Difference between revisions of "Team:Calgary/Software"

 
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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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<h4>GAUSHAUS</h4>
 
<h4>GAUSHAUS</h4>
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   <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">
  
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<center><img style="padding-bottom:20px;"class="img-fluid"src="https://static.igem.org/mediawiki/2020/3/39/T--Calgary--BELLAIC.png">
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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">
  
 
<h4>BELLATRIX</h4>
 
<h4>BELLATRIX</h4>
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     <center><img style="padding-bottom:20px;"class="img-fluid"src="https://static.igem.org/mediawiki/2020/9/97/T--Calgary--Randlecellicon.png">
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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>
 
   <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>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.
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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">
 
  <h4>iGAM 2.0</h4>
 
  <h4>iGAM 2.0</h4>
 
   <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>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.
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   <h4>HARDWARE <br> SOFTWARE</h4>
 
   <h4>HARDWARE <br> SOFTWARE</h4>
 
     <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>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++.
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   <h4>GITHUB</h4>
 
   <h4>GITHUB</h4>
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     <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. <a href="https://github.com/iGEMCalgary">Click Me</a>
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     <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.  
 
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With the subprojects' effort above, we were able to witness and tune Oviita without the lab.  From the protein engineering models, we built confidence in our system's field efficacy with our proteins. These models were then able to influence the design and sequence of our parts directly. Then came issues around our organism's cultivation, and if it could handle the pummeling we were putting it through. This was addressed and answered via the metabolic flux models. These also greatly influenced the design and deployment strategy of our bioreactor.
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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.
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Finally came something unexpected. We were given a subproject through HP, the detection of vitamin A levels in the blood. For this, we had to undergo a project level of modelling so that we could ensure our HP contacts of its viability.  
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Modelling was the gateway inwhich we built Oviita to be physically sustainable. With HP and the preliminary findings in the lab, Oviita can grow from the models to be sustainable for the communities it seeks to help.
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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.