NCBI to help with Rocky Mountain Genomics HackCon, June 17 – 21, 2019

The NCBI will participate in a one-day conference on June 18, 2019 and a hackathon, June 19-21, 2019 as a part of Rocky Mountain Genomics Hackcon 2019 at the BioFrontiers Institute in Boulder Colorado. The conference will feature technical speakers in precision medicine, metagenomics, and advanced RNA-Seq analysis, as well as an exhibitor and poster … … Continue reading

New Lab Matters: The ABCs of PFAS

New Lab Matters: The ABCs of PFAS |

First discovered in the 1930s, per- and polyfluoroalkyl substances (PFAS) now pervade almost every aspect of modern life. In fact, PFAS compounds are found in everything from dental floss to cookware. But human exposure to PFAS comes at a cost, and as old compounds are removed from production, new compounds take their place. So how does a public health laboratory handle this challenge with limited resources? As our feature article shows, by establishing new public-private partnerships.

Here are just a few of this issue’s highlights:

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The post New Lab Matters: The ABCs of PFAS appeared first on APHL Lab Blog.

New lab informatics courses introduce basics to non-specialists  

New lab informatics courses introduce basics to non-specialists |

Two online laboratory informatics courses now on the CDC TRAIN site help laboratory staff to understand how their jobs relate to their laboratory’s informatics system. Developed by APHL and the Centers for Disease Control and Prevention (CDC) in collaboration with the APHL Informatics Committee and members of the target audience, the courses follow a TB specimen as it advances through testing and reporting to inform decisions by clinical care providers and public health agencies.

Historically the term “informatics” evoked fear among laboratory staff who avoided the unfamiliar discipline. Responsibility for the function often devolved to one person who became the de facto informatician more by accident than by intent. When the new skill set proved highly marketable, this individual often departed for new opportunities, leaving the laboratory with no one who could distinguish between LOINC and SNOMED codes, much less maintain the Laboratory Information Management System.

But times have changed. With electronic data now integral to work at both private and public sector laboratories, all staff require a basic knowledge of informatics. With an understanding of how the data they touch flows in and out of their facility, staff can improve the quality and speed of laboratory operations and, ultimately, patient treatment and disease control.

The two online courses, Life of a Specimen and Life of a Result, trace the testing and reporting process in plain language, explaining who comes into contact with the specimen at each point, when errors are most likely to occur and how to avoid them, and how a specimen becomes a result and is reported to stakeholders. Both courses offer P.A.C.E.® credits. Visit CDC TRAIN to register.


  • Life of a Specimen introduces staff roles in laboratory informatics, data relationships, data quality and standards, and the generation and flow of information as a specimen progresses through the pre-analytic, analytic and post-analytic phases.
  • Life of a Result examines how data and information move through and outside the laboratory to impact clinical care and public health decision making.  It covers the recipients of laboratory data, data and results storage, and communication of data and results to stakeholders.

The two courses would be a valuable addition to staff onboarding programs at laboratories of all types. Keith Higginbotham, IT systems manager at the Alabama Department of Public Health, laments that such training was not available earlier in his career:

“I wish I’d had access to this training when I was first starting out. It condenses a year’s worth of knowledge into a few hours, giving lab staff from all backgrounds a real head start. Those in leadership can become stronger advocates for their labs by better understanding their informatics needs and capabilities.”

A third course, which takes the student on a deeper journey into Laboratory Information Management Systems (LIMS), is in production and slated for release in 2019.

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New Lab Matters: Time to welcome the next generation of public health laboratory scientists

New Lab Matters: Time to welcome the next generation of public health laboratory scientists |

The Bureau of Labor Statistics estimates that 12,000 new laboratory professionals are needed each year to meet consumer demand. At the same time, while automation has eliminated some less-skilled laboratory jobs, the growing sophistication of public health laboratory analyses has generated demand for scientists with highly specialized training. As our feature article shows, laboratories are recruiting new talent for the “hidden profession” by taking a hard look into what they really want, and how they want to work.

Here are just a few of this issue’s highlights:

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The post New Lab Matters: Time to welcome the next generation of public health laboratory scientists appeared first on APHL Lab Blog.

Partner, Train, Respond: Increasing Global Emergency Management Capacity

People walking a busy street in Zanzibar.

Countries in Africa are no strangers to major disease outbreaks that can result in illness and death of millions of people.  In the past two years alone the continent has experienced infectious disease outbreaks of cholera, meningitis, Ebola Virus Disease, Lassa fever, and Yellow fever, and other public health emergencies such as drought and famine.

Understanding the big picture

Training participants from Zanzibar discuss the development of an emergency management program
Training participants from Zanzibar discuss the development of an emergency management program.

