Guest Speakers

Science 2.0:
What Every Scientist Needs to Know About
How the Web is Changing the Way They Work

The MaRS Centre, 101 College St., Toronto
Wednesday, July 29, 1:00-6:00 pm, with wine and cheese to follow

Slides from this event are now available online. Our thanks to MITACS, Cybera, the MaRS Centre, SciNet, Prof. Steve Easterbrook, and an anonymous donor for helping to make the event possible.

Titus Brown

Choosing Infrastructure and Testing Tools for Scientific Software Projects

The explosion of free and open source development and testing tools offers a wide choice of tools and approaches to scientific programmers.  The increasing diversity of free and fully hosted development sites (providing version control, wiki, issue tracking, etc.) means that most scientific projects no longer need to self-host. I will explore how three different projects (VTK/ITK; Avida; and pygr) have chosen hosting, development, and testing approaches, and discuss the tradeoffs of those choices.  I will particularly focus on issues of reliability and reusability juxtaposed with the mission of the software.

C. Titus Brown studies developmental biology, bioinformatics, and software engineering at Michigan State University, and he has also worked in the fields of digital evolution and physical meteorology.  A cross-cutting theme of much of his work has been software development for computational science, which has led him into software testing and agile software development practices.  He is also a member of Python Software Foundation and the author of several widely used Python testing toolkits.

Cameron Neylon

A Web Native Research Record: Applying the Best of the Web to the Lab Notebook

Best practice in software development can save researchers time and energy in the critical analysis of data but the same principles can also be applied more generally to recording research process. Successful design patterns on the web tend to be those that successfully couple people into efficient information transfer mechanisms. Can we re-think the way we create, keep, and share our research records by using these design patterns to make it more effective?

Cameron Neylon is a biophysicist who has always worked in interdisciplinary areas and is a leading advocate of data availability. He currently works as Senior Scientist in Biomolecular Sciences at the ISIS Neutron Scattering facility at the Science and Technology Facilities Council. He writes and speaks regularly on the interface of web technology with science and is well-known as one of the leading proponents of open science.

Michael Nielsen

Doing Science in the Open: How Online Tools are Changing Scientific Discovery

Tools like email, preprint servers and Skype have changed the way many scientists work.  In this talk, I argue that such networked tools are in their infancy, and there is enormous untapped potential for online tools to change and improve the way science is done.  I’ll illustrate this using examples such as open data sharing, open notebook science, and mass online collaboration.  The potential is only part of the story, however, for there are also cultural barriers within science that prevent scientists from using online tools to their full potential.  I’ll discuss these cultural barriers, and how they can be overcome.

Michael Nielsen is a writer working on a book about open science and mass online collaboration. In a past life he was a theoretical physicist who co-authored the standard text on quantum computing.

David Rich

Using “Desktop” Languages for Big Problems

This talk will discuss the use of the “M” language (the language used in MATLAB) on clusters and with accelerators including the tradeoff between time to solution and computational efficiency as well as opportunities for additional abstraction.  Language constructs (additions) for parallelism will be described. Opportunities and challenges in using off-site/cloud computing resources will also be discussed and we’ll show some recent benchmarks on large clusters and multi-GPU configurations.  This is a vendor talk, but hype will be minimal.

David Rich is VP Marketing at Interactive Supercomputing.  Previously, he ran the HPC group at AMD (which launched commodity, 64 bit x86 processors in HPC), was president of the HyperTransport Consortium, spent time with high-speed interconnects; InfiniBand, SCI at Fujitsu and Dolphin Interconnect, and started the business which is now TotalView Technologies. In the very old days he worked on the Butterfly at BBN and on networking at Apollo Computer.  David has a BA in Computer Science from Brown University.

Victoria Stodden

How Computational Science is Changing the Scientific Method

As computation becomes more pervasive in scientific research, it seems to have become a mode of discovery in itself, a “third branch” of the scientific method. Greater computation also facilitates transparency in research through the unprecedented ease of communication of the associated code and data, but typically code and data are not made available and we are missing a crucial opportunity to control for error, the central motivation of the scientific method, through reproducibility.  In this talk I explore these two changes to the scientific method and present possible ways to bring reproducibility into today’ scientific endeavor. I propose a licensing structure for all components of the research, called the “Reproducible Research Standard”, to align intellectual property law with longstanding communitarian scientific norms and encourage greater error control and verifiability in computational science.

Victoria Stodden is the Law and Innovation Fellow at the Internet and Society Project at Yale Law School, and a Fellow at Science Commons. She was previously a Fellow at Harvard’s Berkman Center and postdoctoral fellow with the Innovation and Entrepreneurship Group at the MIT Sloan School of Management. She obtained a PhD in Statistics from Stanford University, and an MLS from Stanford Law School.

Jon Udell

Collaborative Curation of Public Events

One of the paradoxes of our era is that we are both more connected and more disconnected than ever before. Online social networks seem to be thriving. But as Robert Putnam observes, although more Americans are bowling than ever before, they are bowling alone rather than in leagues.  The elmcity project aims to help people promote and find out about activities that bring them together in the real world. This talk will explore why and how the project’s core principles of online information management—collaboration, provenance, structure, tagging, and syndication—can be widely taught, understood, and applied.

Jon Udell is an author, information architect, software developer, and new media innovator. His 1999 book Practical Internet Groupware helped lay the foundation for what we now call social software. Udell was formerly a software developer at Lotus, BYTE Magazine’s executive editor and Web maven, and an independent consultant. From 2002 to 2006 he was InfoWorld’s lead analyst, author of the weekly Strategic Developer column, and blogger-in-chief. During his InfoWorld tenure he also produced a series of screencasts and an audio show that continues as Interviews with Innovators on the Conversations Network. In 2007 Udell joined Microsoft as a writer, interviewer, speaker, and experimental software developer. His portfolio includes an interview series, Perspectives, which explores how Microsoft works with universities, governments, and NGOs to develop new and socially impactful uses of its technologies.