Science News & Announcements

Unearthed from the archives

Yesterday, the Geological Society of London revealed that it had recently unearthed rare and important historical artifact: a first edition copy of a geological map first published in 1815. The map, a work of art in its own right, depicts the geology of England, Wales, and portions of Scotland and was created by the influential geologist William Smith.

Smith, often referred to as the “Father of English Geology,” traveled roughly 10,000 miles per year for 15 years to conduct research for his geological map. These years of travel and extensive study of fossils likely led him to one of his most scientific contributions: the principle of faunal succession. In essence, Smith realized that because fossils are layered in the earth one after another in a predictable, linear fashion, different rocks containing similar fossils are similar in age. Based on this principle, geologists have constructed a timetable with which to measure the relative age of rocks.

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Foxfire and fungi: Solving a 2,300 year-old mystery

A 2,300 year-old mystery
An article published Thursday in Current Biology is rekindling interest in a well-known phenomenon— foxfire, or a glowing light emitted by decaying wood and certain species of fungi. The mysterious forest glow, sometimes referred to as “fairy fire,” was first observed thousands of years ago¹, when Aristotle described a “cold fire” light emanating from the woods. Later, in the first century, Roman thinker Pliny the Elder, described luminescent mushrooms on white wood in olive groves¹. In the following centuries, scholars remarked upon the luminescent properties of mushrooms and the cultural uses of these fungi—in the 1500’s, a Swedish scholar noted that Scandinavians used luminescent fungi for light during dark, winter nights, and in the 1600’s, a Dutch physician noted that Indonesian cultures used them as improvised torches². As recently as the 20th century, Micronesian cultures incorporated luminescent fungi into ritual dress and face paint².

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RCC workshops: Three workshops on parallel programming from Intel

The Research Computing Center will be hosting three workshops on parallel programming from Intel during the month of May. All workshops will be held in the Kathleen A. Zar Room in the John Crerar Library. More information on the workshop topics, as well as registration links, are available in the workshop descriptions below:

Intel Software for High-Performance Parallel Applications
Wednesday, May 20, 2015, 9:00 a.m. to 5:00 p.m. | Kathleen A. Zar Room, John Crerar Library

In this workshop, you will be introduced to Intel Parallel Studio XE Cluster Edition, a multi-component software toolkit to create parallel applications, with a focus on trace collection and analysis. You will also be introduced to Intel compilers, along with Intel’s performance and threading analysis tools, such as Intel VTune Amplifier, Intel Inspector, and Intel Advisor. Finally, you will be introduced to the Intel Math Kernel Library, a math library specially designed for high performance on Intel processors.

Register for this workshop here.


 

Parallel Programming and Optimization with Intel Xeon Phi Coprocessors: CDT 101
Thursday, May 21, 2015, 9:30 a.m. to 4:30 p.m. | Kathleen A. Zar Room, John Crerar Library 

This one-day training provides software developers the foundation needed for modernizing their codes to extract more of the parallel compute performance potential found in both Intel Xeon processors and Intel Xeon Phi coprocessors.

 The session will cover:

  • Intel Xeon Phi architecture: purpose, organization, pre-requisites for good performance, future technology
  • Programming models: native, offload, heterogeneous clustering
  • Parallel frameworks: automatic vectorization, OpenMP, MPI
  • Optimization methods: general,  scalar math, vectorization, multithreading, memory access, communication and special topics

Register for this workshop here.


 

Parallel Programming and Optimization with Intel Xeon Phi Coprocessors: CDT 102
Friday, May 22, 2015, 9:30 to 4:30 p.m. | Kathleen A. Zar Room, John Crerar Library

This one-day training provides software developers the foundation needed for modernizing their codes to extract more of the parallel compute performance potential found in both Intel Xeon processors and Intel Xeon Phi coprocessors. It builds on information attendees will have learned in the previous day’s workshop, CDT 101.

The session will cover:

  • Intel Xeon Phi architecture: purpose, organization, pre-requisites for good performance, future technology
  • Programming models: native, offload, heterogeneous clustering 
  • Parallel frameworks: automatic vectorization, OpenMP, MPI
  • Optimization methods: general, scalar math, vectorization, multithreading, memory access, communication and special topics

Please note: You must complete CDT 101 before taking CDT 102.

