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.

Tips for Publishing Your Research

The American Chemical Society (ACS) has put together a series of videos called “Publishing Your Research 101″ that covers important aspects of the publication process.  The series is meant to  “helps authors and reviewers understand how to get a manuscript accepted, respond to reviewer comments, navigate ethical considerations, and improve their manuscript submission process experience.” Done in 10 short videos,  it includes topics such as:

How to Write a Paper to Communicate Your Research

Selecting Peers to Suggest as Reviewers

The Basics of Copyright and Fair Use

ACS has also published a special issue of editor tips called “Mastering the Art of Scientific Publication”. It includes 20 papers about the process of publishing and includes topics such as:

How to Make Your Next Paper Scientifically Effective

The Impact of the Impact Factor

Overcoming the Myths of the Review Process and Getting Your Paper Ready for Publication

Cite with a Sight

 More help with scientific writing and citing is available on the Library’s guide: Citation and Writing Resources, Citation Management Tools and Fair Use.

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.

Lecture: The Future of the Planetarium – Mark SubbaRao, Feb 23

Presented by the Research Computing Center

Mark SubbaRao, Space Visualization Laboratory Director at the Adler Planetarium

Monday, February 23rd, 2:00-3:30PM

Crerar Library, Kathleen A. Zar Room

The first planetarium was developed over 90 years ago.  Today thousands of planetaria exist all across the world.  This talk will argue that the future of the planetarium is to make the transformation to a big data visualization facility.  After reviewing the state of the art in planetarium visualization the talk will conclude with a invitation for University researchers to visualize their data sets at the Adler Planetarium.

Speaker Biography:  Mark SubbaRao is the Director of the Space Visualization Laboratory at the Adler Planetarium.  He received his bachelors degree in engineering physics at Lehigh University and his Ph.D from Johns Hopkins University in astrophysics.  His Ph.D thesis concerned the characterization and evolution of the luminosity function of galaxies.  After obtaining his degree he worked as a post doctoral researcher at the University of Chicago on the Sloan Digital Sky Survey a project to make a 3D map of the Universe.  He has led the development of major exhibition galleries at the Adler such as “The Universe:  A Walk Through Time and Space” and has also produced, written and directed a number of stereoscopic videos and full-dome planetarium shows.  These include the planetarium shows “Welcome to the Universe” and “Cosmic Wonder.”  His visualizations have been widely shown in print and television.  He was part of a team that created a first-prize-winning visualization in the 2011 International Science and Engineering Visualization Challenge.  He was also on a team that was awarded the best visualization at XCEDE 2013.  Dr. SubbaRao chairs the international Planetarium Society’s Task Force on Science and Data Visualization, which seeks to realize the potential of the planetarium as a scientific visualization tool.

For more information contact RCC at info@rcc.uchicago.edu or 773-795-2667

Write-In for science honors students

The science librarians at the Crerar Library invite all students participating in a science honors program to a “Write-In” at Crerar.  Come together with other honors students for an afternoon of dedicated research and/or writing time.  The Write-In provides a quiet space free of distractions, free pizza, and science librarians to answer questions regarding citations and resources.

DATE: Sunday, February 22, 2015

TIME: 12:00-4:00 PM

LOCATION: Kathleen A. Zar Room, 1st Floor, Crerar Library

RSVP to Deb Werner, Librarian for Science Instruction & Outreach, at dwerner@uchicago.edu, indicating your program of study.

Workshop: Endnote Online or Zotero, Feb. 19, 12-1PM

When: Thursday, February 19, 2015 12:001:00 p.m.
Where: Crerar Library, Computer Classroom
5730 South Ellis Avenue, Chicago, IL

Citation managers are powerful, time-saving tools that help you manage your research. They can also help you format your papers in MS Word by creating bibliographies, citations, and footnotes automatically in the style you choose, such as APA or Chicago.

This workshop will compare how EndNote Online and Zotero – two popular citation managers – allow you to save, share, and cite information. In order to provide a side-by-side comparison of tools, the format of this workshop is demonstration rather than hands-on training.

Contact: John Crerar Library
More info: https://training.uchicago.edu/course_detail.cfm?course_id=1455
Tag: Workshops, Training, Graduate Students, Staff
Notes: Persons with disabilities who need an accommodation in order to participate in this event should contact the event sponsor for assistance. For events on the Student Events Calendar, please contact ORCSA at (773) 702-8787.
Information on Assistive Listening Device

COMSOL 5.0 workshop, Feb. 17, 1-4 PM

COMSOL 5.0 and Application Builder Workshop
Mian Qin, COMSOL, Inc.

