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Monday, October 23
 

7:45am EDT

Shuttle Between the Sheraton and the Union
7:45 am -- depart Sheraton, drop off at Union
8:15 am -- depart Sheraton, drop off at Union
8:45 am -- depart Sheraton, drop off at Union
9:15 am -- depart Sheraton, drop off at Union
9:45 am -- depart Sheraton, drop off at Union

Monday October 23, 2017 7:45am - 9:45am EDT
Sheraton Ann Arbor (driveway in front of hotel) 3200 Boardwalk St., Ann Arbor, MI 48108

8:00am EDT

Breakfast and Registration Opens
The Union Opera Lounge is on the first floor near the registration desk and across from the Anderson rooms. You are welcome to bring breakfast food with you to your tutorial room.

Monday October 23, 2017 8:00am - 9:30am EDT
Union Opera Lounge Michigan Union

9:00am EDT

Globus In Your Gateway
This hands-on, 90-minute tutorial explains and demonstrates how to use Globus to add data transfer features to your Web applications and science gateways.Globus is a free service operated by the University of Chicago and is the basis for the XSEDE system’s data transfer services. Participants will learn about Globus’s data transfer service; why it is an easier, more powerful, and more reliable solution than alternatives; how to use it in their own applications and gateway; and how to configure it for specific use cases. During the tutorial, participants will add data transfer features to a running Web application developed in Python.

Experience: Appropriate for all levels

Prerequisites: Participants are expected to be familiar with logging into a Linux shell via SSH and able to use a Linux text editor (e.g., vi/vim, emacs, nano). Familiarity with Python would be helpful but is not required for success in the tutorial.

What to bring: Participants must bring their own WiFi-enabled device with Web browser and SSH client installed. (Linux and Macintosh systems do not require any additional software. Windows and ChromeOS systems must have an SSH client application installed.) A physical keyboard is strongly recommended. The hands-on exercises will use remotely hosted virtual machines provided by the presenters and accessible via SSH and Web browser.

Presenters
avatar for Lee Liming

Lee Liming

Subscriber Engagement Manager, Globus, University of Chicago
I can tell you all about Globus, our services, and our subscriptions for campuses and other research organizations. I am also part of the XSEDE team, focused on user requirements management and integrating other services with XSEDE.
ST

Steven Tuecke

Globus project lead, Globus / UChicago


Monday October 23, 2017 9:00am - 10:30am EDT
Pond Rooms (1st floor) Michigan Union

9:00am EDT

Communication Fundamentals: Effective Strategies to Explain and Pitch Your Work
In this hands-on tutorial, participants will learn and practice the basics of effective communication. Learners will explore tailoring communication efforts for any audience, developing clear and memorable messages, and crafting compelling and engaging narratives. Using these lessons, participants will then create an elevator pitch related to a gateway project.

RELATE (Researchers Expanding Lay-Audience Teaching and Engagement) is a volunteer-based organization at the University of Michigan that offers workshops, educational resources, and outlets for outreach opportunities to enhance researchers’ competency in communication and public engagement. Learn more at www.learntoRELATE.org.

Skill Level: All (Beginner – Advanced)
Prerequisites: None
Necessary software/technology: pen and paper

Presenters
EL

Elyse L. Aurbach

Research Fellow, Lecturer, MBNI University of Michigan
BP

Brandon Patterson

Student, University of Michigan


Monday October 23, 2017 9:00am - 12:30pm EDT
Pendleton Room (2nd floor) Michigan Union

9:00am EDT

Jupyter and its Moons: An introduction to the Jupyter notebook platform and its ecosystem
Tutorial materials are here: https://github.com/Jupyter-Kale/Jupyter-and-its-moons/

In this hands-on introductory tutorial we will cover Jupyter notebook basics, along with a sampling of tools and technologies in the Jupyter ecosystem.

This includes
  • A tour of Jupyter notebooks and their core features for creating literate computing narratives that combine interactive code, documentation and visualizations.
  • Applications in the Jupyter framework (notebook, filebrowser, text editor, terminal and Jupyterlab)
  • IPython goodies
  • Scientific computing support (matplotlib, pandas etc.)
  • Widgets in Jupyter notebooks for interactive computing
  • Customizing Jupyter
  • High level architecture of Jupyter
  • Jupyterhub (if there is time)

Prerequisites:
Attendees are expected to have installed the Continuum Anaconda Distribution [https://www.anaconda.com/download/] which includes all the necessary Jupyter packages.
Optionally, you may also install Docker [https://www.docker.com/community-edition] in order to run various tools. Some basic knowledge of Python will be helpful but is not required.

Presenters
SC

Shreyas Cholia

Group Lead (Usable Software Systems), Lawrence Berkeley National Laboratory
OE

Oliver Evans

Student Assistant, Lawrence Berkeley National Laboratory


Monday October 23, 2017 9:00am - 12:30pm EDT
Anderson Rooms (1st floor) Michigan Union

9:00am EDT

Success Starts Here: A Step-by-Step Approach to Demonstrate the Value of Your Gateway to Your Sponsors, Your Users, and Yourself
You want your gateway to succeed. Whether your gateway is just getting underway or has been operational for some time, it’s never too early or too late to take steps to improve the chances of reaching your gateway’s goals and to show others, including your sponsors and users, that your gateway makes a difference.

This fast-paced tutorial will use worksheets and other practical exercises to help you draft an evaluation plan customized to your gateway. You will learn to:

-- decide where to best invest your limited evaluation resources
--ask questions that matter to determining to your gateway’s success
--choose appropriate methods to answer your questions
--identify meaningful metrics
--effectively report findings from an evaluation

You will leave the tutorial with a draft evaluation plan and with a step-by-step process you can follow as other evaluation needs arise for your gateway. The tutorial will be valuable whether your gateway decides to conduct its own evaluation or to work with an external evaluator.

Requirements: This session is designed for science gateways of all types, in any discipline, and at all stages of development, from proposal writing to mature project. We welcome attendance from gateway leaders or staff who are new to evaluation as well as those who already have responsibility for evaluation. There is no specific skill level required and no technical expertise needed. A laptop or notebook computer is highly recommended.

Presenters
avatar for Ann Zimmerman

Ann Zimmerman

Principal, Ann Zimmerman Consulting
I specialize in program planning and evaluation research with a special focus on working with science-based projects and organizations.


Monday October 23, 2017 9:00am - 12:30pm EDT
Kuenzel Room (1st floor) Michigan Union

10:30am EDT

Coffee Break
Time for a coffee refresh and then make your way back to your tutorial session.

Monday October 23, 2017 10:30am - 11:00am EDT
Union Opera Lounge Michigan Union

11:00am EDT

User Management with Globus Auth
This hands-on tutorial will explain how to use Globus Auth to manage user identities and user accounts in Web applications and science gateways. Globus Auth [1] is a free service operated by the University of Chicago and is the basis for the XSEDE system’s user authentication and federated identity platform. Participants will learn about Globus Auth’s authentication service; why it is an easier, more user-friendly, and more secure solution than alternatives; how to use it in their own applications and gateways; and how to configure it for specific use cases. During the tutorial, participants will add Globus Auth to a running Web application
developed in Python.

Experience: Appropriate for all levels
Prerequisites: Participants are expected to be familiar with logging into a Linux shell via SSH and able to use a Linux text editor (e.g., vi/vim, emacs, nano). Familiarity with Python would be helpful but is not required for success in the tutorial.
What to bring: Participants must bring their own WiFi-enabled device with Web browser and SSH client installed. (Linux and Macintosh systems do not require any additional software. Windows and ChromeOS systems must have an SSH client application installed.) A physical keyboard is strongly recommended. The hands-on exercises will use remotely hosted virtual machines provided by the presenters and accessible via SSH and Web browser.

