Commit ae60bb9d authored by ClovisG's avatar ClovisG
Browse files

2021 update

parent a6ecbe4a
......@@ -29,6 +29,16 @@ document.addEventListener('DOMContentLoaded', function(e) {
});
</script>
<style type="text/css">
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
span.underline{text-decoration: underline;}
div.column{display: inline-block; vertical-align: top; width: 50%;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
</style>
......@@ -214,7 +224,6 @@ padding-left: 1rem;
<h1 class="title toc-ignore">Salmonella Outbreak</h1>
<h3 class="subtitle"><a href="https://clovisg.github.io/teaching/protein-structure-prediction/salmonella_outbreak.mp4">Trailer</a></h3>
<h4 class="author">Clovis Galiez</h4>
<h4 class="date">September 2020</h4>
......@@ -235,7 +244,7 @@ padding-left: 1rem;
<h4><a href="https://project-management-knowledge.com/definitions/w/work-package/">WP1</a>:</h4>
<ul>
<li><p><a href="https://en.wikipedia.org/wiki/Task_(project_management)">T1</a> - one tool that takes two simple <a href="https://en.wikipedia.org/wiki/FASTA_format">FASTA</a> sequencing files (Illumina reads) and outputs a list of <a href="https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism">SNP</a>s (different from <a href="https://en.wikipedia.org/wiki/Scottish_National_Party#Current_ideology">SNP</a>),</p></li>
<li><p>T2 (optional) - one tool that takes a multiple sequence alignment in standard FASTA file format and outputs a protein structure.</p></li>
<li><p>T2 (optional) - Apply your tool to identify mutations between two variants of SARS-Cov-2</p></li>
</ul>
</div>
<div id="wp2" class="section level4">
......@@ -255,14 +264,14 @@ padding-left: 1rem;
</div>
<div id="evaluation-of-your-project" class="section level2">
<h2>Evaluation of your project</h2>
<p>The final evaluation of your proposal will take into account:</p>
<p>The final evaluation of your proposal (max. 5 pages) will take into account:</p>
<ul>
<li>the soundness of your approach (description and mathematical justification of the underlying statistical model)</li>
<li>the soundness of your approach (description and mathematical justification of the underlying statistical model of your method)</li>
<li>algorithmic complexity (more than linear time is not allowed)</li>
<li>the empirical proof you provide to assess the performance of your method on your own simulated data (e.g. <a href="https://en.wikipedia.org/wiki/K-mer">k-mer</a> abundance simulation)</li>
<li>the empirical proof (e.g. using <a href="https://en.wikipedia.org/wiki/K-mer">k-mer</a> abundance simulation) to assess the performance of your method (e.g. up to what sequencing error rate you estimate that your method is robust)</li>
<li>the application on the data provided (correctness of the identified gene)</li>
<li>the biological soundness of the identified mutated gene</li>
<li>the <strong>clarity and simplicity</strong> of the provided code (simple execution like ‘python3 snpDetect.py readsA.fasta readsB.fasta’, and output a list of SNPs)</li>
<li>the <strong>clarity and simplicity</strong> of the provided code (simple execution like ‘python3 snpDetect.py readsA.fasta readsB.fasta’, that outputs the list of SNPs)</li>
</ul>
</div>
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment