Chandrika Sivaramakrishnan

Velo: A Knowledge-Management Framework for Modeling and Simulation

Velo is a reusable, domain-independent knowledge-management infrastructure for modeling and simulation. Velo leverages, integrates, and extends Web-based open source collaborative and data-management technologies to create a scalable and flexible core platform tailored to specific scientific domains. As the examples here describe, Velo has been used in both the carbon sequestration and climate modeling domains.

An Extensible, Scalable Architecture for Managing Bioinformatics Data and Analyses

Systems biology research demands the availability of tools and technologies that span a comprehensive range of computational capabilities, including data management, transfer, processing, integration, and interpretation. To address these needs, we have created the bioinformatics resource manager (BRM), a scalable, flexible, and easy to use tool for biologists to undertake complex analyses. This paper describes the underlying software architecture of the BRM that integrates multiple commodity platforms to provide a highly extensible and scalable software infrastructure for bioinformatics. The architecture integrates a J2EE 3-tier application with an archival experimental data management system, the GAGGLE framework for desktop tool integration, and the MeDICi integration framework for high-throughput data analysis workflows. This architecture facilitates a systems biology software solution that enables the entire spectrum of scientific activities, from experimental data access to high throughput processing and analysis of data for biologists and experimental scientists.

Kepler + MeDICi Service-Oriented Scientific Workflow Applications

Scientific applications are often structured as workflows that execute a series of interdependent, distributed software modules to analyze large data sets. The order of execution of the tasks in a workflow is commonly controlled by complex scripts, which over time become difficult to maintain and evolve. In this paper, we describe how we have integrated the Kepler scientific workflow platform with the MeDICi Integration Framework, which has been specifically designed to provide a standards-based, lightweight and flexible integration platform. The MeDICi technology provides a scalable, component-based architecture that efficiently handles integration with heterogeneous, distributed software systems. This paper describes the MeDICi Integration Framework and the mechanisms we used to integrate MeDICi components with Kepler workflow actors. We illustrate this solution with a workflow application for an atmospheric sciences application. The resulting solution promotes a strong separation of concerns, simplifying the Kepler workflow description and promoting the creation of a reusable collection of components available for other workflow applications in this domain.

A high-performance workflow system for subsurface simulation

The U.S. Department of Energy (DOE) recently invested in developing a numerical modeling toolset called ASCEM (Advanced Simulation Capability for Environmental Management) to support modeling analyses at legacy waste sites. This investment includes the development of an open-source user environment called Akuna that manages subsurface simulation workflows. Core toolsets accessible through the Akuna user interface include model setup, grid generation, sensitivity analysis, model calibration, and uncertainty quantification. Additional toolsets are used to manage simulation data and visualize results. This new workflow technology is demonstrated by streamlining model setup, calibration, and uncertainty analysis using high performance computation for the BC Cribs Site, a legacy waste area at the Hanford Site in Washington State. For technetium-99 transport, the uncertainty assessment for potential remedial actions (e.g., surface infiltration covers) demonstrates that using multiple realizations of the geologic conceptual model results in greater variation in concentration predictions than when a single model is used. Akuna provides integrated toolset needed for subsurface modeling workflow.Akuna streamlines process of executing multiple simulations in HPC environment.Akuna provides visualization tools for spatial and temporal data.Example application demonstrates risk with remediation impacting infiltration rates.

Velo: riding the knowledge management wave for simulation and modeling

Modern scientific enterprises are inherently knowledge-intensive. In general, scientific studies in domains such as geosciences, climate, and biology require the acquisition and manipulation of large amounts of experimental and field data in order to create inputs for large-scale computational simulations. The results of these simulations must then be analyzed, leading to refinements of inputs and models and additional simulations. Further, these results must be managed and archived to provide justifications for regulatory decisions and publications that are based on these models. In this paper we introduce our Velo framework that is designed as a reusable, domain independent knowledge management infrastructure for modeling and simulation. Velo leverages, integrates, and extends open source collaborative and content management technologies to create a scalable and flexible core platform that can be tailored to specific scientific domains. We describe the architecture of Velo for managing and associating the various types of data that are used and created in modeling and simulation projects, as well as the framework for integrating domain-specific tools. To demonstrate a realization of Velo, we describe the Geologic Sequestration Software Suite (GS3) that has been developed to support geologic sequestration modeling. This provides a concrete example of the inherent extensibility and utility of our approach.

