Jan 20 2010
Reducing the Pain of Collaboration
Collaboration tools are becoming legion, and while the individual tools each have unique value, the collection of tools together is creating a real stress in managing the collaboration. Handling identity, access controls, discovery of information, etc is difficult across the tool set, and integrating the tools with the domain science tools is a new frontier. Recently a number of efforts have been started to address these pain points in collaborations. This session will talk about some of those efforts and opportunities to use an integrated set of identity, access and content management mechanisms across the space of computer-aided tools within a collaborative.
Jan 27 2010
Opensource Cloud Computing: The Eucalyptus experience
Over the past decade, cloud computing and storage has transitioned from research concepts into a viable service and a first class citizen and for many large-scale infrastructures in industry, academia and compute intensive research facilities.
Integrating the plethora of cloud and virtualization technologies offered as a service with the traditional in-house computational infrastructure has been a challenge at many fronts. The EUCALYPTUS project (Elastic Utility Computing Architecture Linking Your Programs To Useful Systems) developed at the University of California, Santa Barbara is built upon open-source software stack and holds promise to become the de facto open-source infrastructure to manage both private and public clouds.
Arun Madhavan, a graduate student in the iPlant Core Services Team, will present a technical overview of Eucalyptus, share his experiences of implementing the framework, and provide a live demonstration
June 30th 2010
Mourad Ouzzani (Cyber Center at Purdue) and Ivan Baxter (Donald Danforth Plant Science Center)
LitCloud: A Literature Social Network
In a world that is constantly changing and growing, many researchers are overwhelmed by information overload and consider finding information and people relevant to their areas of interest as extremely time-consuming. For example, there are currently 2000+ papers published every month relevant to Plant Biologists. Most researchers can only scan a small fraction of those and as such miss a significant number of papers that could be of use to their work. There is an urgent need to provide scientists with tools to help them stay abreast the state
Most journals started providing RSS (Really Simple
Syndication) feeds for the papers that they publish, and these feeds are updated as soon as a paper comes online . RSS feeds provide a granular way to seamlessly track various web information sources and can be collated by RSS readers like Google Reader . Such readers provide simple ways for users to select what they are interested in on a single paper level in a way that can be easily tracked, for example , star - specify that a reference is important, add tags - assign a descriptive keyword to a reference for classification, and e-mail to If the RSS reader engagements (actions) of a community of researchers could be captured, the individual and aggregation of these actions could be an immensely valuable resource for researchers and educators . Researchers will be able to find new researchers and information relevant to their work, see which papers are “hot” in their area, follow papers highlighted as being of interest by known In this paper, we describe a literature social network called LitCloud that collects social actions from a community of RSS readers and aggregate this data in a central location. This type of knowledge network would help researchers not only share valuable papers in their areas of interest, but also provide an efficient mechanism for the rapid filtering and refinement of literature in specific areas.
Scientific Workflow and Service Oriented Architecture (SOA) at the LEAD project
Linked Environments for Atmospheric Discovery (LEAD) makes meteorological data, forecast models, and analysis and visualization tools available to anyone who wants to interactively explore the weather as it evolves. The LEAD Portal brings together all the necessary resources at one convenient access point, supported by high-performance computing systems. With LEAD, meteorologists, researchers, educators, and students are no longer passive bystanders or limited to static data or pre-generated images, but rather they are active participants who can acquire and process their own data.
LEAD software enhances the experimental process by automating many of the time consuming and complicated tasks associated with meteorological science. The "workflow" tool links data management, assimilation, forecasting, and verification applications into a single experiment. The experiment's output also includes detailed descriptions of the product, also called "metadata."
Dec 15 2010
Towards supervising the science informatics playground.
Towards supervising the science informatics playground.
For the past decade I have been developing software to help scientists – particularly Life Scientists - collaborate, leverage, integrate and reuse each others results and hopefully accelerate scientific insights and enable reproducible science. The myGrid project (http://www.mygrid.org.uk), launched in 2001 and still going strong, brings computer scientists, software engineers, bioinformaticians, social scientists and biologists to work together to not only investigate novel techniques for information integration, semantic e-science and social computing for scientists, but to also build and run production tools and services. The team, spread over a range of institutions, currently has 24 core members (most at Manchester) and many associated members.
Our work falls into two broad areas: scientific workflows and socially networked e-Laboratories. Our Taverna workflow management system is used by over 400 research organisations worldwide for a full range of Life Science public/private data pipeline tasks, including cloud-based NGS annotation. Our e-Laboratories – myExperiment, SysMO-SEEK, and BioCatalogue – are crowd-contributed and community curated repositories, registries and services that encourage and support the social exchange of scientific assets. myExperiment has over 4000 public members sharing workflows; SysMO-SEEK supports the 13 projects from 91 institutes of the European Systems Biology for MicroOrganisms programme to preserve and exchange models, data and methods; and BioCatalogue has >1700 registered web services for the life sciences curated by the community.
In this talk I will share my experiences in two areas: (a) managing projects and building software for the benefit of all concerned; and (b) the successes and struggles of persuading scientists to share in social environments, when frankly sharing is against their nature. As one might expect these experiences are more to do with socio-political cultural issues rather than technical ones. I will conclude with some remarks on how scientific practice, funding, review and publishing cultures have to adapt if we are to truly enable reproducible and (partially) open science.