Difference between revisions of "Team:Calgary/Software"

 
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<div style="background-color:#FFFFFF; padding-left: 60px; padding-right: 50px; padding-bottom: 60px; border-radius: ;"class = "project-design" id="project-design">
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         <center><h2><b>SOFTWARE OVERVIEW</b></h2></center>
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         <center><h2><b>SOFTWARE</b></h2></center>
 
         <br>
 
         <br>
 
         <p>
 
         <p>
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          Oviita has three main wet lab components that allow <span style="font-style: italic;class="italic">Yarrowia lipolytica</span> to be easy and safe to work with in communities, and be as nutritionally valuable as possible. This year we did extensive planning of experiments, including trouble-shooting plans. Check out our work below!
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Software for this year was completed in hope to provide tools and building blocks for future teams while enabling other aspects of our own project. The following softwares were the fruits of our labour over the summer.
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        </p>
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          </p>
  
  
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   <div style="background-color:#f5b984; border-radius: 25px; padding-bottom: 30px;"class="row resp2">
 
      
 
      
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     <div style="padding-top:30px;"class="col-sm-4"><a href="https://2020.igem.org/Team:Calgary/Bellatrix" class="imglink">
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     <div style="padding-top:30px;"class="col-sm-4"><a href="https://2020.igem.org/Team:Calgary/Gaushaus" class="imglink">
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     <center><img style="padding-bottom:20px;"class="img-fluid"src="https://static.igem.org/mediawiki/2020/3/3a/T--Calgary--partcollection.jpg">
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     <center><img style="padding-bottom:20px;"class="img-fluid"src="https://static.igem.org/mediawiki/2020/b/b3/T--Calgary--GausHaus.png">
  
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<h4>BELLATRIX</h4>
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<h4>GAUSHAUS</h4>
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       <p>Integrating cellulase genes into the <span style="font-style: italic;class="italic">Y. lipolytica</span> genome, thus allowing the yeast to use agricultural waste as a carbon source for energy. </p></center></a>
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       <p>The first portion of our project to benefit from our software development was in our measurement. With our molecular dynamics simulations, we were attempting to characterize data coming out of a firehose. By using the GausHaus measuring software, we can temper the flow to be much more usable and concise. This Software enabled our team to develop models and build confidence in the efficacy of our cellulases. Ultimately this software has impacted the lab where we are currently working on secreting the measured cellulases by our yeast. This software was developed in R.
 +
</p></center></a>
 
     </div>
 
     </div>
 
      
 
      
−
   <div style="padding-top:30px;"class="col-sm-4"><a href="https://2020.igem.org/Team:Calgary/Cellulase_General" class="imglink">
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   <div style="padding-top:30px;"class="col-sm-4"><a href="https://2020.igem.org/Team:Calgary/Bellatrix" class="imglink">
  
−
<center><img style="padding-bottom:20px;"class="img-fluid"src="https://static.igem.org/mediawiki/2020/f/ff/T--Calgary--validate.jpg">
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<center><img style="padding-bottom:20px;"class="img-fluid"src="https://static.igem.org/mediawiki/2020/f/fc/T--Calgary--bellatrixicon.png">
  
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<h4>GAUSHAUS</h4>
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<h4>BELLATRIX</h4>
−
       <p>Integrating cellulase genes into the <span style="font-style: italic;class="italic">Y. lipolytica</span> genome, thus allowing the yeast to use agricultural waste as a carbon source for energy. </p></center></a>
+
       <p>The next aspect of our project to feel the breadth of our software was Modelling. Bellatrix was developed to assist the modelling pathway by allowing arduous pdb files to be decomposed into a new file type known as 'star files' this has allowed relational structure matrices to be easily generated and used by our modelling team. This software was developed in Python.
 +
</p></center></a>
 
     </div>
 
     </div>
 
      
 
      
−
   <div style="padding-top:30px;"class="col-sm-4"><a href="https://2020.igem.org/Team:Calgary/Gaushaus" class="imglink">
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   <div style="padding-top:30px;"class="col-sm-4"><a href="https://2020.igem.org/Team:Calgary/Sticks" class="imglink">
  
−
     <center><img style="padding-bottom:20px;"class="img-fluid"src="https://static.igem.org/mediawiki/2020/7/79/T--Calgary--characterize.jpg">
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     <center><img style="padding-bottom:20px;"class="img-fluid"src="https://static.igem.org/mediawiki/2020/c/c0/T--Calgary--Sticks12.png">
 
<h4>STICKS</h4>
 
<h4>STICKS</h4>
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   <p>Engineering the different strains to be dependent on each other so they can only survive within the bioreactor and not in the environment </p></center></a>
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   <p>For all those computational biologists out there working in R and hate having to jump back and forth with generated pdbs in auxiliary software, we have developed Sticks. Sticks is an R function that allows users to generate dynamic representation Gifs in R. This has saved our drylab a considerable amount of time working on our proteins. This software was developed in R.
 +
</p></center></a>
 
     </div>
 
     </div>
  
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     <div style="padding-top:30px;"class="col-sm-4"><a href="https://2020.igem.org/Team:Calgary/Metabolic_Flux" class="imglink">
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     <div style="padding-top:30px;"class="col-sm-4"><a href="https://2020.igem.org/Team:Calgary/iGAM" class="imglink">
 
   
 
