SWAMI: Integrating Biological Databases and Analysis Tools Within User Friendly Environment

Rifaieh, Rami; Unwin, R. J.; Carver, Jeremy; Miller, Mark A.

doi:10.1007/978-3-540-73255-6_7

Cited by 14 publications

(15 citation statements)

References 16 publications

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“…Workflows are widely used in scientific applications [4,9,16,20,27,28,30]. Workflows orchestrate the execution of tasks by means of a graph that defines the control and data flow between those tasks.…”

Section: Workflow Modelmentioning

confidence: 99%

Efficient lineage tracking for scientific workflows

Heinis

Alonso

2008

Proceedings of the 2008 ACM SIGMOD International Conference on Management of Data

104

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Data lineage and data provenance are key to the management of scientific data. Not knowing the exact provenance and processing pipeline used to produce a derived data set often renders the data set useless from a scientific point of view. On the positive side, capturing provenance information is facilitated by the widespread use of workflow tools for processing scientific data. The workflow process describes all the steps involved in producing a given data set and, hence, captures its lineage. On the negative side, efficiently storing and querying workflow based data lineage is not trivial. All existing solutions use recursive queries and even recursive tables to represent the workflows. Such solutions do not scale and are rather inefficient. In this paper we propose an alternative approach to storing lineage information captured as a workflow process. We use a space and query efficient interval representation for dependency graphs and show how to transform arbitrary workflow processes into graphs that can be stored using such representation. We also characterize the problem in terms of its overall complexity and provide a comprehensive performance evaluation of the approach.

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Section: Workflow Modelmentioning

confidence: 99%

Efficient lineage tracking for scientific workflows

Heinis

Alonso

2008

Proceedings of the 2008 ACM SIGMOD International Conference on Management of Data

104

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“…The CSG consists of two separate, loosely connected software packages: the Web Application (WA) and the Workbench Framework (WF) [25]. The WA is a Java/Struts2 application that creates the graphical user interface in a web browser.…”

Section: Software Architecturementioning

confidence: 99%

Embedding CIPRES science gateway capabilities in phylogenetics software environments

Miller

Schwartz

Pfeiffer

2013

Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery

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The explosive growth in DNA sequence data over the past decade makes it possible to clarify evolutionary relationships among all living things at an unprecedented level of resolution. Phylogenetic inference codes are computationally intensive, so turning this wealth of DNA sequence data into new insights about evolution requires access to high performance computing (HPC) resources. The CIPRES Science Gateway (CSG) was designed to meet this need by providing browser-based access to phylogenetic codes run on XSEDE compute resources. The CSG has lowered the barrier for access to HPC resources for biologists worldwide, supporting more than 6,100 users and enabling more than 600 publications over the past three years. Here we describe plans to create a new set of public CSG web services that can be accessed by any developer through a programmatic interface. These services will allow us to embed access to XSEDE resources within well-established phylogenetics software packages, thus leveraging the investments by developers in creating these rich work environments and by users in learning to use them. The services will also allow any developer with modest scripting skills to access and use CSG capabilities outside of the current browser interface. Our goal in creating these services is to allow scientists to conduct analyses without leaving their preferred work environment, whether that is a complex desktop application, a set of ad hoc scripted workflows, or the existing CSG browser interface. This paper describes the architectural design of the CSG web services, identifies potential issues that will be addressed in exposing programmatic access to HPC resources, and describes plans to embed the CSG web services in eight popular community applications.

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“…Other solutions use a more generic approach to integrate external tools, for example SWAMI 4 . SWAMI tries to provide an integrated environment where biological tools, user data, and public data resources can be easily accessed [4].…”

Section: Related Workmentioning

confidence: 99%

“…SWAMI tries to provide an integrated environment where biological tools, user data, and public data resources can be easily accessed [4]. The used architecture is highly scalable in terms of adding databases and new tools because of using configuration files for providing definitions for tools and data types, and physical descriptions of resource locations.…”

Section: Related Workmentioning

confidence: 99%

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A flexible statistics web processing service - Added value for information systems for experiment data

Heimann

Nieschulze

König‐Ries

2010

Journal of Integrative Bioinformatics

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SummaryData management in the life sciences has evolved from simple storage of data to complex information systems providing additional functionalities like analysis and visualization capabilities, demanding the integration of statistical tools. In many cases the used statistical tools are hard-coded within the system. That leads to an expensive integration, substitution, or extension of tools because all changes have to be done in program code. Other systems are using generic solutions for tool integration but adapting them to another system is mostly rather extensive work. This paper shows a way to provide statistical functionality over a statistics web service, which can be easily integrated in any information system and set up using XML configuration files. The statistical functionality is extendable by simply adding the description of a new application to a configuration file. The service architecture as well as the data exchange process between client and service and the adding of analysis applications to the underlying service provider are described. Furthermore a practical example demonstrates the functionality of the service.

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SWAMI: Integrating Biological Databases and Analysis Tools Within User Friendly Environment

Cited by 14 publications

References 16 publications

Efficient lineage tracking for scientific workflows

Efficient lineage tracking for scientific workflows

Embedding CIPRES science gateway capabilities in phylogenetics software environments

A flexible statistics web processing service - Added value for information systems for experiment data

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