Gateways 2019

The Science Gateways Community Institute (SGCI) is pleased to welcome you to the Gateways 2019 conference, the fourth 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.

Science Gateways provide an easily accessible and powerful computing environment for researchers. These are built around a set of software tools that are heavily used by large research communities in specific domains. Science Gateways have been catering to a growing need of researchers for easy to use computational tools, however, their usage model is typically single user-centric. As scientific research becomes ever more team-oriented, the need for integrated collaborative capabilities in Science Gateways has been emerging. One such need is the ability to share data/results with others. In this article, we will describe and discuss our effort to provide a rich environment for data organization and sharing by integrating the SeedMeLab platform with two Science Gateways: CIPRES and GenApp.

Next-generation sequencing (NGS) allows the characterization of the adaptive immune receptor repertoire (AIRR) in exquisite detail. These large-scale AIRR-seq
data sets have rapidly become critical to vaccine development, understanding the immune response in autoimmune and infectious disease, and monitoring novel therapeutics against cancer. Over the past five years, a grass roots, international community (the AIRR Community - www.airr-community.org) has been working towards establishing standards and recommendations for obtaining, analyzing, curating and comparing/sharing NGS AIRR-seq datasets. Using these standards, the AIRR Community Common Repository Working Group (CRWG) is working towards establishing an international network of AIRR-seq repositories whose data are findable, accessible, interoperable, and reusable (FAIR).

The iReceptor Data Integration Platform (gateway.ireceptor.org) provides an implementation of the AIRR Data Commons envisioned by the AIRR Community. The iReceptor Scientific Gateway links distributed (federated) AIRR-seq repositories,
allowing sequence searches or repertoire metadata queries across multiple studies at multiple institutions, returning sets of sequences fulfilling specific criteria. The data standards developed by the AIRR Community are at the foundation of our ability to implement such a platform. In this paper we use iReceptor as a case study that considers the importance of standards for effective data sharing.

The short paper will discuss the process that the AIRR Community went through to establish its working groups and the standards those working groups produced. This will include discussions of the Minimal Information for AIRR-seq data (MiAIRR), the Standardized Representations for Annotated Immune Repertoires, and the emerging AIRR Data Commons Web API. Each of these standards will be discussed in the context of the iReceptor Platform terms of its importance to the platform's implementation as well as its expected usefulness to the scientific community.

PURR was founded in 2011 as a partnership between Purdue University Libraries, Information Technology at Purdue (ITaP), and the Office of the Executive Vice President for Research as campus-wide support for researchers throughout the data management lifecycle built on the HUBzero® platform, which was developed at Purdue. PURR provides the tools and expertise to help researchers plan for data management, share data with collaborators, publish completed datasets in compliance with federal funding guidelines, safely archive data, and track data publication impact. Every PURR user has access to private space for storing and sharing research data files. When research is completed, PURR takes users through a step-by-step process for selecting and describing data files for publication. Upon publication, PURR mints a DOI for each dataset, and provides archiving services through the MetaArchive network. All published datasets are maintained and accessible on the PURR website for at least 10 years. After which time, they will be reviewed by the libraries and could be decommissioned or moved to library archives.

Over the past eight years, PURR has published 975 datasets, and served over 3,600 researchers with 481 grant awards. In that time, PURR’s services have grown along with the HUBzero® platform to meet the changing needs of the Purdue community as researchers across all fields produce more data. Supporting larger datasets requires a multi-faceted approach far beyond simply acquiring additional storage space. Our recent development has followed a 5-pronged plan: 1) increased storage quotas, 2) new publication series functionality, 3) an online database viewer, 4) publication file preview, and 5) seamless ftp transfers for large publications. Combined, these improvements ensure our increasingly large data publications are not only stored safely, but also are accessible over the long term.

