Matthew R. Hanlon

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.

Araport: the Arabidopsis Information Portal

The Arabidopsis Information Portal (https://www.araport.org) is a new online resource for plant biology research. It houses the Arabidopsis thaliana genome sequence and associated annotation. It was conceived as a framework that allows the research community to develop and release ‘modules’ that integrate, analyze and visualize Arabidopsis data that may reside at remote sites. The current implementation provides an indexed database of core genomic information. These data are made available through feature-rich web applications that provide search, data mining, and genome browser functionality, and also by bulk download and web services. Araport uses software from the InterMine and JBrowse projects to expose curated data from TAIR, GO, BAR, EBI, UniProt, PubMed and EPIC CoGe. The site also hosts ‘science apps,’ developed as prototypes for community modules that use dynamic web pages to present data obtained on-demand from third-party servers via RESTful web services. Designed for sustainability, the Arabidopsis Information Portal strategy exploits existing scientific computing infrastructure, adopts a practical mixture of data integration technologies and encourages collaborative enhancement of the resource by its user community.

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

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

Providing resource information to users of a national computing center

The Texas Advanced Computing Center provides a variety of high‐end resources to state, national, and international computational scientists and engineers. Many users obtain information about these resources via the Texas Advanced Computing Center user interfaces, which are supported by an information gathering and distribution infrastructure. After a number of years of use, we needed to improve our user interfaces by both redesigning the web interface and adding mobile interfaces. To support this, we also needed to update our information infrastructure. This paper presents our new design, describes how it improves over the previous approach, and shows that this design meets our current and expected future needs. Copyright

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

Digital Rocks Portal

Digital Rocks Portal (www.digitalrocksportal.org) Digital Rocks is a data portal for fast storage and retrieval of images of varied porous micro-structures. It has the purpose of enhancing research resources for modeling/prediction of porous material properties in the fields of Petroleum, Civil and Environmental Engineering as well as Geology. This platform allows managing and preserving available images of porous materials and experiments performed on them, and any accompanying measurements (porosity, capillary pressure, permeability, electrical, NMR and elastic properties, etc.) required for both validation on modeling approaches and the upscaling and building of larger (hydro)geological models.

My-Plant.org: A phylogenetically structured social network

My-Plant.org (My-Plant) is a social networking portal for the Plant Sciences community. As part of the iPlant Collaborative, My-Plant is charged with the goal of bringing together scientists, students, educators, and other interested parties by providing a new approach to connecting with others in the plant sciences thereby helping to spark new collaborations and communication among them. Many social networking sites exist where users can form groups and communicate, but the group structure is flat and has no inherent interconnectivity. My-Plant connects users via branches (called clades) of the phylogenetic tree of green plants, thus creating a unique, phylogenetically based social network structure. My-Plant users can join clades at any level of the tree and collaborate with other users interested in these clades. My-Plant is built upon the Drupal open source content management system. This paper discusses My-Plant in detail, its concept and contributions to the iPlant Collaborative, its implementation details, and its efforts to become an information hub for the plant sciences community. In addition, the paper focuses on some of the technology challenges, lessons learned, and future work of My-Plant.