Gateways 2018

The Science Gateways Community Institute (SGCI) is pleased to welcome you to the Gateways 2018 conference, the third sponsored by SGCI. In addition to welcoming you to the next two days of the conference, SGCI's Workforce Development area will announce the winners of the Young Professional of the Year award.

As access to data is becoming central to scientific research, data repositories are becoming a critical component of the research infrastructure. Today's data repositories are not simply a place to store data, but rather they offer a rich set of features to facilitate data sharing and data management. For more than a decade, the Dataverse project has been providing an open-source platform used to build today's data repositories. In this talk, I will present current Dataverse work that aims to provide a solution for tomorrow's data repositories: 1) integrating the data publishing process with replication tools, 2) supporting sensitive data, 3) unifying repositories with multiple cloud storage and computing options. 

Gateways have very specific requirements which makes each gateway unique in its own way. This can become a problem since the architecture, usage, main features, scope, and tools vary depending on the different needs specified by the domain experts. These differences introduce unique obstacles in planning, development, maintenance, and documentation. This panel will discuss the variety of challenges and solutions each member has experienced when developing science gateways. The panelists represent many years of experience and diverse fields of gateway implementation:

• Josue Balandrano Coronel: Designsafe, TACC CEP
• Alejandro Rocha: TUP, CHAMELEON, SGCI, UTRC, TACC CEP
• Carrie Arnold: DARPA SD2E, SGCI, TACC CEP
• Joseph Meiring:  DARPA SD2E, Designsafe, 3DEM, TACC CEP
• John Fonner: NSF Cyverse, DARPA SD2E, NIH VDJ Server, NSF Araport, NSF Agave ToGo, DrugDiscovery@TACC

Join us for a lively discussion of the key phases of any gateway project, and the ways the panelists have approached their varied projects. Audience contributions and questions are also welcome!

Supercomputing resources are used in both interactive and batch computing modes. The interactive mode is typically used for software development and testing purposes, or for running various command-line tools that work in a user-guided manner. The batch mode is often used for running a large number of jobs simultaneously or for large-scale runs that do not require interaction with the users. We needed a gateway (a web-portal) that could support both interactive and batch computing modes. The interactive mode was required for using a command-line tool for code parallelization through a web browser, and the batch mode was required for compiling and running the programs parallelized using the tool on the production systems at open-science data centers. We are iteratively developing this gateway, and its current version is live at https://ipt.tacc.cloud. An overview of the design and implementation of this gateway is presented in this paper. With minimal modifications, the architecture of this gateway can be reused for supporting other similar projects.

In this paper we introduce our system “Kale” that enables Jupyter Notebooks to seamlessly interface with HPC workflows, leveraging distributed computational resources for iterative human-in-the-loop scientific exploration. We discuss the motivation for Jupyter in the context of data-intensive and high-performance computing, and how one can introduce interactivity in this space. Our system, Kale, enables Jupyter notebooks to communicate with backend jobs via a service that can be used to control, monitor and communicate with these tasks. We use iPyWidgets to introduce graphical controls for Kale tasks within the notebook, and enable seamless integration with existing workflow managers. Finally, we discuss a deep learning use case at NERSC where Kale can provide interactive feedback and control to the user.

This demonstration presents Spin, a Docker-based, on-premise cloud platform at NERSC that enables researchers to design, build, and manage their own science gateways and other services using container technology. After explaining the rationale behind building Spin and describing its basic architecture, staff will show how simple services can be created in a few minutes using basic tools. A discussion of science gateways that have been implemented with Spin will follow.

We'll highlight what's ahead for the day, and welcome our first set of the day's presentations.

We introduce DeepForge, a gateway to deep learning for the scientific community. DeepForge is designed to lower the barrier to entry and facilitate the rapid development of deep learning models. Utilizing a cloud-based infrastructure, DeepForge facilitates rapid development by promoting reproducibility, collaboration and remote execution of machine learning pipelines. This represents an interdisciplinary approach to facilitating deep learning development as it leverages the strengths of Model Integrated Computing to provide a powerful hybrid textual-visual programming platform for the scientific community. In the demonstration, we present the core concepts of DeepForge and an image classification example.

Our goal is to create a cloud-ready repository of open-source coastal modeling tools which enable scientists and engineers to use high performance computers to study a variety of physical and ecological processes. The system we are building leverages Jupyter notebooks, Docker, Singularity, and the Agave Platform to create a platform for running jobs and analyzing data in a way that is (1) intuitive, (2) repeatable, (3) and collaborative.

The paper describes the methodology to integrate the four technologies into the system that serves the coastal resilience research collaboratory. Two commonly used open-source numerical models are used to demonstrate the utilities of the system. Simulation results of ocean waves generated by Hurricane Issac (2012) and coastal wave evolution are presented as an illustration. The sustainability of the collaboratory is discussed in detail.

