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July 25, 2014

From the GMR: NCBI Announcements

FYI: NCBI Upcoming events and honors
BLAST in the Cloud webinar July 30th

In one week, NCBI will offer a webinar entitled "BLAST in the Cloud". This presentation will show you how to log on to AWS and deploy the NCBI-BLAST Amazon Machine Image (AMI) quickly. Prior knowledge of using web and standalone BLAST is required.

To register, please go to this link: https://attendee.gotowebinar.com/register/8126572163773355778.

* NCBI News: http://www.ncbi.nlm.nih.gov/news/07-01-2014-BLAST-in-cloud-July-webinar/

NCBI webinar "Using the New NCBI Variation Viewer to Explore Human Genetic Variation" on August 13th

On August 13th, NCBI will host a webinar entitled "Using the New NCBI Variation Viewer to Explore Human Genetic Variation". This presentation will show you how to find human sequence variants by chromosome position, gene, disease names and database identifiers (RefSNP, Variant region IDs) using NCBI's new Variation Viewer.

You will learn how to browse the genome, navigate by gene or exon, filter results by one or more categories including allele frequencies from 1000 Genomes or GO-ESP, and link to related information in NCBI's molecular databases and medical genetic resources such as ClinVar, MedGen, and GTR. You will also be shown how to upload your own data to add to the display and download results.

Anyone who works with clinical or research variation data will find that the Variation Viewer provides a convenient and powerful way to access human variation data in a genomic context that is fully integrated with all other NCBI tools and databases.

To register, please go to this link https://attendee.gotowebinar.com/register/2762824590748330498.

Related Links:
• Variation Viewer: http://www.ncbi.nlm.nih.gov/variation/view
• 1000 Genomes: http://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/
• GO-ESP: http://www.ncbi.nlm.nih.gov/bioproject/165957
• ClinVar: http://www.ncbi.nlm.nih.gov/clinvar/
• MedGen: http://www.ncbi.nlm.nih.gov/medgen/
• GTR: http://www.ncbi.nlm.nih.gov/gtr/?

Announcing major revision of the NCBI genomes FTP site

Within the next two weeks, NCBI will make a major revision to the genomes FTP site. This redesign will expand available content and facilitate data access through an organized, predictable directory hierarchy. The updated site will also provide greater support for downloading assembled genome sequences and/or corresponding annotation data. To give those with automated tools time to update, we plan to maintain the older content and structure of the preexisting /genomes/ FTP site in parallel with the new structure for six months.

The new FTP site structure provides a single entry point to access content representing either GenBank or RefSeq data. Advantages of the updated genomes FTP site include the comprehensive provision of data through a single process flow that is reliant on content in NCBI's Assembly database (which excludes viruses at this time), integration of quality assurance regression tests, and provision of a consistent core set of files for all organisms and assemblies.

Stay tuned for more information about the changes to come and the official launch of the revamped genomes FTP site.

. Current Genomes FTP site: ftp://ftp.ncbi.nlm.nih.gov/genomes/
. GenBank: http://www.ncbi.nlm.nih.gov/genbank/
. RefSeq: http://www.ncbi.nlm.nih.gov/refseq/
. Assembly: http://www.ncbi.nlm.nih.gov/assembly/

NCBI/CDC/FDA/USDA collaboration using whole genome sequencing (WGS) to improve food safety is honored with an HHSinnovates award

A collaborative project between NCBI and several other Federal and state partners to reduce the time and improve the accuracy of detecting foodborne pathogens by using whole genome sequencing (WGS) techniques received an HHSinnovates award on July 21.

The HHSinnovates program was initiated in 2010 to recognize new ideas and solutions developed by HHS employees and their collaborators. Six finalist teams were recognized at the awards ceremony. The WGS Food Safety Project, which also involved the Centers for Disease Control and Prevention (CDC), the Food and Drug Administration (FDA), the U.S. Department of Agriculture (USDA), and state public health laboratories, was one of three projects to be honored as "Secretary's Picks" by HHS Secretary Sylvia Mathews Burwell.

