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Posts from ScienceBlogs, 2006 to 2017, can be found in the archive.

2021 bio database growth

SARS-CoV-2 remains a relevant topic for bio database development. According the the NAR database compendium , and our research, at least 25 SARS-CoV-2 data resources are available to the public. Their Immunoprofiling: How it works specialized topics include immunology, genomics, RNA, proteins, drugs, and SARS-CoV-2 / COVID-19 literature. This post explores the CoV-AbDab database as a resource for studying how antibodies neutralize the virus to protect against serious disease.

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COVID-19 Molecular test EUAs summary

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.

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Molecular profile of a SARS infection

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

Growt of bio databases 2020

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.

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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 Credit: NIAID-RML
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.

Resources for teaching :

1. Coronavirus images from ... Read more

Bioinformatics from google
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 and Bioinformatics in Community Colleges

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.

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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

Shoreline Immuno-Bioininformatics Instance

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

Community colleges: the new frontier for advanced biotechnology education and laboratory services: a recap.

Back in March, we [Digital World Biology,, and the AC2 Bio-Link Regional Center] hosted a panel discussion at the ABRF annual meeting to introduce community colleges to ABRF and vise versa. I am pleased to report that the session was a great success.

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