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Related Concept Videos

Language01:16

Language

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Language is a unique communication system that uses words and systematic rules to organize and transmit information. Unlike other forms of communication, which may involve postures, movements, odors, or vocalizations, language relies on symbols and grammar. This makes human communication distinct from that of other species, who also communicate but do not use language in the same way humans do.
Corballis and Suddendorf (2007) and Tomasello and Rakoczy (2003) highlight the role of language in...
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Components of Language01:24

Components of Language

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Language, whether spoken, signed, or written, consists of specific components: lexicon and grammar. The lexicon is the vocabulary of a language, comprising its words. Grammar is the set of rules used to convey meaning through the lexicon. For example, English grammar adds “-ed” to most verbs to indicate past tense. Words are formed by combining phonemes, which are the basic sound units of a language. Different languages have different sets of phonemes (e.g., “ah” vs.
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Language Development01:22

Language Development

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Children master language quickly and with relative ease, supported by both biological predisposition and reinforcement. B. F. Skinner (1957) proposed that language is learned through reinforcement, while Noam Chomsky (1965) argued that language acquisition mechanisms are biologically determined.
The critical period for language acquisition suggests that the ability to acquire language is at its peak early in life. As people age, this proficiency decreases. Language development begins very...
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Language and Cognition01:27

Language and Cognition

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Language serves as a bridge between ideas and communication, influencing how individuals perceive and interact with the world. Psychologists have long debated whether language shapes thought or vice versa. This discussion gained grip with Edward Sapir and Benjamin Lee Whorf in the 1940s, who proposed that language determines thought, a concept known as linguistic determinism. They suggested that the vocabulary and structure of a language influence how its speakers think and perceive reality.
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Higher Mental Functions of the Brain: Language01:10

Higher Mental Functions of the Brain: Language

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Language is a system of communication that allows the expression of thoughts, ideas, and feelings. The brain processes language in both hemispheres.
Language formation and comprehension take place in the dominant hemisphere. The dominant hemisphere is responsible for understanding the meaning of spoken, written, or sign language, as well as the ability to communicate. For most people, the left hemisphere is the dominant one. The right hemisphere, then, gives tone and emotional context to the...
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ortho–para-Directing Activators: –CH3, –OH, –⁠NH2, –OCH301:11

ortho–para-Directing Activators: –CH3, –OH, –⁠NH2, –OCH3

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All ortho–para directors, excluding halogens, are activating groups. These groups donate electrons to the ring, making the ring carbons electron-rich. Consequently, the reactivity of the aromatic ring towards electrophilic substitution increases. For instance, the nitration of anisole is about 10,000 times faster than the nitration of benzene. The electron-donating effect of the methoxy group in anisole activates the ortho and para positions on the ring and stabilizes the corresponding...
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The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core.

Michael Hucka1, Frank T Bergmann1, Andreas Dräger2

  • 1California Institute of Technology, Pasadena, CA, USA.

Journal of Integrative Bioinformatics
|March 10, 2018
PubMed
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The Systems Biology Markup Language (SBML) is an XML-based file format for computational biological models. Version 2 of SBML Level 3 Core enhances interoperability by standardizing model representation across diverse software tools.

Keywords:
SBMLcomputational biologymodelingstandardssystems biology

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Area of Science:

  • Systems Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Computational models are crucial for interpreting biological data, understanding cellular functions, and making quantitative predictions in life sciences research.
  • The Systems Biology Markup Language (SBML) facilitates the exchange of computational models between different software systems, ensuring a common representation for biological processes like metabolic and signaling pathways.
  • Interoperability in systems biology is essential to prevent translation errors and provide a standardized starting point for model analysis and simulation.

Purpose of the Study:

  • To provide the official specification for Version 2 of the SBML Level 3 Core standard.
  • To define the data structures, XML encoding, and validation rules for SBML documents.
  • To outline the key differences and improvements in Version 2 compared to previous versions, focusing on enhanced mathematical construct support and element identification.

Main Methods:

  • Defining the data structures and their XML encoding for representing computational biological models.
  • Establishing validation rules to ensure the integrity and correctness of SBML documents.
  • Documenting the differences between SBML Version 2 and Version 1, including expanded MathML support and optional child elements.

Main Results:

  • The specification for SBML Level 3 Core Version 2 is established, detailing data structures and XML encoding.
  • New MathML constructs are permitted, more child elements are optional, and all SBML elements now have identifiers, enhancing model expressiveness and flexibility.
  • Validation rules are defined to ensure the quality and consistency of SBML files.

Conclusions:

  • SBML Level 3 Core Version 2 provides an improved and more flexible standard for representing computational biological models.
  • This enhanced specification promotes greater interoperability and reduces errors in data exchange between different software tools in systems biology.
  • The advancements in Version 2 facilitate more robust analysis and simulation of biological systems.