What's in a test? Or better yet what's in 55 SARS-CoV-2 / COVID-19 molecular diagnostic tests? Plenty. 55 FDA EUAs indicate that nine different test formats are used, ranging from RT-PCR, to digital PCR, to isothermal amplification, to LAMP with a CRISPR enzyme.
The numbers of SARS-CoV-2 / COVID-19 diagnostic tests are exploding. These tests detect either viral RNA or antibodies to virus particles. But, which is best? That, of course, depends on what question is being asked. Read more
This year, I'm a little late with my post on the Nucleic Acids Research (NAR) database issue . While I was procrastinating, a pandemic broke out. So, unsurprisingly, this year's database topic is viruses. The NAR archive lists more than 32 databases related to viruses. Of these, 22 are still operational and five of the databases have information about SARS-CoV-2.
Our schools are closed. The farmers market is suspended. Spring sports are not happening. And our grocery stores look like this:
Like many residents, I'm torn between enjoying the sun, or anxiously pacing around the house and getting teary eyed over the #SeattleWeGotThis hashtag on Twitter . The historians say we can cope by ... Read more
Novel Coronavirus SARS-CoV-2
This transmission electron microscope image shows 2019-nCoV, the virus that causes COVID-19, isolated from a patient in the U.S., and emerging from the surface of cells cultured in the lab.
Note: the official name for the disease is COVID-19. The virus that causes the disease is known as nCoV, and 2019-nCoV, and sometimes SARS-CoV-2.
Google image results from a search with "bioinformatics"
This October (9-11, 2019), I attended the 3rd NIBLSE conference entitled: "Integration of Bioinformatics into Life Science Education: Roadmap for the Future." It was held at " Hot Shops " in Omaha Nebraska, a space for artists to work, sell, and meet.
You might ask what is NIBLSE and why are they making a roadmap for the future?
NIBLSE - Network for Integrating Bioinformatics into Life Sciences Education, is five-year NSF funded Research ... Read more
A recent article from STAT news (1) relayed the story of Jaci, a young woman in Iowa dying from a rare form of ALS, and her parents heroic efforts to help her get access to an untested drug.
Interestingly, the drug is an antisense oligonucleotide. Antisense oligos are short pieces of DNA, that bind to complementary molecules of mRNA and target them for destruction. These types of drugs are interesting because they can prevent the production of toxic proteins.
In Jaci’s case, her form of ALS results from a toxic version of the FUS protein. Normally, FUS is found in the ... Read more
Immuno-biotechnology an important field of biotechnology. With the advent of advanced DNA sequencing, and other technologies, immuno-biotechnology has significantly increased the use of computing technologies to decipher the meaning of large datasets and predict interactions between immune receptors (antibodies / T-Cell receptors / MHC) and their targets. Progress toward developing an immuno-bioinformatics course with Shoreline Community College is summarized in the attached presentation.
In early April 2019, the Institute for Systems Biology (ISB, Settle WA) hosted its 18th annual symposium. This year's theme focused on translational biology, which is the practice of commercializing research discovery. Over the two-day symposium, the audience was informed about the latest in the research and development of new products for fighting cancer with immunotherapy and combating research to improve global health.
Meeting Highlights - Immunotherapy
One of ISB's strong values is communicating science to public. This meeting was no exception; much of it ... Read more
It would be unfair to teach an advanced bioinformatics class without getting into the weeds of command line interfaces (CLIs), heading, tailing, greping, and wc-ing files, piping programs together, and running a bioinformatics program and working with its output. Hence, in the final component of the immuno-bioinformatics class that we [Digital World Biology] are developing for Shoreline Community College will use cloud computing in the CyVerse environment to run IgBLAST. Read more
I always look forward to sharing the Nucleic Acids Research (NAR) database issue . This year's blog topic is immunology. The NAR archive lists 31 immunologic databases, but only seven or so are active, and others are not listed in the NAR archive. Read the blog learn more.