eScience Workshop 2011

Advancing Environmental Understanding; the Role of eScience (opens in new tab)—Dan Fay (opens in new tab), Microsoft Research

Our understanding of the world around us is evolving, and with evolution comes the need for adaptation. Environmental scientific research is increasingly having to adapt—from dealing with increasingly large and growing datasets, to trying to credibly inform the public and policy makers. There is a need to have new types of applications grounded in scientific research to move from raw discovery, to knowledge, to informing practical decisions. Understanding environmental changes from the levels of neighborhoods, to regions, to the globe is the focus of scientific study and policy decisions. Technology reinforced by computing is demonstrating the capacity to improve our environmental understanding. This talk contains examples of environmental changes and the challenges that are the focus of scientific investigation; it also identifies technologies and tools that can make an impact on these understandings.

An Open Source Library for Bioinformatics—Simon Mercer, Microsoft Research

Microsoft has created a general-purpose library of useful functions for the assembly, comparison and manipulation of DNA, RNA and protein sequences. Built on the Microsoft .NET platform, this toolkit enables the scientific programmer to rapidly develop the applications needed by genomics scientists to cope with extracting knowledge from the increasing volumes of data common in the field of genomics research. Under development in Microsoft Research for the past three years, it contains a core of standard functions but also enables easy access to a wide range of other Microsoft technologies including Microsoft Silverlight, DeepZoom, and Microsoft Office as well as unique research tools such as Sho and PhyloD. The library is open source under the Apache 2 license, and is freely available for commercial and academic use. Developers are encouraged to adapt and extend the basic library, making their modifications available for others to use at Microsoft Biology Foundation (opens in new tab).

Programming with Massive Data Sources Made Simple, Fast, and Error-Free—Don Syme (opens in new tab), Microsoft Research

The F# 3.0 language is a breakthrough in productivity for programmers working with online data sources, databases, and ontologies. It combines three beautifully tuned features: F# 3.0 type providers, which give the programmer access to massive quantities of scientific data in an intuitive, strongly typed, and navigable way; F# units of measure, which let you attach unit annotations to numerical data; and F# functional programming, which lets you write succinct and efficient transformations of data with a low error rate. With the open source and highly interoperable nature of F#, these features work together to give the scientific programmer a uniquely powerful tool tuned to the needs of scientific programming in the 2010s and beyond.

Cloud Computing for Research—a European Perspective—Fabrizio Gagliardi, Microsoft Research

Cloud computing promises to revolutionise how science and engineering can be carried out by industry, research organisations, and universities alike. To accelerate the adoption of this key technology, it is important that users are able to access cloud resources to best match their real-world applications to this new way of working. VENUS-C (opens in new tab) brings together end-users, developers, and cloud providers to create a seamless framework for cloud computing in Europe and globally. This talk will provide an overview of the VENUS-C project and how it is helping to democratise research.

VENUS-C and the Generic Worker Execution Environment—Götz Brasche, European Microsoft Innovation Center

In this presentation, we provide a technical overview to the VENUS-C (opens in new tab) project. VENUS-C delivers a set of services for researchers and scientists to run scientific applications in the cloud, such as services for data management and processing. In particular, this talk focuses on an implementation of the generic worker pattern, which supports data processing on hybrid clouds deployments, spanning public clouds (such as Windows Azure) and private on-premises deployments. This presentation will highlight implementation tradeoffs, and design and technology choices that were made to build a single extensible code base, which supports a broad variety of deployment models (such as PaaS, IaaS, and on-premises deployments) as well as a broad variety of storage systems.

Data Management in Venus-C—Ilja Livenson, Kungliga Tekniska Hoegeskolan

Data management for cloud applications is an important topic to realize usable services. In this talk, we describe work done in VENUS-C to provide an integration layer for data management facilities.

Drug Design Experiments in the Cloud—Simon Woodman, Newcastle University

This talk describes how VENUS-C is exploiting existing drug-discovery services and components to improve them by experimenting on large-scale infrastructures and ultimately deploying them for the benefit and engagement of pharmaceutical research and healthcare industry.

Green Prefab, Civil Engineering in Cloud Computing—Furio Barzon, Collaboratorio

This talk describes how Collaboratorio is working on the extension of their product GreenPreFab to exploit the VENUS-C platform extensively, as well as adding features and models that will allow civil engineers to simulate building structural behavior in the same integrated environment of the green building commercial value chain. For this scenario, Collaboratorio involves a pilot case building (“Manifattura Domani” in Rovereto, Italy) in order to apply the emerging platform to a real case simulation. We are also engaging with the community of architects, enabling them to approach the e-Infrastructure via specific tools for experimenting with new building solutions and models.

