Gateways 2016: Program
- Published on Friday, 24 September 2021 16:40
Conference Proceedings (papers, slides, and posters) are available on figshare.
|Wednesday, November 2|
|8:00 am||Registration opens; breakfast available [SDSC Auditorium Patio]|
|Morning Tutorials sponsored by San Diego Supercomputer Center and Texas Advanced Computing Center|
|8:30 am||Hands-On Tutorials: Session 1 (choose one from these selections) [SDSC Rooms: See specific tutorial for details]|
|10:00 am||Coffee Break|
|10:30 am||Hands-On Tutorials: Session 2 (choose one from these selections) [SDSC Rooms: See specific tutorial for details]|
|12:00 pm||Lunch (provided)|
|1:00 pm||Introduction and Welcome: Mike Norman, director of the SDSC [SDSC Auditorium]|
|1:15 pm||Keynote 1: Dr. Rajiv Ramnath, Program Director CISE-ACI, National Science Foundation, “Software Programs at the Division of Advanced Cyberinfrastructure, the role of software gateways, and the Science Gateways Community Institute” [SDSC Auditorium] Watch on YouTube|
|2:00 pm||End of Keynote; 10-minute break for switching to concurrent sessions|
|2:10 pm||Concurrent Sessions A|
|Often Overlooked but Always Important: Considerations for Gateway Creation [SDSC Auditorium]|
|Resource Efficiency [RIMAC Green Room]|
|3:10 pm||Coffee Break|
|3:30 pm||Concurrent Sessions B|
|Gateway Case Studies with a Data Focus [SDSC Auditorium]|
|Gateway Case Studies [SDSC Synthesis Center]|
|Using Containers for Gateway Construction [RIMAC Green Room]|
|4:10 pm||10-minute break for switching to next concurrent sessions|
|4:20 pm||Concurrent Sessions C|
|Education and Gateways [SDSC Auditorium]|
|Wrangling Data [RIMAC Green Room]|
|5:30 pm||End of concurrent sessions|
|5:45 pm||Reception, Poster Session and Resource Expo|
|[Ida and Cecil Green Faculty Club: This is a 10-minute walk from SDSC. If you have parked at SDSC, you may leave your car in the Hopkins Parking Structure or park at the Faculty Club for $4. Walking and driving directions are in your conference booklet.]|
|The Poster Session and Resource Expo will be a terrific opportunity for conference participants to connect with colleagues, learn about research, and talk with providers of various gateway-related resources (e.g., software, hardware, consulting services, etc.). There is no additional cost to attend. Refreshments will be served at this event. NOTE: a shuttle bus will provide transportation between the SDSC conference venue and the Sheraton LaJolla at 5:45pm for those who wish to drop off belongings at the hotel, and between the Sheraton and Faculty Club for the remainder of the evening. See the Conference Booklet for the complete schedule. The Reception ends at 8:30pm.|
|Thursday, November 3|
|8:00 am||Registration opens; breakfast available [SDSC Auditorium Patio]|
|8:30 am||Keynote 2: Dr. Fernando Perez, creator of IPython (now Project Jupyter), “Project Jupyter: interactive computing in the context of modern science gateways” [SDSC Auditorium] Watch on YouTube|
|9:15 am||10-minute break for switching to concurrent sessions|
|9:25 am||Concurrent Sessions D|
|Platforms for Gateway Building [SDSC Auditorium]|
|Data Infrastructure Building Blocks (DIBB) [RIMAC Green Room]|
|10:15 am||Coffee Break|
|10:40 am||Lessons Learned Plenary Panel [SDSC Auditorium]
Watch on YouTube
|This panel will feature four 15-minute presentations about gateway building lessons that are broadly applicable to many projects, followed by an open discussion and Q&A.|
|Organizational Attributes of Successful Science Gateways and Cyberinfrastructure Projects (Kerk Kee)|
|Analysis of nanoHUB.org from a Business Perspective (Lynn Zentner, Michael Zentner and Gerhard Klimeck)|
|The CIPRES Science Gateway at Year 6: Lessons learned and best practices (Mark Miller, Terri Schwartz and Wayne Pfeiffer)|
|Evidencing the Value of Australian Science Gateways (Michelle Barker) [CANCELLED]|
|12:00 pm||Lunch sponsored by Omnibond|
|1:00 pm||Concurrent Sessions E|
|Scheduling Strategies [SDSC Auditorium]|
|Gateway Workhorses [RIMAC Green Room]|
|2:00 pm||10-minute break for switching to Open Space part of meeting|
|2:10 pm||Open Space begins [SDSC Auditorium]|
|2:45 pm||Open Space Sessions (30 minutes each) [Various locations determined on site; coffee & snacks available at 3:00 pm]|
|4:15 pm||Wrap up [SDSC Auditorium]|
|Afterwards||Informal dinner for those who are not leaving San Diego immediately after the conference. This is not included in the conference; you will be ordering from a menu. Please sign up near the registration desk so that we can advise the restaurant of how many people to expect.|
