Guide to Data Repositories
The Library has put together a guide to data repositories which includes a Physical Sciences Data Repositories guide http://guides.lib.uchicago.edu/psdrepositories. Please feel free to suggest any additional repositories you are using to store your data or to find new data sets. We are also interested in your knowledge about discipline specific metadata schema and would appreciate hearing from you about the schema you use most often in your research.
Kudos: Kudos is a free service for researchers to increase readership and the impact of your research. With the creation of your Kudos account and linking your author identifiers, like ORCID, you’ll be able to share your work and retrieve multiple metrics relating to your publications including page views, citations, full text downloads, and social media metrics (alternative (alt) metrics). You can sign up for your free account by visiting the site
Why manage your data?
Try BrowZine for the iPad during February
If you haven’t yet tried BrowZine yet, today would be a good day to check it out. BrowZine is a service that allows you to browse, read and follow thousands of the library’s scholarly journals. The Library has recently expanded its BrowZine subscription to include web access from your desktop computer as well as Android mobile devices, in addition to the original iOS mobile device apps. You can keep track of your favorite journals and discover new developments in your field wherever you are.
To learn more or to go ahead and start using BrowZine today, simply visit browzine.com or download the app from the Apple App Store, Google Play Store or Amazon App Store. There is also a BrowZine LibGuide with more information, an introductory video, and links to download the apps.
With BrowZine, you can:
– Browse and read journals: Browse journals by subject, easily review tables of contents, and download full articles
– Use the durable linking capability of browzine.com to easily link to specific “shelves” in BrowZine from your courseware to help guide students to complete assignments, such as familiarizing themselves with journals in their field and writing a summary article or research paper about the material they find.
In the mobile app, you can create a personal experience as well:
– Create your own bookshelf: Add journals to your personal bookshelf and be notified when new articles are published
– Save and export articles: Save articles for off-line reading or export to services such as DropBox, Mendeley, RefWorks, Zotero, Papers and more
We have been experiencing some access issues with UpToDate (UTD) and working closely with the vendor to fix them. We apologize for this inconvenience. Here is a summary of the circumstances under which UTD does, and does not, work.
UpToDate does not currently work:
- On a computer/laptop when using a non-proxied link (i.e. not a Library link to UTD).
- On a mobile device via the UpToDate website, whether using a proxied link or signing in with a personal account.
- The Log In / Register link (i.e. the personal account) does not currently work on a computer/laptop or a mobile device.
UpToDate does currently work:
- On a computer/laptop using the Library’s proxied link:
http://proxy.uchicago.edu/login?url=http://www.lib.uchicago.edu/h/uptodate. Ignore the prominent message “Your clinical information system is not properly configured to integrate with UpToDate” and use the search box as usual.
- On a mobile device via the UTD app. If you do not already have the app, you cannot install it until the personal account feature is functional.
NOTE: The Library’s proxied link also works remotely; you will be prompted to sign in with a CNetID or UCHADID when not at the medical center or when off-campus.
Exhibit Location: The John Crerar Library, Atrium
Exhibit Dates: April 19 – October 31, 2016
The recent affiliation between UChicago and the Marine Biological Laboratory (MBL) is the latest chapter in the long, intertwined history of the two institutions. Charles Otis Whitman, the first director of the MBL, also established biology at the University. Frank Lillie, Zoology chair, became the second director and remained president of the MBL corporation until 1942. Today, as the institutions draw closer, we highlight and celebrate our shared history.
Crerar exhibits website.
University of Chicago researchers have access to Lynda.com, a leading provider of online courses covering business, media, and technology. Researchers can choose from over 4,000 courses, all of which are broken up into short, easy to use videos. Business courses cover everything from leadership and marketing to product management, while media courses cover specific software such as Adobe Photoshop and Adobe InDesign, as well as general techniques for graphic design, video editing and more. Technology courses cover a full range of software and skills, including Java, R, SPSS, data analysis and cyber security. Course levels range from introductory to advanced and instructors are vetted industry experts.