It is vitally important to have a big picture perspective on emergency management and response – if one country is not prepared for a public health emergency, then all the countries in the region are susceptible to public health threats that can easily cross borders and impact surrounding countries. This is where public health emergency management (PHEM) comes in. In-country PHEM capacities and systems can be strengthened to support global health security. When the workforce is trained, emergency management infrastructure is in place, and functional systems exist, a country is better positioned to execute a coordinated response that can mitigate risk and save lives.

CDC and other international partners support ongoing efforts to help countries across Africa build capacity in outbreak detection and response. This includes preventing avoidable epidemics, detecting public health threats early, and responding rapidly and effectively to outbreaks of international concern. CDC provides expertise in PHEM to train emergency management technicians, provide input on emergency management operations, and guide development of functional processes and systems for ministries of health around the globe.

Getting the workforce ready to respond

In August 2017, CDC spearheaded a 5-day PHEM workshop in partnership with the World Health Organization, the United States Defense Threat Reduction Agency, and Public Health England.  The workshop brought together 55 emergency management staff members from across Africa to learn from experts in the field about how to enhance coordination and response capabilities of their country’s PHEM programs.

Participants came from seven countries – Tanzania, Uganda, Kenya, Ethiopia, Liberia, Sierra Leone, and Nigeria – which all share common interests and challenges related to emergency response. The training focused on developing core principles in PHEM, including trained staff, physical infrastructure, and processes to run a fully functional Public Health Emergency Operations Center (PHEOC). The training highlighted best practices, but since many of the participants had first-hand accounts of responding to public health events in their own countries, they were encouraged to share experiences and network with their peers.

Sharing knowledge and expertise

Public health professionals who work in emergency response know that it’s important to build relationships before an incident so that during a response you work effectively and efficiently with partners. One participant noted that the “rich, valuable contributions from other people’s experiences to build upon what I already knew” was one of the most rewarding parts of the workshop.

The tabletop exercises at the end of the workshop emphasized the importance of information and idea sharing. Participants engaged in tabletop exercises that simulated a response to a Yellow Fever outbreak in northern Tanzania. Participants were divided into 7 teams: management, plans, logistics, operations, finance and administration, communication, and partners. Each team had a mix of participants from different countries.  Teams utilized information they had learned throughout the workshop to developed response products, including an organizational structure chart, objectives for the response, and an initial situation report. This exercise led to a robust conversation about different approaches to public health emergency response.

Seeing response in action

Public Health Emergency Operations staff survey the scene after mudslides in Regent, Sierra Leone.
Public Health Emergency Operations staff survey the scene after mudslides in Regent, Sierra Leone.

A highlight of the training was when Dr. Ally Nyanga, the Tanzania Ministry of Health PHEOC Manager and an alumni of the CDC Public Health Emergency Management Fellowship, took workshop participants on a tour of the Tanzania PHEOC, a small room on the third floor of the Ministry of Health building. Previously used as a storage area for the library, the 10 x 20 foot PHEOC is now an efficient space that staff can use when they respond to public health emergencies and outbreaks.  To date, Tanzania’s PHEOC has been activated to respond to widespread cases of Aflotoxicosis, a type of severe food poisoning, and cholera outbreaks in Tanzania.

While the workshop is over and participants have returned home, the work that they do to prepare for the next public health emergency is ongoing. The workshop highlighted some important takeaways – you do not need a big space and high-tech equipment to respond quickly and efficiently to a public health emergency.  Instead, coordination to share information, resources, and ideas is vital to a successful emergency response, both in-country and across an entire region.

Learn more

Building the Future Preparedness and Response Workforce

Woman typing

 TRAIN Learning Network InfographicWhen I think about public health preparedness and response I ask myself three questions:
  • Who provides the infrastructure to train public health responders?
  • Where do they learn what they know?
  • Who helps a responder fulfill their mission?

The answers to these questions may rest in the TRAIN Learning Network (TRAIN). After the September 11th terrorist attacks, public health departments needed a way to track the preparedness-related training of professionals in their state, region, or locality. TRAIN was established in 2003 to offer a solution to the tracking challenge and help train the next generation of the public health workforce.

This network IS the track on which the trains run (pun intended)! If we equip responders with as many skills and as much knowledge as possible before an incident, we can expect:

  • Increased expertise during a response,
  • Just-in-time training that is more readily available,
  • Quicker response and recovery efforts, and
  • Greater resilience.

What is TRAIN?

TRAIN is a national learning network of agencies and organizations that deliver, track, and share trainings for professionals who protect and improve the public’s health. The network identifies, develops, and promotes opportunities for professionals to build their skills and knowledge.

