Abstract We are at the beginning of the new era of``e-science''. Researchers in many areas of sci... more Abstract We are at the beginning of the new era of``e-science''. Researchers in many areas of science, especially in astrophysics, physics, climatology and biology, are now facing tremendous increases in data volumes, as well as corresponding data analysis tools. These increased data and tools demand a better framework to manage the new generation scientific research cycle from data capture, data curation to data analysis, data query and data visualization.
SUMMARY Pheromones trigger reproductive responses of many marine organisms, but little is known a... more SUMMARY Pheromones trigger reproductive responses of many marine organisms, but little is known about how pheromones mediate mate-finding behavior in the marine environment. This paper investigates whether the tetrapeptide nereithione (cysteine-glutathione disulfide), known to be released by females of the polychaete Nereis succinea to trigger spawning in male N. succinea, can also be used at lower concentrations to guide males to the females.
Abstract Scientific workflows have recently emerged as a new paradigm for scientists to formalize... more Abstract Scientific workflows have recently emerged as a new paradigm for scientists to formalize and structure complex and distributed scientific processes to enable and accelerate many scientific discoveries. In contrast to business workflows, which are typically control flow oriented, scientific workflows tend to be dataflow oriented, introducing a new set of requirements for system development. These requirements demand a new architectural design for scientific workflow management systems (SWFMSs).
Abstract Provenance management has become increasingly important to support scientific discovery ... more Abstract Provenance management has become increasingly important to support scientific discovery reproducibility, result interpretation, and problem diagnosis in scientific workflow environments. This paper proposes an approach to provenance management that seamlessly integrates the interoperability, extensibility, and reasoning advantages of semantic Web technologies with the storage and querying power of an RDBMS.
Abstract In this demo, we present the current status of our visual scientific workflow management... more Abstract In this demo, we present the current status of our visual scientific workflow management system called VIEW, highlighting the following two features:(i) the use of Semantic Web technology to represent, store, and query provenance metadata, leading to an interoperable and extensible provenance system, and (ii) the support of visualization of various provenance graphs and intermediate or final data products of a workflow run in the form of medical images or 3-D graphical models.
Pheromones can be used as attractants for the opposite sex in many environments; 23 however, litt... more Pheromones can be used as attractants for the opposite sex in many environments; 23 however, little is known about the search strategies employed in responding to 24 pheromones in the marine environment. The spawning behavior of males of the 25 polychaete Nereis succinea is known to be triggered at close range by a high 26 concentration (>~ 10-7 M) of pheromone, cysteine glutathione disulfide (CSSG), 27 released by females.
Abstract Recently, there has been an increasing need in scientific workflows to solve the shimmin... more Abstract Recently, there has been an increasing need in scientific workflows to solve the shimming problem, the use of a special kind of adaptors, called shims, to link related but incompatible workflow tasks. However, existing techniques produce scientific workflows that are cluttered with many visible shims, which distract a scientist's focus on functional components.
Abstract Scientific workflow has recently become an enabling technology to automate and speed up ... more Abstract Scientific workflow has recently become an enabling technology to automate and speed up the scientific discovery process. Although several scientific workflow management systems (SWFMSs) have been developed, a formal scientific workflow composition model in which workflow constructs are fully compositional one with another is still missing.
Scientific workflows have gained great momentum in recent years due to their critical roles in e-... more Scientific workflows have gained great momentum in recent years due to their critical roles in e-Science and cyberinfrastructure applications. However, some tasks of a scientific workflow might fail during execution. A domain scientist might require a region of a scientific workflow to be “atomic”. Data provenance, which determines the source data that are used to produce a data item, is also essential to scientific workflows.
Abstract Collaborative scientific workflow composition has recently been proposed to support coll... more Abstract Collaborative scientific workflow composition has recently been proposed to support collaborative scientific research projects, which require intensive collaboration among scientists with diverse expertise. A collaborative scientific workflow management system allows participating scientists to design and compose common scientific workflows concurrently.
Abstract. Provenance management has become increasingly important to support scientific discovery... more Abstract. Provenance management has become increasingly important to support scientific discovery reproducibility, result interpretation, and problem diagnosis in scientific workflow environments. This paper proposes an approach to provenance management that seamlessly integrates the interoperability, extensibility, and reasoning advantages of Semantic Web technologies with the storage and querying power of an RDBMS.
Clustering has been one of the most popular approaches used in gene expression data analysis. A c... more Clustering has been one of the most popular approaches used in gene expression data analysis. A clustering method is typically used to partition genes according to their similarity of expression under different conditions. However, it is often the case that some genes behave similarly only on a subset of conditions and their behavior is uncorrelated over the rest of the conditions. As traditional clustering methods will fail to identify such gene groups, the biclustering paradigm is introduced recently to overcome this limitation.
Today many significant scientific discoveries are achieved through complex and distributed scient... more Today many significant scientific discoveries are achieved through complex and distributed scientific computations that are structured and represented as scientific workflows. Although atomicity is a well studied topic in transaction processing and business workflows, such an important capability needs to be revisited in a scientific workflow environment. Firstly, the semantics of atomicity needs to be defined in a dataflow-oriented scientific workflow model, particularly for pipelined execution of hierarchical scientific workflows.
Provenance metadata has become increasingly important to support scientific discovery reproducibi... more Provenance metadata has become increasingly important to support scientific discovery reproducibility, result interpretation, and problem diagnosis in scientific workflow environments. The provenance management problem concerns the efficiency and effectiveness of the modeling, recording, representation, integration, storage, and querying of provenance metadata.
