Rion Dooley

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise plant biology to address Grand Challenges in new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of cyberinfrastructure in research and education. Meeting humanitys projected demands for agricultural and forest products and the expectation that natural ecosystems be managed sustainably will require synergies from the application of information technologies. The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for the physical sciences. iPlant is an open-source project with application programming interfaces that allow the community to extend the infrastructure to meet its needs. iPlant is sponsoring community-driven workshops addressing specific scientific questions via analysis tool integration and hypothesis testing. These workshops teach researchers how to add bioinformatics tools and/or datasets into the iPlant cyberinfrastructure enabling plant scientists to perform complex analyses on large datasets without the need to master the command-line or high-performance computational services.

Distributed Systems of Microservices Using Docker and Serfnode

We review container technology and the challenge of service discovery in micro service architectures and introduce Serf node, a fully decentralized open source solution to the service discovery problem, based on the Serf project. Serf node is a non-intrusive Docker image that composes one or more arbitrary Docker containers. The new images can be deployed into a cluster of Serf nodes, where it advertises itself and provides service discovery mechanisms, monitoring, and self-healing. The resulting cluster is a homogeneous and complete graph, with no master node. We survey existing solutions to the service discovery problem and compare them to Serf node. As an example of the extensibility of Serf node, we show the construction of a file system synchronization solution between Docker containers using Git.

Science Gateways Institute Survey

Science gateways are digital interfaces to advanced technologies that support science/engineering research/education. Frequently implemented as Web and mobile applications, they provide access to community resources such as software, data, collaboration tools, instrumentation, and high‐performance computing. We anticipate opportunities for growth within a fragmented community. Through a large‐scale survey, we measured the extent and characteristics of the gateway community (reliance on gateways and nature of existing resources) to understand useful services and support for builders and users. We administered an online survey to nearly 29,000 principal investigators, senior administrators, and people with gateway affiliations. Nearly 5000 respondents represented diverse expertise and geography. The majority of researchers/educators indicated that specialized online resources were important to their work. They choose technologies by asking colleagues and looking for documentation, demonstrated reliability, and technical support; adaptability via customizing or open‐source standards was another priority. Research groups commonly provide their own resources, but public/academic institutions and commercial services also provide substantial offerings. Application creators and administrators welcome external services providing guidance such as technology selection, sustainability planning, evaluation, and specialized expertise (e.g., quality assurance and design). Technologies are diverse, so flexibility and ongoing community input are essential, as is offering specific, easy‐to‐access training, community support, and professional development. Copyright

Recipes 2.0: Building for today and tomorrow

The history of science gateway development has, in many ways, been a story of the ‘Haves’ vs. the ‘Have‐nots’. Large infrastructure projects led the way, building thick client portals to provide coherent interfaces to an incoherent environment. Contrast this with the way the modern Web is designed using light, front end components, and outsourcing much of the heavy lifting to a mash‐up of REST application programming interfaces, and it is easy to see why modern web applications can be prototyped and refined into stable products in the time it previously took thick client portals to do an initial release. This paper argues that a ‘build for today’ philosophy can lead to the rapid development of science gateways to serve the ‘Have‐nots’. With this philosophy in mind, we are presenting Gateway DNA, a set of responsive front end components built on top of the iPlant Agave application programming interfaces. This toolkit provides the boilerplate for rapid development of lightweight science gateways using only HTML, JavaScript, and CSS. Using Gateway DNA, developers can easily stand up new gateways or quickly add new functionality to existing ones. Copyright

TeraGrid's integrated information service

The NSF TeraGrid project has designed and constructed a federated integrated information service (IIS) to serve its capability publishing and discovery needs. This service has also proven helpful in automating TeraGrids operational activities. We describe the requirements that motivated this work; IISs system architecture, information architecture, and information content; processes that IIS currently supports; and how various layers of the system architecture are being used. We also review motivating use cases that have not yet been satisfied by IIS and outline approaches for future work.