In addition to courses, Lynda.com has created guides using a collection of short videos, articles and checklists, that provide a step by step process for starting a business and becoming a manager. The Starting a Business guide covers everything from evaluating yourself and your business idea to establishing operations. Lynda.com’s Weekly Series feature guarantees that content stays fresh. The most recent video in the Marketing Tips weekly series discusses representing the keyword funnel through SEO.
Questions about how to leverage this powerful tool? Ask us on Twitter, Facebook, or through our reference services.
Location: Crerar Library Computer Classroom.
Endnote is a citation management tool. With it you can keep track of your citations and pdfs and create formatted bibliographies as you write your paper. In this workshop learn how to use the desktop version of EndNote. Topics covered include creating and managing citation libraries, importing citations from online databases and other sources, importing and managing PDFs and creating footnotes and bibliographies. Registration is required. Register for this section.
Location: Crerar Library Computer Classroom
Organizing and keeping track of research documents, whether pdfs, notes, images or other pieces of information, can be time consuming and difficult. Let us help you! This workshop will cover effective naming techniques for documents, citation and pdf management, note taking tools, alerts and feeds, and journal management apps. Registration required.
Are you thinking of writing a systematic review? Biomedical Librarians at Crerar can assist you and your team with various aspects of the review, such as:
- Help formulate the research question
- Conduct searches in multiple databases
- Write search strategy portion of methods section
Take a look at our web page to determine the level of service that is right for your team: http://guides.lib.uchicago.edu/systematicreviewservice. Contact email@example.com to schedule an appointment.
Eckhart Library will be closed Monday, March 21st and Tuesday, March 22nd due to a ceiling repair project. We will reopen Wednesday, March 23rd at 12 PM.
In addition to shortened building hours, Crerar Library circulation hours are reduced for the Spring Interim.
Sunday, March 20: Closed
Monday – Friday, March 21- 25: 8:30am-5:00pm
Saturday, March 26: 9:00am-5:00pm
Sunday, March 27: Noon-5:00pm
For other Libraries or Library departments, see http://hours.lib.uchicago.edu for a complete list.
It is now much easier to search WGS (Whole Genome Shotgun) with stand-alone BLAST on your own computer. New tools from the NCBI allow you to BLAST just the WGS projects you are interested in. You can also search a taxonomic subset of WGS (e.g., all human or all bacterial sequences). These new tools for WGS make the existing search mechanism obsolete.
As of August 5, 2016, the current single WGS BLAST database will be retired from the NCBI FTP site and BLAST server. We suggest moving to the new tools as soon as possible.
Read more at ftp://ftp.ncbi.nlm.nih.gov/blast/WGS_TOOLS/README_BLASTWGS.txt.
This announcement is from NCBI News.
To celebrate Fair Use Week, the Library invited Bridget Madden of the University of Chicago’s Visual Resources Center to contribute this post about the fair use of images.
© 2008 Michael Brewer & ALA Office of Information Technology Policy, CC BY-NC-SA 3.0
The Visual Resources Center (VRC) is one of many places on campus that helps to advise faculty, instructors, and students on issues pertaining to copyright and fair use on campus: our specialty concerns the fair use of images. The VRC cannot make permissions requests or make final decisions regarding fair use, but we can provide advice and guidance. We use the four factors of fair use, published best practices guidelines, and several digital tools to help discuss the appropriate next steps.
For classroom use and academic assignments, we typically recommend embracing fair use to the fullest. For publishing images in books and journal articles, our conversation typically goes through the following questions and relevant tools:
- What image do you want to use? Is the image in the public domain or is it under copyright?
If the image is in the public domain, you may use it however you want. If the image is under copyright, consider the following questions:
- How will you use the image? Based on the four factors of fair use, is your use fair, or do rights need to be cleared?
- What rights need to be cleared? Consider the underlying rights of the work in question and the copyright status of the reproduction.
- Who owns the copyright?
- ARS, VAGA, and artists’ estates and foundations are good places to start if the artist is no longer alive.
- How to approach the copyright holder? Is there a form on their website or do you need to draft a letter?