Development of Technology Readiness Level (TRL) Metrics and Risk Measures

This is an internal project milestone report to document the CCSI Element 7 teams progress on developing Technology Readiness Level (TRL) metrics and risk measures. In this report, we provide a brief overview of the current technology readiness assessment research, document the development of technology readiness levels (TRLs) specific to carbon capture technologies, describe the risk measures and uncertainty quantification approaches used in our research, and conclude by discussing the next steps that the CCSI Task 7 team aims to accomplish.

Scientist-Centered Workflow Abstractions via Generic Actors, Workflow Templates, and Context-Awareness for Groundwater Modeling and Analysis

A drawback of existing scientific workflow systems is the lack of support to domain scientists in designing and executing their own scientific workflows. Many domain scientists avoid developing and using workflows because the basic objects of workflows are too low-level and high-level tools and mechanisms to aid in workflow construction and use are largely unavailable. In our research, we are prototyping higher-level abstractions and tools to better support scientists in their workflow activities. Specifically, we are developing generic actors that provide abstract interfaces to specific functionality, workflow templates that encapsulate workflow and data patterns that can be reused and adapted by scientists, and context-awareness mechanisms to gather contextual information from the workflow environment on behalf of the scientist. To evaluate these scientist-centered abstractions on real problems, we apply them to construct and execute scientific workflows in the specific domain area of groundwater modeling and analysis.

GS3: A Knowledge Management Architecture for Collaborative Geologic Sequestration Modeling

Modern scientific enterprises are inherently knowledge-intensive. In general, scientific studies in domains such as geoscience, chemistry, physics and biology require the acquisition and manipulation of large amounts of experimental and field data in order to create inputs for large-scale computational simulations. The results of these simulations must then be analyzed, leading to refinements of inputs and models and further simulations. In this paper we describe our efforts in creating a knowledge management platform to support collaborative, wide-scale studies in the area of geologic sequestration modeling. The platform, known as GS3 (Geologic Sequestration Software Suite), exploits and integrates off-the-shelf software components including semantic wikis, content management systems and open source middleware to create the core architecture. We then extend the wiki environment to support the capture of provenance, the ability to incorporate various analysis tools, and the ability to launch simulations on supercomputers. The paper describes the key components of GS3 and demonstrates its use through illustrative examples. We conclude by assessing the suitability of our approach for geologic sequestration modeling and generalization to other scientific problem domains.

Knowledge annotations in scientific workflows: an implementation in Kepler

Scientific research products are the result of long-term collaborations between teams. Scientific workflows are capable of helping scientists in many ways including collecting information about how research was conducted (e.g., scientific workflow tools often collect and manage information about datasets used and data transformations). However, knowledge about why data was collected is rarely documented in scientific workflows. In this paper we describe a prototype system built to support the collection of scientific expertise that influences scientific analysis. Through evaluating a scientific research effort underway at the Pacific Northwest National Laboratory, we identified features that would most benefit PNNL scientists in documenting how and why they conduct their research, making this information available to the entire team. The prototype system was built by enhancing the Kepler Scientific Workflow System to create knowledge-annotated scientific workflows and to publish them as semantic annotations.

A collaborative extensible user environment for simulation and knowledge management

In scientific simulation, scientists use measured data to create numerical models, execute simulations and analyze results from advanced simulators executing on high performance computing platforms. This process usually requires a team of scientists collaborating on data collection, model creation and analysis, and on authorship of publications and data. This paper shows that scientific teams can benefit from a user environment called Akuna that permits subsurface scientists in disparate locations to collaborate on numerical modeling and analysis projects. The Akuna application is built on the Velo software platform that provides a desktop client environment for conducting and analyzing simulations, a knowledge management server for project and data management, annotation, collaboration, job execution, and event-based communication, and a Tool Integration Framework for connecting any type of software application - from desktop tools to simulator codes - into the Velo framework. Akuna is a customized Velo deployment that is tailored for subsurface modeling and is designed to support any type of simulator. Simulator extensibility is achieved by providing a customizable suite of desktop tools for simulator setup and execution that utilize Velos Tool Integration Framework and are based on data-driven user interface generation. This paper describes the collaborative aspects of the Velo platform, how Velo was customized for Akuna, and Akunas extensible “toolset” framework that creates a collaborative research environment for subsurface modelers. A use case example is provided, which demonstrates creating and executing a 3D subsurface simulation.