Presenters
avatar for Lee Liming

Lee Liming

Subscriber Engagement Manager, Globus, University of Chicago
I can tell you all about Globus, our services, and our subscriptions for campuses and other research organizations. I am also part of the XSEDE team, focused on user requirements management and integrating other services with XSEDE.
ST

Steven Tuecke

Globus project lead, Globus / UChicago


Monday October 23, 2017 11:00am - 12:30pm EDT
Pond Rooms (1st floor) Michigan Union

12:30pm EDT

Lunch
Food will be served in the Union Opera Lounge, with seating across the hall in the Anderson Rooms.

Monday October 23, 2017 12:30pm - 1:30pm EDT
Union Opera Lounge Michigan Union

1:30pm EDT

Introduction to using the Jetstream Cloud API for Science Gateways
NSF’s Jetstream Cloud is a Infrastructure-as-a-Service platform comprised of two geographically isolated OpenStack+Ceph clusters, each supporting hundreds of virtual machines and data volumes. The two cloud systems are integrated via a user-friendly web application that provides a user interface for common cloud computing operations, authentication to XSEDE via Globus, and an expressive set of service APIs. Jetstream enables on-demand access to interactive, user-configurable computing and analysis capability as well as persistent science gateway functionality. It also seeks to democratize access to cloud capabilities and promote sharable, reproducible research.

This session will describe Jetstream in greater detail, as well as how its unique combination of hardware, software, and user engagement support scientific research and also provide hands-on training for the majority of the time using the Jetstream OpenStack API for basic gateway construction.

Length: 3 hours (30-40 min introduction, the rest hands on)
Experience: Intermediate
Requirements: Laptop. Working SSH client. Working web browser.

Presenters
avatar for Jeremy Fischer

Jeremy Fischer

Manager, Jetstream Cloud, Jetstream - Indiana University
Cloud computing for research and education!


Monday October 23, 2017 1:30pm - 5:00pm EDT
Kuenzel Room (1st floor) Michigan Union

1:30pm EDT

The Biodiversity and Climate Change Virtual Laboratory (BCCVL): an innovative tool for mapping and modelling species distributions
Models play a critical role in synthesising our understanding of the natural world and making forward projections into novel conditions. While they are central to ecological forecasting, models remain inaccessible to most ecologists, in large part due to the informatics challenges of managing the flows of information in and out of such models. The Biodiversity and Climate Change Virtual Laboratory (BCCVL) is a “one stop modelling shop” that simplifies the process of biodiversity and climate impact modelling. It uses national computational infrastructure to provide access to global biodiversity, climate and environmental data integrated with a suite of tools in a coherent online environment. In this tutorial, we will introduce participants to the basics of species distribution modelling and climate change projections and teach how to use the BCCVL to run these models.

Requirements: beginner skill level, no prerequisites, and there are no software requirements necessary. We only advise participants to bring their own laptop and use a browser other than Internet Explorer (e.g. Chrome, Safari, Firefox)

Presenters
SR

Sarah Richmond

Project Manager - BCCVL, Griffith University


Monday October 23, 2017 1:30pm - 5:00pm EDT
Pond Rooms (1st floor) Michigan Union

1:30pm EDT

Think Like an Entrepreneur: Business Strategy for Science Gateways
While project leaders of Science Gateways are often grant-funded, there are many ways in which strategies derived from the for-profit sector are extremely valuable in making sure that the Gateways are successful in offering value to their users. This tutorial will engage participants in hands-on activities designed to help them understand strategic approaches to sustainability, and tactics for better understanding the existing and potential users of their Gateways.

Requirements: This session is designed for leaders of Science Gateways of all types, at all stages of development, from proposal writing to mature project. We encourage leaders from all disciplines to attend. There is no specific skill level required, no technical expertise needed, and no special software or hardware needed.

Presenters
avatar for Juliana Casavan

Juliana Casavan

Science Gateways Community Institute
Juliana Casavan is the Entrepreneurial Programs Manager at The Foundry at Purdue University. Juliana provides educational and workshop opportunities for clients of The Purdue Foundry, a nationally recognized leader in translation of research to market, with the primary workshop called... Read More →
avatar for Nancy Maron

Nancy Maron

BlueSky to BluePrint, LLC
Nancy works with publishers, librarians and other innovative project leaders to define, test and refine assumptions about their new and existing products and services. She honed her skills in over 20 years of experience working at the nexus of publishing, higher education and technology... Read More →


Monday October 23, 2017 1:30pm - 5:00pm EDT
Pendleton Room (2nd floor) Michigan Union

1:30pm EDT

Using the Agave API and Jupyter to Run Simulations, Monitor Events, and Share and Visualize Scientific Results
As science becomes increasingly digital, researchers face new challenges and opportunities to analyze, share, and understand large volumes of data more effectively. Gateways are at the forefront of this challenge, and the Agave Platform has been at the forefront of the gateway movement. Over the last 6 years, the authors have been working to develop this Science-as-a-Service platform, making it possible for users to go from the desktop, to their local data center, to the cloud.But Agave isn’t simply a tool for building web portals–it is, first and foremost, a sophisticated tool chain that enables developers to run jobs, monitor them, collaborate, and share data. As such, it is versatile and adaptable to new environments and interfaces. One such new and innovative variation on the web application is the Jupyter notebook, which combines the best elements of both the command line and the graphical interface.

This tutorial will present a set of hands-on gateway-building techniques using a pair of specific tools: The Agave API and the Jupyter notebook. It will show users how they can (1) take a code and make it run on an HPC resource through both a traditional-style web portal and a notebook, (2) monitor events and notifications in a variety of ways, (3) access, move, and share the data generated by the code, (4) explore and visualize the output (5) trace the provenance records (i.e. the events generated by the job during its execution).

Content Level: Introductory: 40%, Intermediate:60%. For full understanding of the notebooks and their actions, some programming and HPC experience,familiarity with the concepts of batch and interactive computing, and basic competency using Python and the Linux command line are helpful. No specific domain expertise is needed to understand the presentation.

Presenters
avatar for Steven R. Brandt

Steven R. Brandt

Assistant Director, Computational Science, Louisiana State University
avatar for Rion Dooley

Rion Dooley

Director of Platform Services and Solutions, Data Machines Corp
Rion Dooley, PhD is the Director of Platform Services and Solutions at Data Machines Corp. He came to DMC from Texas Advanced Computing Center where he spent the last decade integrating new and emerging technologies to build solutions that make it easier to conduct open, digital science... Read More →
avatar for Kathy Traxler

Kathy Traxler

Outreach and Training Specialist, Center for Computation & Technology at LSU
I have been creating and implementing HPC educational courses and training since 2004. I have worked with XSEDE on student programs and training since it started and have worked with SuperComputing on training and tutorials and student programs since 2007.


Monday October 23, 2017 1:30pm - 5:00pm EDT
Anderson Rooms (1st floor) Michigan Union

3:00pm EDT

Break with snacks, sponsored by Texas Advanced Computing Center (TACC)
Enjoy snacks and mingle with other tutorial attendees.


Monday October 23, 2017 3:00pm - 3:30pm EDT
Union Opera Lounge Michigan Union

5:15pm EDT

Dinner at Menlo Innovations, with bar sponsored by HUBzero
This event will be held at Menlo Innovations, a local software design and development "factory" that uses eXtreme Programming and High-Tech Anthropology® to maximize project management agility and product quality. Brief tours will be offered at the start of the evening for those who are interested. The unusual culture of Menlo Innovations has been documented in the book Joy, Inc.: How We Built a Workplace People Love, by co-founder Rich Sheridan. People come from all over the world to see Menlo's remakable workplace.

No walk-in registration is available. Pre-registration is included if you are registered for Monday, or a la carte registration is available to those who are only registered for Tuesday and Wednesday.

This evening's bar is sponsored by HUBzero.