|[Bella Vista Social Club & Caffé, 2880 Torrey Pines Scenic Dr., La Jolla, CA 92037, Tel: (858) 534-9624]|
Wednesday, 1:15 pm [SDSC Auditorium]
Software Programs at the Division of Advanced Cyberinfrastructure, the role of software gateways, and the Science Gateways Community Institute
Dr. Rajiv Ramnath, Program Director CISE-ACI, National Science Foundation
The Division of Advanced Cyberinfrastructure (ACI) seeks to encourage, support and incentivize its community to create a sustainable national scientific cyberinfrastructure ecosystem. In keeping with this intent ACI’s software programs seek to holistically promote **software-centric** ecosystems that are seen by stakeholder communities as their primary means of furthering and accelerating their science. These software ecosystems comprise reusable software components and frameworks along with a highly-capable workforce. This workforce both uses as well as contributes to this software thus sustaining the ecosystem.
The Software Infrastructure for Sustained Innovation (SI2) program has been the flagship software program within ACI. This year, the SI2 program made major, multi-million dollar awards to establish two Scientific Software Innovation Institutes (S2I2) that will serve as long-term hubs for scientific software development, maintenance and education. The Science Gateways Community Institute (SGCI) is a multi-institutional consortium that will increase the capabilities, number and sustainability of science gateways — mobile or web-based applications that provide broad access to the nation’s shared cyberinfrastructure to scientists and citizens alike.
This talk seeks to present an overview of ACIs programs, in particular its software programs, with a focus on the special role of gateways and the SGCI.
About Rajiv Ramnath: Dr. Ramnath is a Program Director in the Software cluster at the Division of Advanced Cyberinfrastructure (ACI) at the National Science Foundation. He is also a Professor of Practice in Computer Science and Engineering at The Ohio State University where he has extensively collaborated with industry and other departments on research and education programs. Prior to this he worked for many years in industry, leading government-funded research and commercial product development. His industry R&D lab, almost unbeknownst to him, turned into a startup, so Rajiv ended up as an entrepreneur, and so, in addition to his academic work, he has also advised large and small businesses and startups on computing and information technology strategies. At NSF, Rajiv seeks to further the Software cluster’s mission of making scientific software an integral and sustainable part of the national scientific cyberinfrastructure ecosystem.
Thursday, 8:30 am [SDSC Auditorium]
Project Jupyter: interactive computing in the context of modern science gateways
Dr. Fernando Perez, creator of IPython, scientist at Lawrence Berkeley National Laboratory and Berkeley Institute for Data Science at UC Berkeley
Project Jupyter, evolved from the IPython environment, provides a platform for interactive computing that is widely used today in research, education, journalism and industry. The core premise of the Jupyter architecture is to design tools around the experience of interactive computing, building an environment, protocol, file format and libraries optimized for the computational process when there is a human in the loop, in a live iteration with ideas and data assisted by the computer.
The architecture of Jupyter provides a clean separation between the execution context (known as a “kernel” and available for over 70 programming languages) and the user interface; the two communicate via a well-specified, open protocol. Taking advantage of this design, we have built a web-based interface that exposes the computational capabilities of the kernels to users, requiring only a modern web browser. The main component of this interface is the Jupyter Notebook, a system that allows users to compose rich documents that combine narrative text and mathematics together with live code and the output of computations in any format compatible with a web browser (plots, animations, audio, video, etc.). In addition to illustrating the above foundations, in this talk I will discuss the next generation of the Jupyter web interface, JupyterLab.
