakeholder alone could tackle them and that there is a need for greater collaboration. The NIEHS Portal provides a collaboration-enabling, information-laden base necessary to respond to environmental health concerns in the Gulf Coast region while advancing integrative multidisciplinary research. The NIEHS Portal is poised to serve as a national resource to track environmental hazards following natural and man-made disasters, focus medical and environmental response and recovery resources in areas of greatest need, and function as a test bed for technologies that will help advance environmental health sciences research into the modern scientific and computing era.
    Environmental Health Perspectives 05/2007; 115(4):564-71. · 7.26 Impact Factor
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    ABSTRACT: The advent of “Grids,” or Grid computing, has led to a fundamental shift in the development of applications for managing and performing computational or data-intensive analyses. A current challenge faced by the Grid community entails modeling the work patterns of domain or bench scientists and providing robust solutions utilizing distributed infrastructures. These challenges spawned efforts to develop “workflows” to manage programs and data on behalf of the end user. The technologies come from multiple scientific fields, often with disparate definitions, and have unique advantages and disadvantages, depending on the nature of the scientific process in which they are used. In this chapter, we argue that to maximize the impact of these efforts, there is value in promoting the use of workflows within a tiered, hierarchical structure where each of these emerging workflow pieces are interoperable. We present workflow models of the Telescience™ Project1 and BIRN2 architectures as frameworks that manage multiple tiers of workflows to provide tailored solutions for end-to-end scientific processes.
    12/2006: pages 109-125;
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    ABSTRACT: At iGrid 2005 we demonstrated the transparent operation of a biology experiment on a test-bed of globally distributed visualization, storage, computational, and network resources. These resources were bundled into a unified platform by utilizing dynamic lambda allocation, high bandwidth protocols for optical networks, a Distributed Virtual Computer (DVC) [N. Taesombut, A. Chien, Distributed Virtual Computer (DVC): Simplifying the development of high performance grid applications, in: Proceedings of the Workshop on Grids and Advanced Networks, GAN 04, Chicago, IL, April 2004 (held in conjunction with the IEEE Cluster Computing and the Grid (CCGrid2004) Conference)], and applications running over the Scalable Adaptive Graphics Environment (SAGE) [L. Renambot, A. Rao, R. Singh, B. Jeong, N. Krishnaprasad, V. Vishwanath, V. Chandrasekhar, N. Schwarz, A. Spale, C. Zhang, G. Goldman, J. Leigh, A. Johnson, SAGE: The Scalable Adaptive Graphics Environment, in: Proceedings of WACE 2004, 23–24 September 2004, Nice, France, 2004]. Using these layered technologies we ran a multi-scale correlated microscopy experiment [M.E. Maryann, T.J. Deerinck, N. Yamada, E. Bushong, H. Ellisman Mark, Correlated 3D light and electron microscopy: Use of high voltage electron microscopy and electron tomography for imaging large biological structures, Journal of Histotechnology 23 (3) (2000) 261–270], where biologists imaged samples with scales ranging from 20X to 5000X in progressively increasing magnification. This allows the scientists to zoom in from entire complex systems such as a rat cerebellum to individual spiny dendrites. The images used spanned multiple modalities of imaging and specimen preparation, thus providing context at every level and allowing the scientists to better understand the biological structures. This demonstration attempts to define an infrastructure based on OptIPuter components which would aid the development and design of collaborative scientific experiments, applications and test-beds and allow the biologists to effectively use the high resolution real estate of tiled displays.
    Future Generation Computer Systems. 01/2006;
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    ABSTRACT: Electron tomography is a powerful tool for deriving three-dimensional (3D) structural information about biological systems within the spatial scale spanning 1 nm<sup>3</sup> and 10 mm<sup>3</sup>. With this technique, it is possible to derive detailed models of sub-cellular components such as organelles and synaptic complexes and to resolve the 3D distribution of their protein constituents in situ. Due in part to exponentially growing raw data-sizes, there continues to be a need for the increased integration of high-performance computing (HPC) and grid technologies with traditional electron tomography processes to provide faster data processing throughput. This is increasingly relevant because emerging mathematical algorithms that provide better data fidelity are more computationally intensive for larger raw data sizes. Progress has been made towards the transparent use of HPC and grid tools for launching scientific applications without passing on the necessary administrative overhead and complexity (resource administration, authentication, scheduling, data delivery) to the non-computer scientist end-user. There is still a need, however, to simplify the use of these tools for applications developers who are developing novel algorithms for computation. Here we describe the architecture of the Telescience project (http://telescience.ucsd.edu), specifically the use of layered workflow technologies to parallelize and execute scientific codes across a distributed and heterogeneous computational resource pool (including resources from the TeraGrid and OptlPuter projects) without the need for the application developer to understand the intricacies of the grid
    Challenges of Large Applications in Distributed Environments, 2006 IEEE; 01/2006
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    ABSTRACT: The Cybermedia Center (CMC), Osaka University, is a research institution that offers knowledge and technology resources obtained from advanced researches in the areas of large-scale computation, information and communication, multimedia content and education. Currently, CMC is involved in Japanese national Grid projects such as JGN II (Japan Gigabit Network), NAREGI and BioGrid. Not limited to Japan, CMC also actively takes part in international activities such as PRAGMA. In these projects and international collaborations, CMC has developed a Grid system that allows scientists to perform their analysis by remote-controlling the world's largest ultra-high voltage electron microscope located in Osaka University. In another undertaking, CMC has assumed a leadership role in BioGrid by sharing its experiences and knowledge on the system development for the area of biology. In this paper, we will give an overview of the BioGrid project and introduce the progress of the Telescience unit, which collaborates with the Telescience Project led by the National Center for Microscopy and Imaging Research (NCMIR). Furthermore, CMC collaborates with seven Computing Centers in Japan, NAREGI and National Institute of Informatics to deploy PKI base authentication infrastructure. The current status of this project and future collaboration with Grid Projects will be delineated in this paper.