The newly published Rough Cilicia Survey Pottery Study dataset series illustrates both the motivation for and the results of PURR’s recent development. The culmination of four years of close collaboration between PURR’s data curator and a faculty member from Purdue’s classics department, the Rough Cilicia collection is composed of 25 datasets. The collection takes advantage of PURR’s series functionality, which allows authors to separate large data collections into smaller, more manageable, related subsets. These subsets are easier to download than the entire collection, and each subset has a DOI for precise citation. This series makes available images of hundreds of pottery sherds from the ancient Cilicia region of modern-day Turkey, and their associated descriptive information in a series of interactive data tables that allow the user to view, search, and filter data on the PURR website. Users can also download the data files for closer study and reuse. At about 15 GB, the Rough Cilicia series is not exactly “big data,” but it is large enough to stretch the limits of a web-based repository like PURR, and we are increasingly seeing datasets of this size or more. Moderate improvements like the five mentioned here allow us to publish larger datasets while maintaining the ease and convenience of serving users through a web browser.

The Sequence Read Archive (SRA)-https://www.ncbi.nlm.nih.gov/sra houses all publicly available biological DNA sequence data to enhance reproducibility, reduce redundancy, and to allow for new discoveries by comparing data. The SRA stores raw sequencing data and alignment information from high-throughput sequencing platforms, including Roche 454 GS System®, Illumina Genome Analyzer®, Applied Biosystems SOLiD System®, Helicos Heliscope®, Complete Genomics®, and Pacific Biosciences SMRT®.The Sequence Read Archive (SRA), the world’s largest database of sequences, is growing at the alarming rate of 10 TB per day. But this data is inaccessible to most researchers because of the need for large storage and computing facilities to search through the datasets. Most individual laboratories do not have the computing capacity to deal with this volume of data.
Empowering scientists to analyze existing sequence data will provide insight into ecology, medicine, and industrial applications. Together with XSEDE ECSS support, we developed a gateway (https://www.searchsra.org/) to provide computational analysis of a subset of the SRA, focussed on metagenomic sequences. These sequences come from diverse environments, and their analysis is computationally challenging. Our users submit a DNA or protein sequence to be compared to all of the known sequences in the public databases. The computation is performed on XSEDE cloud resource Jetstream and the data housed on the XSEDE Wrangler resource. Results from the computation are only saved shortly to enable the users to download the outputs.
Future improvements will provide data versioning and integrity, a wider range of search algorithms, and integrate other applications into the gateway to streamline direct job submission and result retrieval.

This demonstration presents the Environmental Systems Science Data Infrastructure for a Virtual Ecosystem (ESS-DIVE), a new Department of Energy (DOE) web-based data repository that enables the earth and environmental science community. The multidisciplinary ESS-DIVE team consists of computer scientists, environmental scientists, and digital librarians that have come together to build this system. We will highlight the end-to-end features of ESS-DIVE to showcase its unique capabilities, including (1) Implementation of Data Standards and HTTP API using JSON-LD, (2) Publication workflow and automated DOI generation, (3) Scalable, repeatable containerized infrastructure through Docker, (4) Core capabilities based on the NCEAS Metacat and MetacatUI software, including ORCID based single-sign on, data search and access, data publication and dataset management, and (5) Federated data access and replication on the DataONE network.

Tuesday Learning Labs (1:00-1:45pm)
Table Numbers and Topics for this time slot

1. Cybersecurity Risks for Science Gateways
   This forum, hosted by a cybersecurity analyst affiliated with SGCI, will provide an opportunity for gateway operators and developers to learn more about security risks applicable to gateways and to share their own security challenges. Gateway operators will be able to takeaway solutions to common risks as well as receive direct advice and insight into more unique challenges. Hosted by Mark Krenz.
2. Gateway Ambassadors - Join our community for community builders
   SGCI is in the process of spinning up a community of Gateway Ambassadors. Gateway Ambassadors serve as community builders, making connections between people, experts, and resources on campus and in distributed projects. Come for brainstorming about ideas and concepts what you would like to see in such a community. You can join also if you wouldn't like to fill the role of a Gateway Ambassador yourself - anyone interested is welcome to participate. Hosted by Sandra Gesing.
3. Gateway Data Wrangling
   What do you find most challenging about transferring & managing data in your gateway? Lee is from the Globus team and wants to know what Globus can do to make life easier for gateway developers. Hosted by Lee Liming
4. Workflow Frameworks
   Does your gateway currently support user-defined workflows? If so, what framework do you use and how? Hosted by Rajesh Kalyanam.
5. Self-hosted HUBzero Community
   A call for self-hosted HUBzero site developers and potential open source contributors to brainstorm on ways to foster and sustain a community of support. Hosted by Jack Smith.
6. Training and supporting communities to engage with your Gateway
   Training and supporting researchers to use, extend, or customize a scientific Gateway. This BoF is being organized by Dave Clements and Mo Heydarian, who would be happy to have additional attendees of Gateways 2019 lead the discussion around training.
7. Automation tech and Jetstream
   "Do it once, and it's done. Do it twice, and you should have automated." "Anything that you do more than twice has to be automated." "Three strikes and you automate." Wherever you draw the line, automation is a critical part of running a successful science gateway. Come join other developers, engineers, and DevOps practitioners to share your experiences automating all the things on Jetstream and the commercial cloud. Hosted by Rion Dooley.