Recipes 2.0

The history of science gateway development has, in many ways, been a story of the ‘Haves’ vs. the ‘Have‐nots’. Large infrastructure projects led the way, building thick client portals to provide coherent interfaces to an incoherent environment. Contrast this with the way the modern Web is designed using light, front end components, and outsourcing much of the heavy lifting to a mash‐up of REST application programming interfaces, and it is easy to see why modern web applications can be prototyped and refined into stable products in the time it previously took thick client portals to do an initial release. This paper argues that a ‘build for today’ philosophy can lead to the rapid development of science gateways to serve the ‘Have‐nots’. With this philosophy in mind, we are presenting Gateway DNA, a set of responsive front end components built on top of the iPlant Agave application programming interfaces. This toolkit provides the boilerplate for rapid development of lightweight science gateways using only HTML, JavaScript, and CSS. Using Gateway DNA, developers can easily stand up new gateways or quickly add new functionality to existing ones. Copyright

Dynamically Provisioning Portable Gateway Infrastructure Using Docker and Agave

The iPlant Agave Developer APIs are a Science-as-a-Service platform for developing modern science gateways. One trend we see emerging from our users is the aggregation of many different, distributed compute and storage systems. The rise in popularity in IaaS, PaaS, and container technologies has made the rapid deployment of elastic gateway infrastructure a reality. In this talk we will introduce Docker and the Agave Developer APIs then demonstrate how to use them to provision applications and infrastructure that are portable across any Linux hosting environment. We will conclude by using our lightweight gateway technology, GatewayDNA, to run an application and move data across multiple systems simultaneously.

Authoring a Science Gateway Cookbook

Over the last fifteen years, science gateways have proven to be fertile ground for cyberinfrastructure research, while at the same time dramatically increasing the usage and accessibility of cyberinfrastructure to scientists and educators. Gateway developers, however, still face many challenges in building and operating these complex infrastructures that address the dynamic and emerging challenges of computational infrastructure. Through the XSEDE Science Gateway Program, we propose to solicit information on the knowledge, experience, and software from widely used science gateways. We will compile the information into a “Science Gateway Cookbook” which will democratize the experiences in developing, operating, and sustaining science gateways. We hope this will be a good literature reference and also avoid some repetition in the development process.

Araport: an application platform for data discovery

Araport is an open‐source, online community resource for research on the Arabidopsis thaliana genome and related data. Araport is developed through a partnership between J. Craig Venter Institute, the Texas Advanced Computing Center at The University of Texas at Austin, and The University of Cambridge. Part of the open architecture of Araport is the Science Applications Workspace. Taking an ‘app store’ approach, users can choose applications developed both by the Araport team and community developers to create a customized environment for their work. Araport also provides tooling and support for developing applications for Araport, including an application generator, a rapid development and testing tool, and a straightforward deployment path for publishing applications into the Araport workspace. Copyright

Life science data analysis workflow development using the bioextract server leveraging the iPlant collaborative cyberinfrastructure

In order to handle the vast quantities of biological data gener6ated by high‐throughput experimental technologies, the BioExtract Server (bioextract.org) has leveraged iPlant Collaborative (www.iplantcollaborative.org) functionality to help address big data storage and analysis issues in the bioinformatics field. The BioExtract Server is a Web‐based, workflow‐enabling system that offers researchers a flexible environment for analyzing genomic data. It provides researchers with the ability to save a series of BioExtract Server tasks (e.g., query a data source, save a data extract, and execute an analytic tool) as a workflow and the opportunity for researchers to share their data extracts, analytic tools, and workflows with collaborators. The iPlant Collaborative is a community of researchers, educators, and students working to enrich science through the development of cyberinfrastructure—the physical computing resources, collaborative environment, virtual machine resources, and interoperable analysis software and data services—that are essential components of modern biology. The iPlant AGAVE Advanced Programming Interface, developed through the iPlant Collaborative, is a hosted, Software‐as‐a‐Service resource providing access to a collection of high performance computing and cloud resources. Leveraging AGAVE, the BioExtract Server gives researchers easy access to multiple high performance computers and delivers computation and storage as dynamically allocated resources via the Internet.