JupyterLab combines in a single user interface not only the notebook, but multiple other tools to access Jupyter services and remote computational resources and data. A flexible and responsive UI allows the user to mix Notebooks, terminals, text editors, graphical consoles and more, presenting in a single, unified environment the tools needed to work with a remote environment. Furthermore, the entire design is extensible and based on plugins that interoperate via open APIs, making it possible to design new plugins tailored to specific types of data or user needs. We believe this design is an ideal foundation on which to build modern scientific gateways that support a wide range of user scenarios, from interactive data exploration in high-level languages like Python, Julia or R, to the monitoring and control of traditional HPC resources.
About Fernando Perez: Fernando Pérez (@fperez_org) is a staff scientist at Lawrence Berkeley National Laboratory and a founding investigator of the Berkeley Institute for Data Science at UC Berkeley, created in 2013. He received a PhD in particle physics from the University of Colorado at Boulder, followed by postdoctoral research in applied mathematics, developing numerical algorithms. Today, his research focuses on creating tools for modern computational research and data science across domain disciplines, with an emphasis on high-level languages, literate computing and reproducible research. He created IPython while a graduate student in 2001 and continues to lead its evolution into Project Jupyter, now as a collaborative effort with a talented team that does all the hard work. He regularly lectures about scientific computing and data science, and is a member of the Python Software Foundation as well as a founding member of the Numfocus Foundation. He is the recipient of the 2012 Award for the Advancement of Free Software from the Free Software Foundation.
Hands-On Tutorials: Session 1 (Wednesday, 8:30-10:00)
Data sharing from computer or cluster via SeedMe.org (Data Infrastructure Track) [SDSC Room E-145]
(Amit Chourasia and Dmitry Mishin)
High performance computing processes and workflows often have several steps for example input preparation, computation monitoring, output validation, analysis and visualizations. All these processes yield small-scale consumable data such as computation progress, statistics, plots that are of high value for research team. Sharing and accessing this information by team members is often slow and cumbersome in current HPC environment. SeedMe platform lowers these barriers by providing cyberinfrastructure and necessary tools for data sharing.
This tutorial will introduce attendees to the SeedMe (Stream encode explore and disseminate My experiment) platform and show how this platform can be leveraged to share data rapidly with easy to use tools in ad hoc and/or automated manner. We will also show how to create videos from set of images, which may be useful for sharing visualization results.
Skill Level: Level: Introductory/Beginner
Pre-requisites: Basic familiarity with command line tools like changing directory and executing commands.
Networking: Internet access will be required for this tutorial
1. Computer/Laptop (Mobile devices are not sufficient for this tutorial)
2. Account on SeedMe.org (Attendees can create an account at the tutorial)
3. Download SeedMe Python client
4. Download sample data
Creating Science Gateways with GenApp (Gateway Building Tools Track) [SDSC Auditorium]
(Emre Brookes and Alexey Savelyev)
GenApp is a tool for rapid deployment of applications. GenApp builds fully functioning applications from collections of definition files and libraries of code fragments. Applications are built over a set of modules, each module performing some computation. GenApp can build to a variety of targets, including local GUI and web based applications. Principles of GenApp include facilitating ease of use by tool, framework and application developers, module wrappers and end users. GenApp is currently being successfully used as the generator of multiple production science gateways. In this tutorial, users will learn the basics of developing applications with GenApp and will create both GUI and web based applications running on a cloud resource over the same set of modules.
The instructors suggested that it might be helpful to review the 1 May presentation here:
Requirements: Participants should bring a laptop with an SSH client and modern web browser installed. Working knowledge of some text editor under linux is required, such as nano, vi or emacs. The instructors will arrange for students to have access to cloud based training accounts.
