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Related Concept Videos

Lewis Acids and Bases02:33

Lewis Acids and Bases

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In 1923, G. N. Lewis proposed a generalized definition of acid-base behavior in which acids and bases are identified by their ability to accept or to donate a pair of electrons and form a coordinate covalent bond.
A coordinate covalent bond (or dative bond) occurs when one of the atoms in the bond provides both bonding electrons. For example, a coordinate covalent bond occurs when a water molecule combines with a hydrogen ion to form a hydronium ion. A coordinate covalent bond also results when...
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Some compounds produce hydroxide ions when dissolved by chemically reacting with water molecules. In all cases, these compounds react only partially and so are classified as weak bases. These types of compounds are also abundant in nature and important commodities in various technologies. For example, global production of the weak base ammonia is typically well over 100 metric tons annually, being widely used as an agricultural fertilizer, a raw material for chemical synthesis of other...
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Base Excision Repair01:54

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One of the common DNA damages is the chemical alteration of single bases by alkylation, oxidation, or deamination. The altered bases cause mispairing and strand breakage during replication. This type of damage causes minimal change to the DNA double helix structure and can be repaired by the base excision repair (BER) pathways. BER corrects damaged DNA sequences by removing the damaged base and restoring the original base sequence using the complementary strand as a template.
The first step of...
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Ions as Acids and Bases02:54

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Salts with Acidic Ions
Salts are ionic compounds composed of cations and anions, either of which may be capable of undergoing an acid or base ionization reaction with water. Aqueous salt solutions, therefore, may be acidic, basic, or neutral, depending on the relative acid-base strengths of the salt’s constituent ions. For example, dissolving the ammonium chloride in water results in its dissociation, as described by the equation:
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Erwin Chargaff’s rules on DNA equivalence paved the way for the discovery of base pairing in DNA. Chargaff’s rules state that in a double-stranded DNA molecule,
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Bronsted-Lowry Acids and Bases02:58

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The acid-base reaction class has been studied for quite some time. In 1680, Robert Boyle reported traits of acid solutions that included their ability to dissolve many substances, to change the colors of certain natural dyes, and to lose these traits after coming in contact with alkali (base) solutions. In the eighteenth century, it was recognized that acids have a sour taste, react with limestone to liberate a gaseous substance (now known to be CO2), and interact with alkalis to form neutral...
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Container-based bioinformatics with Pachyderm.

Jon Ander Novella1, Payam Emami Khoonsari2, Stephanie Herman1,2

  • 1Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.

Bioinformatics (Oxford, England)
|August 14, 2018
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Summary
This summary is machine-generated.

Computational biologists can now use Pachyderm, an open-source system, for reproducible and scalable data science workflows. This framework simplifies complex analyses and manages data pipelines efficiently on modern infrastructures.

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Area of Science:

  • Bioinformatics and Computational Biology
  • Data Science and Workflow Management

Background:

  • Computational biology research faces significant challenges with large datasets and complex, multi-stage analyses.
  • Reproducibility and efficient data management are critical for modern computational biology infrastructure.

Purpose of the Study:

  • To adapt and demonstrate the utility of the Pachyderm workflow system and data management framework for bioinformatics applications.
  • To address the need for reliable processing, orchestration, and data tracking in computational biology pipelines.

Main Methods:

  • Adapted the open-source Pachyderm system, utilizing Kubernetes for container orchestration.
  • Developed a Helm Chart for versatile Pachyderm deployment and extended its file system for block storage.
  • Created a wrapper for cloud-agnostic virtual infrastructure deployment and illustrated benefits with a metabolomics workflow.

Main Results:

  • Pachyderm was successfully adapted for bioinformatics, offering a data pipelining and versioning layer.
  • Enhancements included a Helm Chart, extended file system, and a cloud-agnostic deployment wrapper.
  • A large-scale metabolomics workflow demonstrated Pachyderm's efficiency, sustainability, reproducibility, and scalability.

Conclusions:

  • Pachyderm provides a robust solution for managing complex computational biology workflows and data.
  • The framework enhances reproducibility and scalability, crucial for handling large biological datasets.
  • Pachyderm facilitates efficient and sustainable data science practices in bioinformatics.