My Favorite Computing Videos on YouTube

I have often been asked what are my favorite computing videos on YouTube. There are so many, it’s hard to give a definitive answer and I keep discovering more, some posted several years ago. As of today only, here are some of my favorites.

The annual SciPy conferences, held each year in the US and Europe, post videos of the presentations in dedicated channels each. They provide an enormous amount of information on the rapid developments in Python.  You can find the SciPy 2016 talks here, and one of my favorites is “Python and R Together at Last: Writing Cross Language Tools,” by Bill Lattner:

There are many talks and videos on cloud computing. Eli the Computer Guy has a fine introduction to cloud computing, intended as a class:

Some of my favorites though are talks and interviews on the history and philosophy of computing that are hard to find anywhere else. Here is Grady Booch of IBM talking on The History (and the Future) of Software:

It is part of the Computer History Museum channel.

Here is the Professor Linux himself, Linus Torvalds (very funny in parts):




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Community Building Through Software Design

This the title of a very interesting talk (which I wish I had given myself!) by Jed Brown of CU Boulder at the 2017 NSF SI2 meeting. Jed is involved in writing code for the Portable, Extensible Toolkit for Scientific Computation (PETSc) , which is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. The practices he describes came largely out of supporting PETSc, yet are applicable across many disciplines. I would recommend anyone wishing to build a software community read these slides before diving into the development.

I am not able to post the slides here, but I will show some “slideshots” that I think have particularly broad applicability; in particular, note the comments about forking in the slide on “Upstreaming and community building,” something I haven’t given a lot of thought to.




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A guide to sustainability models for research software projects.

.. subtitled “How can we find funding for our open source project?”

This is a GitHub page started by my colleague Dan Katz of NCSA. This is a living document that lists, with examples, techniques for sustaining software once initial development funding has ended.  To maximize the value of the page, Dan is soliciting contributions and examples from the scientific community.  As of this writing, he lists the following categories:

Donation button
Crowdfunding (one-time)
Crowdfunding (recurring)
Books & merchandise
Advertising & sponsorships
Industry support
Consulting & services
Dual license
Open core
Foundations & consortiums
Venture capital
Trademark licensing & franchising

Here is a sample content, from Industry Support:

“Companies sometimes support particular projects via paying for some development in that project, or by supporting a PhD or researcher to undertake a specific development project. Find a company that uses your project, and determine something the project wants to do that the company is willing to put work into.
(Note that this might overlap Consulting & services below.)


Taps into those who have resources (i.e. companies)
Can be well-aligned with company needs
In certain areas, industrial support for PhD or researcher positions is already an established mechanism


Usually involves “getting lucky”: no clear, repeatable path to finding this arrangement
Project already needs to be well-known and used
Governance issues, company could have undue influence over project
Can affect project dynamics + balance
Case Studies

BoneJ – with F + P Specialist Modelling Group”

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Defending Science and Scientific Integrity in the Age of Trump

This week’s blog is a little off my usual beat, but in the current climate, I think it’s a good choice.  This is a 75 minute podcast, prepared by Robert Frederick of American Scientist, of a panel discussion held at the annual meeting of the American Association for the Advancement of Science this past month.

The panelists were:

  • Lewis Branscomb, University of California, San Diego
  • John Holdren, former director, White House Office of Science and Technology Policy
  • Jane Lubchenco, Oregon State University
  • Amy Luers, Skoll Global Threats Fund
  • Gretchen Goldman, Union of Concerned Scientists
  • Andrew Rosenberg, Union of Concerned Scientists (moderator)

You can also read the transcript at

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Free the Science: One Scholarly Society’s bold vision for open access and why it matters now more than ever

This is a repost of a very interesting article by Ellen Finnie in  the IO:In The Open Blog. Ellen is a member of the ECS Group of Advisory Librarians (EGALs).

The Electrochemical Society, a small nonprofit scholarly society founded in 1902, has an important message for all of us who are concerned about access to science.   Mary Yess, Deputy Executive Director and Chief Content Officer and Publisher, could not be clearer about the increased urgency of ECS’ path:  “We have got to move towards an open science environment. It has never been more important – especially in light of the recently announced ‘gag orders’ on several US government agencies– to actively promote the principles of open science.”    What they committed to in 2013 as an important open access initiative has become, against the current political backdrop, truly a quest to “free the science.”

ECS’s “Free the Science” program is designed to accelerate the ability of the research ECS publishes — for example, in sustainable clean energy, clean water, climate science, food safety, and medical care — to generate solutions to our planet’s biggest problems.  It is a simple and yet powerful proposition, as ECS frames it:

“We believe that if this research were openly available to anyone who wished to read it, anywhere it the world, it would contribute to faster problem solving and technology development, accelerate the pace of scientific discovery, encourage innovation, enrich education, and even stimulate the economy.”