Secure Software Engineering Practices [SDSC Synthesis Center]
(Randy Heiland and Von Welch)
Software engineering (SE) is concerned with developing and maintaining software systems that behave reliably and efficiently, and satisfy defined requirements. This tutorial presents an overview of SE, with a focus on security and science gateways. Some of the topics covered will include: software repositories, continuous integration, testing, code signing, vulnerability management, static analysis, and secure coding. CTSC (trustedci.org) and SGCI (sciencegateways.org) have partnered to help make science gateways more secure. Tutorial participants will get an introductory understanding of how security concerns are relevant to their gateways and how the partnership of the CTSC and SGCI may be able to help them.
Special Tutorial for Students and Young Professionals: Getting Started with the Chemistry Gateway SEAGrid [SDSC Room 408]
The Science and Engineering Applications Grid (SEAGrid) empowers researchers to easily use scientific applications deployed across a wide range of supercomputers, campus clusters, and computing cloud. SEAGrid features both a powerful desktop client and go-anywhere Web application. SEAGrid helps scientist create model inputs, simplifies access to computing resources, enables visualizations of outputs, and provides archives for simulation data. It supports computational chemistry, molecular dynamics, structural mechanics, and fluid dynamics. This tutorial will help participants learn the basics of making use of this powerful gateway. (This tutorial is open to all, but will be geared toward students and young professionals new to gateway use.)
Requirements: Participants should bring a Mac or Windows laptop.
Hands-On Tutorials: Session 2 (Wednesday, 10:30-12:00)
Building a Modern Research Data Portal with Globus (Data Infrastructure Track) [SDSC Synthesis Center]
Globus is an established service that is widely used for managing research data on XSEDE, DOE, and campus computing resources, and it continues to evolve with the addition of data publication capabilities, and enhancement of the core data transfer and sharing functions. Over the past year we have added new identity and access management functionality that will simplify access to Globus using campus logins, and facilitate the integration of Globus, XSEDE, and other research cyberinfrastructure services into web and mobile applications. In this session we will describe the Globus platform-as-a-service for research data management, and for identity and access management, and demonstrate how developers can use the Globus platform in portals, science gateways, and web applications to deliver advanced data and identity management capabilities to their research communities. A combination of presentation, demonstrations, and code walkthroughs will allow attendees to develop a good understanding of the platform’s capabilities and how it can be used in their own work.
Requirements: It is recommended that participants bring a laptop with Python and Git in order to perform tutorial exercises.
Agave ToGo Micro Sites: Phenomenal Gateway Power, Itty Bitty Living Space (Gateway Building Tools Track) [SDSC Room E-145]
(Rion Dooley, Manuel Rojas, and Joe Stubbs)
The Agave Platform is an open Science-as-a-Service platform that empowers users to run code, manage data, collaborate meaningfully, and integrate easily with the world around them. A common requirement of many projects, is to provide a single-purpose science gateway that allows project members to collaborate on computational experiments and publish data for external consumption. In this short tutorial, we walk attendees through the creation, branding, configuration, and automated deployment of a single-purpose science gateway based on Agave ToGo Micro Sites. At the end of the tutorial, attendees will have a fully functional, zero-maintenance gateway hosted free of charge.
Requirements: Users should have at minimum, the following requirements in order to effectively participate in and complete the tutorial: A laptop with Git installed, GitHub account, Basic HTML competency.
Tools for Building Science Gateway Communities: Apache Airavata and HUBzero (Gateway Building Tools Track) [SDSC Auditorium]
(Supun Nakandala, Suresh Marru, Marlon Pierce, and Betsy Hillery)
This tutorial will be split between Airavata and HUBzero. In Part 1 of this tutorial, we present SciGaP, which includes participation from the CIPRES, UltraScan, Neuroscience, and SEAGrid Gateways combined with the Apache Airavata middleware for managing jobs and data. Our goal is to show participants how to build and run gateways using both software and collected experience from some of the most heavily used XSEDE science gateways. Example tutorial material is available from https://cwiki.apache.org/confluence/display/AIRAVATA/XSEDE+2016+Tutorials.
Requirements for Part 1: Laptop or mobile phone to follow along with the demonstration.
