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Rosalind: Learn bioinformatics by programming it

167 pointsby mnemonicslothover 5 years ago

8 comments

xvilkaover 5 years ago
Would have been nice to have a Julia version too. Some time ago I suggested [1] to create a Julia flavor of Biostar Handbook [2]. And now there is an initiative[3] to create similar, but open source book instead. So anyone can contribute already.<p>[1] <a href="https:&#x2F;&#x2F;discourse.julialang.org&#x2F;t&#x2F;biostar-handbook-computational-genomics-and-julia-to-be-or-not-to-be&#x2F;25732" rel="nofollow">https:&#x2F;&#x2F;discourse.julialang.org&#x2F;t&#x2F;biostar-handbook-computati...</a><p>[2] <a href="https:&#x2F;&#x2F;www.biostarhandbook.com&#x2F;" rel="nofollow">https:&#x2F;&#x2F;www.biostarhandbook.com&#x2F;</a><p>[3] <a href="https:&#x2F;&#x2F;github.com&#x2F;BioJulia&#x2F;biojulia_handbook&#x2F;issues&#x2F;1" rel="nofollow">https:&#x2F;&#x2F;github.com&#x2F;BioJulia&#x2F;biojulia_handbook&#x2F;issues&#x2F;1</a>
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divbzeroover 5 years ago
If by chance anyone is not aware, the namesake is Rosalind Franklin [1] who made seminal contributions in the fields of X-ray crystallography and electron microscopy.<p>[1]: <a href="https:&#x2F;&#x2F;en.wikipedia.org&#x2F;wiki&#x2F;Rosalind_Franklin" rel="nofollow">https:&#x2F;&#x2F;en.wikipedia.org&#x2F;wiki&#x2F;Rosalind_Franklin</a><p>It was her X-ray image that led to the discovery of the molecular structure of DNA.
eesmithover 5 years ago
So, I picked one at semi-random - <a href="http:&#x2F;&#x2F;rosalind.info&#x2F;problems&#x2F;prtm&#x2F;" rel="nofollow">http:&#x2F;&#x2F;rosalind.info&#x2F;problems&#x2F;prtm&#x2F;</a> and found a usability problem (a popup that doesn&#x27;t work; in FF or Safari) and a wrong example answer. Here&#x27;s the description.<p>&gt; Given: A protein string P of length at most 1000 aa.<p>&gt; Return: The total weight of P. Consult the monoisotopic mass table.<p>The &quot;monoisotopic mass table&quot; appears to be a link. I get a pop-up, but nothing appears in it, other than a spinner. I had to do a web search to find <a href="http:&#x2F;&#x2F;rosalind.info&#x2F;glossary&#x2F;monoisotopic-mass-table&#x2F;" rel="nofollow">http:&#x2F;&#x2F;rosalind.info&#x2F;glossary&#x2F;monoisotopic-mass-table&#x2F;</a> .<p>The page continues:<p>&gt; Sample Dataset - SKADYEK<p>&gt; Sample Output - 821.392<p>Using the monoisotopic mass table I computed:<p><pre><code> &gt;&gt;&gt; d = {&#x27;A&#x27;: 71.03711, &#x27;C&#x27;: 103.00919, &#x27;D&#x27;: 115.02694, &#x27;E&#x27;: 129.04259, &#x27;F&#x27;: 147.06841, &#x27;G&#x27;: 57.02146, &#x27;H&#x27;: 137.05891, &#x27;I&#x27;: 113.08406, &#x27;K&#x27;: 128.09496, &#x27;L&#x27;: 113.08406, &#x27;M&#x27;: 131.04049, &#x27;N&#x27;: 114.04293, &#x27;P&#x27;: 97.05276, &#x27;Q&#x27;: 128.05858, &#x27;R&#x27;: 156.10111, &#x27;S&#x27;: 87.03203, &#x27;T&#x27;: 101.04768, &#x27;V&#x27;: 99.06841, &#x27;W&#x27;: 186.07931, &#x27;Y&#x27;: 163.06333} &gt;&gt;&gt; sum(d[c] for c in &quot;SKADYEK&quot;) 821.3919199999999 </code></pre> This matches the example. BUT!!!!<p>This is <i>NOT</i> the correct answer because as the expanded text says, &quot;the mass of a protein is the sum of masses of all its residues plus the mass of a single water molecule.&quot;<p>The table says &quot;the monoisotopic mass of water is considered to be 18.01056&quot; so<p><pre><code> &gt;&gt;&gt; 821.3919199999999 + 18.01056 839.40248 </code></pre> This latter number matches the value given by <a href="https:&#x2F;&#x2F;web.expasy.org&#x2F;cgi-bin&#x2F;compute_pi&#x2F;pi_tool" rel="nofollow">https:&#x2F;&#x2F;web.expasy.org&#x2F;cgi-bin&#x2F;compute_pi&#x2F;pi_tool</a> .<p>Which means the example answer ... is wrong. Yes?<p>How (in)correct are the other answers? I-am-not-a-bioinformatics-programmer.
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dangover 5 years ago
A thread from 2012: <a href="https:&#x2F;&#x2F;news.ycombinator.com&#x2F;item?id=4761831" rel="nofollow">https:&#x2F;&#x2F;news.ycombinator.com&#x2F;item?id=4761831</a><p>(Reposts are fine after a year: <a href="https:&#x2F;&#x2F;news.ycombinator.com&#x2F;newsfaq.html" rel="nofollow">https:&#x2F;&#x2F;news.ycombinator.com&#x2F;newsfaq.html</a>)
fao_over 5 years ago
First off, the login page doesn&#x27;t redirect to the HTTPS version of the page, so it&#x27;s sending my password over plaintext. What makes this worse is that when I manually go to the TLS page, it gives me a PF_END_OF_FILE_ERROR (I&#x27;m running firefox 72.0.2, on Alpine Linux).<p>The second thing is picking the first example (the character counting problem). Clicking on the thing, it told me that the important words are highlighted, and that the words &#x27;figure N&#x27; refer to the figures on the right -- which felt unnecessary, because it&#x27;s something that anyone visiting wikipedia, or browsing a book, would know.
danielecookover 5 years ago
It’s a great site and greatly accelerated my learning of programming.<p>The form of learning which I call “problem based” learning is a great format for me. You learn from reading up on a topic. You learn from trying different solutions. Finally, you learn from seeing other people’s answers once you’ve solved it.<p>Also check out:<p>Hackerrank.com - all around focus Project Euler- math focus Leetcode - more oriented towards interview training but still useful and fun.
acomjeanover 5 years ago
We used a version of this site for a bio informatics algorithm class a couple years ago (we used the site for part of the homework assignments, I guess the auto grading of code saves the instructors time...)<p>The problems are interesting and fun to solve, they didn’t have a lot of context, though They seemed to have added some at the start of each problem.
rjkennedy98over 5 years ago
Surprised to see this here as this has been around for quite some time. I used to do these problems on the weekends in 2013-14.
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