Category Archives: SciPy

SciPy 2013 Conference Recap

Author: Eric Jones

Another year, another great conference.  Man, this thing grew a ton this year.  At final count, we had something like 340 participants which is way up from last year’s 200 or so attendees.  In fact, we had to close registration a couple of weeks before the program because that is all our venue could hold.  We’ll solve that next year.  Invite your friends.  We’d love to see 600 or even more.

Many thanks to the organizing team.  Andy Terrell and Jonathan Rocher did an amazing job as conference chairs this year both managing that growth and keeping the trains on time.  We expanded to 3 parallel sessions this year, which often made me want to be in 3 places at once.  Didn’t work.  Thankfully, the videos for all the talks and sessions are available online.  The video team really did a great job — thanks a ton.

I’ve wondered whether the size would change the feel of the conference, but I’m happy to report it still feels like an gathering of friends, new and old.  Aric Hagberg mentioned he thinks this is because it’s such a varied (motley?) crowd from disparate fields gathered to teach, learn, and share software tools and ideas.  This fosters a different atmosphere than some academic conferences where sparring about details of a talk is a common sport.  Hmh.  Re-watching the videos, I see Fernando Perez mentions this as well.

Thanks again to all who organized and all who attended.  I’m already looking forward to seeing you again next year.  Below are my personal musings on various topics at the conference:

  • The tutorials were, as usual, extremely well attended.  I spent the majority of my time there in the scikits learn track by Gael VaroquauxOlivier Grisel, and Jake VanderPlas.  Jeez, has this project gone far.  It is stunning to see the breath and quality of the algorithms that they have.  It’s obviously a hot topic these days; it is great to have such an important tool set at our disposal.
  • Fernando Perez gave a keynote this year about IPython.  We can safely say that 2013 is the year of the IPython notebook.  It was *everywhere*.  I’d guess 80+% of the talks and tutorials for the conference used it in their presentations.  Fernando went one step further, and his slide deck was actually live IPython notebooks.  Quite cool.  I do believe it’ll change the way people teach Python…  But, the most impressive thing is that Fernando still has and can execute the original 250 line script that was IPython 0.00001.  Scratch that.  The most impressive thing is to hear how Fernando has managed to build a community and a project that is now supported by a $1.1M grant from the Sloan foundation.  Well done sir.  The IPython project really does set the standard on so many levels.
  • Olivier Grisel, of scikits learn fame, gave a keynote on trends in machine learning.  It was really nice because he talked about the history of neural networks and the advances that have been made in “deep learning” in recent years.  I began grad school in NN research, and was embarrassed to realize how recent (1986) the back propagation learning algorithm was when I first coded it for research (1993).  It seemed old to me then — but I guess 7 years to a 23 year is, well, pretty old.  Over the years, I became a bit disenchanted with neural nets because they didn’t reveal the underlying physical process within the data.  I still have this bias, but Olivier’s discussion of the “deep learning” advances convinced me that I should get re-educated.  And, perhaps I’m getting more pragmatic as the gray hairs fill in (and the bald spot grows).  It does look like it’s effective for multiple problems in the detection and classification world.
  • William Schroeder, CEO of Kitware, gave a keynote on the importance of reproducible research which was one of the conference themes.  It was a privilege to have him because of the many ways Kitware illuminated the path for high quality scientific software in the open source world with VTK.  I’ve used it both in C++ and, of course, from Python for many, many years.  In his talk, Will talked about the existing scientific publication model doesn’t work so well anymore, and that, in fact, with the web and tools that are now available, direct publishing of results is the future together with publishing our data sets and code that generated them.  This actually dovetailed really well with Fernando’s talk, and I can’t help but think that we are on this track.
  • David Li has been working with the SymPy team, and his talk showed off the SymPy Live site that they have built to interactively try out symbolic calculations on the web.  I believe David is the 2nd high school student to present in the history of SciPy, yes? (Evan Patterson was the other that I remember)  Heh.  Aaand, what were you doing your senior year?  Both were composed, confident, and dang good — bodes well for our future.
  • There are always a few talks of the “what I have learned” flavor at Python.  This year, Brian Granger of IPython fame gave one about the dangers of features and the benefits of bugs.  Brian’s talks are almost always one of my favorites (sorta like I always make sure to see what crazy stuff David Beazley presents at PyCon).  Part of it is that he often talks about parallel computing for the masses which is dear to my heart, but it is also because he organizes his topics so well.
  • Nicholas Kridler also unexpectedly hooked me with another one of these talks.  I was walking out of conference hall after the keynote to go see what silly things the ever smiling Jake Vanderplas might be up to in his astronomy talk.  But derned if Nicholas didn’t start walking through how he approaches new machine learning problems in interesting ways.  My steps slowed, and I finally sat down, happy to know that I could watch Jake’s talk later.  Nicholas used his wits and scikits learn to win(!) the Kaggle whale detection competition earlier this year, and he gave us a great overview of how he did it.  Well worth a listen.
  • Both Brian and Nicholas’ talks started me thinking how much I like to see how experts approach problems.  The pros writing all the cool libraries often give talks on the features of their tools or the results of their research, but we rarely get a glimpse into their day-to-day process.  Sorta like pair programming with Martin Chilvers is a life changing experience (heh.  for better or worse… :-)), could we have a series of talks where we get to ride shotgun with a number of different people and see how they work?  How does Ondrej Certik work through a debugging session on SymPy development?  Does his shiny new cowboy hat from Allen Boots help or not?  When approaching a new simulation or analysis, how does Aric Hagberg use graph theory (and Networkx) to set the problem up?  When Serge Rey gets a new set of geospatial data, what are the common things he does to clean and organize the data for analysis with PySAL?  How does Wes McKinney think through API design trade-offs as he builds Pandas?  And, most importantly, how does Stefan Van Der Walt get the front of his hair to stand up like that? (comb or brush? hair dryer on low or high?)  Ok, maybe not Stefan, but you get the idea.  We always see a polished 25 minute presentation that sums up months or years of work that we all know had many false starts and painful points.  If we could learn about where people stubbed their toe and how to avoid it in our work, it would be pretty cool.  Just an idea, but I will run it by the committee for next year and see if there is any interest.
  • The sprints were nothing short of awesome.  Something like 130+ people were there on the first day sprinting on 10-20 different libraries including SymPy, NumPy, IPython, Matplotlib as well as more specific tools like scikits image and PySal.  Amazing to see.  Perhaps the bigger surprise was that at least half also stayed for Saturday’s sprints.  scikits learn had a team of about 10 people that worked two full days together (Friday and Saturday activity visible on the commit graph), and I think multiple other groups did as well.  While we’ve held sprints for a while, we had 2 top 3 times as many people as 2012, and this year’s can only be described as wildly successful.

  • While I was there, I spent most of my time checking in on the PySide sprint where John Erhsman of Wingware got a new release ready for the 4.8 series of Qt (bless him), and Robin Dunn, Corran Webster, Stefan Landgovt, and John Wiggins investigated paths forward toward 5.x compatibility.  No one was too excited about Shiboken, but the alternatives are also not a walk in the park.  I think the feeling is, long term, we’ll need to bite the bullet and go a different direction than Shiboken.

TGIF: SciPy 2012 Recap Video

As we wait for the SciPy talk videos to make their way onto the web, we’d like to share a short film recapping SciPy 2012.

The latest iteration of the SciPy conference was another great example of the scientific python community coming together to share “the latest and greatest.” Most organizations want to change the world in some way or another. At Enthought, we attempt to do this by building tools that help our customers – in both academia and industry – concentrate on solving their actual problems rather than wrestling with technology. We believe Python’s ability to operate smoothly in different contexts (e.g., desktop, web, array-based and distributed computing, etc.) makes it a highly productive and pragmatic tool with which to build solutions.