In recent years, the explosion of social media platforms and the public collection of social data has brought forth a growing desire and need for research capabilities in the realm of social media and social data analytics. Research on this scale, however, requires a high level of computational and data-science expertise, limiting the researchers who are capable of undertaking social media data-driven research to those with significant computational expertise or those who have access to such experts as part of their research team. The Social Media Macroscope (SMM) is a science gateway with the goal of removing that limitation and making social media data, analytics, and visualization tools accessible to researchers and students of all levels of expertise. The SMM provides a single point of access to a suite of intuitive web interfaces for performing social media data collection, analysis, and visualization via for open-source and commercial tools. Within the SMM social scientists are able to process and store large datasets and collaborate with other researchers by sharing ideas, data, and methods. This document functions as a brief primer on the initial build of the SMM. As a clarifying note, the SMM is currently in a proof-of-concept stage.

The science gateway and online community nanoHUB hosts over 4000 technical resources related to nanoscience and nanotechnology and online capabilities for nano community engagement. nanoHUB also hosts over 500 online simulation tools. nanoHUB serves the nano community spectrum ranging from undergraduate students to high profile researchers. In this paper, the evolution of nanoHUB online simulation is discussed along with the impact of that simulation on student behavior. With over 52,000 simulation users, the nanoHUB team is not personally aware of most new classrooms that adopt simulation in their syllabi. Yet, these classroom users feed the next generation of nano community contributors. A method is presented to detect classroom by clustering coordinated behavior among simulation users, thereby automatically detecting adoption of simulation tools in a classroom environment. Several prototypical patterns of clustered behavior are analyzed, ranging from peripheral to systemic classroom integration of simulation. Visualizations of detailed user behavior illustrate the varying behavior structures. Between the fall of 2000 and the fall of 2011, in 846 clustered behaviors have been detected. This number of classroom settings is on a continuous growth trend as nanoHUB becomes more widely adopted. A discussion on the rate of adoption of published simulation tools in clustered behaviors is presented.

Neuroscientists are increasingly relying on parallel and distributed computing resources for analysis and visualization of their neuron simulations. This requires expert knowledge of programming and cyberinfrastructure configuration, which is beyond the repertoire of most neuroscience programs. This paper presents early experiences from development efforts of a next-generation science gateway for research and training purposes of novice/expert users. The development efforts were enabled by a one-credit graduate research training course titled ECE 8001 "Software and Cyber Automation in Neuroscience" at the University of Missouri for engendering multi-disciplinary collaborations between computational neuroscience and cyberinfrastructure students and faculty. Specifically, we discuss how the course organization has led to the exemplar outcomes involving design of a novel science gateway to support use cases with custom configurations with tools such as e.g., NEURON using both local campus resources and the Neuroscience Gateway resources. The ultimate goal of these efforts is to improve access to high-performance and distributed computing resources for a set of neuroscience research and education use cases.

The Materials Project (MP) has served as an effective dissemination platform for computational materials science data for nearly 8 years. In its capacity as a Science Gateway, it serves over 50,000 users from around the world with data on over 70,000 crystalline materials. In recent years, MP's growing popularity has been facilitated by educational resources developed by its core team and diligently maintained documentation of the methodology and provenance associated with its data. In this report, we highlight a recent effort by MP to standardize a set of educational materials for its user base in its annual \textit{Materials Project Workshop}, which was conducted in the summers of 2016 and 2017. More specifically, we describe our insights on how organization of material, presentation format, formative assessment, and active learning were integrated to produce an effective educational experience for our attendees. We also highlight the lessons we've learned, in the hopes other Science Gateway efforts may draw on our experiences in crafting their own educational and training resources.

While interest in new technologies can be immediately apparent, barriers to access are not always clear. Iterative, participatory, interface design is one approach to bridging disciplinary barriers to democratizing new technologies. Here we discuss what we learned applying these methods to the development of Immerj, an application to simplify the post-production of immersive video content, developed by students at the Texas Advanced Computing Center. Much like gateways, Immerj provides easy access to high-end technologies. Students had the opportunity to engage with stakeholders including journalists at the Washington Post, National Public Radio, and many other local and national organizations in order to guide the design of their Knight Foundation funded prototype. We will discuss what we learned and how stakeholder input helped our engineers understand and meet the stakeholders' needs, offering implications for gateways of all types. 

See the full explanation on the schedule at 1:15pm on Wednesday.

This is the wrap-up of the four Jumpstart Conversation periods on Thursday. At 2:55 pm, we’ll gather in the Lil’ Tex Auditorium to hear about the “aha!” moments and great ideas that came from these conversations. We’ll discuss what ways we can use these ideas to further improve our gateway community.