About Learning Labs
“Learning Labs” may be one of several styles of impromptu learning:

• Pop-up BOFs (Birds-of-a-Feather Sessions)
• Mini Hacks
• Coffee-Break Conversations

We will have three 45-minute periods devoted to your ideas. Round tables will be set up for you to meet with others and discuss the topics of your choice. Here are the ways you can get involved:

1. Propose a topic that you’d be willing to host. (You don’t have to be an expert, just interested!) 
2. Find a topic that interests you, and join a table!

Submit your topic with this Google form by Tuesday, September 24 at 7pm Pacific: https://forms.gle/1Th5svq13VeKreLE7.

We’ll announce when and where the first round are happening by Tuesday morning on Sched, second round on Wednesday morning. We may be able to insert additional topics after the deadline if space is available.

Science gateways, also known as advanced web portals, virtual research environments and more, have changed the face of research and scholarship over the last two decades. Scholars world-wide leverage science gateways for a wide variety of individual research endeavors spanning diverse scientific fields. Evaluating the value of a given gateway to its constituent community is critical in obtaining the financial and human resources to sustain gateway operations. Accordingly, those who run gateways must routinely measure and communicate impact. Just as gateways are varied, their success metrics vary as well. In this survey paper, a variety of different gateways briefly share their approaches.

Neuroscientists are increasingly relying on high performance/throughput computing resources for experimentation on voluminous data, analysis and visualization at multiple neural levels. Though current science gateways provide access to computing resources, datasets and tools specific to the disciplines, neuroscientists require guided knowledge discovery at various levels to accomplish their research/education tasks. The guidance can help them navigate through relevant publications, tools, topic associations and cloud platform options as they accomplish important research and education activities. To address this need and to spur research productivity and rapid learning platform deployment, we present "OnTimeRecommend", a novel recommender system that comprises of several integrated recommender modules through RESTful web services. We detail a neuroscience use case in a CyNeuro science gateway, and show how the OnTimeRecommend design can enable novice/expert user interfaces, as well as template-driven control of heterogeneous cloud resources.

Dr. Songjie Wang will be presenting this paper on behalf of the project.

In this paper and demo, we will present and showcase the Data Release Infrastructure we have developed and deploy using state of the art technologies like Kuberentes, Jupyter, Celery and Python to allow scientist to access, explore and analyze the catalogs and images generated by the Dark Energy Survey project, which is a scientific community-based project (with over 500 scientists) with the goal of understanding the origin of dark matter and dark energy by surveying the night sky and observe millions of galaxies and stars for a 5 year period. This Infrastructure includes novel data visualizations and exploration tools to enable scientific discovery. I will review the deployment and development process, the scientific output and feedback as well as the main features of our gateway.

