Tag: Software

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Derivations by Noah Farberman

I recently started using the Logic2010 software for school and fell, madly, in love with solving simple derivations. These two poems derive from that love:

I Love Derivations, and They Love Me

If I love you well
Then you’ll be well loved, my love
Love, derivations

This poem is in reference to the basic derivation rule “Modus Ponens” which dictates that a given variable, if equal to an antecedent present in a conditional statement, can be used to derive a consequent. In other symbols: If I have the premises of “X” and “X->Y” I can use Modus Ponens to derive “Y.”

Derivations Hate Me, So I Hate Them

If you are unloved
Then I have no choice. I do
Not love you either

This poem refers to the derivation inference rule “Modus Tollens.” Logicians can use Modus Tollens to derive a negative antecedent.

An acting inverse of Modus Ponens, Tollens applies to a scenario in which a variable is the negation of a conditional consequent. In other symbols: If I have the premises “~X” and “Y->X” I can use Modus Tollens to derive “~Y.”

You too can have fun solving simple derivations using Logic2010 here: https://logiclx.humnet.ucla.edu/

Noah “Noah Farberman” Farberman is a Toronto writer and Comedian. You can catch up with him on Twitter @NoahFarr

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Click click go! by Dr Jolene Ramsey

Galaxy applied
Eyes scan Apollo data
To annotate phage

By Jolene Ramsey

Studying the genetic makeup of an organism helps us understand how they tick. Scientists often make precise notes about the position and function of important features within a genome, called annotation, akin to marking and reviewing the restaurants on a city map. Viruses tend to have smaller genomes, but they are packed with information. We annotate the genomes of bacteriophages, the viruses that infect and kill bacteria, to reveal their genetic secrets. While there are automated annotation programs, manual review by human eyeballs is necessary to ensure high quality outcomes. With the number of interesting new phage genomes rising daily, the need for user-friendly tools to analyze their genomes has grown as well.

Using our curated toolbox in an open-source, online bioinformatic portal called Galaxy (https://cpt.tamu.edu/galaxy-pub), features common to bacterial and phage genomes can be spotted and cataloged by novices and experts. There are many feature types, each one detected by a different tool. Instead of manually passing the genome through each tool, we are able to speed up and standardize the process using automatic pipelines that run a prescribed list of analyses. We can visualize the results in context using another linked platform called Apollo, and also compare to known genomes. The coupled Center for Phage Technology Galaxy and Apollo suite have allowed us to annotate >130 bacteriophage genomes, and train many students and researchers along the way.

Original research: https://doi.org/10.1371/journal.pcbi.1008214

Jolene Ramsey studies bacterial viruses (phage) as a Center for Phage Technology postdoctoral researcher. She tries to understand how phages orchestrate their escape plan at the molecular level. You can catch up with her on Twitter: @jrrmicro

Enjoyed Jolene’s sciku? Check out her excellent sciku ‘Privateer, the phage’, ‘TF gets in on the bud’, ‘The Phriendly Phage’ and ‘Saba, the morning breeze’.

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Only our minds by Nishant Mehrotra

lab reunion –
we play Chinese whispers with
only our minds

by Nishant Mehrotra

The idea of communicating with our thoughts alone is the stuff of science fiction that, thanks to a team at the University of Washington (Seattle) and Carnegie Mellon University (Pittsburgh), may soon become a reality. In their work (Jiang et. al., 2019), the researchers demonstrate the feasibility of multi-person brain-to-brain communication for the first time. Their system, BrainNet, is an exciting first step towards the future where the Internet might have human brains directly linked to it.

Original research: http://dx.doi.org/10.1038/s41598-019-41895-7

Nishant Mehrotra (@NMehrotratweets) is an  electrical engineer by profession, but a poet by (his) admission. He  blogs at nm30.blogs.rice.edu about RF and wireless research.

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Algorithmic Complexity by Dr David Keyes

It’s not the flop count

But the data location;

The paradigm shifts.

 

Until recently, the analysis of algorithms emphasized finding the minimum number of operations required to complete a task to a given precision – the algorithmic complexity. This is natural when the operations are both the most time-consuming steps of the computation and a reasonable proxy for all other costs, including data motion.

Today, floating point operations (“flops”) are much cheaper in time and in energy than moving the data into and out of the processing unit while memory hierarchies based on multilevel caches deliver operands at latencies and energy costs that vary by several orders of magnitude, depending upon where the freshest copies of the data are found. This situation results in the resurrection of old algorithms and the design of new ones that may do many more flops than previously “optimal” methods, but move less data back and forth from remote locations, and thus finish in less time, with smaller energy expenditure.

The author’s group has created several pieces of software that have displaced previous choices by optimizing memory transfers rather than flops. An example of a singular value decomposition that overcomes a flops handicap of as much as an order of magnitude is given in Sukkari et al (2016). For a community discussion of new paradigms on the path to exascale, see Dongarra et al (2011).

Original research:

Sukkari et al, 2016, https://doi.org/10.1145/2894747

Dongarra et al, 2011 https://doi.org/10.1177/1094342010391989

David Keyes directs the Extreme Computing Research Center at KAUST, where he was a founding dean in 2009. He inhabits the intersection of Mathematics, Computer Science, and applications, with a focus on colonizing emerging energy-efficient architectures for scientific computations. He is a Fellow of SIAM and AMS and has received the ACM Gordon Bell Prize and the IEEE Sidney Fernbach Award. As a lover of poetry, he is delighted to discover the Sciku community.

Enjoyed this sciku? Check out David’s other sciku: Low-rank representation.