Tuesday, February 17, 2015, 1:00–4:00 p.m.
Kathleen A. Zar Room, John Crerar Library

 Join us for this unique opportunity to advance your skills in multiphysics simulation. This half-day workshop begins with a walk-through of the fundamental modeling steps in COMSOL Multiphysics. Attendees will then have the chance to set up and solve a simulation through a hands-on exercise, guided by a COMSOL expert. You will leave with new skills to work on your own applications using your free, two-week COMSOL trial.

  • Discover the capabilities and features of COMSOL Multiphysics and get a quick overview of the add-on products
  • Learn the natural workflow of the COMSOL Desktop user interface through which all physical phenomena are set up
  • See how to efficiently create and modify your models, and optimize your designs, step-by-step
  • Experience the speed and ease of modeling in the COMSOL environment, shown through a hands-on multiphysics simulation example
  • Learn to convert an existing COMSOL model into an app using the COMSOL Application Builder
  • Set up and solve your first simulation
  • Have a conversation with a COMSOL specialist about your application area
  • Start your two-week free trial and work through your own simulations helped by the COMSOL Technical Support Team
  • Try the Application Builder for designing COMSOL applications

Prerequisites: A computer running Windows is needed for the Application Builder. To participate in the hands-on session you will need to bring a laptop to run a free two-week trial license of the COMSOL software. If you are unable to bring a laptop, we’ll ask you to pair up with another attendee during the hands-on part of the workshop.

Register here.

Sweet science at the John Crerar Library

February 14th: Whether you love it or hate it, Valentine’s Day is a holiday that brings out strong sentiments. The flurry of gift-, flower-, card-, and candy-exchanging observed today is, in fact, nothing new– a rise of the American middle class in the mid-19th century brought these traditions and customs to the fore.  Food, and especially candy and confectionery items, became inextricably tied to Valentine’s Day after the American Civil War, when the U.S. economy witnessed a decrease in the price of sugar and a subsequent rise of the confectionery industry.

The John Crerar Library is home to a veritable treasure trove of cookbooks, both vintage and modern. This Valentine’s Day, we have chosen to highlight some of the library’s more “vintage” confectionery cookbooks. To the left, you will find two recipes selected directly from our turn-of-the-century holdings, and below, the products of these recipes made nearly a century after their original publication.

Lovers' Layer-Cake, baked February 11, 2015. Lovers' Layer-Cake and Cocoa Fudge, baked February 11, 2015.





More from these cookbooks:

Title Page: Choice Recipes, by Maria Parloa. Published 1899.

Walter Baker & Co's Vanilla Chocolate Color Label

Walter Baker & Co's Breakfast Cocoa and Baker's Chocolate. Color Labels.

Walter & Baker Co's German Sweet Chocolate, Color Label

Cover: The Everyday Cake Book, by Gertrude Paul. Published 1921.





More at The University of Chicago Library:

Sweet Home Chicago: Chocolate and Confectionery Production and Technology in the Windy City

Selected Valentine’s Day Readings

GSA Bulletin historical issues online from 1890 to present


Image from C. H. Hitchcock, “Geology of Oahu,” Geological Society of America Bulletin, January 1900, v. 11, p. 15-60, doi:10.1130/GSAB-11-15

The Geological Society of America has completed digitizing the earliest years of the Geological Society of America Bulletin, extending access online back to 1890.  These historical issues are included in the Library’s subscription to th GSA Bulletin on the GeoScienceWorld publishing platform.  

University of Chicago students, faculty and staff can see a list of all the available full text PDF issues of the GSA Bulletin by visiting the GeoScienceWorld site.


Workshop: Managing Your Online Presence as a Researcher, Feb. 10 and 12


Tuesday, February 10, 4–5 PM or Thursday February 12, 12-1PM

Where: Crerar Library, Kathleen Zar Room
5730 South Ellis Avenue, Chicago, IL
Description: You want to establish an effective online presence, but what are the best ways to make your identity visible to potential collaborators? Join us for a 60 minute workshop to learn how to build your online profile as a scholar/researcher. We’ll cover online scholarly communities, author identifiers (like ORCID), and other ways to carve out a space online for your professional self.

Another session of this same workshop will be held on February 12th at 12pm. See more info link for details.

