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Identical blocks of code found in 2 locations. Consider refactoring.
Open

        return (self.gR*self.VmPFK*x[3]*(-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)*(1 + x[3]/self.KmPFKF6P + (-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)/((2 - 8*self.KeqAK)*self.KmPFKATP) + (self.gR*x[3]*(-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5))/((2 - 8*self.KeqAK)*self.KmPFKATP*self.KmPFKF6P)))/((2 - 8*self.KeqAK)*self.KmPFKATP*self.KmPFKF6P*((self.L0*(1 + (self.CPFKF26BP*self.F26BP)/self.KPFKF26BP + (self.CPFKF16BP*x[2])/self.KPFKF16BP)**2*(1 + (2*self.CPFKAMP*self.KeqAK*(self.SUMAXP - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)**2)/((-1 + 4*self.KeqAK)*self.KPFKAMP*(self.SUMAXP - x[12] + 4*self.KeqAK*x[12] - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)))**2*(1 + (self.CiPFKATP*(-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5))/((2 - 8*self.KeqAK)*self.KiPFKATP))**2*(1 + (self.CPFKATP*(-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5))/((2 - 8*self.KeqAK)*self.KmPFKATP))**2)/((1 + self.F26BP/self.KPFKF26BP + x[2]/self.KPFKF16BP)**2*(1 + (2*self.KeqAK*(self.SUMAXP - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)**2)/((-1 + 4*self.KeqAK)*self.KPFKAMP*(self.SUMAXP - x[12] + 4*self.KeqAK*x[12] - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)))**2*(1 + (-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)/((2 - 8*self.KeqAK)*self.KiPFKATP))**2) + (1 + x[3]/self.KmPFKF6P + (-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)/((2 - 8*self.KeqAK)*self.KmPFKATP) + (self.gR*x[3]*(-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5))/((2 - 8*self.KeqAK)*self.KmPFKATP*self.KmPFKF6P))**2))
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/model_composition.py and 1 other location - About 4 days to fix
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 292..292

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 465.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

        return (self.VmPGK*((self.KeqPGK*x[1]*(self.SUMAXP - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5))/(1 - 4*self.KeqAK) - (x[9]*(-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5))/(2 - 8*self.KeqAK)))/(self.KmPGKATP*self.KmPGKP3G*(1 + x[1]/self.KmPGKBPG + x[9]/self.KmPGKP3G)*(1 + (self.SUMAXP - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)/((1 - 4*self.KeqAK)*self.KmPGKADP) + (-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)/((2 - 8*self.KeqAK)*self.KmPGKATP)))
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/model_composition.py and 1 other location - About 4 days to fix
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 271..272

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 437.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

        return (self.VmGLK*(-((x[4]*(self.SUMAXP - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)) /
                              ((1 - 4*self.KeqAK)*self.KeqGLK)) + (x[5]*(-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5))/(2 - 8*self.KeqAK)))/(self.KmGLKATP*self.KmGLKGLCi*(1 + x[4]/self.KmGLKG6P + x[5]/self.KmGLKGLCi)*(1 + (self.SUMAXP - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)/((1 - 4*self.KeqAK)*self.KmGLKADP) + (-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)/((2 - 8*self.KeqAK)*self.KmGLKATP)))
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/model_composition.py and 1 other location - About 4 days to fix
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 307..307

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 437.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

        return (self.VmPYK*((x[10]*(self.SUMAXP - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5))/(1 - 4*self.KeqAK) - ((-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)*x[11])/((2 - 8*self.KeqAK)*self.KeqPYK)))/(self.KmPYKADP*self.KmPYKPEP*(1 + (self.SUMAXP - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)/((1 - 4*self.KeqAK)*self.KmPYKADP) + (-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)/((2 - 8*self.KeqAK)*self.KmPYKATP))*(1 + x[10]/self.KmPYKPEP + x[11]/self.KmPYKPYR))
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/model_composition.py and 1 other location - About 1 day to fix
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 271..271

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 145.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

            m_percentiles[i, :] = [
                numpy.percentile(m[i, :], 1),
                numpy.percentile(m[i, :], 5),
                numpy.percentile(m[i, :], 33.33),
                numpy.percentile(m[i, :], 50),
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py and 1 other location - About 1 day to fix
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 898..905

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 134.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

            n_percentiles[i, :] = [
                numpy.percentile(n[i, :], 1),
                numpy.percentile(n[i, :], 5),
                numpy.percentile(n[i, :], 33.33),
                numpy.percentile(n[i, :], 50),
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py and 1 other location - About 1 day to fix
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 889..896

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 134.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

class Specie(Base):
    """ Represents a species

    Attributes:
        name (:obj:`str`): name
Severity: Major
Found in intro_to_wc_modeling/concepts_skills/software_engineering/databases/core.py and 1 other location - About 6 hrs to fix
intro_to_wc_modeling/concepts_skills/software_engineering/databases/core.py on lines 44..58

