Gateways 2016

This conference series is for gateway creators and users who want to connect with and learn from others like them. The Gateways 2016 proceedings are hosted on figshare. In addition, video from our keynotes and other sessions are linked below.


Proceedings on figshare

How to cite a paper, demo, tutorial, or poster (choose one of these options for the citation below, not all):

Author(s). 2016. "Title." Paper/Demo/Tutorial/Poster presented at Gateways 2016, San Diego, CA, USA, November 2–3, 2016. URL/DOI to paper in figshare.

Video Highlights

Watch the following keynotes and panel on our Gateways 2016 YouTube playlist.

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. 

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.

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. 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. 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. 

“Lessons Learned” Plenary Panel 

This panel featured three 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)


While much of the adoption and diffusion of science gateways and/or computational tools for e-science is driven by the attributes of the tools [see 1], the organizations behind the tools play a critical role in determining the ultimate diffusion. This paper reports 10 organizational attributes of successful gateways and cyberinfrastructure projects. Based on a systematic analysis of 135 interviews, the organizational attributes include having leaders with credibility, multidisciplinary expertise, collaborative environment, shared goals, a common language, strategic structure, productive routines, organizational capacity, sustainable funding, and personnel continuity.


Analysis of from a Business Perspective (Lynn Zentner, Michael Zentner and Gerhard Klimeck)


Science Gateways are typically implemented by scientists and cyberinfrastructure experts to serve a specific, externally-funded scientific focus. Sustainability of those gateways and the knowledge and tools they contain continues to be of strong interest to both the gateways and the funding agencies that support their creation and initial operation. is an established gateway entering its 15th year of operation and now serving over 1.4 million visitors annually. The leadership at nanoHUB have utilized a partnership with Purdue’s Krannert School of Management to collaborate on examining nanoHUB from a business perspective. The results of these collaborations are outlined in this extended abstract and will be expanded upon in the corresponding presentation.


The CIPRES Science Gateway at Year 6: Lessons learned and best practices (Mark Miller, Terri Schwartz and Wayne Pfeiffer)


The CIPRES Science Gateway was created in 2009 to provide the international phylogenetic community with easy access to parallel versions of community codes run on High Performance Computing resources available through the XSEDE project. After six years of operation, job submissions continue to increase each month, and more than 19,000 individual users have been provided with access. Here we describe the lessons learned and best practices acquired over the lifetime of the CIPRES Science Gateway.