Presenting the award, HHS Deputy Secretary Bill Corr said: "Together all these folks engaged in a demonstration project to showcase the benefits of using whole genome sequencing for food surveillance and detection purposes. They showed that whole genome sequencing can produce faster detection of foodborne pathogens than the traditional method, helping us stop an outbreak of disease in its tracks, and for that we deeply appreciate your work." The award went to the specific individuals leading the project in the various agencies; in the case of NCBI, Senior Scientist William Klimke, Ph.D., was honored for his work in heading NCBI's part of the project.

WGS provides greater specificity than other techniques, such as the commonly used pulsed-field gel electrophoresis (PFGE), in identifying the DNA fingerprint of bacteria. It also can more rapidly determine whether isolates are related to a foodborne disease outbreak.

The demonstration project involves real-time sequencing of Listeria monocytogenes isolates from human DNA as well as the food supply chain. In the project, the whole genomes of isolates are sequenced and the sequencing data are sent to NCBI, which performs assembly, annotation, and analysis and then sends results back to CDC, FDA, USDA, and the labs.

Collaborative projects using WGS for other pathogens related to food safety are also underway.

* HHSinnovates: http://www.hhs.gov/idealab/pathways/hhs-innovates/

July 24, 2014

New Issue of Liblog: The Newsletter of the Mayo Clinic Libraries

Dear Colleagues: The 51st issue of our online newsletter Liblog: Newsletter of the Mayo Clinic Libraries has been published. Hope you are enjoying your summer. Best regards - Michael

J. Michael Homan | Director of Libraries | Mayo Clinic Libraries | Assistant Professor of Medical Informatics | College of Medicine | 507-284-9595 | homan@mayo.edu | Assistant: 507-284-2543 | Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | www.mayoclinic.org

From the GMR: Save the Date announcement for "A Librarian's Guide to NCBI"

Some of you have been waiting for this class to come again.

The required online class will be offered:
January 12 - February 20, 2015
Registration opens September 29th
The in-person five-day class in Bethesda, MD runs:
March 9-13, 2015
Registration will be offered to those who complete the online class.

Enjoy - and be aware the class fills up quickly.


---------- Forwarded message ----------
From: Sharon E. Dennis
Date: Tue, Jul 15, 2014 at 11:12 AM
Subject: [NNLMout] Save the Date announcement for "A Librarian's Guide to NCBI"
To: "nnlmout@uw.edu"

Hi everyone,

We have posted the "Save the Date" announcement for the 2015 session of "A Librarian's Guide to NCBI." You can see the announcement on NTC's blog: http://nnlm.gov/ntc/2014/07/10/save-the-dates-2015-a-librarians-guide-to-ncbi-course/

Or in the NLM Technical Bulletin: http://www.nlm.nih.gov/pubs/techbull/ja14/ja14_libguide_ncbi.html

Let me know if you have questions. Thanks!

Best regards,

Sharon Dennis
Assistant Director
National Library of Medicine Training Center (NTC)
Spencer S. Eccles Health Sciences Library
University of Utah
10 North 1900 East
Salt Lake City, UT 84112

800-338-7657, press 2
Fax: 801-581-3632

July 23, 2014

Aug. 7 SLA-MN Salon: Associations - who needs them?

The next SLA Minnesota Salon will be held at the Walker Art Center Open Field. Open Field offers a mash-up of experiences and a chance to get together. For this Salon we are mashing up discussion, mingling with other associations and picnicking.

The topic up for discussion will be "Associations. Who Needs Them?" We'll explore what the benefits/challenges are of belonging to professional associations and attending professional conferences.

Bring your picnic blanket or chair and enjoy a summer evening with SLA-MN.

