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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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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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Weak Base Solutions03:21

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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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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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DNA Base Pairing02:27

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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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SciApps: a cloud-based platform for reproducible bioinformatics workflows.

Liya Wang1, Zhenyuan Lu1, Peter Van Buren1

  • 1Cold Spring Harbor Laboratories, Cold Spring Harbor, Ithaca, NY, USA.

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

SciApps is a web-based platform that automates bioinformatics workflows for reproducible analysis of large datasets. It simplifies data management across distributed systems, making complex analyses accessible and repeatable.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • High-throughput methods generate vast amounts of sequence and phenotype data.
  • Managing and analyzing this data on distributed systems presents significant challenges.
  • Efficient data management is crucial for reproducible and accessible large-scale bioinformatics analyses.

Purpose of the Study:

  • To develop a web-based platform for reproducible bioinformatics workflows.
  • To automate the execution of modular bioinformatics applications.
  • To support workflow execution on both local clusters and cloud environments.

Main Methods:

  • Developed SciApps, a web-based platform.
  • Implemented automation for modular Agave applications.
  • Enabled execution of workflows on diverse computing infrastructures.
  • Provided exemplar workflows for association and annotation analyses.

Main Results:

  • SciApps facilitates the automation of bioinformatics workflows.
  • The platform supports execution across local clusters and cloud environments.
  • Exemplar workflows for association and annotation demonstrate usability.
  • Enhances accessibility and reproducibility of large-scale bioinformatics analyses.

Conclusions:

  • SciApps provides a robust solution for reproducible bioinformatics workflow management.
  • The platform addresses the need for efficient data analysis in the era of big biological data.
  • Facilitates seamless integration of modular applications for complex analyses.