Emanuele Santos

VisTrails: visualization meets data management

Scientists are now faced with an incredible volume of data to analyze. To successfully analyze and validate various hypothesis, it is necessary to pose several queries, correlate disparate data, and create insightful visualizations of both the simulated processes and observed phenomena. Often, insight comes from comparing the results of multiple visualizations. Unfortunately, today this process is far from interactive and contains many error-prone and time-consuming tasks. As a result, the generation and maintenance of visualizations is a major bottleneck in the scientific process, hindering both the ability to mine scientific data and the actual use of the data. The VisTrails system represents our initial attempt to improve the scientific discovery process and reduce the time to insight. In VisTrails, we address the problem of visualization from a data management perspective: VisTrails manages the data and metadata of a visualization product. In this demonstration, we show the power and flexibility of our system by presenting actual scenarios in which scientific visualization is used and showing how our system improves usability, enables reproducibility, and greatly reduces the time required to create scientific visualizations.

Provenance for Computational Tasks: A Survey

The problem of systematically capturing and managing provenance for computational tasks has recently received significant attention because of its relevance to a wide range of domains and applications. The authors give an overview of important concepts related to provenance management, so that potential users can make informed decisions when selecting or designing a provenance solution.

Managing rapidly-evolving scientific workflows

We give an overview of VisTrails, a system that provides an infrastructure for systematically capturing detailed provenance and streamlining the data exploration process. A key feature that sets VisTrails apart from previous visualization and scientific workflow systems is a novel action-based mechanism that uniformly captures provenance for data products and workflows used to generate these products. This mechanism not only ensures reproducibility of results, but it also simplifies data exploration by allowing scientists to easily navigate through the space of workflows and parameter settings for an exploration task.

The ALPS project release 2.0: open source software for strongly correlated systems

We present release 2.0 of the ALPS (Algorithms and Libraries for Physics Simulations) project, an open source software project to develop libraries and application programs for the simulation of strongly correlated quantum lattice models such as quantum magnets, lattice bosons, and strongly correlated fermion systems. The code development is centered on common XML and HDF5 data formats, libraries to simplify and speed up code development, common evaluation and plotting tools, and simulation programs. The programs enable non-experts to start carrying out serial or parallel numerical simulations by providing basic implementations of the important algorithms for quantum lattice models: classical and quantum Monte Carlo (QMC) using non-local updates, extended ensemble simulations, exact and full diagonalization (ED), the density matrix renormalization group (DMRG) both in a static version and a dynamic time-evolving block decimation (TEBD) code, and quantum Monte Carlo solvers for dynamical mean field theory (DMFT). The ALPS libraries provide a powerful framework for programmers to develop their own applications, which, for instance, greatly simplify the steps of porting a serial code onto a parallel, distributed memory machine. Major changes in release 2.0 include the use of HDF5 for binary data, evaluation tools in Python, support for the Windows operating system, the use of CMake as build system and binary installation packages for Mac OS X and Windows, and integration with the VisTrails workflow provenance tool. The software is available from our web server at http://alps.comp-phys.org/.

Managing the Evolution of Dataflows with VisTrails

Scientists are now faced with an incredible volume of data to analyze. To successfully analyze and validate various hypotheses, it is necessary to pose several queries, correlate disparate data, and create insightful visualizations of both the simulated processes and observed phenomena. Data exploration through visualization requires scientists to go through several steps. In essence, they need to assemble complex workflows that consist of dataset selection, specification of series of operations that need to be applied to the data, and the creation of appropriate visual representations, before they can finally view and analyze the results. Often, insight comes from comparing the results of multiple visualizations that are created during the data exploration process.