How this small society — which currently publishes just 2 journals — came to this conclusion, and how they plan to move to an entirely open access future, is, I believe, broadly instructive at a time when our political environment has only one solid state: uncertainty.

ECS’s awakening to OA was jump-started by the 2013 OSTP memorandum on public access to research.   It became clear to the ECS that while their technical audience had perhaps not at that time fully embraced open access, the OSTP memo represented a sea change.  By spring of 2013, the board had resolved that ECS was heading towards OA, and they launched a hybrid open access option for their key journals in 2014.

And here’s where the story gets even more interesting.  If you look only at their first offering in 2014 or even their current offerings, you won’t immediately see their deeper plan, which goes well beyond hybrid OA.  For ECS, as Yess clearly indicates, “Gold open access is not the way to go.”   In fact, ECS “doesn’t believe in gold open access,” seeing it as “just a shell game.”

As Yess explains it, “If we hit tipping point to all gold OA, the big commercial players will simply flip all their journals to OA, and the subscription money from library budgets will come out of author budgets, costs will spiral up and we’ll be in the same escalating price environment we’ve been suffering from for years.”  So Yess is “skeptical about gold working.  Given the size and market share of the large STM publishers, they will make Gold OA work to their stakeholders’ benefit, and it will not benefit researchers and their communities.”

There is broad (though hopefully not divisive or overly distracting) debate about whether the APC market will function well for research libraries, and what adjustments to this APC market might make it work.  But meanwhile, what’s a society – the sole nonprofit society to still be publishing their own journals in the relevant disciplines — to do?  ECS’s multi-pronged and contingency-based path is one we could all benefit from watching.  What they envision is “a community of people supporting the content.”  Their insight is to work in the same framework they have had since 1902 — community support– but to evolve what that community support looks like.

Under their subscription-based publishing model, they had relied on a combination of library subscriptions, the Society’s own coffers, and authors’ page charges. Competition from commercial publishers forced ECS to eliminate page charges and to rely on subscriptions and other revenue to support the publications program.  This model has already shown signs of falling apart, with ECS, like many smaller societies, increasingly edged out by big deals from major publishers which preclude cancellations of their journals.

So ECS felt they needed to think differently.  Starting with offering hybrid OA in their flagship journals (rather than launching new OA-specific titles) has allowed the ECS to “test the waters” and has introduced OA to their community of scholars, generating interest around all of the issues.   They started with a two-year program offering generous numbers of APC waivers to members, meeting attendees, and all library subscribers.  This has resulted, as they hoped, in raised awareness, good uptake, and recognition for their OA program.

Then in 2016 they introduced ECS Plus, through which libraries can opt to pay a bit more than the cost of single ECS APC (which is $800) to upgrade their subscription to the package of ECS journals, and as a result have all APCs waived for authors on their campuses who choose the OA option.  Since its launch, ECS has seen a small but encouraging growth in this program. They now have about 800 subscribers, and “there is some evidence the library community feels this is a valuable program,” Yess says.

ECS aims to become “platinum OA” by 2024 – entirely open access, with no APCs, operating fully in what Yess calls an “open science environment.”  They expect to take many roads to achieve this goal.  One is reducing publication costs.  Toward that end, they have entered an agreement with the Center for Open Science to build, at no cost to ECS, a new digital library platform which, once adopted, will reduce ECS’s publication costs.

In addition, this platform will allow ECS to fulfill the“need to move beyond the original concept of open access in standard journals, and beyond the idea of being a publisher in the old sense of journals, articles, issues – to get beyond containerized thinking,” Yess says.

Moving beyond those ‘containers’ will be more possible given their work with the Center for Open Science to offer a preprint server.  The preprint server will be built on the same platform and framework as the preprint servers SocArXiv and PsyArXiv, and will integrate with preprint servers outside of the Open Science Framework such as bioRxiv and arXiv.  ECS hopes to launch this preprint server in beta next month.

While reducing costs and breaking out of old containers, ECS will also need to generate non-subscription revenue if they want to balance the books.  They want to work with the library community to obtain a commitment to pay some kind of cost, possibly looking at a model inspired by SCOAP3.  They also plan to seek donations and endowments from organizations and research funders.  And if the cost reductions and new revenue streams don’t provide a sufficient financial foundation, Yess says that APCs are “a contingency plan” for ECS.

Regardless of which of these roads the ECS takes, for Yess, the overall direction is clear:  “Scholarly publishing has to change. Period.”  Their solutions to the need for change are generated from their own context, and are certainly not one-size-fits-all.   But regardless of whether the specific mechanisms work for other societies, what is instructive from the ECS approach is that they are embracing new realities, envisioning a new, open, scholarly sharing environment, and are building their future from their original base in a community of science and technology.  They are finding a way to maximize the potential of the digital age to support their mission to “free the science” for the betterment of humanity.