    Journal of Clinical Monitoring and Computing 11/2005; 19(4-5):279-94. · 0.71 Impact Factor
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    ABSTRACT: The Telescience Project™ (https://telescience.ucsd.edu) aims to provide a complete, end-to-end, single sign-on solution for biomedical image analysis and structure-function correlation. Telescience merges advanced solutions for remote instrumentation (via Telemicroscopy™), distributed data computation and storage, and transparent access to federated databases of cell structure. Here, we describe the Grid-based system architecture that enables the Telescience Project. This Grid service architecture provides a fabric for seamless interoperability among user interfaces (Web portals and applications) and externally addressable Grid resources (instruments and computers). Although many software components and tools provide some capabilities relating to enabling usable scientific grids, few systems offer the required complete interactions with grid infrastructures "out of the box". Significant time and effort, therefore, are needed for software evaluation, testing, and integration. Here we describe an emerging layer of the overall Grid infrastructure that provides a complete solution for application and portal developers to interact with core Grid functionality.
    18th IEEE Symposium on Computer-Based Medical Systems (CBMS 2005), 23-24 June 2005, Dublin, Ireland; 01/2005
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    ABSTRACT: For over the last decade, researchers at the National Center for Microscopy and Imaging Research (NCMIR, http://ncrrdr.ucsd.edu) have been developing and implementing novel technologies to propel collaborative research. NCMIR has built flexible high throughput, cyber infrastructure environments which connect researchers to advanced imaging instruments datagrids and computational grids. Through the integration of pioneering research in remote instrumentation research (known as Telemicroscopy™) and grid based distributed computing and data management, this group demonstrated this vision in the context of The Telescience Project (https://telescience.ucsd.edu). Telescience provides an end-to-end, single sign-on solution for biomedical image analysis and structure-function correlation that integrates users with resources and applications with unified security and without prohibitive complexity. Here, we describe the flattening and generalization of the layers of software that make up the Grid-based system architecture of the project. In particular, we focus on the maturation and generalization of the architecture, including the development of an Application to middleware interaction component (ATOMIC) services fabric that streamlines application integration with core grid middleware. This broadening of the overall grid service architecture is the product of over 6 years of user-developer iterative software refinement cycles which have resulted in a suite of Telescience Tools that provide generalized solutions for increasing the interoperability of user interfaces (Web portals and applications) and externally addressable grid resources (instruments and computers).
    First International Conference on e-Science and Grid Technologies (e-Science 2005), 5-8 December 2005, Melbourne, Australia; 01/2005
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    ABSTRACT: Scientific imaging instruments are used in a variety of disciplines to gather vital data for research and study. Specifically, in the biomedical field various types of biological imaging instruments, such as electron microscopes and light microscopes, are used everyday to acquire 2D and 3D datasets for further understanding of biological structures. Remote operation or "teleoperation" of instruments has become a popular solution for research scientists to acquire and share data across research domains separated by geographical barriers. A generalized software architecture solution is presented in this paper to use emerging software technologies to develop a reusable framework to easily integrate instruments for remote-operation in a safe and secure fashion. Web services have emerged as a popular technology to provide software applications with a framework to achieve interoperability and integration with other applications. This generalized software architecture was developed to take advantage of Web service middleware technology and to provide a solution for easily plugging in scientific imaging instruments for teleoperation. The architecture has also incorporated grid technology to achieve a more scalable and robust solution for handling the enormous data sets produced from these instruments. Finally a set of client libraries is presented to demonstrate a useful API for developers to quickly develop a graphical user interface to communicate and acquire data from these instruments.
    First International Conference on e-Science and Grid Technologies (e-Science 2005), 5-8 December 2005, Melbourne, Australia; 01/2005
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    ABSTRACT: The Cybermedia Center, Osaka University (CMC) is a research institution that offers resource with knowledge and technology of all advanced research in the area of large-scale computation, information and communication, multimedia content and education. Currently, CMC involves in Japanese national grid projects such as JGN II (Japan Gigabit Network) and BioGrid. Not limited to Japan, CMC also takes an active part in international activities such as PRAGMA. In these projects and international collaboration, CMC has developed the Grid system that allows scientists to perform their analysis by remotely controlling the world-largest ultra-high voltage electron microscope located in Osaka University. On the other, CMC has been taking a leading role at BioGrid sharing experience and knowledge on the system development for biology. In this paper, we will describe BioGrid project overview and introduce progress of Telescience group which collaborates with Telescience project lead by National Center for Microscopy and Imaging Research (NCMIR).
