Shoreline Community College

Growth of NAR BioDBs

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. Read more

Odysseus at battle

Bioinformatics is full of unexpected adventures. Some are related to data discoveries, but many more are related to navigating the maize of software needed to implement a solution. Read more

Immunoprofiling sample preparation

DNA sequencing-based immunoprofiling quantitatively measures AR diversity in samples by determining the sequences of V(D)J junctions. AR receptor diversity is vast due to a combinatorial rearrangement process that inserts a variable number of random DNA bases at each junction. In the sequencing process V(D)J junctions are amplified with V and J gene specific primers and, to be quantitative, differences in amplification rates that are due to primer sequences must be factored into each assay. Read more

Immunoprofiling steps of the general workflow

Immunoprofiling is the quantitative measurement of antigen receptors (ARs; antibodies or T-cell receptors) in a sample and is a hot area in biotechnology. Immunoprofiling is used to assess the diversity of antigen receptors (ARs: antibodies and T-Cell receptors) and how this diversity changes in response to allergens, infections, or vaccines. In cancer therapy, Immunoprofiling is used to develop biomarkers and understand how an individual’s immune cells fight tumors, and predict individuals' response to immunotherapy.

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Infographic: BCRs vs TCRs

BCRs (antibodies) and TCRs (T cell receptors) are the recognition molecules of our immune system; the molecules they bind are called antigens. BCRs and TCRs are similar in many ways, but their differences form the core of how self and non-self are recognized. Read more

Immuno-Bioinformatics Infographic

Immuno-bioinformatics is a fast growing subdiscipline of immuno-biotechnology. New technologies like immune-profiling and targeted cancer therapies are leading to job growth and demands for new skills and knowledge in biomanufacturing, quality systems, informatics, and cancer biology. Read more

Molecule in Space
Singularity: the point at which a function takes an infinite value.

"Eew!" Is how high performance computing (HPC) admins react to Docker, according to Dr. Vanessa Saurus when she described the motivation for developing Singularity [1] at the Cyverse Container Camp . Like Docker, Singularity allows one to package programs and their dependencies in ways that they can be run as virtual instances with low overhead. Singularity improves on Docker to make it possible to run containers in HPC environments such as super computers.

Why ... Read more

Container on a train

Containerization technologies like Docker are designed to solve challenges associated with installing and running complex software such as bioinformatics pipelines and web servers. Docker will change the world ... maybe. While clearly powerful and enabling, the magic of Docker can also be an overpromise. To understand why, you need to understand the “ The Law of Leaky Abstractions .”

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Infrared Cacti
Saguaro National Park - Tucson AZ

The technological Singularity is the moment beyond which "technological progress will become incomprehensibly rapid and complicated [1].” Hmmm. That sounds like bioinformatics.

Surviving the Singularity requires reducing complexity. This was the topic of a recent three-day Cyverse Container Camp hosted at the University of Arizona, Tucson AZ. I attended the camp as part of Digital World Biology's ... Read more

MHC-I with antigen from Molecule World

Lately I’ve been thinking about immunology, and not just because it is flu season, it is because Digital World Biology (DWB) is collaborating with Shoreline Community College to design a five-week bioinformatics course that will be component of their one year immuno-biotechnology certificate (1).

An aspect of the course will cover the ways in which industry studies and utilizes components of the immune system from vaccines to making antibodies to measuring T-Cell Receptor (TCRs) repertoires as biomarkers. In the classes, bioinformatics methods will be used to to reinforce ... Read more

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