- Do you already have a publication quality image? Most publishers are looking for an image that is at least 300 DPI. Can the VRC scan one for you out of a book, or will you need to purchase one from the repository or rights owner?
We invite you to get in touch with the VRC at firstname.lastname@example.org if you have any questions related to image use and copyright.
This workshop provides an overview of NCBI molecular resources for cancer researchers. In the first part of the Webinar you will learn to more effectively use the Entrez text-based search system and the BLAST sequence similarity search tool to find data relevant to cancer research including sequence, variation, gene and expression information. The second part of the presentation will focus on accessing large-scale genomics datasets. You will learn how to search for, access and download DNA-seq, RNA-seq, Epigenomics and Metagenomics datasets and how to access the tools and APIs at NCBI that can be used to extract relevant subsets of that data for cancer research.
Date: Wednesday, March 2, 2016
Time: 12:00 pm CST
After the live presentation, the Webinar will be uploaded to the NCBI YouTube channel. Any related materials will be accessible on the NCBI Webinars and Courses homepage: https://www.ncbi.nlm.nih.gov/home/coursesandwebinars.shtml where you can also find information about future Webinars.
Above information from: NLM Tech Bull. 2016 Jan-Feb;(408):b7.
Location: Crerar Library Computer Classroom.
Endnote is a citation management tool. With it you can manage your citations and pdfs and create formatted bibliographies as you write your paper. In this workshop learn how to use the desktop version of EndNote. Topics covered include creating and managing citation libraries, importing citations from online databases and other sources, importing and managing PDFs and creating footnotes and bibliographies. Registration is required. Register for this section.
NCBI provides series of 5-15 minute webinars that introduce new NCBI tools or provide quick tips for using popular resources. View them on the NCBI YouTube Channel at: https://www.youtube.com/playlist?list=PLH-TjWpFfWrv-ezUBX2b53vNnDp6Dnd7P
The Computer Science Instructional Laboratory (CSIL) at Crerar
CSIL (Photo by Jason Smith)
Looking for statistical software tools like Stata, R or MATLAB? Want to do some geographical data visualization with ArcGIS? Need to do coding in Java or Python? Edit some photos with Adobe Photoshop or create a soundtrack Edit Edit date and timeusing Audacity? You can do all that and more in the John Crerar Library. Using either computer workstations provided by the Library or by the Computer Science Instructional Laboratory (CSIL, pronounced “see-sill”) you can access a plethora of software applications.
The Library’s Windows workstations have Microsoft Office products and a variety of web browsers, as well as a desktop shortcut to the IT Services vLab. Click on the icon, and login in using your cNetID and password and you can access a broad range of software utilities, including R, MATLAB, and Stata. For a full list of the software options, visit https://answers.uchicago.edu/page.php?id=19919.
CSIL computers include Mac and Linux machines (Linux machines require a separate computer science account), and offer a broad array of software development and engineering tools, multimedia applications, and image processing applications. CSIL tutors are available to assist with any questions. During the academic year, the facility is open all hours that the Crerar Library is open. There are twelve Mac workstations located outside the CSIL classrooms; workstations inside the classrooms are available for use when not in use for a class. For a full list of software and hardware resources offered by CSIL, as well as more information on hours, contacts, and policies, visit https://csil.cs.uchicago.edu/facilities.shtml.
The Library has created a guide to help researchers with Data Management issues such as how to write a Data Management Plan (DMP) and Data Repository and Storage Options available.
Why manage your data?
Many funding agencies such as the NSF now require that researchers write a data management plan in order to receive funding. Preserving your data also ensures it will be available in the long term. In addition documenting and managing your data saves you time because it will be easier to use in an organized and understandable form. Putting your data in a repository and letting the repository handle any requests about it also saves you time that you can focus on your own research.
We also offer a guide to creating and using Author identifiers, including ORCID IDs. Creating an ORCID ID gives you a persistent, unique numeric identifier that links together all of your research work, including any name changes over the course of your career. It distinguishes you from others with the same name and ensures that your work is attributed to you. It also makes it easy for others to locate all of your research, since it is all linked by an identifier.