Discovering Biology in a Digital World™

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

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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Timeline of the National Science Foundation's Advanced Technology Education program

Last week I attended my first NSF ATE PI meeting. As a contributing member of Digital World Biology's ATE project entitled " A Bridge to Bio-Link's Future ," I participated in the conference by preparing and staffing our booth in the first evening's showcase.

As a brief background, the NSF (National Science Foundation) ATE (Advanced Technology Eduction) program celebrated its 25 th anniversary this year. ATE's mission is to support innovations in technical education at two-year colleges. These colleges, ... Read more

A fun thing we can do with molecular models is to create art. In Molecule World™ , the residue coloring option applies a different color to each amino acid and nucleotide. When we're characterizing a protein and trying to understand its function, the residue coloring option helps us identify repetitive or unusual amino acid sequences, but we can also use this coloring option to have fun.

The video at the end shows all the steps put together.

1. Find and download a spherical protein structure.

To make pumpkin-like molecular ... Read more

Cytochrome C oxidase is a molecule that none of us air-breathing creatures can live without. It's also really interesting. This protein complex is a dimer of two smaller complexes. Each of the smaller complexes contains 13 different proteins and two heme groups.

Oxidized Cytochrome C Oxidase. Each protein chain is colored differently.
Arrows point to the active site in subunit I.

The two heme groups are both part of the cytochrome c oxidase subunit I protein. The DNA sequence of this protein is used for many types of DNA barcoding.

The two heme groups in Cytochrome C ... Read more

Learn how to identify biomolecules quickly by playing games with Biochemi cards. Read more

We created the structure collection feature in Molecule World because I knew it would be useful in teaching my courses. A request from the Weisman Art Museum at the University of Minnesota taught us structure collections could be useful in other ways, too.

The Weisman Art Museum collaborated with neuroscientists at the University of Minnesota and Ricardo Martinez Murillo, a neuroscientist in Spain, to produce the traveling Beautiful Brain exhibit featuring the drawings of Santiago Ramón y Cajal. Cajal is considered the father ... Read more

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

Amino Rummy

Digital World Biology (DWB) has released three new kinds of card decks inspired by the essential units of proteins: the amino acids. The card deck, Amino Rummy,™ has a biological twist. 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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