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Archive for the ‘Technology and Libraries’ Category

PubMed Commons Update

Monday, August 4th, 2014

PubMed Commons set the stage for commenting on any publication in PubMed, the world’s largest searchable database of biomedical literature. New infrastructure and design enhancements have been implemented to improve the user experience and support the PubMed Commons community, and they are now live on PubMed and PubMed Commons.

At center stage is new artwork that has been adopted for the PubMed Commons blog, Twitter account, and home page, to present a clear, unified identity across platforms. The home page has also been streamlined to consolidate information about joining and using PubMed Commons in a single page to help users get started. A synopsis of the most recent blog post is now available at the top of the home page to help users stay up-to-date on PubMed Commons.

 

For several months, comment rating has given members the chance to weigh in on what comments they find useful. Visitors to PubMed can see these ratings alongside comments. Ratings are a key element in calculating the comment and commenter scores that determine the appearance of comments in the “Selected comments” stream on the home page. Some new site modifications will highlight contributions to PubMed Commons.

 

On the home page, “Top comments now” will feature the top three recent comments. On PubMed records, “Selected comments” (from the home page stream) prompt the appearance of an icon above abstracts, directing readers to comments below. And now the most recent tweet about a PubMed Commons comment appears on the home page for PubMed searches.  Check it out!

New England Journal of Medicine Articles on Cybersecurity and Health Care

Monday, August 4th, 2014

Share with your Chief Information Officers, heads of IT, and anyone else with an interest in patient data privacy. Both articles will require a subscription.

When ‘Hacktivists’ Target Your Hospital

http://www.nejm.org/doi/full/10.1056/NEJMp1407326

Cybersecurity in Health Care

http://www.nejm.org/doi/full/10.1056/NEJMp1404358

NTIS Reports of Possible Interest

Monday, August 4th, 2014

Big Data: Seizing Opportunities, Preserving Values.

Report produced in 2014 by the Executive Office of the President, Washington, DC.

A White House report on big data released May 1 concludes that the explosion of data in today’s world can be an unprecedented driver of social progress, but it also has the potential to eclipse basic civil rights and privacy protections. The report drew praise from business and technology groups for its grasp of how big data analytics could improve education and healthcare, uncover wasteful government spending, and help with the nation’s continuing economic recovery. But those same groups cautioned that government attempts to regulate data collection could interfere with productivity and job growth.

For NTIS Customers click here / For NTRL Customers click here

 

Frontiers in Massive Data Analysis.

Report produced in 2013 by the National Research Council, Washington, DC. Board on Mathematical Sciences.

Experiments, observations, and numerical simulations in many areas of science and business are currently generating terabytes of data, and in some cases are on the verge of generating petabytes and beyond. Analyses of the information contained in these data sets have already led to major breakthroughs in fields ranging from genomics to astronomy and high-energy physics and to the development of new information-based industries. Traditional methods of analysis have been based largely on the assumption that analysts can work with data within the confines of their own computing environment, but the growth of big data is changing that paradigm, especially in cases in which massive amounts of data are distributed across locations. While the scientific community and the defense enterprise have long been leaders in generating and using large data sets, the emergence of e-commerce and massive search engines has led other sectors to confront the challenges of massive data.

For NTIS Customers click here / For NTRL Customers click here

 

Data Mining Meets HCI: Making Sense of Large Graphs.

Report produced in 2012 by Carnegie Mellon Univ., Pittsburgh, PA. Machine Learning Department.

We have entered the age of big data. Massive datasets are now common in science, government and enterprises. Yet, making sense of these data remains a fundamental challenge. Where do we start our analysis. Where to go next. How to visualize our findings. We answers these questions by bridging Data Mining and Human-Computer Interaction (HCI) to create tools for making sense of graphs with billions of nodes and edges, focusing on (1) Attention Routing: we introduce this idea, based on anomaly detection, that automatically draws people’s attention to interesting areas of the graph to start their analyses. We present three examples Polonium unearths malware from 37 billion machine- file relationships NetProbe fingers bad guys who commit auction fraud. (2) Mixed-Initiative Sensemaking: we present two examples that combine machine inference and visualization to help users locate next areas of interest: Apolo guides users to explore large graphs by learning from few examples of user interest; Graphite finds interesting subgraphs, based on only fuzzy descriptions drawn graphically. (3) Scaling Up: we show how to enable interactive analytics of large graphs by leveraging Hadoop, staging of operations, and approximate computation. This thesis contributes to data mining, HCI, and importantly their intersection, including: interactive systems and algorithms that scale theories that unify graph mining approaches; and paradigms that overcome fundamental challenges in visual analytics. Our work is making impact to academia and society: Polonium protects 120 million people worldwide from malware; NetProbe made headlines on CNN, WSJ and USA Today; Pegasus won an open source software award; Apolo helps DARPA detect insider threats and prevent exfiltration. We hope our Big Data Mantra ‘Machine for Attention Routing Human for Interaction’ will inspire more innovations at the crossroad of data mining and HCI.