Monday October 23, 2017 5:15pm - 7:30pm EDT
Menlo Innovations LLC Offices at Liberty Square, 505 East Liberty, LL500 (Lower Level)

6:30pm EDT

Shuttle Between the Union and the Sheraton
6:30 pm -- depart Union, drop off at Sheraton
7:00 pm -- depart Union, drop off at Sheraton
7:30 pm -- depart Union, drop off at Sheraton
8:30 pm -- depart Union, drop off at Sheraton

Monday October 23, 2017 6:30pm - 8:30pm EDT
Michigan Union Bus Stop State Street, just north of South University
 
Tuesday, October 24
 

7:45am EDT

Shuttle Between the Sheraton and the Union
7:45 am -- depart Sheraton, drop off at Union
8:15 am -- depart Sheraton, drop off at Union
8:45 am -- depart Sheraton, drop off at Union
9:15 am -- depart Sheraton, drop off at Union
9:45 am -- depart Sheraton, drop off at Union

Tuesday October 24, 2017 7:45am - 9:45am EDT
Sheraton Ann Arbor (driveway in front of hotel) 3200 Boardwalk St., Ann Arbor, MI 48108

8:00am EDT

Breakfast, sponsored by Indiana University Pervasive Technology Institute), Registration Opens
Breakfast will be available in the Rogel Ballroom, adjacent to the Registration Desk. This breakfast is sponsored by Indiana University's Pervasive Technology Institute.


Tuesday October 24, 2017 8:00am - 9:30am EDT
Rogel Ballroom (2nd floor) Michigan Union

8:45am EDT

Welcome & Announcement of Awards
Grab your breakfast and join us for a brief welcome to the conference, an overview of the two days ahead, and the announcement of the Young Professional of the Year Awards, sponsored by the Science Gateways Community Institute. You'll also get to see the other Young Professionals attending the conference so that you can keep an eye out for them and welcome them to the community of science gateway creators and users!

Tuesday October 24, 2017 8:45am - 9:15am EDT
Rogel Ballroom (2nd floor) Michigan Union

9:15am EDT

Your Audience Comes First: The Key to Communication and Engagement
Connecting people through scientific or engineering gateways requires effective communication. All gateway users – researchers, educators, public audiences – must understand the purpose, utility, and significance of the gateway if it is to be successful. Therefore, establishing effective communication practices to explain the project becomes critical to developing the gateway and ensuring its longevity. Fortunately, communication skills can be learned and practiced by anyone. Developing communication efforts with goals that align with those of the target audience, using storytelling to convey clear messages, and using appropriate language and visual elements are all key skills of a successful communication strategy. Putting these skills into practice can maximize the utility and benefits of your gateway for all parties involved.

Slides are available at https://doi.org/10.6084/m9.figshare.5613217 (19MB).

Elyse L. Aurbach is a co-founder and co-director of the science communication and public engagement organization, RELATE (www.learntoRELATE.org). She uses evidence-based research, active learning techniques, improv exercises, and best practices to develop curricula to teach communication skills and facilitate public engagement. Aurbach holds a PhD in neuroscience from the University of Michigan, and her current research uses informatics techniques to examine network changes in the brain associated with psychiatric illnesses.

Presenters
EL

Elyse L. Aurbach

Research Fellow, Lecturer, MBNI University of Michigan


Tuesday October 24, 2017 9:15am - 10:30am EDT
Rogel Ballroom (2nd floor) Michigan Union

10:30am EDT

Coffee Break
Time for a coffee refresh and then make your way to your choice of concurrent sessions.

Tuesday October 24, 2017 10:30am - 10:50am EDT
Rogel Ballroom (2nd floor) Michigan Union

10:49am EDT

Concurrents A
"Concurrents A" has two themed sets of presentations:

  1. Tools for Secure Access (Pendleton)
  2. Gateway Journeys (Rogel)

Each presentation is 20 minutes total, including 5 minutes of Q&A. Approximate start times of the papers (which are displayed in presentation order) are:
  • 10:55am
  • 11:15am
  • 11:35am


Tuesday October 24, 2017 10:49am - 11:55am EDT
2nd floor meeting rooms Michigan Union

10:50am EDT

A1.1 Demo: The OSiRIS User Interface
Our OSiRIS (Open Storage Research InfraStructure) demo will focus on the flexibility of our resource provisioning process. We’ll show how a prospective OSiRIS user can authenticate to our system with their InCommon member institute credentials and receive a provision of storage space using the protocol(s) of their choice - POSIX mount or S3. The demonstration will also show how users can self-organize access groups for other users within their organization and quickly authorize their client software to connect to their storage allocation. The key points of this demo are that users will be able to use credentials administered not by us but by their home institutions and they’ll easily be able to invite others to collaborate in their OSiRIS VO with access rights of their choosing.

Presenters
SM

Shawn McKee

Research Scientist, University of Michigan Physics
BM

Benjeman Meekhof

OSiRIS Lead Engineer, UM ARC-TS


Tuesday October 24, 2017 10:50am - 11:55am EDT
Pendleton Room (2nd floor) Michigan Union

10:50am EDT

A1.2 Short Paper: Secure Web-Based Access for Productive Supercomputing
US Department of Defense High Performance Computing (HPC) Modernization Program communities are increasingly in need of access to highly capable computing, networking, storage, and software resources from their user enclaves that are administratively prevented from installation of applications due to malicious software risks. The HPC Portal enables a productive and secure computational science environment.


Tuesday October 24, 2017 10:50am - 11:55am EDT
Pendleton Room (2nd floor) Michigan Union

10:50am EDT

A1.3 Short Paper: Using Keycloak for Gateway Authentication and Authorization
Establishing users’ identities before they access research infrastructure resources is a key feature of science gateways. With many science gateways now relying on general purpose gateway platform services, the challenges of managing identity-derived features have expanded to include authorization between science gateway tenants, middleware, and third party identity provider services. The latter include campus identity management systems. This paper examines the use of Keycloak as an implementation of an identity management system for Apache Airavata middleware, replacing our previous WSO2 Identity Server-based implementation. This effort raises larger issues that software-as-a-service communities should consider when embedding dependencies on third party software and services, including developing selection criteria and future-proofing systems.

Presenters
avatar for Marcus Christie

Marcus Christie

Principal Science Gateway Research Consultant, Indiana University
Apache Airavata, scientific computing, high performance computing, Vue.js, Django, big data, cloud computing
SM

Suresh Marru

Gateway Architect, Indiana University
SP

Sudhakar Pamidighantam

Senior Scientist, Indiana University
MP

Marlon Pierce

Director, Science Gateways Research Center, Indiana University


Tuesday October 24, 2017 10:50am - 11:55am EDT
Pendleton Room (2nd floor) Michigan Union

10:50am EDT

A2.1 Short Paper: REMEDI - Where Hospitals Share Data for the Improvement of Patient Safety
The Regenstrief National Center for Medical Device Informatics (REMEDI) is an evidence-based community of practice for medical device informatics to promote and improve patient safety. REMEDI collects data that have been captured and stored on medical devices such as smart infusion pumps. It enables users to conduct complex analyses via a point-and-click web interface. These analyses can be conducted on both specific hospitals and groups of hospitals to enable comparative examinations and benchmarking. Members of the REMEDI community voluntarily contribute data and identify themselves to each other. In this short paper, we describe REMEDI community and discuss technical aspects and challenges of the platform. Next, we examine different applications of the REMEDI platform and how each application serves the community. Finally, we highlight areas of future work on the platform.

Presenters
DJ

Damion Junk

Senior Data Scientist, Purdue University / HubZero
avatar for Michael Zentner

Michael Zentner

Director, HUBzero Platform, Purdue University / HUBzero
Entrepreneurship, Leadership of large cyberinfrastructure projects.


Tuesday October 24, 2017 10:50am - 11:55am EDT
Rogel Ballroom (2nd floor) Michigan Union

10:50am EDT

A2.2 Short Paper: Development of the Nanoconfinement Science Gateway
The nanoconfinement science gateway empowers users to simulate the distributions of ions confined between material surfaces that are nanometers apart. The gateway facilitates investigations for a wide array of ionic and environmental parameters using standard molecular dynamics (MD) techniques for unpolarizable interfaces and an advanced MD technique for polarizable interfaces. In this paper, we discuss the goals of the nanoconfinement science gateway and elucidate the plans for building it.