In this time of tumult and doubt on our national stage, when the merits of science – and even the existence of facts  — are questioned at the highest levels, ECS’s doubling down on OA and open science can help those of us committed to leveraging science and scholarship for all of humanity, everywhere, see a hopeful way forward, a way that keeps us moving toward our aim of democratized access to science.


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Spherical Panoramas for Astrophysical Data Visualization

This is the title of a paper by Brian Kent (NRAO), which has been accepted for publication in the PASP Special Focus Issue: Techniques and Methods for Astrophysical Data Visualization. You can download the paper from arXiv at .(I understand that the special issue will be published in the Spring). This is a timely publication, given the growing number of wide-area image products released in astronomy.

Brian shows to use the the  three-dimensional software package Blender and the Google Spatial Media module are used in tandem to immerse users in data exploration. The spherical panoramas that can be output from these open-source technologies include static panoramas, single-pass fly-throughs and orbit flyovers.  Briefly, Blender is a 3D graphics suite whose output can be processed by Google Spatial Media to create 360 degree video, and that output can be exported to youTube (with the appropriate metadata added to the header).

All-sky astronomy maps are well suited to this spherical panorama approach. The paper gives an itemize workflow for creating such panoramas. It involves combing images in equirectangular, cylindrical equal are or Hammer-Aitoff projections. Tools such as Montage can perform the projections calculations.

Brian maintains a web page called “An Introduction to 3D Graphics and Visualization for the Sciences.” It includes some panoramic video demos, and I embed a couple below; use your mouse to pan across the images.



Finally, if you really want to learn this technology, consider reading Brian’s book “3D Scientific Visualization with Blender.




Posted in Astronomy, computer videos, Computing, computing videos, cyberinfrastructure, High performance computing, information sharing, Milky Way, Montage, programming, publishing, Scientific computing, software engineering, visualization, workflows | Tagged , , , , , , | Leave a comment

From The Front Lines of SPIE Astronomical Telescopes and Instrumentation 2016

I attended the SPIE meeting on Astronomical Telescopes and Instrumentation in Edinburgh, Scotland from June 26 through July 1, and I am sharing my views on the conference presentations. Approximately 2,000 astronomers, software engineers and instrumentation specialists crowded the Edinburgh International Conference Center (EICC) for the week.  You can see a detailed review of the meeting and a large collection of photographs on the SPIE web page. Parts of this post are based on the SPIE review.

As a software specialist, I gravitated towards the software presentations, which focused on software solutions to challenges in cyberinfrastructure. There were many interesting talks. Paul Hirst of Gemini described how building the next generation of the Gemini archive in the Amazon cloud is proving cost effective, given the high cost of power in Hawaii. Steve Berukoff’s team described how they are building a  Petascale data system for the Daniel K. Inouye Solar Telescope, under construction on Maui. Trey Roby described how his team was modernizing the underpinnings of the Firefly web-based presentation system by replacing the Google Web Toolkit with Javascript. Joerg Retzlaff discussed lessons learned in the Publication of science data products through the ESO archive. Tom McGlynn described the NASA archive model for the implementation and operation of the Virtual Observatory.

Tim Jenness described the challenges of handling large amounts of data and efforts of the LSST team to join the Astropy community leveraging and contributing to those software packages within the confines set by current funding limits and methodologies. Marco Molinaro  shared the results of his team’s EU-FP7 program, VIALACTEA, which provides an infrastructure for handling and manipulating diverse datasets into a more homogeneous database. I described work at the Keck Observatory Archive using R-tree indexing schemes to enable fast, more efficient searches of solar system objects.

My favorite talk was by Asher Baltzell, who discussed a cloud-based data reduction scheme applied to Magellan AO (MagAO) images and the resulting development of a free cyberinfrastructure for community use. The MagAO system featured prominently at the meeting. See the presentations in the MagAO blog at

See the SPIE review for excellent talks on gravitational waves, the operation of the Large Millimeter Telescope (LMT), and four NASA Science Technology Definition Teams presentations on submissions for the Decadal 2020 survey, among others.

The conference reconvenes in 2018 in Austin, Texas.

Posted in astroinformatics, Astronomy, computer modeling, cyberinfrastructure, Data Management, databases, Gemini, Grid Computing, High performance computing, informatics, information sharing, programming, Scientific computing, software engineering, software maintenance, software sustainability, TMT, user communities, Virtual Observatory, visualization, W. M. Keck Observatory | Tagged , , , , , , , , , , , , | 2 Comments