Earth scientists expend significant effort synthesizing data often from multiple data sources for both modeling and empirical analyses. We introduce BASIN-3D (Broker for Assimilation, Synthesis and Integration of eNvironmental Diverse, Distributed Datasets) as a data brokering approach to reduce the scientist's data processing burden. BASIN-3D synthesizes diverse data from a variety of remote sources in real-time without the need for additional storage. BASIN-3D is an extendable Django web framework application using a generalized data synthesis model that makes the synthesized data available via REpresentational State Transfer (REST) Application Programming Interface (API). We have currently implemented our data synthesis model to represent sensor-based time series earth science observations across a hierarchy of spatial locations. Supporting our data synthesis model is a plugin framework that allows developers to map data sources of interest to the BASIN-3D synthesis model. In this demo, we give an overview of BASIN-3D's synthesis model and plugin framework and compare direct time-series queries to a public data source with queries to BASIN-3D. Additionally, we demonstrate a web interface built on top of BASIN-3D that provides a usable interface for scientific users including features such as an interactive map, data visualization, and download.

The BEACO2N website offers an easy-to-use tool for visualizing, comparing and downloading air quality data. Used in science curriculum K-12 and by academic researchers, these data provide measurements of the air we breath and the factors that influence them.

The initial idea for a science gateway is often driven by requirements in research and/or teaching; however, the knowledge about implementing an extensible, scalable, easy-to-use, and sustainable science gateway is not necessarily in the knowledge portfolio of the researcher behind the idea. On the development side, someone knowledgeable on the topic of creating science gateways may not necessarily be an expert in the research area serviced by an envisioned science gateway. The close collaboration between researchers and science gateway creators is crucial to gather all necessary information and requirements on a science gateway. This is usually an underestimated design task, and the exact layout for the science gateway is a continuous and iterative process. Suggestions come from developers for the design and layout while feedback and comments come from the user community. While each community and its requirements for a science gateway are unique, the questions that need to be answered for planning and designing a particular science gateway are very similar for any domain. The panel will discuss effective checklists to support developers communicating with diverse domain experts. Such checklists may be the basis for starting a Software Requirement Specification for an envisioned science gateway.

This panel will be useful for both software developers creating gateways and researchers/educators who specialize in the content of a gateway, as it will illuminate both sides of the process. Additional questions for the panelists will be accepted in advance during the Tuesday afternoon Learning Labs. More details will follow.

There is currently no consensus on how quickly the Greenland ice sheet is melting due to global warming, and what the ramifications will be for the rise in sea level. Sea level rise is a grave concern, due to its potential impact on coastal populations, global economies, and national security. Therefore, the ice-sheet science community is striving to improve their understanding of the problem. This community consists of two groups that perform related but distinct kinds of science: a data community, and a model building community. Broadly, the data community characterizes past and current states of the ice sheets, by assembling data from past events and from satellite observations. The modeling community, meanwhile, seeks to explain and forecast the speed and extent of ice sheet melting and subsequent sea level rise, by developing and validating computational models to explain these changes. Although ice sheet experimental data and models are dependent on one another, these two groups of scientists are not well integrated; better coordination is needed between data collection efforts and modeling efforts if we are to improve our understanding of ice sheet melting rates. These two scientific communities must build closer ties in order to better validate models and reduce prediction uncertainties.

We present a new science gateway, GHub, that is taking form as a collaboration space for ice sheet scientists in academia and government agencies alike. This gateway, built on the HUBzero platform, will host datasets and modeling workflows, and provide access to codes for community tool building. First, we aim to collect, centralize, and fuse existing datasets, creating new data products that more completely catalog the ice sheets of Greenland and Antarctica. Second, we plan to build workflows that provide support for correct model validation and improve uncertainty quantification, thus extending existing ice sheet models. Finally, we will host existing community codes. We will install codes such as CmCt on the gateway server itself, and others, such as ISSM, on gateway-accessible high-performance computing resources, so that scientists can build new tools utilizing them. A natural objective of this gateway is to provide a unifying location where these disparate scientific communities may gather, mingle, and collaborate, using collaborative gateway features with the goal of doing better science. Overall, this gateway will be a major step towards accomplishing goals that were identified by a recent NSF workshop on the Greenland ice sheet. With this new cyberinfrastructure, ice sheet scientists will gain improved tools to quantify the rate and extent of sea level rise, for the benefit of human societies around the globe.