Abstract We are at the beginning of the new era of``e-science''. Researchers in many areas of sci... more Abstract We are at the beginning of the new era of``e-science''. Researchers in many areas of science, especially in astrophysics, physics, climatology and biology, are now facing tremendous increases in data volumes, as well as corresponding data analysis tools. These increased data and tools demand a better framework to manage the new generation scientific research cycle from data capture, data curation to data analysis, data query and data visualization.
SUMMARY Pheromones trigger reproductive responses of many marine organisms, but little is known a... more SUMMARY Pheromones trigger reproductive responses of many marine organisms, but little is known about how pheromones mediate mate-finding behavior in the marine environment. This paper investigates whether the tetrapeptide nereithione (cysteine-glutathione disulfide), known to be released by females of the polychaete Nereis succinea to trigger spawning in male N. succinea, can also be used at lower concentrations to guide males to the females.
Abstract Scientific workflows have recently emerged as a new paradigm for scientists to formalize... more Abstract Scientific workflows have recently emerged as a new paradigm for scientists to formalize and structure complex and distributed scientific processes to enable and accelerate many scientific discoveries. In contrast to business workflows, which are typically control flow oriented, scientific workflows tend to be dataflow oriented, introducing a new set of requirements for system development. These requirements demand a new architectural design for scientific workflow management systems (SWFMSs).
Abstract Provenance management has become increasingly important to support scientific discovery ... more Abstract Provenance management has become increasingly important to support scientific discovery reproducibility, result interpretation, and problem diagnosis in scientific workflow environments. This paper proposes an approach to provenance management that seamlessly integrates the interoperability, extensibility, and reasoning advantages of semantic Web technologies with the storage and querying power of an RDBMS.
Abstract In this demo, we present the current status of our visual scientific workflow management... more Abstract In this demo, we present the current status of our visual scientific workflow management system called VIEW, highlighting the following two features:(i) the use of Semantic Web technology to represent, store, and query provenance metadata, leading to an interoperable and extensible provenance system, and (ii) the support of visualization of various provenance graphs and intermediate or final data products of a workflow run in the form of medical images or 3-D graphical models.
Pheromones can be used as attractants for the opposite sex in many environments; 23 however, litt... more Pheromones can be used as attractants for the opposite sex in many environments; 23 however, little is known about the search strategies employed in responding to 24 pheromones in the marine environment. The spawning behavior of males of the 25 polychaete Nereis succinea is known to be triggered at close range by a high 26 concentration (>~ 10-7 M) of pheromone, cysteine glutathione disulfide (CSSG), 27 released by females.
Abstract Recently, there has been an increasing need in scientific workflows to solve the shimmin... more Abstract Recently, there has been an increasing need in scientific workflows to solve the shimming problem, the use of a special kind of adaptors, called shims, to link related but incompatible workflow tasks. However, existing techniques produce scientific workflows that are cluttered with many visible shims, which distract a scientist's focus on functional components.
Abstract Scientific workflow has recently become an enabling technology to automate and speed up ... more Abstract Scientific workflow has recently become an enabling technology to automate and speed up the scientific discovery process. Although several scientific workflow management systems (SWFMSs) have been developed, a formal scientific workflow composition model in which workflow constructs are fully compositional one with another is still missing.
Scientific workflows have gained great momentum in recent years due to their critical roles in e-... more Scientific workflows have gained great momentum in recent years due to their critical roles in e-Science and cyberinfrastructure applications. However, some tasks of a scientific workflow might fail during execution. A domain scientist might require a region of a scientific workflow to be “atomic”. Data provenance, which determines the source data that are used to produce a data item, is also essential to scientific workflows.
Abstract Collaborative scientific workflow composition has recently been proposed to support coll... more Abstract Collaborative scientific workflow composition has recently been proposed to support collaborative scientific research projects, which require intensive collaboration among scientists with diverse expertise. A collaborative scientific workflow management system allows participating scientists to design and compose common scientific workflows concurrently.
Abstract. Provenance management has become increasingly important to support scientific discovery... more Abstract. Provenance management has become increasingly important to support scientific discovery reproducibility, result interpretation, and problem diagnosis in scientific workflow environments. This paper proposes an approach to provenance management that seamlessly integrates the interoperability, extensibility, and reasoning advantages of Semantic Web technologies with the storage and querying power of an RDBMS.
Clustering has been one of the most popular approaches used in gene expression data analysis. A c... more Clustering has been one of the most popular approaches used in gene expression data analysis. A clustering method is typically used to partition genes according to their similarity of expression under different conditions. However, it is often the case that some genes behave similarly only on a subset of conditions and their behavior is uncorrelated over the rest of the conditions. As traditional clustering methods will fail to identify such gene groups, the biclustering paradigm is introduced recently to overcome this limitation.
Today many significant scientific discoveries are achieved through complex and distributed scient... more Today many significant scientific discoveries are achieved through complex and distributed scientific computations that are structured and represented as scientific workflows. Although atomicity is a well studied topic in transaction processing and business workflows, such an important capability needs to be revisited in a scientific workflow environment. Firstly, the semantics of atomicity needs to be defined in a dataflow-oriented scientific workflow model, particularly for pipelined execution of hierarchical scientific workflows.
Provenance metadata has become increasingly important to support scientific discovery reproducibi... more Provenance metadata has become increasingly important to support scientific discovery reproducibility, result interpretation, and problem diagnosis in scientific workflow environments. The provenance management problem concerns the efficiency and effectiveness of the modeling, recording, representation, integration, storage, and querying of provenance metadata.
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