 

For NTIS Customers click here / For NTRL Customers click here

ClinicalTrials.gov: Results Reporting, Unique Evidence, and the Role of Medical Librarians

Monday, July 28th, 2014

Presenter:      Kate Flewelling, Outreach Coordinator, NN/LM MAR

Dates:              September 2 – 22, 2014

Where:             Online

Details:             http://nnlm.gov/ntcc/classes/class_details.html?class_id=661

Summary: This 3-week, self-paced course will explain what a clinical trial is and why ClinicalTrials.gov is a significant resource; demonstrate ways to search and interpret studies with results on ClinicalTrials.gov; and discuss the unique position of health science librarians to provide education and to advocate for the results database and submission requirements.

Note: Several regions are offering this course. If you are in NY, NJ, PA or DE, please take the session provided by the Middle Atlantic Region.

Ready, Set, Go: Easy-to-Use Online Tools to Create Effective “How-To” Tutorials (TechTime session)

Monday, July 28th, 2014

MAR offers 1 MLA Continuing Education (CE) credit per session—details will be provided at the end of the session.

Presenter:      Andrew Youngkin, Emerging Technologies / Evaluation Coordinator, NN/LM Southeastern/Atlantic Region (SE/A)

Date / Time: Wednesday, July 30, 2014 / 11 am – Noon (ET)

Where:             https://webmeeting.nih.gov/techtime/

Online / No Registration Required

Summary: This presentation will feature a select group of easy-to-use, (mostly) free online tools to plan and create online tutorials (aka, screencasts). Key features of these online tutorial creation tools will be demonstrated and best practices for screencasting, including voice-over narration and
storyboarding, will be discussed.

NCBI Webinar: Using the New NCBI Variation Viewer to Explore Human Genetic Variation

Monday, July 28th, 2014

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: http://www.nlm.nih.gov/pubs/techbull/ja14/brief/ja14_ncbi_reprint_webinar.html

NCATS Announces the Toxicology in the 21st Century (Tox21) Data Challenge 2014 Competition

Monday, July 28th, 2014

The National Center for Advancing Translational Sciences (NCATS) has announced the Toxicology in the 21st Century (Tox21) Data Challenge 2014 competition.

The goal of the challenge is to crowdsource data analysis by independent researchers in order to develop computational models that can better predict chemical toxicity. It is designed to improve current toxicity assessment methods, which are often slow and costly. The model submission deadline is November 14, 2014. NCATS will showcase the winning models in January 2015. Registration for the challenge and more information is available on the web site.

Tox21 scientists are currently testing a library of more than 10,000 chemical compounds in NCATS’s high-throughput robotic screening system. To date, the team has produced nearly 50 million data points from screening the chemical library against cell-based assays. Data generated from twelve of these assays form the basis of the 2014 challenge. For more information on the Tox21 Modeling Challenge and Tox21 Program, contact Anna Rossoshek.

Seeking the next Head of the National Network of Libraries of Medicine (NN/LM) at NLM

Tuesday, July 22nd, 2014

We are pleased to share with you the recruitment announcement for the next Head of the National Network of Libraries of Medicine,
commonly referred to as the national Network Office (NNO):

The Head of the National Network Office of the NN/LM serves as a national leader in developing collaborations among the varied types of libraries in the Network, including health sciences libraries, and academic and public institutions, to improve access to and the sharing of biomedical information resources.  The NNO Head is responsible for monitoring, evaluating, and advising on all aspects of providing biomedical information, for outreach to groups experiencing health disparities, and for providing access to medical information in national and international emergency and disaster situations.  The NNO Head advises on public health information policy issues, as related to programs conducted throughout the Network.   This is an exciting time for an incoming Head because plans for the 2016-2021 Regional Medical Library contracts are underway.

The very short posting time of July 22July 31 reflects the government’s effort to hire talented people quickly.  Please see the postings on USAJobs.gov and follow the instructions to apply.  One posting is for “Status Candidates” (Merit Promotion and VEOA Eligibles) and the other is for for “All US Citizens.”

The jobs will also be linked from “Careers @ NLM” on the NLM home page:  www.nlm.nih.gov.