Contact: John Crerar Library
More info: https://training.uchicago.edu/course_detail.cfm?course_id=1339
Tag: Workshops, Training, Graduate Students, Staff
Notes: Persons with disabilities who need an accommodation in order to participate in this event should contact the event sponsor for assistance. For events on the Student Events Calendar, please contact ORCSA at (773) 702-8787.
Information on Assistive Listening Device

Workshop: Introduction to EndNote (Online Version), Feb. 6

When: Friday, February 6, 2015 12:001:00 p.m.
Where: Crerar Library, Computer Classroom
5730 South Ellis Avenue, Chicago, IL
Description: EndNote offers an online version of its popular citation manager that is available to the University of Chicago community freely through the Library. The online version offers the key features of the popular EndNote software, but with added enhancements of cloud storage, syncing, and the ability to easily share and collaborate. Come to this workshop and see if EndNote’s online version works for you.
Contact: John Crerar Library
More info: https://training.uchicago.edu/course_detail.cfm?course_id=1339
Tag: Workshops, Training, Graduate Students, Staff
Notes: Persons with disabilities who need an accommodation in order to participate in this event should contact the event sponsor for assistance. For events on the Student Events Calendar, please contact ORCSA at (773) 702-8787.
Information on Assistive Listening Device

Workshop “Introduction to R” Feb.12 and 19, 2-4 PM

Introduction to R
Lian Huan Ng, Instructor, Research Computing Center

Thursday, February 12, and Thursday, February 19, 2015, 2:00–4:00 p.m. | Kathleen A. Zar Room, John Crerar Library

This workshop is a two-part series on an introduction to the statistical software R. 

Session 1 (February 12): Attendees will gain hands-on experience working with an example data set using R while learning about the basic features of R.  Topics to be covered include: using R as a calculator, common data types (vector, matrix, list, data frame), importing and exporting data in R, and some basic statistical analyses.  No prior experience with R is required.

Session 2 (February 19): We will continue from where we have left off from the first workshop.  Topics to be covered include: additional basic statistical analyses, plotting, the “apply” family, using external packages, and basic programming syntax (if time permits).  Attendance at the previous first workshop is not required but you should be comfortable with some basic R commands, such as how to import a data set into R as a data frame.

Prerequisites: Attendees are strongly encouraged to bring a laptop to participate in the hands-on session and have access to both R and the RStudio software.  If you already have access to an RCC account, then you can use the RStudio software via RCC’s ThinLinc.  Otherwise, you can download and install the stand-alone R and RStudio software onto your laptop prior to attending the workshop.

Register here.

The science of snowstorms

Although the snowfall from winter storm Juno has not quite measured up to the predictions of a dangerous and historic snowstorm made this past weekend, the storm has had a heavy impact on New England, causing flooding, power outages, and dumping up to 30 inches of snow on parts of the region. The National Weather Service’s predictions prompted swift action from public officials and an avalanche of media coverage across the nation (including a map from the Smithsonian allowing viewers to track the storm through social media).

According to the National Snow and Ice Data Center (NSIDC), forecasting snowfall is a difficult science. This observation from the NSIDC seems to resonate strongly with the spotty snowfall observed during winter storm Juno:

“In addition, snow does not fall evenly everywhere. Even during the same storm, one neighborhood may receive deep snow, while an adjacent neighborhood may only receive a light dusting. At the local scale, variations in snow depth are caused primarily by wind during and after the storm, and by melting after the storm. At the larger scale, say across an entire state, it also depends on the storm track. Places in the middle of the storm track may receive significant snowfall, while locations along the edges of the storm may receive much less.”


Interested in keeping warm, snuggling up indoors, and reading about weather and climatology? The John Crerar Library offers a multitude of resources that will allow you to explore the storm from a safe distance:

In Print


Other Online Resources

PubAg: new search engine for published USDA research

National Agricultural Library“The National Agricultural Library (NAL) has unveiled PubAg, a user-friendly search engine that gives the public enhanced access to research published by U.S. Department of Agriculture (USDA) scientists. NAL is part of USDA’s Agricultural Research Service (ARS).

PubAg, which can be found at PubAg.nal.usda.gov, is a new portal for literature searches and full-text access of more than 40,000 scientific journal articles by USDA researchers, mostly from 1997 to 2014. New articles by USDA researchers will be added almost daily, and older articles may be added if possible. There is no access fee for PubAg.”

Text from the USDA Agricultural Research Service.

The Science Writing Prize for College Students accepting submissions for 2015


The annual John Crerar Foundation Science Writing Prize for College Students honors the memory of John Crerar – industrialist and philanthropist whose estate established the John Crerar Library.

This competitive award for excellence and clarity in science writing acknowledges the ability of a University of Chicago College student to produce a paper, on a scientific topic, which is thorough in its arguments but accessible to a broad readership.

Students will submit a 2,500-3,000 word essay on a topic in science, medicine and/or technology. Essays should describe how the topic is relevant to the student’s studies and describe the topic’s impact on society today and into the future. Submissions must be scientifically and technically accurate, make reference to the relevant literature, and be accessible to a readership with a general knowledge of science. We encourage and welcome submissions from all perspectives.