   
−
       <center><img style="padding-bottom:20px;"class="img-fluid"src="https://static.igem.org/mediawiki/2020/7/79/T--Calgary--characterize.jpg">
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       <center><img style="padding-bottom:20px;"class="img-fluid"src="https://static.igem.org/mediawiki/2020/0/0a/T--Calgary--iGAMIcon.png">
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  <h4>METABOLIC FLUX</h4>
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  <h4>iGAM 2.0</h4>
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   <p>Engineering the different strains to be dependent on each other so they can only survive within the bioreactor and not in the environment </p></center></a>
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   <p>In a blast from the past, iGAM has received a few small updates to increase usability. These updates allow the program to work better on other proteins and allow users to insert their own fitness functions. Thereby allowing this software to be used by many more teams. This software was developed in R.
 +
</p></center></a>
 
     </div>
 
     </div>
  
−
     <div style="padding-top:30px;"class="col-sm-4"><a href="https://2020.igem.org/Team:Calgary/Cellobiohydrolase" class="imglink">
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     <div style="padding-top:30px;"class="col-sm-4"><a href="https://2020.igem.org/Team:Calgary/Hardware" class="imglink">
 
    
 
    
−
       <center><img style="padding-bottom:20px;"class="img-fluid"src="https://static.igem.org/mediawiki/2020/7/79/T--Calgary--characterize.jpg">
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       <center><img style="padding-bottom:20px;"class="img-fluid"src="https://static.igem.org/mediawiki/2020/f/fb/T--Calgary--Randlecellnew.png">
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   <h4>HARDWARE</h4>
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   <h4>HARDWARE <br> SOFTWARE</h4>
−
     <p>Engineering the different strains to be dependent on each other so they can only survive within the bioreactor and not in the environment </p></center></a>
+
     <p>Finally, our hardware-software was developed to allow our hardware projects to operate efficiently and reliably. We have provided these scripts to give other teams looking to work on hardware projects a point of reference. This will allow other teams to learn from our mistakes, strengthening their projects. This software was developed in C++.
 +
</p></center></a>
 
       </div>
 
       </div>
  
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       <div style="padding-top:30px;"class="col-sm-4"><a href="https://2020.igem.org/Team:Calgary/Endoglucanase1" class="imglink">
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       <div style="padding-top:30px;"class="col-sm-4"><a href="https://github.com/iGEMCalgary" class="imglink">
 
    
 
    
−
         <center><img style="padding-bottom:20px;"class="img-fluid"src="https://static.igem.org/mediawiki/2020/7/79/T--Calgary--characterize.jpg">
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         <center><img style="padding-bottom:20px;"class="img-fluid"src="https://static.igem.org/mediawiki/2020/3/33/T--Calgary--GitHub.png">
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   <h4>ENDOGLUCANASE</h4>
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   <h4>GITHUB</h4>
−
     <p>Engineering the different strains to be dependent on each other so they can only survive within the bioreactor and not in the environment </p></center></a>
+
     <p>If you are looking to find any of the softwares above, please visit our GitHub. While you are hunting around you can also view our software from the last few years.
 +
</p></center></a>
 
       </div>
 
       </div>
  
 
      
 
      
 
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<br><br>
 +
<p>
 +
The fingerprints of our software can be traced throughout our entire project. This has benefited not only the project but also the software as well. Our team is extremely interdisciplinary, and through more and more members of the team using the software, we have been able to gain user input from individuals that we would not normally consider in our development strategy. The result is software that considers the biologist and the engineer. We hope that this will increase its usefulness to other teams allowing it to become a part of many different projects in both the dry and wetlab.
 +
 +
</p>
  
  

Latest revision as of 03:11, 28 October 2020



SOFTWARE


Software for this year was completed in hope to provide tools and building blocks for future teams while enabling other aspects of our own project. The following softwares were the fruits of our labour over the summer.

GAUSHAUS

The first portion of our project to benefit from our software development was in our measurement. With our molecular dynamics simulations, we were attempting to characterize data coming out of a firehose. By using the GausHaus measuring software, we can temper the flow to be much more usable and concise. This Software enabled our team to develop models and build confidence in the efficacy of our cellulases. Ultimately this software has impacted the lab where we are currently working on secreting the measured cellulases by our yeast. This software was developed in R.

BELLATRIX

The next aspect of our project to feel the breadth of our software was Modelling. Bellatrix was developed to assist the modelling pathway by allowing arduous pdb files to be decomposed into a new file type known as 'star files' this has allowed relational structure matrices to be easily generated and used by our modelling team. This software was developed in Python.

STICKS

For all those computational biologists out there working in R and hate having to jump back and forth with generated pdbs in auxiliary software, we have developed Sticks. Sticks is an R function that allows users to generate dynamic representation Gifs in R. This has saved our drylab a considerable amount of time working on our proteins. This software was developed in R.

iGAM 2.0

In a blast from the past, iGAM has received a few small updates to increase usability. These updates allow the program to work better on other proteins and allow users to insert their own fitness functions. Thereby allowing this software to be used by many more teams. This software was developed in R.

HARDWARE
SOFTWARE

Finally, our hardware-software was developed to allow our hardware projects to operate efficiently and reliably. We have provided these scripts to give other teams looking to work on hardware projects a point of reference. This will allow other teams to learn from our mistakes, strengthening their projects. This software was developed in C++.

GITHUB

If you are looking to find any of the softwares above, please visit our GitHub. While you are hunting around you can also view our software from the last few years.



The fingerprints of our software can be traced throughout our entire project. This has benefited not only the project but also the software as well. Our team is extremely interdisciplinary, and through more and more members of the team using the software, we have been able to gain user input from individuals that we would not normally consider in our development strategy. The result is software that considers the biologist and the engineer. We hope that this will increase its usefulness to other teams allowing it to become a part of many different projects in both the dry and wetlab.