Registration open: The Changing Ecosystem of Scholarly Communication Symposium

The 4th Biennial Kathleen A. Zar Symposium, The Changing Ecosystem of Scholarly Communication, will be held on May 1, 2015, at the University of Chicago’s John Crerar Library.

Scholarly communication in the sciences is in a state of rapid evolution. In addition to conventional journal and book publishing, scientists have many modes of consumption and dissemination of research: videos, interactive charts, linked data, blogs, social media, visualizations, and more. The metrics system has also had to adapt, as impacts are now measured far more extensively than by citations alone, including downloads, bookmarks, blog posts, Tweets, and mainstream news coverage. Technology is a big driver of change, but so too is a dynamic funding landscape, with mandates for wider public sharing of research. 

Researchers, librarians, and publishers all benefit from field guides to this novel ecosystem. The 2015 Zar Symposium will explore this new information ecosystem and its impacts on those who inhabit it. 

Registration and full schedule at: http://www.lib.uchicago.edu/e/crerar/zar/

Zar Symposium 2015

The symposium is a biennial event held at the John Crerar Library of the University of Chicago and made possible through the support of the Kathleen and Howard Zar Science Library Fund.

Winter quarter loans to quarterly borrowers automatically extended to June 26

Items checked out by current quarterly borrowers with privileges in good standing and due April 3 will be automatically renewed by the Library for spring quarter. As of March 23, all such items will have a new due date of June 26, 2015. No action by borrowers is necessary.

The automatic renewal is being performed because the functionality to manually renew items is currently unavailable in the Catalog. The Library is working to restore this functionality as soon as possible.

Users may view a list of all items out, including current due dates, via My Account.

For assistance, please contact Circulation or visit a Library circulation desk.

POSTPONED: Wikipedia Edit-a-thon: University of Chicago Edition

editathon graphic

A new date will be announced soon for this event.

On March 28, 2015 the University of Chicago Library will host a Wikipedia edit-a-thon in the Special Collections Research Center. The subject focus of the event is great women in University of Chicago history. Experienced Wikipedia editors and new users alike are welcome to participate. Librarians in Special Collections have chosen specific events, organizations, and people without existing Wikipedia articles to be created as part of this event.  As well as short articles that can be expanded upon. The list includes some notable names to be researched and added to Wikipedia: Georgiana Simpson, Gertrude Dudley, and Marlene Dixon. This is a great opportunity to learn how to edit Wikipedia but also learn about the role of women in shaping and sustaining the University. 

Those in attendance will be able to consult primary source material in special collections as well as print and electronic secondary sources to verify facts. Staff will be on site to offer help navigating online resources to help editors build new articles or enhance existing articles.

Wikipedia has a lot to offer and gain from working with the University Library. This event provides an opportunity to learn how articles are built and maintained and provide on-site access to databases and one-on-one assistance from reference librarians in navigating these sources. New users shouldn’t shy away from attending.

The day-long event begins at 9:30 a.m. and ends at 4:00 p.m. Coffee and pastries will be provided in the morning and lunch will be served in the afternoon. Come for all or part of the day. Registration required, please RSVP by 3/25/15. Email: specialcollections@lib.uchicago.edu or sign up on Facebook

Participants are asked to bring their own laptop and power cord.

 

New to Wikipedia?

Create an account on Wikipedia, if you don’t have one already.  There are a lot of benefits for doing so, particularly with collaborative events like edit-a-thons.  

Once your account is made, try running through The Wikipedia Adventure, an automated tutorial that will help cover some of the basics of using Wikipedia.  It takes about an hour to complete, and it’s an excellent resource for getting started.    

Crerar Library interim hours, March 21-29

Crerar Library will have reduced building and circulation hours for spring interim, March 21-29. 

Building
Sunday – Thursday 8:00 a.m. – 10:00 p.m.
Friday – Saturday 8:00 a.m. – 8:00 p.m.

Circulation
Monday – Friday 8:30 a.m. – 5 p.m
Saturday 9:00 a.m. – 5 p.m.
Sunday, March 22  Closed
Sunday, March 29 Noon – 5:00 p.m.

For a complete list of hours for all locations and departments, see hours.lib.uchicago.edu.

Celebrating Pi Day

As New York Times columnist Gary Antonick playfully pointed out this week, 03/14/15 only rolls around once every century, with the full sequential time arriving on 03/14/15 at 9:26:53. The “Pi Day of the Century” has made a significant splash in news media outlets, with the New York TimesPBS, and CBS, among others, reporting.