  • First Prize is $1500
  • Second Prize is $500
  • Deadline for submission is: APRIL 20, 2015


Click here for more details and competition guidelines.


Email questions to crerar-prize@lib.uchicago.edu.





New Library Director and University Librarian arrives on campus

Brenda Johnson

Brenda Johnson

Dear University of Chicago Faculty, Students and Staff,

As I begin my second week on campus, I would like to say how very happy I am to have arrived at the University of Chicago. The warm welcome I have received from so many of you in the last few days has made me feel immediately at home.

The University of Chicago’s status as one of the world’s premier academic and research institutions and its Library’s role in fueling intellectual inquiry and a transformative education are well known internationally. As the year unfolds, I look forward to learning much more about your work; about the ways you rely on the Library to support your research, teaching and study; and about the ways you see your needs evolving as you break new scholarly ground or advance in your education.

It will be my great pleasure to meet many more of you and to discuss these matters with you in the coming months.

With warm regards,

Brenda L. Johnson
Library Director and University Librarian
The University of Chicago Library

Save the date: 4th Biennial Kathleen A. Zar Symposium, May 1, 2015

CrerarGuide09_arch_color2Save the date for the 4th Biennial Kathleen A. Zar Symposium, “The Changing Ecosystem of Scholarly Communication,” held on Friday, May 1, 2015 at the 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.

Information about previous symposia is available at http://www.lib.uchicago.edu/e/crerar/zar/.

Introduction to EndNote Online Version: workshop

When: Monday, January 12, 2015 12:001:00 p.m.
Where: Crerar Library, Computer Classroom
5730 South Ellis Avenue, Chicago, IL
Description: EndNote offers an online version of its popular citation manager that is available to the University of Chicago community freely through the Library. The online version offers the key features of the popular EndNote software, but with added enhancements of cloud storage, syncing, and the ability to easily share and collaborate. Come to this workshop and see if EndNote’s online version works for you.
Contact: John Crerar Library
More info: https://training.uchicago.edu/course_detail.cfm?course_id=1339
Tag: Workshops, Training, Graduate Students, Staff
Notes: Persons with disabilities who need an accommodation in order to participate in this event should contact the event sponsor for assistance. For events on the Student Events Calendar, please contact ORCSA at (773) 702-8787.
Information on Assistive Listening Device

Lecture: Dynamic Execution for Exascale Computing – Thomas Sterling, Jan 14

thomassterling-mw2015Friday, January 15, 2015, 3:00-4:30 PM Lecture
Dynamic Execution for Exascale Computing
Thomas Sterling
Professor, Informatics and Computing, Indiana University | CREST, Executive Associate Director, Chief Scientist
Kathleen A. Zar Room, John Crerar Library

The challenge of achieving useful exascale computing will demand innovations in computer architecture, parallel programming models, and system software. This presentation will describe the areas where advances are anticipated and the concepts behind them. It will provide examples from experimental systems demonstrating early results that support these approaches. The talk will include current findings from the recently developed HPX-5 runtime system and the new XPI asynchronous programming interface.

Speaker biography: 

Dr. Thomas Sterling holds the position of Professor of Informatics and Computing at the Indiana University (IU) School of Informatics and Computing as well as serves as Chief Scientist and Executive Associate Director of the Center for Research in Extreme Scale Technologies (CREST). Since receiving his Ph.D from MIT in 1984 as a Hertz Fellow Dr. Sterling has engaged in applied research in fields associated with parallel computing system structures, semantics, and operation in industry, government labs, and academia. Dr. Sterling is best known as the “father of Beowulf” for his pioneering research in commodity/Linux cluster computing. He was awarded the Gordon Bell Prize in 1997 with his collaborators for this work. He was the PI of the HTMT Project sponsored by NSF, DARPA, NSA, and NASA to explore advanced technologies and their implication for high-end system architectures. Other research projects included the DARPA DIVA PIM architecture project with USC-ISI, the Cray Cascade Petaflops architecture project sponsored by the DARPA HPCS Program, and the Gilgamesh high-density computing project at NASA JPL. Thomas Sterling is currently engaged in research associated with the innovative ParalleX execution model for extreme scale computing to establish the foundation principles to guide the co-design for the development of future generation Exascale computing systems by the end of this decade. ParalleX is currently the conceptual centerpiece of the XPRESS project as part of the DOE X-stack program and has been demonstrated in proof-of-concept in the HPX runtime system software. Dr. Sterling is the co-author of six books and holds six patents. He was the recipient of the 2013 Vanguard Award. In 2014, he was named a fellow of the American Association for the Advancement of Science.

