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<oai_dc:dc xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd">
  <dc:title>Predict Dominant Direction of Reactions of a Biochemical Network</dc:title>
  <dc:title>R package ReDirection version 1.0.1</dc:title>
  <dc:description>Biologically relevant, yet mathematically sound constraints are used
    to compute the propensity and thence infer the dominant direction of reactions
    of a generic biochemical network. The reactions must be unique and their 
    number must exceed that of the reactants,i.e., reactions &gt;= reactants + 2.  
            'ReDirection', computes the null space of a user-defined stoichiometry
    matrix. The spanning non-zero and unique reaction vectors (RVs) are 
    combinatorially summed to generate one or more subspaces recursively.  
            Every reaction is represented as a sequence of identical components 
    across all RVs of a particular subspace. The terms are evaluated with 
    (biologically relevant bounds, linear maps, tests of convergence, descriptive
    statistics, vector norms) and the terms are classified into forward-, reverse- 
    and equivalent-subsets. Since, these are mutually exclusive the probability 
    of occurrence is binary (all, 1; none, 0).
            The combined propensity of a reaction is the p1-norm of the 
    sub-propensities, i.e., sum of the products of the probability and maximum
    numeric value of a subset (least upper bound, greatest lower bound). This, 
    if strictly positive is the probable rate constant, is used to infer dominant
    direction and annotate a reaction as "Forward (f)", "Reverse (b)" or 
    "Equivalent (e)".
            The inherent computational complexity (NP-hard) per iteration suggests
    that a suitable value for the number of reactions is around 20.
            Three functions comprise ReDirection. These are check_matrix() and 
    reaction_vector() which are internal, and calculate_reaction_vector()
            which is external.</dc:description>
  <dc:type>Software</dc:type>
  <dc:relation>Depends: stats, MASS, pracma</dc:relation>
  <dc:relation>Imports: gtools</dc:relation>
  <dc:relation>Suggests: testthat (&gt;= 3.0.0)</dc:relation>
  <dc:creator>Siddhartha Kundu &lt;siddhartha_kundu@aiims.edu&gt;</dc:creator>
  <dc:publisher>Comprehensive R Archive Network (CRAN)</dc:publisher>
  <dc:contributor>Siddhartha Kundu &lt;2021: Manuscript Under Preparation&gt;</dc:contributor>
  <dc:rights>GPL-3</dc:rights>
  <dc:date>2021-10-04</dc:date>
  <dc:format>application/tgz</dc:format>
  <dc:identifier>https://CRAN.R-project.org/package=ReDirection</dc:identifier>
  <dc:identifier>doi:10.32614/CRAN.package.ReDirection</dc:identifier>
</oai_dc:dc>
