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| </div> | | </div> |
| <div class="text"> | | <div class="text"> |
− | <p>n order to do that, we decided to utilize Poly, an open-source Go package for organism engineering. | + | <p>In order to do that, we decided to utilize Poly, an open-source Go package for organism engineering. |
| As a Go package, Poly has intrinsic properties that allow easy reusability, compatibility, and good | | As a Go package, Poly has intrinsic properties that allow easy reusability, compatibility, and good |
| performance. Poly also has a very vivid and funny community, guided by a very active maintainer and | | performance. Poly also has a very vivid and funny community, guided by a very active maintainer and |
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| <ol> | | <ol> |
| <li> | | <li> |
− | <p><mark><b><a href="https://github.com/igemsoftware2021/friendzymes-cookbook/blob/main/tutorials/01_Understanding_Poly.ipynb">Understanding Poly</a></b></mark></p> | + | <p><b><a href="https://github.com/igemsoftware2021/friendzymes-cookbook/blob/main/tutorials/01_Understanding_Poly.ipynb">Understanding Poly</a></b></p> |
| <p>Poly is our key tool for the software. It was a planned decision to build workflows that | | <p>Poly is our key tool for the software. It was a planned decision to build workflows that |
| integrate with Poly, to show ways to use the package, as well as create some new features; | | integrate with Poly, to show ways to use the package, as well as create some new features; |
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| </li> | | </li> |
| <li> | | <li> |
− | <p><b><mark><a href="https://github.com/igemsoftware2021/friendzymes-cookbook/blob/main/tutorials/02_Codon_Optimization.ipynb">Codon Optimization</mark></a></b></p> | + | <p><b><a href="https://github.com/igemsoftware2021/friendzymes-cookbook/blob/main/tutorials/02_Codon_Optimization.ipynb">Codon Optimization</a></b></p> |
| <p>A very common task for the design of parts is Codon Optimization, so here we will show how | | <p>A very common task for the design of parts is Codon Optimization, so here we will show how |
| you can create customized Codon Tables and how you can use this to do codon optimization of | | you can create customized Codon Tables and how you can use this to do codon optimization of |
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| </li> | | </li> |
| <li> | | <li> |
− | <p><b><mark><a href="https://github.com/igemsoftware2021/friendzymes-cookbook/blob/main/tutorials/03_Automatic_Annotation_Of_Problematic_Sequences.ipynb">Annotation of problematic sequences</a></mark></b></p> | + | <p><b><a href="https://github.com/igemsoftware2021/friendzymes-cookbook/blob/main/tutorials/03_Automatic_Annotation_Of_Problematic_Sequences.ipynb">Annotation of problematic sequences</a></b></p> |
| <p>Have you designed your sequence? Now it is time to remove small forbidden parts that can | | <p>Have you designed your sequence? Now it is time to remove small forbidden parts that can |
| hinder you, not only when sequencing (e.g. hairpins, repetitive regions), but also when | | hinder you, not only when sequencing (e.g. hairpins, repetitive regions), but also when |
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| </li> | | </li> |
| <li> | | <li> |
− | <p><b><mark><a href="https://github.com/igemsoftware2021/friendzymes-cookbook/blob/main/tutorials/04_Fix_CDS.ipynb">CDS fix</a></mark></b></p> | + | <p><b><a href="https://github.com/igemsoftware2021/friendzymes-cookbook/blob/main/tutorials/04_Fix_CDS.ipynb">CDS fix</a></b></p> |
| <p>In this notebook, you will input your CDS sequence(s) and receive your CDS corrected without | | <p>In this notebook, you will input your CDS sequence(s) and receive your CDS corrected without |
| the problematic sequences. This is done by replacing the codons with synonymous ones, thus | | the problematic sequences. This is done by replacing the codons with synonymous ones, thus |
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| | | |
| <li> | | <li> |
− | <p><b><mark><a href="https://github.com/igemsoftware2021/friendzymes-cookbook/blob/main/tutorials/05_Create_Parts_With_Overhangs.ipynb">Automatically create parts with correct overhangs</a></mark></b></p> | + | <p><b><ma<a href="https://github.com/igemsoftware2021/friendzymes-cookbook/blob/main/tutorials/05_Create_Parts_With_Overhangs.ipynb">Automatically create parts with correct overhangs</a></b></p> |
| <p>How about designing your final plasmid without worrying about each separate part and using a | | <p>How about designing your final plasmid without worrying about each separate part and using a |
| script to add the restriction binding sites, spacer, and overhangs? That’s what you find | | script to add the restriction binding sites, spacer, and overhangs? That’s what you find |
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| | | |
| <li> | | <li> |
− | <p><b><mark><a href="https://github.com/igemsoftware2021/friendzymes-cookbook/blob/main/tutorials/06_Simulate_a_Golden_Gate_simulation_for_checking_parts.ipynb">Golden Gate Simulation</a></mark></b></p> | + | <p><b><a href="https://github.com/igemsoftware2021/friendzymes-cookbook/blob/main/tutorials/06_Simulate_a_Golden_Gate_simulation_for_checking_parts.ipynb">Golden Gate Simulation</a></b></p> |
| <p>In this notebook, you will run a simulation of a Golden Gate reaction and see if everything | | <p>In this notebook, you will run a simulation of a Golden Gate reaction and see if everything |
| is theoretically acceptable before physically synthesizing your parts.</p> | | is theoretically acceptable before physically synthesizing your parts.</p> |
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| <ol> | | <ol> |
| <li> | | <li> |
− | <p><b><mark><a href="https://github.com/igemsoftware2021/dna-annotate">DNA Annotator</a</mark></b></p> | + | <p><b><a href="https://github.com/igemsoftware2021/dna-annotate">DNA Annotator</a></b></p> |
| <p>This action allows users to process Genbank files and reannotate them with problematic | | <p>This action allows users to process Genbank files and reannotate them with problematic |
| regions as Hairpins, Repetitive sequences, and forbidden restriction binding sites, allowing | | regions as Hairpins, Repetitive sequences, and forbidden restriction binding sites, allowing |
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| </li> | | </li> |
| <li> | | <li> |
− | <p><b><mark><a href="https://github.com/igemsoftware2021/dna-is-synthesizable">Is this DNA Synthesizable?</a></mark></b></p> | + | <p><b><a href="https://github.com/igemsoftware2021/dna-is-synthesizable">Is this DNA Synthesizable?</a></b></p> |
| <p>Instead of copying and pasting each sequence that you have in the IDT gBlock Analyzer page to | | <p>Instead of copying and pasting each sequence that you have in the IDT gBlock Analyzer page to |
| see if your sequence is synthesizable, we created this action to check this for you. We have | | see if your sequence is synthesizable, we created this action to check this for you. We have |
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| </li> | | </li> |
| <li> | | <li> |
− | <p><b><mark><a href="https://github.com/igemsoftware2021/codon-optimize">Codon Optimization</a></mark></b></p> | + | <p><b><a href="https://github.com/igemsoftware2021/codon-optimize">Codon Optimization</a></b></p> |
| <p>You could, with this action, automatically codon- optimize a list of sequences for different | | <p>You could, with this action, automatically codon- optimize a list of sequences for different |
| organisms based on the codon tables you share. This is good if you’re working with multiple | | organisms based on the codon tables you share. This is good if you’re working with multiple |