Top Reasons to Attend:
Arrive before 5:45 and your first drink is free!
Meet and mix (we'll be shouting distance/mingling distance of the Library as Incubator Project group)
Air your grievances or proclaim your pride for what professional associations have to offer
Picnicking at Open Field
Stay for The Acoustic Campfire (8-10 pm) or take advantage of the free gallery admission (5-9 pm)

When: 5:30-7:30 p.m., Thursday, Aug. 7
Where: Walker Art Center Open Field
What to bring: picnic blanket or chair, money for food or additional beverages available for purchase.
Who should attend: Anyone interested in picnics, lively discussion and mingling with other information professionals

RSVP: To Alisa Coddington: alisa.coddington@padillacrt.com

*Reminder* SLA MN Salon Series is open to everyone. Anyone can organize and host a SLA-MN Salon event. Please contact Alisa Coddington for details.

PadillaCRT | 1101 West River Parkway, Suite 400, Minneapolis, Minnesota 55415
o. (612) 455-1734 | alisa.coddington@padillacrt.com

July 21, 2014

Sharon Kambeitz's Retirement Tea

Allina Health Services is celebrating the career of their colleague, Sharon Kambeitz at a tea on July 31, 2014 at their headquarters.

July 18, 2014

From the GMR: The July 2014 GMR Update is live!

Hello, Network Members,

The GMR Update for July 2014 is now live. You may view it online at the following link: http://nnlm.gov/gmr/about/gmrupdate.html

Of note in this issue is the announcement of the Library Student Outreach Award recipients and a message from the GMR Associate Director, Beth Layton.

Be sure to check it out!


Jacqueline Leskovec, MLIS, MA, RN
Outreach, Planning and Evaluation Coordinator
National Network of Libraries of Medicine
Greater Midwest Region
1750 W. Polk St. M/C 763
Chicago, IL 60612-4330

312.996-2464 Phone
312.996-2226 FAX

July 11, 2014

Remembering Sunny Worel

Many of you have already heard about our communities loss of Sunny Worel. I was not fortunate enough to know Sunny, but I know many in HSLM did. Pam Barnard passed this along:

It is with sadness that I mention for anyone not following her journey on Facebook or Caring Bridge (I wasn't following either) or who doesn't read the Star Tribune obituaries, Sunny Worel passed away from colon cancer on July 1. I never worked with Sunny, but she was an inspiration to those of us who strive to have an authentic voice in the varied library work that we all do in different places and in different ways ... I know she had many friends and colleagues at the U of MN, as well as her other places of employ and from her interests. As the entry in her obituary said, she was an original and will be deeply missed by many.


Feel free to leave memories of Sunny in the comments.

July 7, 2014

Update: Minnesota electronic Health Library (MeHL), July 2014

Good Morning HSLM Members!

At the HSLM Annual meeting on June 13, Anne Beschnett gave a presentation
about the Minnesota Electronic Health Library (MeHL), an Initiative of the
University of Minnesota Health Sciences Libraries. The vision for MeHL is
to provide equal access to a core set of clinical, evidence-based, online
information resources for all Minnesotans. This includes all health
providers, researchers, students, and educators, as well as caregivers and
patients who need quality information to engage in the patient care
partnership. For more information, see: http://hsl.lib.umn.edu/about/mehl.

Currently, the MeHL project team is engaging with various groups throughout
the state who would both benefit from access to information and help
support the initiative. The team's goal is to develop a wide base of
support as prepare to request state funding during the 2015 legislative

The presentation highlighted the request for information (RFI) was issued
in the spring to vendors. Responses have been reviewed by the project
team, and four possible funding scenarios were drafted for MeHL.

The presentation's Q&A section and subsequent discussion among the HSLM
members was helpful in raising many good points, which are being reviewed
by the project team for follow-up.

Additional feedback and comments are welcomed, and can be directed to Erinn
Aspinall (MeHL Project Manager) at aspin005@umn.edu. You can also leave
feedback on the "Tell Us Your Story" section of the MeHL webpage.