In addition to an interesting, challenging work environment, NLM has a great location on the campus of the National Institutes of Health (NIH) in Bethesda, Maryland.  NIH is a short Metro ride from Washington, DC and a short walk from Bethesda’s thriving restaurant and retail district.  As a supervisory librarian at the GS15 level, the position has a salary range of $124,995-$157,100, and reports to the Associate Director for Library Operations, Joyce Backus.

If you have questions about this job, please contact Zenaida Olivero, PHR, (301) 435-5716, or Oliverozm@mail.nih.gov.

Dianne Babski

Deputy Associate Director of Library Operations
National Library of Medicine

Discovering TOXNET Class

Friday, July 18th, 2014

Free Online TOXNET® Class Offered This Fall by the National Library of Medicine Training Center (NTC)

 

The National Library of Medicine Training Center (NTC) is offering an online, asynchronous class called “Discovering TOXNET” from October 20 – November 14, 2014.

 

Discover TOXNET and other NLM environmental health databases through videos, guided tutorials, and discovery exercises. The class is taught online in 13 independent modules.

 

TOXNET is a web-based system of databases covering hazardous chemicals, environmental health, toxic releases, chemical nomenclature, poisoning, risk assessment and regulations, and occupational safety and health. The independent modules cover TOXLINE, ChemIDplus, TRI, TOXMAP, Hazardous Substances Data Bank, IRIS, Haz-Map, LactMed, WISER, CHEMM, REMM, LiverTox, and more.   You’ll learn about the resources through videos, guided tutorials, and discovery exercises.

 

Who should take the class?

Health sciences librarians and health or environmental sciences professionals interested in unlocking the information in TOXNET and the other environmental health and toxicology resources.

 

How much time?

You will work on your own time over a period of 4 weeks to complete the modules that are of interest to you. There is one required module; the remaining modules are optional. This class is offered for variable MLA Continuing Education credit. Each module will be offered for 0.5 to 2.0 credit hours, for a total of up to 12 hours. Credit will not be awarded for partial completion of a module. Total credit awarded will be based on completed modules with a minimum of 1.0 credit hours.

 

What happens during the class?

This course is offered asynchronously through Moodle; you will work at your own pace. Each module consists of guided interactive online tutorials AND/OR tutorial videos as well as discovery exercises. Instructors will be available to answer questions and provide assistance throughout the course.

 

The modules are:

  1. Introduction to TOXNET: 0.5 hour (Required)
  2. TOXLINE: 1.0 hour
  3. ChemIDplus: 2.0 hours
  4. Integrated Risk Information System & Risk Assessment: 1.0 hour
  5. Hazardous Substances Databank: 1.5 hours
  6. Toxic Release Inventory: 1.0 hour
  7. TOXMAP: 1.5 hours
  8. Household Products Database: 0.5 hour
  9. LactMed: 0.5 hour
  10. Haz-Map: 0.5 hour
  11. WISER & CHEMM: 1.0 hour
  12. REMM: 0.5 hour
  13. LiverTox: 0.5 hour

 

How do I register?

Space in the class are limited, so don’t delay!  Register now at:

http://nnlm.gov/ntcc/classes/class_details.html?class_id=809

 

For questions, contact the NTC at ntc@utah.edu.

New Features Added to ChemIDplus

Friday, July 18th, 2014

ChemIDplus is a dictionary of over 400,000 chemicals (names, synonyms, and structures). It includes links to NLM and other databases and resources, including ones to over 100 federal, state and international agencies. ChemIDplus Lite is designed for simple searching on name or registry number. ChemIDplus Advanced helps users draw their own structures and perform similarity and substructure searches. ChemIDplus records are updated daily. The following new features are now available:

A new “3D” button on search results pages provides calculated three dimensional structure models for over 300,000 chemicals and 645,000 variations.  Users can adjust the rotation speed, the image type (ball and stick, space fill, wireframe), and 3D angle of viewing; dragging the image changes its orientation. Right clicking on the structure box provides other control options such as color, style, measurements, and computation.  The open source JSMol program is used for viewing these models.  Another feature offers 3D when viewed with Red/Cyan, Red/Green or Red/Blue glasses, allowing for unique visualization of a molecule with depth perception.

The ChemIDplus structure box now uses quick-loading Marvin for JavaScript (free; requires IE9 or above). The Marvin Applet version is also available in a pull-down for legacy browsers.

ChemIDplus is now IPhone IOS and Android OS friendly. Buttons collapse to neatly fit the phone screen, and the structures can be displayed.