*Refreshments will be served*

 For more information contact RCC at info@rcc.uchicago.edu or 773-795-2667

Introduction to Endnote (Desktop Version), Wednesday, Jan.14, 12-1 PM

Endnote imageLocation: Crerar Library Computer Classroom.

Learn how to use the bibliographic software EndNote.  Topics covered include creating and managing libraries, importing references from online databases, importing and managing PDFs and creating formatted bibliographies and citations in Microsoft Word. Registration is required.  Register for this section.

Exhibits Coal Swamp Fossils: The Robert Springfield Fossil Collection – new web exhibit

Calamites sp.

A branch of Calamites sp. that shows multiple spore producing cones of a sphenopsid.

A web version is now available of the current Crerar Library exhibit: Coal Swamp Fossils: The Robert Springfield Fossil Collection.  The physical exhibition, consisting of 16 fossils, is on view in the Crerar Library’s First Floor Reading Room for the 2014-2015 academic year.  It was curated by Benjamin Rhind, University of Chicago Laboratory Schools high school senior.

Exhibit Description: This collection of fossils was collected by Robert Springfield in mines in southern Tennessee and northern Alabama.  They contain many fossils from the Carboniferous Period, ranging from 330,000,000 -300,000,000 BCE.  The period was defined by the large deposits of coal beds that it left behind.  This massive amount of coal was because of the development of bark bearing trees and the fact that a lower sea level during this age left behind large lowland, swampy forests.  Plant life during the period was diverse, and although this collection of fossils contains several different genera and species, they all fit into one of three categories: sphenopsids, lycopods and pteridosperms.

The University of Chicago Library is grateful to the Springfield family for their gift of fossil specimens, which brings unique materials to the Library’s collections.  The Robert Springfield Fossil Collection is on loan from the Library’s Special Collections Research Center.


Best of science and medicine in 2014

Here’s a look back on some of the best and most read of science and medicine in 2014:


imedapps’ Best Medical Apps Released in 2014

Cleveland Clinic’s Top 10 Medical Innovations for 2014

Hercules A galaxy

Hercules A galaxy (Photograph by X-ray: NASA/CXC/SAO, Optical: NASA/STScI, Radio: NSF/NRAO/VLA)

Docphin’s Top 50 Most Viewed Medical Journal Articles in 2014

Read by QxMD’s Top 50 Articles from 2014



Science’s Breakthrough of the Year 2014

Nature’s 2014: The Year in Science

Wired’s The Craziest Sci-Fi Fantasies That Got Closer to Reality This Year

Science Friday’s The Best of 2014

National Geographic’s Nature Photo of the Year

National Geographic’s Best Space Pictures of 2014

Something’s Brewing web exhibit launched


Drawing of beer barrels in storage.

Something’s Brewing. The Art, Science and Technology of Beer Brewing 

(an online exhibit)

There is more to brewing than barley and hops. Beverages have been brewed from beans, oatmeal, honey, molasses, rye, wheat, old bread, and even whole chickens. Ancient Egyptians, medieval monks, and Chicago city founders have all practiced the art of brewing.

The Crerar Library exhibit, Something’s Brewing: The Art, Science and Technology of Brewing, was originally shown January 8 – March 31, 2007 and explored the development of brewing, from the ancient Sumerians’ rice-based beverages to the rise and fall of the Chicago brewing industry.  The Library is pleased to present a web version of the exhibit, including links to original works in digital online libraries where available.  

This exhibit was curated by Andrea Twiss-Brooks and Debra Werner.  The images and text were adapted for the web exhibit by Jennifer Hart and Andrea Twiss-Brooks.

NIH Manuscript Submission (NIHMS) system getting a new look

In January 2015, a redesign of the NIH Manuscript Submission (NIHMS) system will be launched.  The redesign includes a new interface, streamlined log in and manuscript submission processes, and screen-specific help information.  Additional details about the new interface are at http://www.nihms.nih.gov/NIHMS_Announcement.pdf.

More information about the NIH Public Access Policy is available on Crerar’s NIH Public Access Policy Guide.

new NIHMS home page preview

Preview of the new NIH Manuscript Submission (NIHMS) home page.

Alert Fall quarter loans to quarterly borrowers automatically extended to April 3

Items checked out by current quarterly borrowers with privileges in good standing and due January 9 will be automatically renewed by the Library for winter quarter. As of December 18, all such items will have a new due date of April 3, 2015. No action by borrowers is necessary.

The automatic renewal is being performed because the functionality to manually renew items is temporarily 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 online or visit a Library circulation desk.