CrowdLabs: social analysis and visualization for the sciences

Managing and understanding the growing volumes of scientific data is one of the most challenging issues scientists face today. As analyses get more complex and large interdisciplinary groups need to work together, knowledge sharing becomes essential to support effective scientific data exploration. While science portals and visualization Web sites have provided a first step towards this goal, by aggregating data from different sources and providing a set of predesigned analyses and visualizations, they have important limitations. Often, these sites are built manually and are not flexible enough to support the vast heterogeneity of data sources, analysis techniques, data products, and the needs of different user communities. In this paper we describe CrowdLabs, a system that adopts the model used by social Web sites, allowing users to share not only data but also computational pipelines. The shared repository opens up many new opportunities for knowledge sharing and re-use, exposing scientists to tasks that provide examples of sophisticated uses of algorithms they would not have access to otherwise. CrowdLabs combines a set of usable tools and a scalable infrastructure to provide a rich collaborative environment for scientists, taking into account the requirements of computational scientists, such as accessing high-performance computers and manipulating large amounts of data.

A Provenance-Based Infrastructure to Support the Life Cycle of Executable Papers

As publishers establish a greater online presence as well as infrastructure to support the distribution of more varied information, the idea of an executable paper that enables greater interaction has developed. An executable paper provides more information for computational experiments and results than the text, tables, and figures of standard papers. Executable papers can bundle computational content that allow readers and reviewers to interact, validate, and explore experiments. By including such content, authors facilitate future discoveries by lowering the barrier to reproducing and extending results. We present an infrastructure for creating, disseminating, and maintaining executable papers. Our approach is rooted in provenance, the documentation of exactly how data, experiments, and results were generated. We seek to improve the experience for everyone involved in the life cycle of an executable paper. The automated capture of provenance information allows authors to easily integrate and update results into papers as they write, and also helps reviewers better evaluate approaches by enabling them to explore experimental results by varying parameters or data. With a provenance-based system, readers are able to examine exactly how a result was developed to better understand and extend published findings.

VisMashup: Streamlining the Creation of Custom Visualization Applications

Visualization is essential for understanding the increasing volumes of digital data. However, the process required to create insightful visualizations is involved and time consuming. Although several visualization tools are available, including tools with sophisticated visual interfaces, they are out of reach for users who have little or no knowledge of visualization techniques and/or who do not have programming expertise. In this paper, we propose VisMashup, a new framework for streamlining the creation of customized visualization applications. Because these applications can be customized for very specific tasks, they can hide much of the complexity in a visualization specification and make it easier for users to explore visualizations by manipulating a small set of parameters. We describe the framework and how it supports the various tasks a designer needs to carry out to develop an application, from mining and exploring a set of visualization specifications (pipelines), to the creation of simplified views of the pipelines, and the automatic generation of the application and its interface. We also describe the implementation of the system and demonstrate its use in two real application scenarios.

Using VisTrails and Provenance for Teaching Scientific Visualization

Over the last 20 years, visualization courses have been developed and offered at universities around the world. Many of these courses use established visualization libraries and tools (e.g. VTK, ParaView, AVS, VisIt) as a way to provide students a hands‐on experience, allowing them to prototype and explore different visualization techniques. In this paper, we describe our experiences using VisTrails as a platform to teach scientific visualization. VisTrails is an open‐source system that was designed to support exploratory computational tasks such as visualization and data analysis. Unlike previous scientific workflow and visualization systems, VisTrails provides a comprehensive provenance management infrastructure. We discuss how different features of the system, and in particular, the provenance information have changed the dynamics of the Scientific Visualization course we offer at the University of Utah. We also describe our initial attempts at using the provenance information to better assess our teaching techniques and student performance.

Bridging workflow and data provenance using strong links

As scientists continue to migrate their work to computational methods, it is important to track not only the steps involved in the computation but also the data consumed and produced. While this provenance information can be captured, in existing approaches, it often contains only weak references between data and provenance. When data files or provenance are moved or modified, it can be difficult to find the data associated with the provenance or to find the provenance associated with the data. We propose a persistent storage mechanism that manages input, intermediate, and output data files, strengthening the links between provenance and data. This mechanism provides better support for reproducibility because it ensures the data referenced in provenance information can be readily located. Another important benefit of such management is that it allows caching of intermediate data which can then be shared with other users. We present an implemented infrastructure for managing data in a provenance-aware manner and demonstrate its application in scientific projects.