January 18, 2017

More Badges to Earn, Hackathoners!

Several months ago, I posted on the beginnings of the OpenWorm Foundation's badge system. Contributions have been made by several senior contributors, including myself (see the Literature Mining series). Another of my contributions is a series of three badges focused on planning and executing a successful Hackathon [1]. Hackathons are get-togethers of expertise for the purpose of facilitating social coding and solving big, multistep problems. These types of events can be held live or via Skype, and even involve non-coding problem domains [2].

An active in-person Hackathon. 

Check out the Hackathon badges today! For people unaccostomed to earning badges, badges are a quick credential earned by working through the evidence points and submitting an answer in the form of short pieces of computer code, images/graphs, or links acquired through wrking with a piece of technology. The points of evidence are meant to encourage problem-solving and learning on your own, so there is no time limit on completion. Let me know if working through this badge encourages you to host a Hackathon event of your own.

[1] Badges must be earned in sequence: Hackathon I, Hackathon II, and Hackathon III.

[2] Hackathons can also be used to collaboratively solve interdisciplinary problems in a short period of time. For more information, please see: Marshall, J. (2016). In first 72 Hours of Science, SFI postdocs test the limits of transdisciplinary science. Santa Fe Institute News, April 20.

January 10, 2017

How to Kick-Start a Crypto-Currency

Here is an infographic (see below) I received from interested reader Steve Rogen, which follows up on a critique of Bitcoin I published back in 2014). He pointed me to a blogpost by Dinar Durham (a Financial Tech startup) explaining the concept of an initial coin offering (ICO). 

An ICO is a way for a new crypto-currency to distribute its coinage across a broader number of users than the more standard Bitcoin approach, and eliminates severe favoritism towards early adopters. The infographic itself demonstrates the process of public offering for a new coin. 

According to Dinar Durham's blogpost, ICOs have a mixed track record of success; while some are successful, others are not. However, they are becoming more popular as the number of altcoin types increases

December 30, 2016

New Paper at The Winnower

I have a new paper up at The Winnower, just in time for holiday (New Year's Day) reading. The Winnower is a publishing platform that allows people to post manuscripts and other writing while sharing it with the general public and receive feedback. They use a post-publication peer review system, and allows people to gather reviews and revise the original submission (winnowing) before assigning a formal doi (publication). This is my second experience with this type of publication system.

The paper is titled "On Braitenberg's Vehicles, Compound Polygons, and Evolutionary Developmental Structural Complexity", and network theory to analyzing the geometry and spatial composition of biological phenotypes. The paper is currently open for review (which you can submit at the site). I invite you to read and evaluate!

December 1, 2016

Searching for Food and Better Data Science at the Same Time

Two presentations to announce, both of which are happening live on 12/2. The first is the latest OpenWorm Journal Club, happening via YouTube live stream. The title is "The Search For Food", and is a survey of a recently-published paper on food search behaviors in C. elegans [1].

While the live-stream will be available in near-term perpetuity [2] on YouTube, the talk will begin at 12:45 EST [3]. The abstract is here:
Random search is a behavioral strategy used by organisms from bacteria to humans to locate food that is randomly distributed and undetectable at a distance. We investigated this behavior in the nematode Caenorhabditis elegans, an organism with a small, well-described nervous system. Here we formulate a mathematical model of random search abstracted from the C. elegans connectome and fit to a large-scale kinematic analysis of C. elegans behavior at submicron resolution. The model predicts behavioral effects of neuronal ablations and genetic perturbations, as well as unexpected aspects of wild type behavior. The predictive success of the model indicates that random search in C. elegans can be understood in terms of a neuronal flip-flop circuit involving reciprocal inhibition between two populations of stochastic neurons. Our findings establish a unified theoretical framework for understanding C. elegans locomotion and a testable neuronal model of random search that can be applied to other organisms.
The other presentation is one that I will give at the Champaign-Urbana Data Science Users' Group. This will be a bit more informal (20 minutes long), and part of the monthly meeting. The meeting will be live (12 noon CST) at the Enterprise Works building in the University Research Park. The archived slides are located here. The title is "Open Data Science and Theory", and the abstract is here:
Over the past few years, I have been working to develop a way to use secondary data and Open Science practices and standards for the purpose of establishing new systems-level discoveries as well as confirming theoretical propositions. While much of this work has been done in the field of comparative biology, many of the things I will be highlighting will apply to other disciplines. Of particular interest is in how the merger of data science and Open Science principles will facilitate interdisciplinary science.

[1] Subtitle: To boldly go where no worm has gone before. Yup, Star Trek pun. Full reference: Roberts, W. et.al   A stochastic neuronal model predicts random search behaviors at multiple spatial scales in C. elegans. eLife, 2016; 5: e12572.

[2] for as long as YouTube exists.

[3] Click here for UTC conversion.

November 21, 2016

Be as Brief as Possible but no Briefer

Nature Highlights article on the Journal of Brief Ideas, which itself is brief.

No, this is not an Einstein quote. But Einstein very well may have submitted to the Journal of Brief Ideas [1], an open access version of Occam's razor. I just submitted a brief paper called "Playing Games with Ideas: when epistemology pays off", which is the equivalent of a fully-indexed abstract [2]. While some people might find 200 words to be too brief, the Journal allows for attachments to be submitted, thus allowing a bit of circumventing with regard to the word limit [3].

According to the Journal FAQ, submitting such brief reports is part of establishing something below the current standard for the minimal publishable unit. It is also important for enforcing good scientific citizenship practices [4]. Very short papers have occasionally been published in regular journals. Mathematics papers by Lander and Parkin [5] and Conway and Soifer [6] accomplished mathematical proofs in less than a paragraph (but with multiple figures). Other than these rather mythical examples, it is quite the challenge to integrate a well-formulated idea into the Journal of Brief Ideas' 200 word limit.

[1] Woolston, C. (2015). Journal publishes 200-word papers. Nature, 518, 277.

[2] Indexing done via document object identification on Zenodo, doi:10.5281/zenodo.167647

[3] If a picture is worth 1000 words, then the Journal of Brief Ideas become less brief than its name implies.

[4] Neisseria (2015). All you need to publish in this journal is an idea. Science Made Easy blog, February 13.

[4] Lander, L.J. and Parkin, T.R. (1966). Counterexample to Euler's Conjecture on sums of like powers. Bulletin of the American Mathematical Society, 72(6), 1079.

[5] Conway, J.H. and Soifer, A. (2004). Can n2 + 1 unit equilateral triangles cover an equilateral triangle of side > n, say n + ɛ? American Mathematical Monthly, 1.