Monthly updates on the MeHL project will also be shared with HSLM members
through the duration of the initiative.

Thank you for your continued interest and support.

MeHL Project Team:

Erinn Aspinall
Anne Beschnett
Katherine Chew
Janice Jaguszewski
Nicole Theis-Mahon

July 3, 2014

From the GMR: 2014 Sewell stipend for librarians with an interest in public health

Librarians with an interest in public health, make this the year you attend the American Public Health Association Annual Meeting. Stipends funded by The Grace and Harold Sewell Memorial Fund for this purpose will be awarded to at least 10 librarians in 2014. This year's APHA meeting will take place in New Orleans, LA from November 15-19, 2014. Its theme is Healthography: How Where You Live Affects Your Health and Well-Being. For more information on the meeting see APHA's website: http://www.apha.org/meetings/annual/.

Applications are now being accepted. The deadline for application is July 24, 2014, 5pm EST. For the complete Call for Applicants, application forms, and FAQs, go to http://www.phha.mlanet.org/blog/activities/sewell-stipend/.

For more information on the 2014 APHA meeting see http://www.apha.org/meetings/highlights/.

For more information on the Sewell Fund, see http://www.sewellfund.org/ -

What is the Value of Attending APHA as a Sewell Stipend recipient?

The mission of the Fund is to increase librarians' identification with medical and health care professionals. Stipends have been awarded annually since 2001. Past participants testify to the value of attending APHA:

"Connecting with my fellow library and information professionals and public health colleagues was energizing...The spirit of true collaboration shone through the programs." (Feili Tu)

"Many of the things I learned were not specific, as in tangible facts, more of an understanding of what Public Health is. I learned it covers just about everything...for Public Health you need to be knowledgeable about the issues, the potential impact of legislation, and knowledgeable about the 'agendas' of the interested parties..." (Kristin Kroger)

"Overall the conference really helped me to better understand the scope of public health as well as the latest development in the areas of public health that I am most likely to have to deal with as a librarian....It was an incredible learning experience." (Manju Tanwar)

"The fact that I'm working on a Masters in Public Health was very interesting to her (public health colleague) because she didn't realize that some librarians also have another graduate degree. I think this helped solidify the idea that librarians could be peers to teaching faculty." (Amber Burtis)

"As a result of the meeting I gained a deeper understanding of my patrons' needs" (Peggy Gross)

"I feel like I now have a cohort of people to whom to turn when I have questions about what I am doing as I move into supporting my institution's public health program." (Laure Zeigen)

The committee is looking forward to reading your applications!

Barbara Folb, Chair, Client Relations Committee

Helena VonVille, Chair-elect, Client Relations Committee

Public Health/ Health Administration Section
Medical Library Association

July 2, 2014

From the GMR: Check with NLM Before Discarding Journals

NLM's Journal Donation System makes it possible for libraries to determine whether NLM needs any volumes of the print journals they plan to discard. The system can be used by DOCLINE and non-DOCLINE libraries to offer any title, including titles not owned by NLM. The system can be accessed at http://www.nlm.nih.gov/journaldonation/ or by searching "Journal Donation System" on NLM's home page. In the system, click on "Help" for detailed instructions. For additional assistance, contact NLM at (301) 496-0081 or NLMJournalDonation@mail.nlm.nih.gov . NLM will pay shipping for volumes we need. To donate pre-1871 journal volumes to the History of Medicine Division, see http://www.nlm.nih.gov/hmd/about/donate.html.

Since the beginning of the online donation system in April 2009, over 10,000 gifts have been added to the collection. With the help of libraries planning to discard journal volumes, NLM can build on the success achieved to date.

Karen Sinkule
Preservation and Collection Management Section
Journal Donation Unit
National Library of Medicine
8600 Rockville Pike
Bethesda, MD 20894