Thrilled to be starting work with the AnVIL and the curriculum development team to bring the power of this computational genomics research system to students and teachers all across the country! Through Johns Hopkins University and NIH’s genome research branch (NHGRI), college faculty from around the country are coming together to design curriculum and classroom lab exercises to teach students how to use this powerful data resource.
What would you like to do with genetic data? What would you like to investigate? Send in your questions or project suggestions for consideration!
What is AnVIL?
The task of turning the masses of generated biology healthcare data into useful information has been a problem since the advent of genetic sequence data production. With exponential increase in genomic data produced over the last 10 years, researchers are swimming in data. Without a centralized system for storing data generated in labs, datasets were not freely comparable because of silo-like storage. AnVIL, a data storage project sponsored by the NIH’s NHGRI uses Google cloud storage to serve anyone interested in computational genomics research.
This means students, teachers, and anyone curious who has internet access large data sets and run analytic programs. The promise of the internet breaking down barriers to information is finally being realized for genetics data.
This question was posed by a student in a recent class. You can help the National Institutes of Health with their studies of the COVID vaccine (these studies are called “clinical trials”). For more information, visit:
Many students (and non-students alike) have expressed concern about vaccine safety and wondered how a COVID-19 vaccine can be made on an accelerated timeline. They question safety and doubt effectiveness because speed is presumed to translate into sloppiness. However, vaccine research (prior to the COVID pandemic) has focused on how to make all-purpose delivery mechanisms that are then custom tailored to a particular pathogen. If you’d like to dive into the details and see how researchers have done this, years in advance of COVID, watch a lecture by NIH researchers at:
Unlocking the DNA sequence was celebrated in the early 2000s as providing the key to curing disease. Overlooked is the relative lack of information about the structure of folded proteins. Most of the known protein structures studied are bacterial; of all the known protein structures, only 25% are human (2017 data). The proteins in our bodies are responsible for everything from sending signals in autoimmune disease to driving the uncontrolled growth in cancer. Knowing the structure of proteins allows researchers to design and build drugs that impair their action.
You can contribute to unlocking the structure of proteins with your desktop/laptop computer and internet connection. Through the Folding@Home research project run by a Stanford professor, you can load a free program onto your computer that runs in the background. Using your computer’s processing power, folding simulations are run and the data you generate contributes to research. The program runs mathematical calculations to determine how the proteins will fold in the most energetically favorable shape. By unlocking the computer power of computers all over the world, protein structures can be determined and used by researchers to better understand disease.
At a recent National Institutes of Health Grand Rounds Lecture in October, Curtis Langlotz, a Stanford Univ. medical doctor and bioinformatics researcher, gave a lecture detailing his work to bring artificial intelligence to radiology image interpretation. What was striking about his one-hour lecture is how his research not only involves medical expertise, but also an in-depth knowledge of computer science and linguistics. Traditionally, experts have been viewed as individuals who know much about one specific area. To be on the cutting edge of research, one often has to be an expert in multiple areas. Of course, Prof. Langlotz probably didn’t expect that his work would take him into linguistics, but interdisciplinary work requires an open mind and frequently takes detours into new and exciting areas.
The future? A computer assisting doctors to be sure that small masses are detected before they become massive tumors!
It’s not too early to start thinking about summer opportunities. Through the federal-funded National Science Foundation, researchers from across the country can pay undergraduate summer researchers in their labs. Though you will have to apply to the individual lab (and be accepted), you will have the opportunity to work on your own research project and contribute to the lab’s research. Start your search by visiting the link below to see a list of universities and researchers in the NSF’s Research Experience for Undergraduates program (if the link is disabled, search for “NSF REU sites Biological Sciences”):
Great opportunity to attend a web conference sponsored by the Alan Alda Center for Science Communication at Stony Brook University last week. Simply amazing to be selected for this online conference. The Alda Center brought together a group of people from all over the world who all communicate about science in their work (other professors, government researchers, consultants). We spent the session engaged in a role-playing improvisation session to stimulate brainstorming. We then fruitfully discussed how to better explain science topics to audiences with varying levels of expertise. Highly recommend the Alda Center’s programs to other science teachers and anyone else who explains science as part of their everyday work. Hope to be invited back for another conference!
Great panel discussion session at the United States Geological Survey (USGS) where new discoveries made in USGS labs were presented to find new applications. Imagine a hockey-puck sized gas sensor, originally designed to monitor water oxygen, being adapted for use in a doctor’s office to measure arterial blood gas.
Privileged to recently visit this world-class research facility to learn about their leading research in neuroscience, tour the facilities, and discover research opportunities for students. A neuroscience research powerhouse in the metro DC area often unknown to students and faculty alike, is the Howard Hughes Medical Institute (HHMI) Janelia Farms facility. Like the National Institutes of Health (NIH), most of the money awarded by HHMI is awarded to researchers to support their work at a home university (unlike NIH, HHMI is a private organization not affiliated with any government body and was started by oil billionaire Howard Hughes, as seen in the movie The Aviator). The beautiful Janelia Farms facility attracts leading scientists from all over the world featuring world-class lab space, a beautiful physical facility, fantastic dining service available nearly 24-7…all located in the beautiful countryside of Loudoun County on a former farm. Student research awards are available, though competition for these research awards is fierce (with applicants from all over the world) and requires extensive prior research experience. Inspiring architecture, beautiful artwork (with a brain science theme), and an atmosphere of intense science made for an unforgettable visit to an unparalleled facility.