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 106.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

class Compartment(Base):
    """ Represents an compartment

    Attributes:
        name (:obj:`str`): name
Severity: Major
Found in intro_to_wc_modeling/concepts_skills/software_engineering/databases/core.py and 1 other location - About 6 hrs to fix
intro_to_wc_modeling/concepts_skills/software_engineering/databases/core.py on lines 61..74

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 106.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

    def v_2(self, x):
        # Glucose-6-phosphate isomerase
        # G6P <=> F6P
        return (self.VmPGI*(-(x[3]/self.KeqPGI) + x[4]))/(self.KmPGIG6P*(1 + x[3]/self.KmPGIF6P + x[4]/self.KmPGIG6P))
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/model_composition.py and 1 other location - About 6 hrs to fix
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 309..312

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 102.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

    def v_9(self, x):
        # Phosphoglycerate mutase
        # P3G <=> P2G
        return (self.VmPGM*(-(x[8]/self.KeqPGM) + x[9]))/(self.KmPGMP3G*(1 + x[8]/self.KmPGMP2G + x[9]/self.KmPGMP3G))
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/model_composition.py and 1 other location - About 6 hrs to fix
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 274..277

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 102.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Identical blocks of code found in 2 locations. Consider refactoring.
Open

    def __init__(self, k_m=5, k_n=20, gamma_m=numpy.log(2) * 60 / 3, gamma_n=numpy.log(2) / 10, m_0=1, n_0=98):
        """
        Args:
            k_m (:obj:`float`, optional): mRNA synthesis rate constant (molecules h\ :sup:`-1`)
            k_n (:obj:`float`, optional): protein synthesis rate constant (\ :sup:`-1`\  h\ :sup:`-1`)
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py and 1 other location - About 5 hrs to fix
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 36..51

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 94.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Identical blocks of code found in 2 locations. Consider refactoring.
Open

    def __init__(self, k_m=5, k_n=20, gamma_m=numpy.log(2) * 60 / 3, gamma_n=numpy.log(2) / 10, m_0=1, n_0=98):
        """
        Args:
            k_m (:obj:`float`, optional): mRNA synthesis rate constant (molecules h\ :sup:`-1`)
            k_n (:obj:`float`, optional): protein synthesis rate constant (\ :sup:`-1`\  h\ :sup:`-1`)
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py and 1 other location - About 5 hrs to fix
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 674..689

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 94.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

    def dNAD_dt(self, x):
        return 1.0 * self.v_15(x) + 1.0 * self.v_16(x) - 1.0 * self.v_7(x) - 3.0 * self.v_13(x)
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/model_composition.py and 1 other location - About 4 hrs to fix
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 375..376

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 76.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

    def dNADH_dt(self, x):
        return 1.0 * self.v_7(x) + 3.0 * self.v_13(x) - 1.0 * self.v_15(x) - 1.0 * self.v_16(x)
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/model_composition.py and 1 other location - About 4 hrs to fix
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 372..373

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 76.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

    def dACE_dt(self, x):
        return 1.0 * self.v_12(x) - 1.0 * self.v_15(x) - 2.0 * self.v_13(x)
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/model_composition.py and 1 other location - About 2 hrs to fix
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 396..397

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 58.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

    def dTRIO_dt(self, x):
        return 2.0 * self.v_6(x) - 1.0 * self.v_16(x) - 1.0 * self.v_7(x)
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/model_composition.py and 1 other location - About 2 hrs to fix
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 354..355

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 58.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

def main(output_directory=DEFAULT_OUTPUT_DIRECTORY):
    """ Run simulation, plot results, and save plots

    Args:
        output_directory (:obj:`str`, optional): directory to save plots
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/submodel_simulation.py and 1 other location - About 2 hrs to fix
intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/simulation.py on lines 211..228

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 57.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

def main(output_directory=DEFAULT_OUTPUT_DIRECTORY):
    """ Run simulation and plot results

    Args:
        output_directory (:obj:`str`, optional): directory to save plots
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/simulation.py and 1 other location - About 2 hrs to fix
intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/submodel_simulation.py on lines 175..191

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 57.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Identical blocks of code found in 2 locations. Consider refactoring.
Open

    def calcIdName(self):
        self.id = '%s[%s]' % (self.species.id, self.compartment.id)
        self.name = '%s (%s)' % (self.species.name, self.compartment.name)
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py and 1 other location - About 2 hrs to fix
intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py on lines 574..576

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 54.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Identical blocks of code found in 2 locations. Consider refactoring.
Open

    def calcIdName(self):
        self.id = '%s[%s]' % (self.species.id, self.compartment.id)
        self.name = '%s (%s)' % (self.species.name, self.compartment.name)
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py and 1 other location - About 2 hrs to fix
intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py on lines 605..607

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 54.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

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