TRAIN is an open platform, meaning that anyone, anywhere can access the training. Learners have access to thousands of health knowledge and skill-related courses. An emergency management specialist at a state health department can take courses in other disciplines or topic areas with content that is curated by the CDC or another partner in the network.

Learners are able to search TRAIN for courses that are tagged with PHEP Capabilities or PHPR Core Competencies. You can register as a learner through your state’s TRAIN affiliate or through CDC TRAIN.TRAIN has more than 1.5 million registered learners in all 50 states, 5 U.S. territories, and 177 countries.

How does TRAIN work?

TRAIN is a collaboration between 27 state health agencies and partners, as well as 3 federal partners – Centers for Disease Control and Prevention, Veterans Health Administration, and Medical Reserve Corps – who serve as TRAIN Learning Network affiliates. More than a thousand CDC-developed learning opportunities are available to all the registered learners in the TRAIN network.

TRAIN affiliates operate branded online portals, which allow them to:

  • Identify specific groups of learners for targeted courses or training plans
  • Monitor training and completion of specific groups of learners, including the use of custom reports
  • Partner on training with state, tribal, local, territorial, national, and international providers

Meanwhile, organizations that provide training, including other government agencies, academic institutions, and nongovernmental organizations can:Why is TRAIN a wise investment? Over 12 years (2005 – 2016), the Kansas Department of Health and Environment saw a cost savings of $35 million as a result of staff taking trainings through its portal, KS TRAIN. Learners and the agency saved travel expenses as well as personal costs.

  • Assign training to a specific group of learners and monitor their progress towards completion
  • Test knowledge and collect feedback, develop custom curricula, and access course data

The TRAIN approach fosters collaboration, saves cost by reducing duplication, and reaches learners across jurisdictional lines. This ensures that together, we can train the entire workforce with all the tools at our collective disposal.

Get more information

If you have additional questions, please send an email to

NLM Webinar series: “Insider’s Guide to Accessing NLM Data: EDirect for PubMed”

Beginning February 21, 2017, the National Library of Medicine (NLM) will present the three-part webinar series “Insider’s Guide to Accessing NLM Data: EDirect for PubMed.” This series of workshops will introduce new users to the basics of using EDirect to … Continue reading

Ready or Not: Communicating During an Emergency in the Country of Georgia


Emergencies don’t wait for you to be ready.

In 2015, the country of Georgia invited CDC to conduct a training on the principles of Crisis and Emergency Risk Communication (CERC). But before we could get there, the capital city of Tblisi was struck by a major flood.

The flash flood and ensuing mudslide killed 20 people and covered much of the city in water and mud. There were news reports about the massive damage, human casualties, and even escaped zoo animals.  Ready or not, responders had to jump in and communicate clearly about the emergency.

This is exactly the type of situation CERC training is intended to prepare for. When a crisis hits, people need understandable, trustworthy, and accurate information they can act on. And they need it fast.  CERC helps communicators ensure that the right messenger is delivering the right message at the right time.

CERC saves lives

When we arrived in Georgia, my co-worker Kellee Waters and I discovered that the news reports hadn’t captured the intensity of the flood the way firsthand accounts could. We heard sobering stories from our colleagues about the impact of the disaster: a stream that turned into a raging river; a landslide that caught everyone off guard.

In the aftermath of the flood, many of our Georgian colleagues found themselves needing to use CERC principles — with or without training. They had to quickly and clearly inform people about threats in different parts of the city and communicate what actions the government was taking to rescue people and animals.

Lessons from the flood

When we began our training, we found that participants’ experiences from the flood gave them valuable insight. Those who had been involved in communicating about the flood stressed the importance of consistent messaging. They recalled that messages about safety had been quickly reported and repeated in the news and on social media; making information readily available to reporters allowed important safety messages to be disseminated faster and wider and increased their credibility. The government had helped by being the first to report accurate, credible messages that offered action steps for citizens to stay safe – before, during and after the crisis.

Class participants also talked about identifying and connecting with groups of people who did not speak Georgian as their first language. This was crucial so all Georgians could return to a more familiar and normal life as quickly as possible after the flood.

While not everyone in our class had a role in communicating during the flood, they all recognized the value of effective communication in an emergency response. They also noted that good communication takes experience, knowledge, and expertise.

None of the participants would have wished this tragedy on their country, but they all had a strong resolve to use the experience to prepare for future events.

Shaking things up!

Participants with trainers after receiving their CERC certificates.
Participants with trainers after receiving their CERC certificates.

During class, participants learned about the different agencies where they worked and considered how each agency might play a role in future responses. They practiced developing messages and explored strategies for making sure those messages reached the right people.

As part of the training, we used an earthquake scenario to identify the types of information different audiences need in a response, and we looked at how those needs evolved over time.