In Part 2 of this tutorial, we feature HUBzero (hubzero.org), which is a powerful, open source software platform for creating dynamic web sites that support scientific research and educational activities. Used by communities ranging from nanotechnology, composite design, earth sciences, data curation, to healthcare, it is a proven framework for building a science gateway and a key part of many organizations’ cyberinfrastructure.
The HUBzero platform provides an application framework for developing and deploying interactive computational tools. This tutorial will provide an overview of the HUBzero integrated cyberinfrastructure, describe communities actively using it, and demonstrate how to build a web platform to support collaboration, data sharing, and computation.
Requirements for Part 2: Laptop. In order to expedite the install of HUBzero, participants will need to create an AWS Marketplace Account https://aws.amazon.com/marketplace/. When doing the HUBzero install, if you terminate the image right after the tutorial it will cost you nothing. If you leave it running it will cost roughly .03 cents a minute. Correction: The cost is $0.04 / hour $0.01 t2.micro EC2 Instance usage fees + $0.03 hourly software fee. If you have any questions, please email the instructor at eahillery [at] purdue [dot] edu.
Concurrent Sessions A (Wednesday at 2:10pm)
Often Overlooked but Always Important: Considerations for Gateway Creation [SDSC Auditorium]
- Science Gateways and Cybersecurity: Learning from the Past and Preparing for the Future (Randy Heiland and Von Welch)
- SciStarter 2.0: A Gateway to Drive Research, Participation, and Community-building in Citizen Science (Catherine Hoffman, Caren Cooper, Steve Gano, Ira Bennett, and Darlene Cavalier)
- Capturing the “Whole Tale” of Computational Research: Reproducibility in Computing Environments (Bertram Ludascher, Kyle Chard, Niall Gaffney, Matthew Jones, Jaroslaw Nabrzyski, Matthew Turk and Victoria Stodden)
Resource Efficiency [RIMAC Green Room]
- MyGeoHub Science Gateway for Spatial Data and a Model for Sustainability (Lan Zhao, Carol Song and Larry Biehl)
- Interactive Leaderboard for Requesting and Tracking Expensive Calculations of Optional Properties across a Database of Materials (Donald Winston, Joseph Montoya and Kristin Persson)
- Better Data Discoverability in Science Gateways (Supun Nakandala, Sudhakar Pamidighantam, Suresh Marru and Marlon Pierce)
Concurrent Sessions B (Wednesday at 3:30pm)
Gateway Case Studies with a Data Focus [SDSC Auditorium]
- A Novel Gateway for Visual Exploratory Analysis and Sharing of Survey Data (Ilya Zaslavsky, Side Li, Stephan Lamont, David Valentine and Thomas Whitenack)
- The DesignSafe-CI Architecture (Stephen Mock, Matthew Hanlon, Dan Stanzione and Ellen Rathje)
Gateway Case Studies [SDSC Synthesis Center]
- The Renaissance Simulations Laboratory (Kacper Kowalik, Michael Norman, Britton Smith and Matthew Turk)
- CoESRA: From virtual desktop to science gateway (Hoang Anh Nguyen, David Abramson, Siddesware Guru and Yi Sun)
Using Containers for Gateway Construction [RIMAC Green Room]
- Containers-as-a-service via the Actor Model (Joe Stubbs, Rion Dooley and Matthew Vaughn)
- Demo: Creating Sandboxed User Environments with Jupyterhub and Docker (Shreyas Cholia, Donald Winston and Daniel Gunter)
Concurrent Sessions C (Wednesday at 4:20pm)
Education and Gateways [SDSC Auditorium]
- Creating a Gateway for Collaborative Learning (Bev Corwin, Christie Ewen, Sean Auriti, John Ulmer, Janine Medina and Noreen Whysel)
- The Barcode of Life Student Data Portal: Supporting a National Network of Students in Cataloging Multicellular Life with DNA Barcodes (Ralph Imondi, Linda Santschi and Sujeevan Ratnasingham)
