Difference between revisions of "Team:Calgary/Software"

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<h2 class="page-subtitle">Computing Biology</h2>
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<h1 class="page-title">Software</h1>
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                <p>iGAM</p>
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                <img style="width: 100%" src="https://static.igem.org/mediawiki/2019/3/33/T--Calgary--DynaGixWhite.gif" />
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                <p>BioBrick Optimization Tool</p>
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            <h1>Inspiration</h1>
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            <h2>iGAM</h2>
  
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<img style="width: 100%" src="https://static.igem.org/mediawiki/2019/3/33/T--Calgary--DynaGixWhite.gif"/><p>iGAM</p>
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<img style="width: 100%" src="https://static.igem.org/mediawiki/2019/3/33/T--Calgary--DynaGixWhite.gif"/><p>BioBrick Optimization Tool</p>
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<h1>Inspiration</h1>
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                                        <h2>iGAM</h2>
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            <b>Proteins are widely used in the iGEM community,</b>  but there is very little iGEM teams can do to understand their protein’s atomic behaviour. At iGEM Calgary we wanted to generate a quantitative way to allow other teams to characterize each amino acid of their proteins.
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<b>Proteins are widely used in the iGEM community,</b> but there is very little iGEM teams can do to understand their protein’s atomic behaviour. At iGEM Calgary we wanted to generate a quantitative way to allow other teams to characterize each amino acid of their proteins.
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            <h1>Inspiration</h1>
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            <h2>B.O.T.</h2>
  
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            Our team ran into the difficulties of optimizing a DNA sequence for expression while making it still possible to order from IDT. WE built a tool that could easily and quickly optimize sequences so synthetic biologists can focus on their experiments not ordering.
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            <h1>Measurement</h1>
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            <h2>WHAT DID WE QUANTIFY?</h2>
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            <b>To assist in the dynamic characterization by other teams</b> we looked to develop a methodology that allows for the calculation and aggregation of Brownian motion measurements for each amino acid in a sequence. The Brownian motion measurement chosen was the Root Mean Square Fluctuation(RMSF) calculated for every atom of a protein in ten picosecond intervals.
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            <b>The RMSF data</b> was calculated from a nanosecond Molecular Dynamic Simulation(MDS) completed within GROMACS, an industrial MDS software.  These values were then averaged over each amino acid, this ensured that the unit of measurement was observed on a scale that was modifiable by teams. This resulted in a series of curves that quantitatively expressed the dynamics for each amino acid.
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<p>Our team ran into the difficulties of optimizing a DNA sequence for expression while making it still possible to order from IDT. WE built a tool that could easily and quickly optimize sequences so synthetic biologists can focus on their experiments not ordering.
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<h1>Measurement</h1>
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<h2>WHAT DID WE QUANTIFY?</h2>
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<p><b>To assist in the dynamic characterization by other teams</b> we looked to develop a methodology that allows for the calculation and aggregation of Brownian motion measurements for each amino acid in a sequence. The Brownian motion measurement chosen was the Root Mean Square Fluctuation(RMSF) calculated for every atom of a protein in ten picosecond intervals.  
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<b>The RMSF data</b> was calculated from a nanosecond Molecular Dynamic Simulation(MDS) completed within GROMACS, an industrial MDS software.  These values were then averaged over each amino acid, this ensured that the unit of measurement was observed on a scale that was modifiable by teams. This resulted in a series of curves that quantitatively expressed the dynamics for each amino acid.
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Above is a complete view of the movement attributed to every amino acid of a protein. Having all of the curves present at the same time can be quite confusing. The true power of this measurement can be harnessed when amino acids are displayed in smaller clusters. Below is the dynamics of the 25th, 80th, and 90th amino acid of the 6GIX protein.
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            Above is a complete view of the movement attributed to every amino acid of a protein. Having all of the curves present at the same time can be quite confusing. The true power of this measurement can be harnessed when amino acids are displayed in smaller clusters. Below is the dynamics of the 25th, 80th, and 90th amino acid of the 6GIX protein.
  
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<h1>Functionality</h1>
 
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<h2>WHAT CAN RMSF ACCOMPLISH</h2>
 
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                <h1>Functionality</h1>
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                <h2>WHAT CAN RMSF ACCOMPLISH</h2>
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<h1>Appendix A</h1>
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<h2>Procedure of data collected <i>in vitro</i></h2>
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                <h1>Appendix A</h1>
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                <h2>Procedure of data collected <i>in vitro</i></h2>
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Revision as of 02:28, 14 October 2019

Page Template

iGAM

BioBrick Optimization Tool

Inspiration

iGAM

Proteins are widely used in the iGEM community, but there is very little iGEM teams can do to understand their protein’s atomic behaviour. At iGEM Calgary we wanted to generate a quantitative way to allow other teams to characterize each amino acid of their proteins.

Inspiration

B.O.T.

Our team ran into the difficulties of optimizing a DNA sequence for expression while making it still possible to order from IDT. WE built a tool that could easily and quickly optimize sequences so synthetic biologists can focus on their experiments not ordering.

Measurement

WHAT DID WE QUANTIFY?

To assist in the dynamic characterization by other teams we looked to develop a methodology that allows for the calculation and aggregation of Brownian motion measurements for each amino acid in a sequence. The Brownian motion measurement chosen was the Root Mean Square Fluctuation(RMSF) calculated for every atom of a protein in ten picosecond intervals.

The RMSF data was calculated from a nanosecond Molecular Dynamic Simulation(MDS) completed within GROMACS, an industrial MDS software. These values were then averaged over each amino acid, this ensured that the unit of measurement was observed on a scale that was modifiable by teams. This resulted in a series of curves that quantitatively expressed the dynamics for each amino acid.

Above is a complete view of the movement attributed to every amino acid of a protein. Having all of the curves present at the same time can be quite confusing. The true power of this measurement can be harnessed when amino acids are displayed in smaller clusters. Below is the dynamics of the 25th, 80th, and 90th amino acid of the 6GIX protein.

Functionality

WHAT CAN RMSF ACCOMPLISH

Appendix A

Procedure of data collected in vitro