For example, class participants recognized that a large earthquake would likely receive global news coverage, but that the first priority would be getting safety information to the affected people. They had to make decisions about how to get life-saving information to first responders and those affected while providing enough information for all audiences so that rumors and misinformation would not spread.

Armed with new knowledge, our colleagues in Georgia are now prepared to act more swiftly and effectively to make sure everyone receives the information they need, no matter when or where disaster might strike.

CDC Ebola Training in Anniston



Making the decision to volunteer in an Ebola Treatment Unit (ETU) in West Africa shows a lot of courage and takes support from friends, loved ones, and other healthcare workers. It also requires the knowledge and skills to safely treat very sick patients in a challenging environment. CDC understands that healthcare workers preparing to deploy to West Africa need to know the infection prevention and control principles necessary for working in an ETU. To help meet this need, CDC offers an introductory training course at the Federal Emergency Management Agency’s (FEMA) Center for Domestic Preparedness in Anniston, Alabama.

CDC’s Preparing Healthcare Workers to Work in Ebola Treatment Units (ETUs) in Africa training course allows students to work in a mock ETU, where they practice putting on and taking off (donning and doffing) personal protective equipment (PPE). They also practice triaging patients, drawing blood, and safely cleaning up body fluid spills. In addition to this hands-on training, participants attend lectures to better understand the disease and how to protect themselves physically and mentally when working in an ETU. For most of the trainees, working in an ETU will be a new experience. This course gives them an opportunity to practice the required skills and prepare themselves psychologically.

People at a hand washing stationA recent graduate of the training, Kwan Kew Lai, is back in the United States after serving as a doctor with the International Medical Corps (IMC) in an ETU in Liberia. Kwan Kew volunteered for the Ebola outbreak response because she understood the critical need for healthcare personnel on the ground to help combat the epidemic. Kwan Kew knew the work was going to be dangerous, but she knew her skills were desperately needed, especially since so many local healthcare workers in West Africa had already lost their lives to Ebola while providing care. Kwan Kew has spent the last nine years volunteering during public health emergencies and natural disasters; however, she described the Ebola outbreak as one of the most difficult and heart-wrenching experiences she has ever faced.

Her journey began with CDC’s 3-day training course, which she completed along with 35 other healthcare workers. Kwan Kew traveled to West Africa in mid-October. When she arrived in Bong, Liberia, she was greeted by a huge sign announcing “Ebola is real and it is here in Liberia.” At a roadblock performing temperature checks, another banner read, “Fight the Ebola virus. Protect yourself. Protect your family. Protect your community.”  These signs were a striking reminder of the reality Liberia faces as a country plagued by the largest Ebola outbreak in history.

Her first day at the 52-bed ETU began at 6:45 a.m. with caring for 33 patients, 15 confirmed and 18 suspected to have Ebola. Each day, Kwan Kew had to use her training, meticulously donning and doffing her PPE, a process which took 15 to 20 minutes each time. Even with temperatures reaching 89 degrees Fahrenheit during training in Alabama, those conditions were nothing like the humid weather the trainees would face in West Africa.

Kew in front of an Ebola treatment unit sign.Kwan Kew, an avid runner, compared wearing layers of PPE and treating patients in the sweltering heat of Liberia to running a marathon on a very hot day.

“At mile 17, I began to hit the wall, but somehow pushed myself to mile 20, at which point I invariably asked myself why I was running this marathon or any marathon at all. But at the stretch to the finish line and at the end, the emotional boost to have finished running 26.2 miles was just indescribable.”

The physical demands, weather, and hot gear worn in the ETU were not the only challenge Kwan Kew faced. She also wrote about how hard it was to care for patients and encourage them to be hopeful while being encumbered by PPE.

“What makes it even more poignant is that when the patients need close human contact the most, in times of extreme suffering, pain, and fear, there is none to offer except with a barrier of protective covering. In the beginning, it hit home to me that there was a real possibility of a true exposure; however, as time went on, inspired by the persistence, dedication, and selfless caring of my colleagues, that fear was pushed to the back of my mind and the goal of getting the patients better overwhelmingly became my main concern.”

Now back in the United States, Kwan Kew’s 21-days of self-monitoring are over. While she is ready to return to her normal job as an infectious disease doctor in Boston, Massachusetts, she can’t help thinking about the uncertainty facing people in West Africa as Ebola continues to spread.

The Second Offering of “A Librarian’s Guide to NCBI” at NIH

NCBI, in collaboration with NLM and the National Network of Libraries of Medicine NLM Training Center (NTC) at the University of Utah, recently presented the second offering of A Librarian’s Guide to NCBI. Health Sciences Librarians from 17 universities and … Continue reading