- VIDIA: a HUBzero Gateway for Data Analytics Education, plus a demo of the VIDIA Gateway: a Virtual Infrastructure for Data Intensive Analysis (Jeanette Sperhac and Steven M. Gallo) (30-minute presentation and demo)
Wrangling Data [RIMAC Green Room]
- DARE-BigNGS : A Science Gateway Model for Scalable NGS Data Analytics Over Distributed HPCs and Clouds (Joohyun Kim, Shayan Shams, Nayong Kim, Mohammad Jalalzai and Seung-Jong Park)
- Demo: Interactive Access to Internet Topology Data (Kc Claffy, Marina Fomenkov, Bradley Huffaker and Young Hyunn)
- Effective and interactive dissemination of diffusion data using MPContribs, plus a demo of UW/SI2 and MPContribs (Patrick Huck, Kristin Persson, Dan Gunter, Dane Morgan, Henry Wu and Tam Mayeshiba) (30-minute presentation and demo)
Concurrent Sessions D (Thursday at 9:25am)
Platforms for Gateway Building [SDSC Auditorium]
- GenApp: Extensible Tool for Rapid Generation of Science Gateways and Standalone GUI Applications (including Building applications from definition files with GenApp) (Alexey Savelyev and Emre Brookes) (30-minute presentation and demo) Enabling Interactive Notebooks on Supercomputers with Jupyterhub (Shreyas Cholia, R. Shane Canon and Rollin Thomas)
Data Infrastructure Building Blocks (DIBB) [RIMAC Green Room]
- SeedMe2: Data sharing building blocks (Amit Chourasia, David Nadeau, John Moreland, Dmitry Mishin and Michael Norman), plus a demo of SeedMe.org – Share data and visualization (Amit Chourasia, Mona Wong, Dmitry Mishin, David Nadeau and Michael Norman) (30-minute presentation and demo)
- Brown Dog A Science Driven Data Transformation Service (Kenton McHenry, Jong Lee, Praveen Kumar, Barbara Minsker, Jay Alameda, Shannon Bradley, Luigi Marini, Rob Kooper, Christopher Navarro, Smruti Padhy, Marcus Slavenas, Sandeep Satheesan, Yan Zhao, Bing Zhang, Inna Zharnitsky and Eugene Roeder)
“Lessons Learned” Plenary Panel (Thursday at 10:40am) [SDSC Auditorium]
This panel will feature four 15-minute presentations about gateway building lessons that are broadly applicable to many projects, followed by an open discussion and Q&A.
- Organizational Attributes of Successful Science Gateways and Cyberinfrastructure Projects (Kerk Kee)
- Analysis of nanoHUB.org from a Business Perspective (Lynn Zentner, Michael Zentner and Gerhard Klimeck)
- The CIPRES Science Gateway at Year 6: Lessons learned and best practices (Mark Miller, Terri Schwartz and Wayne Pfeiffer)
- Evidencing the Value of Australian Science Gateways (Michelle Barker) [CANCELLED]
Concurrent Sessions E (Thursday at 1:00pm)
Scheduling Strategies [SDSC Auditorium]
- MultiCloud Resource Management using Apache Mesos with Apache Airavata (Pankaj Saha, Madhusudhan Govindaraju, Suresh Marru and Marlon Pierce)
- Demo: Co-Scheduling HPC and BigData jobs using Apache Mesos (Shameera Yodage, Suresh Marru and Marlon Pierce)
- Reactive, Interactive, and High Throughput Computation in the Agave Platform (Rion Dooley and Joe Stubbs)
Gateway Workhorses [RIMAC Green Room]
- Dressing Apache Airavata Services With Automatically User-Generated Interfaces (Daniele D’Agostino, Luca Roverelli, Gabriele Zereik, Emanuele Danovaro, Andrea Clematis and Antonella Galizia)
- Demo: Pegasus Scientific Workflows within HUBzero (Mats Rynge, Karan Vahi and Steven Clark)
- The Globus Platform for Science Gateways (Steven Tuecke)
About Open Space
“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. There will also be two breakout rooms with a projector, for those who might like to offer a demo or impromptu presentation.
There will be three 30-minute sets of concurrent sessions. Approximately 9 locations will be designated for these sessions, but additional sessions/topics may be added at impromptu locations (e.g., outdoors).
We’ll be gathering your ideas, placing them into a basic agenda, and letting the conversation go!