Presenters
SM

Suresh Marru

Gateway Architect, Indiana University


Tuesday October 24, 2017 10:50am - 11:55am EDT
Rogel Ballroom (2nd floor) Michigan Union

10:50am EDT

A2.3 Short Paper: nSides: An interactive drug--side effect gateway
Adverse drug events are a leading cause of morbidity and mortality around the world. Regulatory agencies, such as the Food and Drug Administration (FDA), maintain large collections of adverse event reports. These spontaneous reporting systems provide an opportunity to retrospectively study drug effects from patient population data. To make our results more accessible, we present a gateway to a new database of drug interactions (nSides) developed using the FDA Adverse Event Reporting System. Side effects for a variety of drugs and drug interactions are presented. Additionally, for high order drug combinations, with the support of the Science Gateway Community Institute's Extended Developer Support, we develop a novel system to request new models to be generated using the Open Science Grid on-demand.

Presenters
RV

Rami Vanguri

Postdoctoral Research Scientist, Columbia University
avatar for Choonhan Youn

Choonhan Youn

computer scientist, SDSC at UCSD


Tuesday October 24, 2017 10:50am - 11:55am EDT
Rogel Ballroom (2nd floor) Michigan Union

11:55am EDT

Lunch, sponsored by CloudyCluster by Omnibond
This lunch, sponsored by CloudyCluster by Omnibond, also features themed tables. If you are interested in any of the topics, feel free to join that table for a lively discussion with your colleagues. Topics will be announced at the conference.


Tuesday October 24, 2017 11:55am - 12:55pm EDT
Rogel Ballroom (2nd floor) Michigan Union

12:54pm EDT

Concurrents B
"Concurrents B" has two themed sets of presentations:

  1. Systems to Connect Resources (Pendleton)
  2. Platforms (Rogel)

Each presentation is 20 minutes total, including 5 minutes of Q&A. Approximate start times of the papers (which are displayed in presentation order) are:
  • 1:00pm
  • 1:20pm
  • 1:40pm
  • 2:00pm

Tuesday October 24, 2017 12:54pm - 2:20pm EDT
2nd floor meeting rooms Michigan Union

12:55pm EDT

B1.1 Demo: Extending Jupyter to Support Interactive High Performance Computing
This demonstration will showcase our work in integrating the Jupyter platform with HPC resources, including extensions and modifications that enable “human in the loop” interactive supercomupting.

Presenters
SC

Shreyas Cholia

Group Lead (Usable Software Systems), Lawrence Berkeley National Laboratory
OE

Oliver Evans

Student Assistant, Lawrence Berkeley National Laboratory


Tuesday October 24, 2017 12:55pm - 2:20pm EDT
Pendleton Room (2nd floor) Michigan Union

12:55pm EDT

B1.2 Short Paper: Evaluating Big Data Frameworks To Simplify Distributed Task Execution In Apache Airavata
Apache Airavata powers users to run scientific applications on remote computing resources. Airavata integrates with science gateways to moderate computational jobs on diverse resources. Some of the job may require to execute multiple tasks. Newer technology trends such as Cloud Computing, BigData and Internet of Things are yielding open source software frameworks which are built for scale and reliability. In this paper we share our experiences in exploring the use of such frameworks and adapt for science gateway task management needs implemented by Apache Airavata.

Presenters
SM

Suresh Marru

Gateway Architect, Indiana University
MP

Marlon Pierce

Director, Science Gateways Research Center, Indiana University
GS

Gourav Shenoy

Research Assistant, Indiana University


Tuesday October 24, 2017 12:55pm - 2:20pm EDT
Pendleton Room (2nd floor) Michigan Union

12:55pm EDT

B1.3 Short Paper: Managing Computational Gateway Resources with XDMoD
The U.S. National Science Foundation (NSF) has invested heavily in research computing, funding XSEDE to integrate supercomputers with science gateways and datasets for researchers in the U.S. and around the world. It is important to understand how these tools contribute to knowledge, plan wisely for future resource investments, and enable end users to make better use of these resources. Enter XDMoD (XD Metrics on Demand), a comprehensive tool that collects and presents detailed data about resource usage, for program managers, developers, support staff, and end users alike. As XSEDE adds non-traditional resources and diversifies its computational resources, the considerable capabilities offered by XDMoD must keep pace. In this short paper, we introduce XDMoD's current capabilities, describe the state of its support for gateway resources, and outline our plans to further enhance these offerings.


Tuesday October 24, 2017 12:55pm - 2:20pm EDT
Pendleton Room (2nd floor) Michigan Union

12:55pm EDT

B1.4 Demo: CloudLaunch as a Gateway for Discovering and Launching Cloud Applications
Global presence of cloud computing infrastructure and increasing demand by researchers to be able to easily gain access to research software is putting pressure on application deployers to make their applications easily accessible. In this demo, we present CloudLaunch as a portal for discovering and launching cloud-enabled applications on a variety of cloud providers. The portal makes it possible for deployers to readily integrate their application into the portal while end-users can easily browse and launch available applications. CloudLaunch provides necessary abstractions to make either task uniform and accessible across all supported cloud providers.

Presenters
avatar for The Other Enis Afgan

The Other Enis Afgan

Research scientist, Johns Hopkins University
avatar for Marcus Christie

Marcus Christie

Principal Science Gateway Research Consultant, Indiana University
Apache Airavata, scientific computing, high performance computing, Vue.js, Django, big data, cloud computing


Tuesday October 24, 2017 12:55pm - 2:20pm EDT
Pendleton Room (2nd floor) Michigan Union

12:55pm EDT

B2.1 Demo: Developing Apps to Extend Open OnDemand
The Open OnDemand Project is an open-source software project that enables high- performance computing (HPC) centers to install and deploy advanced web and graphical interfaces for their users. We have seen OnDemand’s bundled applications significantly lower the barrier to entry for novice users. In addition, OnDemand can be easily extended for a given user community through the development of custom applications. In this demonstration, we show the creation, development and deployment of a simple example application.

Presenters
EF

Eric Franz

Web & Interface Applications Senior Engineer, Ohio Supercomputer Center
JN

Jeremy Nicklas

Web and Interface Application Engineer, Ohio Supercomputer Center


Tuesday October 24, 2017 12:55pm - 2:20pm EDT
Rogel Ballroom (2nd floor) Michigan Union

12:55pm EDT

B2.2 Short Paper: Integrating Web Applications into the HUBzero Gateway Platform
The HUBzero(R) Platform has a long history of supporting interactive simulation tools with X11-based graphical user interfaces through the web browser. In recent years, new HTML and JavaScript based development environments have matured and are being utilized by researchers to help them perform research, develop simulations, clean and explore data, and present results. In this paper, we look at how the HUBzero Platform supports the use and publication of web applications built with Jupyter Notebooks and RStudio’s Shiny and RMarkdown libraries, and how this infrastructure is generic enough to support other web application platforms.

Presenters
MH

Martin Hunt

Senior Software Enginer, Purdue University
DK

Derrick Kearney

Software Engineer, Purdue University


Tuesday October 24, 2017 12:55pm - 2:20pm EDT
Rogel Ballroom (2nd floor) Michigan Union

12:55pm EDT

B2.3 Short Paper: SLATE and the Mobility of Capability
SLATE (Services Layer at the Edge) implements “cyberinfrastructure as code” by augmenting the canonical Science DMZ pattern with a generic, programmable, secure and trusted underlayment platform. This platform hosts advanced container-centric services needed for higher-level capabilities such as data transfer nodes, software and data caches, workflow services and science gateway components. SLATE uses best-of-breed data center virtualization components, and where available, software defined networking, to enable distributed automation of deployment and service lifecycle management tasks by domain experts. As such it simplifies creation of scalable platforms that connect research teams, institutions and resources to accelerate science while reducing operational costs and development cycle times. Since SLATE needs only commodity components for its functional layers, it is used in building distributed systems across all data center types and scales thus enabling creation of ubiquitous, science-driven cyberinfrastructure. By providing automation and programmatic interfaces to distributed HPC back-ends and other cyberinfrastructure resources, SLATE can amplify the reach of science gateways and therefore the domain communities they support.