The SciPy community is changing the world by continually pushing technical computing forward in a pragmatic way. One just has to look at the content and tools presented at SciPy historically to know that this community has been been up to its neck in “data science” for some time. One could also argue, however, that SciPy is one of the best kept secrets in technical computing. As the recent focus on MapReduce solutions illustrates, the world is in the grips of “big computation.” It will only get tougher in the foreseeable future. At the same time, “big data” is a relative term. “Big” for a bioinformatician is different than for a macro hedge fund analyst, and these differences can often be measured in orders of magnitude. And when it comes to solutions, rarely does one size fit all.

In contrast, SciPy addresses a broad array of problems. SciPy 2012 offered High Performance Computing and Visualization tracks, with tutorials on machine learning, plotting, parallel computing, and time series analysis. Sometimes all these topics could be found in a single talk (see VisIt). The community also demonstrated some open-mindedness by inviting Jeff Bezanson, one of the authors of Julia, to share his experience building a language specifically designed for technical computing. It turns out there is a fair amount of overlap between what the SciPy community and the Julia team are planning. With LLVM IR increasingly being viewed as a common target, there is real excitement about what the future holds for language development and interaction.

This is all to say that SciPy has a lot to offer the world. Stay tuned for a bigger and better SciPy next year!

Scipy 2012

No Mas

Scipy 2012 is wrapping up today tomorrow as bands of sprinters come together to hack away on their projects of interest. Many thanks to the sponsors and volunteers that made this year’s Scipy another success. The Scipy conference has always been highly technical. Although “data science” and “big data” have become buzzwords recently, Scipy has been exploring these themes for many years. Projects featuring machine learning, high performance computing, and visualization were in full attendance at this year’s Scipy. Stay tuned for links to talk videos (care of Next Day Video)!

BioInformatics at Scipy: It’s Alive!

It's Alive!

We are pleased to announce the 2012 SciPy Bioinformatics Workshop held in conjunction with SciPy 2012 this July in Austin, TX.

Python in biology is not dead yet… in fact, it’s alive and well!

Remember just a few short years ago when BioPerl ruled the world? Just one minor paradigm shift* later and Python now has a commanding presence in bioinformatics. From Python bindings to common tools all the way to entire Python-based informatics platforms, Python is used everywhere** in modern bioinformatics.

If you use Python for bioinformatics or just want to learn more about how its being used, join us at the 2012 SciPy Bioinformatics Workshop. We will have speakers from both academia and industry showcasing how Python is enabling biologists to effectively work with large, complex data sets.

The workshop will be held the evening of July 19 from 5-6:30.

More information about SciPy is available on the conference site: http://conference.scipy.org/scipy2012/

!! Participate !!

Are you using Python in bioinformatics? We’d love to have you share your story. We are looking for 3-4 speakers to share their experiences using Python for bioinformatics.

Please contact Chris Mueller at chris.mueller [at] lab7.io and Ray Roberts at rroberts [at] enthought.com to volunteer. Please include a brief description or link to a paper/topic which you would like to discuss. Presentations will last for 15 minutes each and will be followed by a panel Q&A.

* That would be next generation sequencing

** Yes, we aRe awaRe of that otheR language used eveRywhere, but let’s celebRate Python Right now.

SciPy for .NET & IronPython

This week Enthought and Microsoft are announcing the availability of NumPy and SciPy for IronPython and the .NET Framework, released in conjunction with the release of Microsoft’s Python Tool for Visual Studio release. These packages implement a fast and flexible multi-dimensional array package (NumPy) and a large collection of scientific and numerical algorithms built on top of the array (SciPy) andare two fundamental building blocking for technical computing in Python. CPython users are well familiar with both but up until now they have not been available on other Python environments. This is because both packages include many heavily optimized native-code (typically C or FORTRAN) implementation of the algorithms, thus requiringcustom wrappers to integrate them into each Python environment.

The result of the project isIronPython ports of NumPy and SciPy, which are full .NET ports and include custom C#/C interfaces to a common native C core. This means that the full functionality is available not only to IronPython but to all .NET languages such as C# or F# by directly accessing the C# interface objects.