Panel Session – Supporting Scientific Users in the Cloud

Session Chair: Fabrizio Gagliardi, Microsoft Research

• Götz Brasche, European Microsoft Innovation Center
• Ignacio Blanquer, Universitat Politècnica de València
• Andrea Manieri, Ingegneria Informatica SpA

While cloud computing promises to be a key enabling technology for eScience, its success relies not only on technical capabilities, but also on socio-economic factors. VENUS-C (opens in new tab) has been addressing a broad spectrum of areas: software architecture, cloud infrastructure, user scenarios, dissemination, cooperation, and training. In this panel session, we will discuss how all of these factors are suppport scientific users in using cloud computing. We will also highlight the most important issues from both end-user and service provider perspectives.

Session Chair: Donald Brinkman, Microsoft Research

Big Archaeology: Creation, Integration, Analysis, and Dissemination of Archaeological Data—Graeme Earl, University of Southampton

This presentation will introduce the work of the Archaeological Computing Research Group at Southampton, tracing the archaeological data life-cycle from creation in the field and lab to public and academic dissemination. Our work at sites such as Portus, the Port of Imperial Rome, has demonstrated the potential of an integrated digital approach to archaeological practice on a large scale. In addition to the data processing and management needs implied by techniques such as laser scanning, three-dimensional geophysics, and reflectance transformation imaging, the use of digital technologies on site has a transformative role to play in interpretation and field practice. We are therefore exploring potentials for building wearable prototypes to blur the digital:physical research environments of laboratories and field sites, and examining their impact on the archaeological research process. In partnership with the Southampton μ-VIS Centre we have also begun to employ micro computed tomography on the imaging of archaeological materials, which presents considerable data visualisation and management tasks to be explored in the paper. Finally, having explored the production of these datasets, the paper will explore modes for integrated examination of rich, spatial information at micro and geographic scales, the construction of graphical simulations for analysis and dissemination, and methods for creating rich publications.

The Archive Without Walls—Jeffrey Schnapp, Harvard University

This presentation will focus on a metaLAB project entitled extraMUROS: an open-source HTML5 infrastructure built on public APIs that enables faculty, students, and the general public to view, annotate, and remix digital multimedia collections and to interconnect them with other high-quality digital repositories across the web. While books (in material and digital form alike) are vital to the future of libraries, we believe that in an increasingly audiovisual world of scholarship and public discourse, it is essential that libraries play a major role in preserving, making available, and providing innovative tools for interpreting and disseminating society’s audiovisual past, present, and future across media.

Session Chair: Donald Brinkman, Microsoft Research

TextGrid – An Architecture to Store, Access and Manage Diverse Humanities Data—Andreas Witt, Institut für Deutsche Sprache, Zentrale Forschung

TextGrid is a virtual research environment for scholars in the humanities, currently focusing on German literature, art history, classics, linguistics, and musicology. TextGrid’s architecture includes a repository accessible via dedicated web service APIs. It consists of a storage component, which manages file access and replication and uses a storage grid as data backend, and another component that handles role-based access control. In addition to access rights, certain license policies must be enforced for published content. A TextGrid middleware component, called TG-license, has been designed for published content. For high scalability, these three TextGrid middleware components are designed to be distributed.

The presentation will give a general overview of the TextGrid architecture and the content of the TextGrid repository. It then will focus on license requirements and describe how the TG-license can handle licensing issues such as data that is:

• Only publicly accessible 70 years after the death of the author
• Only accessible if the user has acknowledged the license

The tool to solve these license issues is based on XACML policies that refer to attributes of the user and of the resources, information that is stored in a distributed LDAP directory.

Large-Scale Music Analysis in the Key of E-Science—Stephen Downie, University of Illinois – Urbana, Champaign

The use of eScience technologies in the digital arts and digital humanities research domains represents a fast-growing area of scholarly activity. The Structural Analysis of Large Amounts of Music Information (SALAMI) project is an excellent example of the fruitful union of classic musicology and eScience. SALAMI is a multinational (Canada, United Kingdom, and United States) and multidisciplinary (music theory, library science, and computer science) digital humanities research collaboration. Exploiting 250,000 hours of compute time donated by the National Center for Supercomputing Applications (NCSA) at the University of Illinois, the SALAMI project is conducting the structural analysis of some 20,000 hours (in other words, roughly 2.3 years) of music audio.

Thus, the SALAMI team is undertaking formal music analyses at a scale that no individual human scholar could ever hope to undertake. They will also contextualize the SALAMI project within the broader frameworks of the ongoing Networked Environment for Music Analysis (NEMA) and the Music Information Retrieval Evaluation eXchange (MIREX) projects. The motivations, goals, and developments of these three interrelated projects are presented to help illustrate the kinds of questions being explored by music informatics scholars and the roles that the eScience suite of tools—including HPC, semantic web, and Linked Data techniques—can play in answering those questions.