Presenters
SM

Shawn McKee

Research Scientist, University of Michigan Physics


Tuesday October 24, 2017 12:55pm - 2:20pm EDT
Rogel Ballroom (2nd floor) Michigan Union

12:55pm EDT

B2.4 Short Paper: cvfHUB: A Gateway Supporting Microsoft Windows in Engineering Workflows
The HUBzeroR platform enables scientists to build off one another’s research by providing a robust collaborative platform to allow them to share the software they created and utilized for their work. Customized tools, code, and data were no
longer forgotten after a research effort was complete. HUBzero enabled researchers to offer their tools for anyone to use and modify so they could continue to collaborate long after the initial project concluded. Early versions of HUBzero focused on providing researchers a Linux based environment to host their software. Our group realized there was growing interest in HUBzero hosting commercial, licensed software, which often requires Microsoft Windows, so we began to investigate how we could integrate Microsoft Windows into HUBzero. A key partner, the Institute for Advanced Composites Manufacturing Innovation (IACMI) joined the effort. In this paper, we discuss the approach of our solution and associated
learnings.

Presenters
DB

David Benham

Senior Software Engineer, Purdue University
avatar for Michael Zentner

Michael Zentner

Director, HUBzero Platform, Purdue University / HUBzero
Entrepreneurship, Leadership of large cyberinfrastructure projects.


Tuesday October 24, 2017 12:55pm - 2:20pm EDT
Rogel Ballroom (2nd floor) Michigan Union

2:20pm EDT

Break with snacks, sponsored by San Diego Supercomputer Center
Enjoy some snacks, sponsored by the San Diego Supercomputer Center, and then make your way to your choice of concurrent sessions.


Tuesday October 24, 2017 2:20pm - 2:50pm EDT
Rogel Ballroom (2nd floor) Michigan Union

2:49pm EDT

Concurrents C
"Concurrents C" has two themed sets of presentations:

  1. Supporting Data Use Through Infrastructure and Best Practices (Pendleton)
  2. Drawing on Experience to Promote Quality and Sustainability (Rogel)

Each presentation is 20 minutes total, including 5 minutes of Q&A. Approximate start times of the papers (which are displayed in presentation order) are:
  • 2:55pm
  • 3:15pm
  • 3:35pm (The last presentation in Concurrents C.1, which is a paper and demo combined, is 30 minutes total.)

Tuesday October 24, 2017 2:49pm - 4:05pm EDT
2nd floor meeting rooms Michigan Union

2:50pm EDT

C1.1 Short Paper: Improving Online Data Sharing with the W3C Data on the Web Best Practices
In January 2017, the World Wide Web Consortium (W3C) approved a new recommendation, Data on the Web Best Practices (DWBP), with the intention of providing guidance for those who publish datasets of all kinds on the Web. The goals were to enhance communication between publishers and consumers, to promote the re-use of data, and to foster trust in data by consumers. We review the best practices in the context of science gateways and discuss the applicability of each guideline in scientific data sharing.

Presenters
AG

Annette Greiner

web application developer, NERSC, LBNL


Tuesday October 24, 2017 2:50pm - 4:05pm EDT
Pendleton Room (2nd floor) Michigan Union

2:50pm EDT

C1.2 Short Paper: xDCI - Accelerating Data Cyberinfrastructure and Research for Community Science Gateways
Authors: Ray Idaszak • Stan Ahalt • Kira Bradford • Chris Calloway • Claris Castillo • Jason Coposky • Jon Crabtree • Sarah Davis  • Yue Guo • Fan Jiang • Ashok Krishnamurthy • Howard Lander • W. Christopher Lenhardt • Arcot Rajasekar • Kimberly Robasky • Terrell Russell • Erik Scott • Don Sizemore  • Michael Stealey • Hao Xu • Hong Yi • Wenzhao Zhang

Abstract: This presentation discusses xDCI, a Data Cyberinfrastructure environment that accelerates deployment of Science Gateways. Recognizing the growing importance of Science Gateways, xDCI builds on their elements in making it efficient for individuals and organizations to launch and sustain customizable Science Gateways[ #_ftn1]while growing their respective communities and accelerating resultant science.

Presenters
RI

Ray Idaszak

Director of DevOps, RENCI / University of North Carolina at Chapel Hill


Tuesday October 24, 2017 2:50pm - 4:05pm EDT
Pendleton Room (2nd floor) Michigan Union

2:50pm EDT

C1.3 Short Paper + DEMO: SeedMe: Data sharing building blocks
The need for data sharing and rapid data access has become central with the rise of collaborative research in many disciplines. Several data sharing approaches have emerged for consumer use cases that primarily need an easy way to share files using web browsers. However, these approaches are not well suited to the particular demands of large-scale data sharing for computational research. Whereas consumer approaches primarily support manual user interfaces to add and remove files, the huge number of files that can be generated during and after a large-scale computation job make manual data sharing interfaces impractical. Instead, these tasks require mechanisms that integrate into computation workflows to automatically post files during and after computation jobs. Furthermore, scientific data sharing requires additional metadata and descriptive information that characterizes shared data to record job and compute platform characteristics, input data, job parameters, job completion status, and other record-keeping required to document the trajectory of computational research. Without these features, consumer data sharing approaches are not well suited for computational science.

In this work we describe SeedMe2 (Stream, Encode, Explore and Disseminate My Experiments) as a data sharing platform that caters to unique needs of computational scientists to support data sharing, context descriptions, discussion, light visualization of supported small data format and easy workflow integration.

Presenters
AC

Amit Chourasia

Visualization group leader, University of California San Diego


Tuesday October 24, 2017 2:50pm - 4:05pm EDT
Pendleton Room (2nd floor) Michigan Union

2:50pm EDT

C2.1 Short Paper: Science Gateways: Sustainability via On-Campus Teams
The challenges for creators of specific science gateways are manifold, and the expertise needed for well-designed science gateways is very diverse. The sustainability of science gateways is crucial to serve communities effectively, efficiently and reliably. One measure to achieve greater sustainability of science gateways is establishing on-campus teams. Researchers are served more efficiently since the support by experienced developers reduces individual project investments, and a team can bring the diversity of required expertise for a well-designed science gateway. This paper goes into detail about the challenges and the benefits of on-campus groups and of sharing resources across a campus. We provide four successful cases, describe the services of the Science Gateways Community Institute (SGCI) to support the process in building such groups, and recommend strategies for using free campus resources.

Presenters
avatar for Maytal Dahan

Maytal Dahan

Manager, Portals & Gateways Infrastructure Group, Texas Advanced Computing Center
PEARC17 Tech Program Chair, come by and say hi!
avatar for Katherine Lawrence

Katherine Lawrence

Associate Director, Community Engagement & Exchange, U of Michigan/Science Gateways Community Institute
I help people creating advanced digital resources for research and education connect their projects with helpful services, expertise, and information. Ask me how the Science Gateways Community Institute can support your projects--at no cost--to better leverage the people and money... Read More →
MP

Marlon Pierce

Director, Science Gateways Research Center, Indiana University
avatar for Nancy Wilkins-Diehr

Nancy Wilkins-Diehr

Associate Director, San Diego Supercomputer Center
Science gateways and running
avatar for Michael Zentner

Michael Zentner

Director, HUBzero Platform, Purdue University / HUBzero
Entrepreneurship, Leadership of large cyberinfrastructure projects.


