Tag Archives: Open Science

SciPy 2013: Day Three

Opening Remarks:

With tutorials concluding yesterday, today began the talks. This is the largest SciPy to date. The registration increase of ~75% over last year was easily noticeable at the opening remarks as I sat in a packed room of fellow coders and scientists.  Co-hosts Andy and John announced that the primary themes for this years conference are reproducibility and machine learning before introducing the keynote speaker Fernando Perez.

Keynote: Fernando Perez of IPython — IPython: from the shell to a book with a single tool – The method behind the madness

As you would expect from Fernando, the talk was fast paced, informative, and enjoyable. The real icing on the cake however, was the delivery — an IPython Notebook slide show. I’ve already gone into who excited I am about the IPython notebook; I think it will make an awesome medium for teaching CS students. The slide show only further enhances the usefulness of the IPython tool set. -steps down from soapbox- Anyway, I’ve tried to summarize points from Fernando’s talk I found to be of interest.

After a brief set of opening remarks about the amazing spirit of the community and the phases of the research life cycle, Fernando explained some of IPython’s major mile stones:

  • 2001 – First version of IPython (it was only 259 lines of code!) It’s primary goal was to provide a better interactive Python shell.
  • 2004 – Interactive plotting with matplotlib.
  • 2005 – Interactive parallel computing.
  • 2007 – IPython embedding embedding in Wx apps.
  • 2010 – An improved shell and a protocol to go along with it.
  • 2010 – After 5 attempts, a sixth leads to what we now know as IPython notebook.
  • 2010 – Sharing notebooks with zero-install via nbviewer
  • 2012 – Reproducible research with IPython.parallel and StarCluster
  • 2012 – IPython notebook-based technical blogging
  • 2013 – The first White House hackathon (IPython and NetworkX go to DC)
  • 2013 – IPython notebook-based books: “Literate Computing” Probabilistic Programming and Bayesian Methods for Hackers.

Continuing, Fernando explained many of the lessons he’s learned since starting the project, highlighted alternative use cases written around IPython and IPython notebooks, thanked the community, and gave us some ideas into what lays ahead for IPython (1.0 in a few weeks!). Once the video becomes available, I will be sure to add it here and I highly recommend you watch it!

“The purpose of computing is insight, not numbers” — Hamming ’62


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Center for Open Science APS Pre-Conference

Last Thursday I attended the Center for Open Science’s (OSF) APS Pre-Conference. It was a small, but pleasant affair. The morning kicked off with a variety of lightning talks from various academics and developers who focused on what open source / open science are and how they are beneficial to the community. I may be biased but my favorite talk was about the Open Science Framework (OSF).

The OSF is the infrastructure that allows the COS to accomplish its goals: Developing infrastructure to assist the scientific workflow, community building on open practices, and metascience (researching the science of science). Dr. Jeffery Spies, the co-founder of the COS and lead developer of the OSF gave an excellent overview of where the project is at, what it hopes to accomplish, and where we plan to work toward next.

After a quick coffee break, a second round of lightning talks commenced; this time the talks focused on open source / open science projects currently in development. One of the COS’s lead developers gave a brief, but well-rounded, talk demonstrating how even non-technical users can contribute to open source projects through a GitHub issue submission tutorial. Additionally, I spoke about a project I’m working on called Scholarly and another intern at the COS gave an overview of his project pydocx — a very useful collaboration tool.

Following a tasty lunch at Noodles & Company the group formed into a very informal round table discussion about the morning’s talks as well as comments and concerns about related areas. Although slow to start, a lot of interesting and varying view points were brought up that lead to well-mannered debates and insights into things I would have otherwise never been aware of.

The pre-conference ended with small group discussions. Individuals broke into conversations with others maintaining similar interests, networked with potential colleagues, and caught up with old ones.

All in all, the pre-conference was a lot of fun. I was able to practice my public speaking skills, make connections with lots of other like-minded individuals, and gain a deeper understanding of what I’m working on and why it’s so important.


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