This paper discusses the design and implementation of the ‘Ike Wai Hawai‘i Groundwater Recharge Tool, an application for providing data and analyses of the impacts of land-cover and climate modifications on groundwater-recharge rates for the island of O‘ahu. This application uses simulation data based on a set of 29 land-cover types and two rainfall scenarios to provide users with real-time recharge calculations for interactively defined land-cover modifications. Two visualizations, representing the land cover for the island and the resultant groundwater-recharge rates, and a set of metrics indicating the changes to groundwater recharge for relevant areas of the map are provided to present a set of easily interpreted outcomes based on the user-defined simulations. Tools are provided to give users varying degrees of control over the granularity of data input and output, allowing for the quick production of a roughly defined simulation, or more precise land-cover models that can be exported for further analysis. Heuristics are used to provide a responsive user interface and performant integration with the database containing the full set of simulation data. This tool is designed to provide user-friendly access to the information on the impacts of land-cover and climate changes on groundwater-recharge rates needed to make data-driven decisions.

Wednesday Learning Labs (11:15-12:00pm)
Table Numbers and Topics for this time slot

1. Building gateways shouldn't be this hard   
   It's no secret that science gateways are more than, "just a website." But what makes them so challenging (and expensive) to build? People from every area of the gateway community are invited to come exchange problems, solutions, and ideas about how to make gateway development better for everyone. Hosted by Rion Dooley.
2. Containers: The Why and How
   Do you currently use containers in your gateway? If so, why did you choose to? If not, could you benefit from their use? Hosted by Rajesh Kalyanam.
3. New User Adoption of Gateways
   What can we do to promote new user adoption of gateways? Come share your tips, strategies, and ideas, and learn from others too. Hosted by Kerk Kee.
4. iReceptor: Gateways and Data Standards
   Following up on my talk on Tuesday, discussing iReceptor, a gateway for Immune Genetics, including both the gateway architecture and how we use data standards in our platform. Hosted by Brian Corrie.
5. HPC in the Cloud with Tapis
   Discussions around how to use the Tapis API framework for high throughput and high performance computing. Hosted by Joe Stubbs.
6. SGCI Cloudify Science Gateways
   This solicitation seeks proposals from the SGCI Community to Cloudify Science Gateways for operation in the public cloud. Stop by to talk to us about your idea. Hosted by Boyd Wilson and Amy Cannon.

About Learning Labs
“Learning Labs” may be one of several styles of impromptu learning:

• Pop-up BOFs (Birds-of-a-Feather Sessions)
• Mini Hacks
• Coffee-Break Conversations

We will have three 45-minute periods devoted to your ideas. Round tables will be set up for you to meet with others and discuss the topics of your choice. Here are the ways you can get involved:

1. Propose a topic that you’d be willing to host. (You don’t have to be an expert, just interested!)
2. Find a topic that interests you, and join a table!

Submit your topic with this Google form by Tuesday, September 24 at 7pm Pacific: https://forms.gle/1Th5svq13VeKreLE7.

We’ll announce when and where the first round are happening by Tuesday morning on Sched, second round on Wednesday morning. We may be able to insert additional topics after the deadline if space is available.

Powered by the HUBzero platform, nanoHUB is the science gateway built and operated by the Network for Computational Nanotechnology (NCN). Like many science gateways, nanoHUB offers a variety of content. Among all HUBzero hubs, nanoHUB is unique for its large catalog of simulation tools and its community of tool users. In 2018, nanoHUB saw 16,750 users execute more than 750,000 simulation jobs using some 600 simulation tools. The resources applied to computing these jobs totaled some 145,000 CPU hours.

While the CPU allocation is significant, what is arguably more significant is the “wall” time experienced by the users running the simulation. Our own internal studies have shown a relationship between usage and wall time. Tools that have a low expected wall time typically have the highest utilization. The bulk of nanoHUB Rappture tools typically execute jobs in the range of almost 0.0 seconds to the maximum allowed session time of 2 weeks. Across these jobs, the expected (median) wall time is approximately 17.0 seconds.