Tuesday October 24, 2017 2:50pm - 4:05pm EDT
Rogel Ballroom (2nd floor) Michigan Union

2:50pm EDT

C2.2 Short Paper: Evaluating Interactive Archives
Consequently, software preservation has become a new focus of the scientific world; commercial and academic projects have sprouted to fill the void for software preservation. There are emerging standards for packaging content in projects such as Popper, Research Objects, and DataMill. Websites such as RunMyCode, MyExperiment, Research Compendia, Zenodo, Open Science Framework, and two independent projects both called Datahub have been created to host scientific code and data. There are also software frameworks that a researcher can leverage to build their own software, such as torch.ch and GenePattern. There are tools to capture and replay the dynamic execution of software such as ReproZip, CDE, and Sumatra. Another strategy are curated collections of software such as Madagascar, including Taverna, Galaxy, Wings, VisTrails, and Kepler. A plethora of literate programming solutions to combine code and prose such as knitr, SOLE, Jupyter, Zeppelin, Collage, Binder, and Beaker Notebook have appeared. Services have sprung up to run science code in the cloud, like Chameleon Cloud, NanoHub, and two commercial services: defunct Wind River Helix Lab Cloud and newcomer Code Ocean. Finally, there are tools that describe a software environment and generate virtual machines on the fly such as Umbrella, Simulocean, and OCCAM. In fact, the problem has shifted somewhat from a reproducibility crisis to an issue of there being too many solutions and knowing which ones to use!

It is obvious that there is every motivation to create software archives that can keep digital artifacts for scientific research running. Yet, we have no means to evaluate these archival systems. The broader scientific software community needs to put effort into defining what quality means for both artifacts and archives. We will define such a criteria, look at existing archives and their drawbacks, and how it shows through experience that this metric is appropriate.

Presenters
DW

David Wilkinson

System Designer, University of Pittsburgh


Tuesday October 24, 2017 2:50pm - 4:05pm EDT
Rogel Ballroom (2nd floor) Michigan Union

2:50pm EDT

C2.3 Short Paper: Science Gateway Patterns and Practices: Experiences Deploying Web Portals for Science at the NERSC Supercomputing Center
In this work we catalog patterns, practices and trends we have seen from our experiences deploying science gateways at the NERSC supercomputing center. We cover the following topics: Sharing Data Over The Web, Web Frameworks for Science, Web IDEs and Interactive HPC, REST APIs, Authentication and Authorization, Edge Services, Data Transfer Services, Cloud based Portals, and Containers. This is our attempt to share what we have learned with the community, and to identify key aspects of science gateway deployment and development.

Presenters
SC

Shreyas Cholia

Group Lead (Usable Software Systems), Lawrence Berkeley National Laboratory
AG

Annette Greiner

web application developer, NERSC, LBNL


Tuesday October 24, 2017 2:50pm - 4:05pm EDT
Rogel Ballroom (2nd floor) Michigan Union

4:15pm EDT

Open Space Kickoff (Proposal of Session Topics)
“Open Space” sessions allow you, as a participant, to determine part of our conversational agenda. “Open Space Technology” was born from the realization that the most exciting, satisfying, useful parts of a conference are often the coffee breaks. The goal of an Open Space Technology (OST; sometimes called an “unconference”) meeting is to create time and space for participants to engage deeply and creatively around issues of concern to them. The agenda is set by the participants and emerges from their individual and collective interests. There is no need to have prior experience with an OST event to participate — just bring your interests and ideas!

We invite you to think about topics that you would like to discuss with your colleagues. It could be a problem you face in your science gateway work, a question you have about gateway technologies, a discovery you’d like to share with others, or an idea that occurs to you during the course of the conference. 

On Tuesday afternoon, we'll collect your ideas to organize "Open Space" conversations. There will be two 25-minute "sets" of concurrent sessions on Wednesday afternoon, plus a lunch "set" on Wednesday. Also, based on your registration ideas, we'll provide a variety of "Open Space" tables during Tuesday lunch. Think of them as mini BoFs!

We’ll be gathering your ideas, placing them into a basic agenda, and letting the conversation go!

Tuesday October 24, 2017 4:15pm - 5:00pm EDT
Rogel Ballroom (2nd floor) Michigan Union

5:00pm EDT

Shuttle Between the Union and the Sheraton
5:00 pm -- depart Union, drop off at Sheraton
5:15 pm -- depart Sheraton, drop off at Union
5:30 pm -- depart Union, drop off at Sheraton
5:45 pm -- depart Sheraton, drop off at Union
6:00 pm -- depart Union, drop off at Sheraton
6:15 pm -- depart Sheraton, drop off at Union
6:30 pm -- depart Union, drop off at Sheraton
6:45 pm -- depart Sheraton, drop off at Union
7:00 pm -- depart Union, drop off at Sheraton
7:15 pm -- depart Sheraton, drop off at Union
7:30 pm -- depart Union, drop off at Sheraton
7:45 pm -- depart Sheraton, drop off at Union
8:00 pm -- depart Union, drop off at Sheraton
8:15 pm -- depart Sheraton, drop off at Union
8:30 pm -- depart Union, drop off at Sheraton

Tuesday October 24, 2017 5:00pm - 8:30pm EDT
Michigan Union Bus Stop State Street, just north of South University

5:30pm EDT

Poster Session, Resource Expo, and Reception, with bar sponsored by HUBzero
This event is at the University of Michigan Museum of Art, which is across the street from our conference venue at the Michigan Union. While you're waiting for our event to begin (and while presenters are setting up), you can browse the museum galleries from 5:30 to 6:00pm. The full reception with the Poster Session and Resource Expo begins at 6:00pm. The Resource Expo is an opportunity to mingle and talk with resource providers, vendors, and other organizations relevant to science gateways. The reception will include heavy hors d'oeuvres, a bar, and music. Mix it all together for a lively evening of conversation and learning. This event is included in the full conference registration and is also available to attend a la carte if you are only joining part of the conference.

The bar is sponsored by HUBzero, including their private-label beer. Have a bottle!


Tuesday October 24, 2017 5:30pm - 8:00pm EDT
University of Michigan Museum of Art (UMMA) 525 South State Street (across from Michigan Union)
 
Wednesday, October 25
 

7:45am EDT

Shuttle Between the Sheraton and the Union
7:45 am -- depart Sheraton, drop off at Union
8:15 am -- depart Sheraton, drop off at Union
8:45 am -- depart Sheraton, drop off at Union
9:15 am -- depart Sheraton, drop off at Union
9:45 am -- depart Sheraton, drop off at Union

Wednesday October 25, 2017 7:45am - 9:45am EDT
Sheraton Ann Arbor (driveway in front of hotel) 3200 Boardwalk St., Ann Arbor, MI 48108

8:00am EDT

Breakfast and Registration Opens
Wednesday October 25, 2017 8:00am - 9:30am EDT
Rogel Ballroom (2nd floor) Michigan Union

8:45am EDT

Panel: The Business of Gateways: Experiences in the First Science Gateways Community Institute Incubator Bootcamp
On 24-28 of April, 2017, the Science Gateways Community Institute Incubator held its first in-person training session, a Science Gateways Bootcamp, comprised of 22 people, representing 10 different projects, all facing the same issue: how to make their projects sustainable over the long term. This panel invites 4 cohort members and 3 instructors to discuss the outcomes and lessons learned from the workshop, and to reflect more generally on issues of critical importance to sustaining Gateways.

Presenters
CA

Catrina Adams

Education Director, Botanical Society of America
avatar for Juliana Casavan

Juliana Casavan

Science Gateways Community Institute
Juliana Casavan is the Entrepreneurial Programs Manager at The Foundry at Purdue University. Juliana provides educational and workshop opportunities for clients of The Purdue Foundry, a nationally recognized leader in translation of research to market, with the primary workshop called... Read More →
avatar for Michael LaMar

Michael LaMar

Associate Professor, College of William and Mary
avatar for Nancy Maron

Nancy Maron

BlueSky to BluePrint, LLC
Nancy works with publishers, librarians and other innovative project leaders to define, test and refine assumptions about their new and existing products and services. She honed her skills in over 20 years of experience working at the nexus of publishing, higher education and technology... Read More →
avatar for Michael Zentner

Michael Zentner

Director, HUBzero Platform, Purdue University / HUBzero
Entrepreneurship, Leadership of large cyberinfrastructure projects.