Why all the irrational celebration?

In 1988, a San Francisco physicist named Larry Shaw designated March 14th as a day to acknowledge and celebrate the irrational number, Pi. In 2009, the United States House of Representatives passed a resolution supporting Shaw’s designation of March 14th as National Pi Day. Since Shaw’s 1988 designation, Pi Day has been celebrated worldwide, and typical festivities range from pie baking and eating competitions to writing Pi poetry and rap. True enthusiasts who wish to celebrate more than once a year often acknowledge Pi Approximation Day on July 22– Archimedes proved, in the 3rd Century BC, that the fraction 22/7 is a close approximation of Pi (an approximation that is still sometimes used by calculators).

Albert Einstein’s (1879–1955) birthday also happens to be March 14th, furthering the cause for celebration in mathematically- and scientifically-minded communities.

A brief history of Pi:

Archimedes was able to approximate the area a circle, πr², where r is the radius.  He accomplished this by drawing a polygon around a circle and inscribing a polygon within the same circle then calculating the areas of each.

Archimedes’ method for approximating the area of a circle.

The first calculation of pi was done by the ancient Greek mathematician Archimedes (287–212 BC). Archimedes was able to approximate the area a circle, πr², where r is the radius.  He accomplished this by drawing a polygon around a circle and inscribing a polygon within the same circle then calculating the areas of each (pictured left). The area of the circle was between these two. Archimedes was able to demonstrate using this method that pi is between 3 1/7 and 3 10/71. 

Euclid's proof that the ratio of the area of a circle is to the square of its radius is the same for all circles

Euclid, & Simson, R. (1829). The Elements of Euclid: Viz, the first six books, together with the eleventh and twelfth ; the errors, by which Theon, or others, have long ago vitiated these books, are corrected, and some of Euclid’s demonstrations are restored ; also the book of Euclid’s data, in like manner corrected. Philadelphia: Desilver.

Later Euclid (323–283 BC) the “father of geometry”   was able to prove that the ratio of the area of a circle to the square of its diameter is the same for all circles.  This proof appears in Book XII of his Elements.

Highlights from the Library’s collections:

Blatner, D. (1997). The joy of [pi]. New York: Walker and Co..

Posamentier, A. S., & Lehmann, I. (2004). [Pi]: A biography of the world’s most mysterious number. Amherst, N.Y.: Prometheus Books.

Euclid, & Simson, R. (1756). The Elements of Euclid: Viz. the first six books, together with the eleventh and twelfth. In this edition, the errors, by which Theon, or others, have long ago vitiated these books, are corrected, and some of Euclid’s demonstrations restored. Glasgow: Printed by R. and A. Foulis


 

Want to learn more about Pi? The Library’s math and history of science research guides are an excellent place to start.

 

Webinar: NCBI and the NIH Public Access Policy – PMC Submissions, My NCBI, My Bibliography and SciENcv, Mar. 5

On Thursday, March 5, 2015, NCBI will host a webinar outlining how to use My NCBI to report public access policy compliance for NIH grant holders. Topics will include the NIH Public Access Policy, NIHMS and PubMed Central (PMC) submissions, creating My NCBI accounts, use of My Bibliography to report compliance to eRA Commons, and using SciENcv to create BioSketches.

To register for this Webinar, go here: https://attendee.gotowebinar.com/register/4507901281168213249

Text from the NLM Technical Bulletin.

Workshop: Introduction to OpenMP, Wednesday, Feb. 25

Wednesday, February 25, 1–3 PM, Crerar Library, Kathleen A. Zar Room

Douglas Rudd, Research Computing Center

This workshop will give a brief introduction to shared-memory parallel programming using the OpenMP standard. It is designed to give people with little to no parallel programming experience knowledge of basic parallel programming topics, examples of applying OpenMP to existing problems, and strategies for avoiding common errors and pitfalls. The tutorial will begin with an introduction to the concept of parallel programming and a discussion of how to identify problems that may benefit from parallelization. This will be followed by an introduction to the OpenMP API, with an emphasis on parallelizing existing serial codes. Examples in both C and Fortran will be provided.  

 Prerequisites: Familiarity with C, C++, or Fortran.

Register here.