    5th International Symposium on Cluster Computing and the Grid (CCGrid 2005), 9-12 May, 2005, Cardiff, UK; 01/2005
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    ABSTRACT: Electron tomography is a powerful technique for deriving 3D structural information from biological specimens. As advanced instrumentation, networking, and grid computing are applied to electron tomography and biological sciences in general, much work is needed to integrate and coordinate these advanced technologies in a transparent way to deliver them to the end user. The Telescience Portal (http://gridport.npaci.edu/Telescience) is a web-based solution for end-to-end electron tomography that centralizes applications and seamlessly interfaces with the grid to accelerate the throughput of data results. In this paper we will describe the architecture and design of the Telescience Portal in the context of our experiences leading up to and including the iGrid2002 workshop. We will examine the lessons learned in developing the production Telescience environment, leveraging a successful international collaboration with groups in Japan and Taiwan, building end-to-end native IPv6 networks across continents, and examining IPv6 enabled mechanisms for transferring large data from two unique, remotely accessible high performance scientific instruments. Traditional computer science communities develop next generation technologies. Applications like Telescience drive these next generation technologies into production quality applications for everyday research needs.
    Future Generation Computer Systems. 08/2003;
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    ABSTRACT: Electron tomography is a powerful technique for deriving 3D structural information from biological specimens. As advanced instrumentation, networking, and grid computing are applied to electron tomography and biological sciences in general, much work is needed to integrate and coordinate these advanced technologies in a transparent way to deliver them to the end user. The Telescience Portal (http://gridport.npaci.edu/Telescience) is a web-based solution for end-to-end electron tomography that centralizes applications and seamlessly interfaces with the grid to accelerate the throughput of data results. In this paper we will describe the architecture and design of the Telescience Portal in the context of our experiences leading up to and including the iGrid2002 workshop. We will examine the lessons learned in developing the production Telescience environment, leveraging a successful international collaboration with groups in Japan and Taiwan, building end-to-end native IPv6 networks across continents, and examining IPv6 enabled mechanisms for transferring large data from two unique, remotely accessible high performance scientific instruments. Traditional computer science communities develop next generation technologies. Applications like Telescience drive these next generation technologies into production quality applications for everyday research needs.
    Future Generation Comp. Syst. 01/2003; 19:1031-1039.
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    ABSTRACT: Electron tomography is a powerful tool for deriving three-dimensional (3D) structural information about biological systems within the spatial scale spanning 1 nm3 and10 mm3: With this technique, it is possible to derive detailed models of subcellular components such as organelles andsynaptic complexes andto resolve the 3D distribution of their protein constituents in situ. While there continues to be progress towards the integration of high-performance computing technologies with traditional electron tomography processes, there is a significant needfor more transparent integration with applications andto minimize the administrative overhead and complexity (resource administration, authentication, scheduling, data delivery) passed on to the non- computer scientist enduser. Here we present the ''Telescience Portal'' ( https://gridport.npaci.edu/Telescience) as an example of a fully integrated, web-based solution for performing end-to-end electron tomography. More than just a collection of individual applications, the Portal provides a transparent workflow, where simple intuitive interfaces for grid-enabled parallel computation, resource scheduling, remote instrumentation, advanced image processing and visualization, access to distributed/federated databases, and network-enabled data management and archival are tightly coupled within a secure environment which promotes increasedcollaboration between researchers. This tightly integratedTelescience system is a test-bedapplication for using grid resources to accelerate the throughput of data acquisition and processing, increase access to scarce and/or expensive instrumentation, and improve the accuracy of derived data products.
    J. Parallel Distrib. Comput. 01/2003; 63:539-550.
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    ABSTRACT: The Telescience™ Project (https://telescience.ucsd.edu) provides a complete, end-to-end, single sign-on solution enabling remote and collaborative biomedical image analysis for structure-function correlation studies. The service based system architecture that enables the Telescience Project provides a fabric for seamless interoperability among user interfaces (web portals and applications) and externally addressable Grid resources (instruments and computers). The Telescience architecture addresses an imminent need for domain scientists: the amount of data that is possible to collect from instruments is out-pacing the traditional methods use to compute, analyze, and collaborate upon that data. Current solutions call for a "Grid-based cyber-infrastructure" managed resources to solve the problems of such extreme amounts of data. The degree to which these resources can be effectively utilized, however, is hampered by the user overhead required for the current generation of scientific analysis applications and programs to natively mesh with the emerging infrastructure. The Telescience Applications to Middleware Interaction Components (ATOMIC) bundles to ease that overhead for both users and developers alike. Here we describe the implementation of Telescience ATOMIC to enable scientific researchers to transparently connect to large scale, national cyber- infrastructure providers.