Wednesday October 25, 2017 8:45am - 9:45am EDT
TBA

9:54am EDT

Concurrents D
"Concurrents D" has two themed sets of presentations:

  1. Tools for Data Systems (Pendleton)
  2. Educational Gateways and Their Design (Rogel)

Each presentation is 20 minutes total, including 5 minutes of Q&A. Approximate start times of the papers (which are displayed in presentation order) are:
  • 10:00am
  • 10:20am
  • 10:40am


Wednesday October 25, 2017 9:54am - 11:00am EDT
2nd floor meeting rooms Michigan Union

9:55am EDT

D1.1 Short Paper: Novel Network Services for Supporting Big Data Science Research
To interconnect research facilities across wide geographic areas, network operators deploy science networks, also referred to as Research and Education (R&E) networks. These networks allow experimenters to establish dedicated network connections between research facilities for transferring large amounts of data. Recently, R&E networks have started using Software-Defined Networking (SDN) and Software-Defined Exchanges (SDX) for deploying these connections. AtlanticWave/SDX is a response to the growing demand to support end-to-end network services spanning multiple SDN domains. However, requesting these services is a challenging task for domain-expert scientists, because the interfaces of the R&E networks have been developed by network operators for network operators. In this paper, we propose interfaces that allow domain-expert scientists to reserve resources of the scientific network using abstractions that focus on their data transfer needs for scientific workflow management. Recent trends in the networking field pursue better interfaces for requesting network services (e.g., intent-based networking). Although intents are sufficient for the needs of network operations, they are not abstract enough in most cases to be used by domain-expert scientists. This is an issue we are addressing in the AtlanticWave/SDX design: network operators and domain-expert scientists will have their own interfaces focusing on their specific needs.


Wednesday October 25, 2017 9:55am - 11:00am EDT
Pendleton Room (2nd floor) Michigan Union

9:55am EDT

D1.2 Short Paper: Extending Gateways into the Field: Geospatial Extensions and Remote Data Services
Science gateways are generally accessed via web browsers from workstation or laptop computers. However, activities such as fieldwork and data collection have prompted an increasing call for new methods of access using a wide range of mobile and specialized devices. Our work to extend the HUBzero gateway framework with new access routes is described. Specifically, an emphasis is placed on enabling the flow of geospatial data and metadata between geo-enhanced HUBzero hubs and devices in the field.

Presenters
RK

Rajesh Kalyanam

Research Scientist, Purdue University
avatar for Carol Song

Carol Song

Senior Scientist, Purdue University/Rosen Center for Advanced Computing
LZ

Lan Zhao

Research Scientist, Purdue University


Wednesday October 25, 2017 9:55am - 11:00am EDT
Pendleton Room (2nd floor) Michigan Union

9:55am EDT

D1.3 Short Paper: Database Versioning in Apache Airavata
A powerful feature for many science gateways is the ability to record and preserve a user’s cyberinfrastructure sessions. This capability can be straightforwardly developed using database technologies but two important requirements need to be taken into account. First, many gateways are open source software projects, which means that multiple developers from different organizations may be modifying the code base. Second, the records stored in a gateway’s database need to be preserved as the gateway’s codebase evolves, and we must find effective strategies for migrating legacy data to new implementations. As with many other challenges faced by gateways, we may turn to the broader fields of Web and cloud development, particularly continuous integration and deployment strategies used by “software as a service” systems. In this paper, we examine two tools, Liquibase and Flyway, that are designed to solve the general data versioning problem. We evaluate them using requirements from the Apache Airavata project. We conclude that Liquibase is the most appropriate solution.

Presenters
SM

Suresh Marru

Gateway Architect, Indiana University
MP

Marlon Pierce

Director, Science Gateways Research Center, Indiana University


Wednesday October 25, 2017 9:55am - 11:00am EDT
Pendleton Room (2nd floor) Michigan Union

9:55am EDT

D2.1 Short Paper: SEAGrid Use Case - Science Gateways Community Institute Training and Workforce Development
SEAGrid Science gateway is an infrastructure for computational science and engineering research and education primarily. It integrates computational chemistry application software and computational hardware resources and provides end to end environments with pre and post processing tools in a community oriented fashion. The environments are provided as web browser based interfaces and desktop clients where the former provides file upload and downloads required for computations while the latter provides molecular editors and graphical application input generation interfaces and output parsers to extract output components for visualization. The infrastructure is extensible such that other open tools can be integrated tightly or loosely. Such tools have been used in the classrooms for project oriented computational chemistry topics at undergraduate level. Here we discuss recent use of SEAGrid infrastructure for training and workforce development for computational chemistry, focussed at Minority serving institutions.

Presenters
avatar for LINDA HAYDEN

LINDA HAYDEN

SGCI ASSOCIATE DIRECTOR FOR WORKFORCE DEVELOPMENT, ECSU/SGCI
SP

Sudhakar Pamidighantam

Senior Scientist, Indiana University


Wednesday October 25, 2017 9:55am - 11:00am EDT
Rogel Ballroom (2nd floor) Michigan Union

9:55am EDT

D2.2 Short Paper: Redesigning PlantingScience.org: The Role of User Experience Evaluation in Improving a HUBZero Gateway for Plant Science Mentoring
PlantingScience.org, an online mentoring platform, enlisted the help of the Science Gateways Community Institute to conduct a usability evaluation. The process included workflow analysis, heuristic evaluation, comparative analysis, usability testing, and a final report that together have been instrumental to improving how teachers, scientists, and students use the PlantingScience.org online mentoring platform. Key friction points were identified in website navigation, in matching teams of students with appropriate mentors, and in facilitating teacher front-end registration and password management for student users. In this paper, we discuss the process of evaluation that led to identifying areas of friction for users. We also discuss how identified problem areas were redeveloped, and include feedback from our users about the new features. Other gateways will gain insight into approaches for evaluating website user experience and then using that evaluation to generate website changes that improve usability and reduce administrative support, making it possible to comfortably serve a much larger user community.

Presenters
CA

Catrina Adams

Education Director, Botanical Society of America
SG

Sue Gyoung Kim

Student, University of Michigan
PS

Purva Sane

User Experience Intern, Science Gateways Community Institute


Wednesday October 25, 2017 9:55am - 11:00am EDT
Rogel Ballroom (2nd floor) Michigan Union

9:55am EDT

D2.3 Short Paper: Building a gateway between classrooms and data science using QUBESHub
This paper addresses the gap between the practice of biological science and biology education as it pertains to data science and quantitative literacy. We discuss one way to address this gap through the development of a new web application called BioRadiant, an open-source R Shiny application that will be deployed on the scientific gateway QUBES (Quantitative Undergraduate Biology Education and Synthesis).

Presenters
avatar for Michael LaMar

Michael LaMar

Associate Professor, College of William and Mary


Wednesday October 25, 2017 9:55am - 11:00am EDT
Rogel Ballroom (2nd floor) Michigan Union

11:00am EDT

Very Short Break -- Coffee available
Fresh coffee available in Rogel.

Wednesday October 25, 2017 11:00am - 11:10am EDT
Rogel Ballroom (2nd floor) Michigan Union

11:09am EDT

Concurrents E
"Concurrents E" has two sets of concurrent demos, part 1 (Pendleton) and part 2 (Rogel).