Completing the port required considerably more work than just writing new interfaces IronPython. To start with large parts of the NumPy C code were written specifically for CPython and made free use of the CPython APIs. To support additional Python environments the codebase had to be refactored into a Python-independent core library plus a CPython-specific interface layer. A big advantage to this architectural separation is that the core NumPy library can now be used from applications written in C or C++ much more easily and ports to other Python environments will require less work.

The second supporting project was an extension of Cython to support IronPython. Cython, not to be confused with CPython, is a tool that allows C extensions to be written for Python using a language based on Python with extensions for interacting with native code libraries. Up until now Cython has only supported the CPython environment. We have extended Cython to be able to generate C++/CLI code interfaces for .NET, and thus IronPython. Using a single Cython input file it is now possible to target both CPython and IronPython environments.

The main driver for the Cython project was the nature of the SciPy library. SciPy consists of dozens of different packages, many of which have a hand-written C interface for CPython. One option was to write a matching C# interface for each of these to support IronPython. While this would have taken less time, the result would have been a significant duplication of code and more maintenance work in the future. Instead we chose to port Cython to .NET and then rewrite each C module in Cython so one a single source file is needed.

The first release of SciPy and NumPy for .NET are available now as binary distributions from SciPy.org or directly from Enthought. All of the code for these and the supporting projects are open source and available at the links below.

Travis Oliphant announces…

Travis announces project to extend NumPy/SciPy to .Net

Travis announces project to extend NumPy/SciPy to .Net

Travis Oliphant kicked off today’s SciPy 2010 Day 2 with a great keynote talk. He told the story of his own path to Python, filling his slides with the faces and work of other developers, scientists, and mathematicians inspiration, teachers, and collaborators. He explained how his academic trajectory, from electrical engineering, through a brief affair with neuroscience, to a biomedical engineering PhD, both drove and competed with his work creating NumPy.
Last, but not least, Travis closed his talk with rather large announcement: Enthought has undertaken the extension of NumPy and SciPy to the .NET framework. For details on the project refer to the official release.

SciPy 2010 underway!

Everyone minus Ian, the most valiant photographer!

Everyone minus Ian, the most valiant photographer!

We were thrilled to host SciPy 2010 in Austin this year. Everyone seems to be enjoying the cool weather (so what if its borne of thunderstorms?) and the plush conference center/hotel (even if we had to retrain their A/V team).
After two days of immensely informative Tutorials, the General Session began yesterday with speaker Dave Beazley’s awesome keynote on Python concurrency. In addition to the solid line-up of talks at the main conference, we had two very well-attended specialized tracks: Glen Otero, chaired the Bioinformatics track, while Brian Granger and Ken Elkabany coordinated the Parallel Processing & Cloud Computing talks. The day then closed with a conference reception and guacamole-fueled Birds of a Feather sessions.
SciPy 2010

EPD 6.1: MKL on Linux, Windows, & OSX

epd-6-1-long
There were several reasons we initially decided to include MKL, an extensively threaded, highly optimized library, in the Enthought Python Distribution. For one thing, we like that MKL detects the processing capability of the machine and then runs optimal algorithm for that hardware. Secondly, we knew that MKL would offer faster linear algebra routines than the ATLAS framework, previously used for EPD Linux and Windows, and Accelerate library, previously used for OSX.

We didn’t anticipate, however, just how dramatic that speed up would be. Our benchmarking tests document the astounding increases in processing speed that MKL lends to EPD.

In EPD 6.1, NumPy and SciPy are dynamically linked against the MKL linear algebra routines. This allows EPD users to seamlessly benefit from the highly optimized BLAS and LAPACK routines in the MKL. In addition, EPD 6.1 comes bundled with all of the MKL run-time libraries so that advanced users can take advantage (with ctypes) of even more of the MKL library such as fast Fourier transforms, trust-region optimization methods, sparse solvers, and vector math.

We’re really pleased with the optimizations MKL offers to our EPD users. Try out EPD 6.1 for yourself!