Starting in 2011, the combined efforts of the leadership teams of both nanoHUB and HUBzero were awarded an NSF grant for the “Instant On” project. This project invested in several strategies to reduce resource consumption and improve user experience by reducing the turn around time between submitting a simulation job and receiving the computed result. One of the strategies would invest in developing a system to re-use
simulation results when possible. This development ultimately became a part of the HUBzero middleware as a caching system. It is this caching system upon which the remainder of this paper will focus.

In Section 2, we will describe the design goals of the “Instant On” cache and highlight some of the implementation details and features. In Section 3, we will discuss the operation of the cache with respect to utility and economy and also some of the pitfalls both experienced and potential. Section 4 will present some future directions in which the cache is but one of several services built on top of the underlying archive of simulation results. We will conclude in Section 5 with an invitation for other science gateways to use “Instant
On” as part of their tool and workflow pipelines.

In this paper we are introducing SimTools, a simple way to create tools with well-defined inputs and outputs. Ease-of-use is a priority; a SimTool is a Jupyter notebook which can be a self-contained simulation or a wrapper that calls a larger tool. Inputs and outputs are described in YAML embedded in the notebook. A new copy of the notebook is returned as the result of the run, with the cells showing the progress of the simulation, including intermediate results for debugging. Outputs are embedded in the notebook metadata as data or database references. Published SimTools can be deployed as Docker or Singularity images and will be runnable on any platform that can run those containers.

The Chem Compute Science Gateway provides access for undergraduate chemistry students to perform computational chemistry jobs. These jobs are mostly run within a typical 3 - 4 hour laboratory period. Thus, the users and usage of our gateway is quite different from a typical research based gateway. We will demonstrate the usage of the gateway and the aspects of it that are geared towards interfacing with undergraduates in a short lab period.

Wednesday Learning Labs (2:00-2:40pm)
Table Numbers and Topics for this time slot

1. Kubernetes for Fun and Science
   With Kubernetes establishing itself as the de facto container orchestration platform in the cloud, what happens when the gateway community adopts Kubernetes into their projects. Meet fellow developers, designers, and community builders to talk Kubernetes for science and what the availability of open platforms means for gateway sustainability. Hosted by Rion Dooley.
2. Code and Coffee
   We get it. Sometimes you just need a fix. Take a break from the program to grab some coffee, knock out some code. No host, but open to anyone.
3. Jupyter(Hub) in Gateways
   This is a discussion about all things related to the jupyter project, including integrating JupyterHub with Gateways, running Jupyter Notebooks as jobs, and deploying JupyterHub on Jetstream with Kubernetes. Hosted by Andrea Zonca and Julia Looney.
4. Gateways for classroom education
   Let's talk about the challenges of focusing on education in a research oriented world. Hosted by Mark Perri.
5. Research Software Engineers - Challenges of a career path in academia
   One major concern in achieving software sustainability is improving career paths for RSEs, research programmers and/or facilitators - whether they are staff or faculty at academic institutions or national labs. Software contributions are generally not a factor in career advancement in academia. While several initiatives and projects such as US-RSE show the interest in changing the culture in academia to support career paths, the interaction between these initiatives is still sparse. This could be a good time to join forces and use the momentum of the diverse communities thinking about similar challenges. Hosted by Sandra Gesing.

About Learning Labs
“Learning Labs” may be one of several styles of impromptu learning:

• Pop-up BOFs (Birds-of-a-Feather Sessions)
• Mini Hacks
• Coffee-Break Conversations

We will have three 45-minute periods devoted to your ideas. Round tables will be set up for you to meet with others and discuss the topics of your choice. Here are the ways you can get involved:

1. Propose a topic that you’d be willing to host. (You don’t have to be an expert, just interested!)
2. Find a topic that interests you, and join a table!

Submit your topic with this Google form by Tuesday, September 24 at 7pm Pacific: https://forms.gle/1Th5svq13VeKreLE7.

We’ll announce when and where the first round are happening by Tuesday morning on Sched, second round on Wednesday morning. We may be able to insert additional topics after the deadline if space is available.

We're eager for your input about growing the gateway community and shaping upcoming conferences into "can't miss it" events. Join us for a quick chat before grabbing a snack and heading home!