Each demo is 20 minutes total, including 5 minutes of Q&A. Approximate start times of the demos (which are displayed in presentation order) are:
  • 11:15am
  • 11:35am


Wednesday October 25, 2017 11:09am - 11:55am EDT
2nd floor meeting rooms Michigan Union

11:10am EDT

E1.1 Demo: I-TASSER Gateway for Protein Structure Prediction and Structure-based Function Annotation
I-TASSER (Iterative Threading ASSembly Refinement) is a composite approach for protein structure prediction and structure-based protein function annotation. Starting from sequence of a target protein, structure templates are identified by threading. The full-length target structure is constructed by fragment re-assembly simulation. The final structure model is further compared to entries in BioLiP structure-function database for biological function interference. Recently, the I-TASSER protocol is implemented as an XSEDE science gateway, which has helped 14,503 users to decipher the structure and function of 38,545 proteins. I-TASSER gateway is available at http://zhanglab.ccmb.med.umich.edu/I-TASSER/.

Presenters
CZ

Chengxin Zhang

Graduate Student Research Assistant, University of Michigan


Wednesday October 25, 2017 11:10am - 11:55am EDT
Pendleton Room (2nd floor) Michigan Union

11:10am EDT

E1.2 Demo: COSMIC2 – A science gateway for cryo-electron microscopy
Recent advances in cryo-electron microscopy (cryo-EM) have led to the wide-spread adoption of the technique worldwide to allow the determination of atomic protein structures. In order to use this powerful technique, however, scientists must use high performance computing resources in order to calculate protein structures from terabytes of image data. We have built the COSMIC2 science gateway to provide researchers with access to the computing resources available on the Comet supercomputer located at the San Diego Supercomputer Center. In order to handle terabyte-sized data uploads, we have integrated the file transfer service Globus into the gateway. During this demonstration, we will highlight the user interface and data ingestion process used by the gateway, while also discussing considerations for user interface and design.

Presenters
MC

Michael Cianfrocco

Assistant Professor, University of Michigan
MW

Mona Wong

Software engineer, UCSD SDSC
avatar for Choonhan Youn

Choonhan Youn

computer scientist, SDSC at UCSD


Wednesday October 25, 2017 11:10am - 11:55am EDT
Pendleton Room (2nd floor) Michigan Union

11:10am EDT

E2.1 Demo: MyGeoHub Geospatial Gateway
MyGeoHub is a science gateway for researchers working with geospatial data. Based on the HUBzero cyberinfrastructure framework, it provides general-purpose software modules enabling geospatial data management, processing and visualization. Termed "GABBs" (Geospatial Data Analysis Building Blocks), these modules can be leveraged to build geospatial data driven tools with minimal programming and construct dynamic workflows chaining both local and remote tools and data sources. We will present examples of such end-to-end workflows demonstrating the underlying software building blocks that have also found use beyond the MyGeoHub gateway in other science domains.

Presenters
RC

Rob Campbell

Scientific Programmer, Purdue University
RK

Rajesh Kalyanam

Research Scientist, Purdue University
DK

Derrick Kearney

Software Engineer, Purdue University
avatar for Carol Song

Carol Song

Senior Scientist, Purdue University/Rosen Center for Advanced Computing
LZ

Lan Zhao

Research Scientist, Purdue University


Wednesday October 25, 2017 11:10am - 11:55am EDT
Rogel Ballroom (2nd floor) Michigan Union

11:10am EDT

E2.2 Demo: An innovative tool for mapping and modelling species distributions: the Biodiversity and Climate Change Virtual Laboratory
Models play a critical role in synthesising our understanding of the natural world and making forward projections into novel conditions. While they are central to ecological forecasting, models remain inaccessible to most ecologists, in large part due to the informatics challenges of managing the flows of information in and out of such models. The Biodiversity and Climate Change Virtual Laboratory (BCCVL) is a “one stop modelling shop” that simplifies the process of biodiversity and climate impact modelling. It uses national computational infrastructure to provide access to global biodiversity, climate and environmental data integrated with a suite of tools in a coherent online environment. In this demo, we will showcase how the BCCVL enables researchers to investigate, explore and accelerate biodiversity and climate change research.

Presenters
SR

Sarah Richmond

Project Manager - BCCVL, Griffith University


Wednesday October 25, 2017 11:10am - 11:55am EDT
Rogel Ballroom (2nd floor) Michigan Union

12:00pm EDT

Lunch, including Open Space discussion tables
Find people who share your interests by joining a table with an Open Space topic for discussion. Topics will be proposed during the Open Space kick-off session on Tuesday afternoon. 

Are you a note-taker looking for the online Google Doc? Here it is: http://tinyurl.com/gateways17open

Wednesday October 25, 2017 12:00pm - 12:55pm EDT
Rogel Ballroom (2nd floor) Michigan Union

12:55pm EDT

Beyond the Science Gateway: Connecting Cyberinfrastructure Back to the Laptop
Science Gateways today are generally built to provide a web-accessible interface for a particular scientific community to access a combination of software, hardware, and data deployed in an expertly managed computing center. But what happens when the scientist wants to repatriate their data? Or perform some analysis that is not supported by the gateway?  Both for the purposes of encouraging innovative workflows and serving an audience with a wide range of computational experience, it is important to consider how a gateway can fit into the broader computational ecosystem of a particular researcher or research group. One simple starting point for this is to ask the question "how can the gateway connect back to the laptop?" This talk will consider how this is being done today in science gateways and present some ideas for how this could be expanded in the future.

Link to slides on figshare: https://figshare.com/articles/2017_10_SGCI_Keynote_pptx/5585500

Presenters
avatar for Ian Stokes-Rees

Ian Stokes-Rees

Computational Scientist, Anaconda Inc
Ian Stokes-Rees is a computational scientist at Anaconda. He has worked in the field of grid and cloud computing for the past decade and consulted in the area of large scale data modelling, processing, analytics and visualization. His primary interest is in developing software and... Read More →


Wednesday October 25, 2017 12:55pm - 1:55pm EDT
Rogel Ballroom (2nd floor) Michigan Union

2:05pm EDT

Open Space Sessions
On Tuesday afternoon, we collected your ideas to organize "Open Space" conversations. To read about how that worked, see this: http://sched.co/Bl3o

Today there will be two 25-minute "sets" of concurrent sessions, plus a lunch "set." 

See the agenda posted on the wall for your options.

Are you a note-taker looking for the online Google Doc? Here it is: http://tinyurl.com/gateways17open

Wednesday October 25, 2017 2:05pm - 2:55pm EDT
Rogel Ballroom (2nd floor) Michigan Union

3:00pm EDT

Closing Session
We invite you to gather after Open Space to discuss next steps and future opportunities for the science gateways community.

Presenters
avatar for Katherine Lawrence

Katherine Lawrence

Associate Director, Community Engagement & Exchange, U of Michigan/Science Gateways Community Institute
I help people creating advanced digital resources for research and education connect their projects with helpful services, expertise, and information. Ask me how the Science Gateways Community Institute can support your projects--at no cost--to better leverage the people and money... Read More →


Wednesday October 25, 2017 3:00pm - 3:30pm EDT
Rogel Ballroom (2nd floor) Michigan Union

5:30pm EDT

Dinner gathering at Zingerman's Deli (optional; not included in registration)
Join us for an Ann Arbor classic: Zingerman's Deli. Zingerman's is a true destination for visitors to Southeast Michigan. It is a pleasant 20-minute walk from the Michigan Union, though you'll have a couple of hours to enjoy Ann Arbor after the conference ends. The cost of dinner is not included in your registration; the deli offers not just sandwiches, soups, and salads, but also a cheese and meat counter, freshly baked breads and goodies, and a wide variety of specialty foods. Just so you're prepared, sandwiches range between $9-$19, but many are large enough to share. After you order your meal, we'll gather in a reserved space upstairs at the Zingerman's Next Door Coffeehouse, where they also sell coffee, baked desserts, gelato, and chocolate.

Wednesday October 25, 2017 5:30pm - 7:30pm EDT
Zingerman's Deli 422 Detroit St. Ann Arbor, Michigan 48104
 
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