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<!DOCTYPE html>
<html>
<a title="Scientific Programming">
<body>
<h1>Scientific Programming</h1>
<h4> To Do List </h4>
<ul>
<li>Learn html</li>
<li>Learn JavaScript</li>
<li>Learn SQL</li>
<li>Learn CSS (for webpage layout)</li>
</ul>
<a href="https://validator.w3.org/#validate_by_input">html validator</a>
<h4> Literature Mandatory Reading </h4>
<ul>
<li><a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002802">Prlić A, Procter JB. Ten Simple Rules for the Open Development of Scientific
Software. PLoS Computational Biology. 2012 Dec 6;8(12):e1002802.</a></li>
<li><a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003285">Sandve GK, Nekrutenko A, Taylor J, Hovig E. Ten Simple Rules for Reproducible
Computational Research. Bourne PE, editor. PLoS Computational Biology. 2013
Oct 24;9(10):e1003285.</a></li>
<li>Wiegley, John. Git from the Bottom Up. 2018. https://jwiegley.github.io/git-fromthe-bottom-up/</li>
<li>(behind paywall) Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C.Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017
Apr;35(4):316–9.</li>
<li><a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004947">Perez-Riverol Y, Gatto L, Wang R, Sachsenberg T, Uszkoreit J, Leprevost F da V,
et al. Ten Simple Rules for Taking Advantage of Git and GitHub. Markel S, editor. PLOS Computational Biology. 2016 Jul 14;12(7):e1004947.
</a></li>
<li><a href="https://riojournal.com/articles.php?journal_name=rio&id=7573">Mietchen D, Hagedorn G, Willighagen E, Rico M, Gómez-Pérez A, Aibar E, et al. Enabling Open Science: Wikidata for Research (Wiki4R). Research Ideas and Outcomes. 2015 Dec 22;1:e7573.</a></li>
<li>List M, Ebert P, Albrecht F. Ten Simple Rules for Developing Usable Software in Computational Biology. Markel S, editor. PLOS Computational Biology. 2017 Jan 5;13(1):e1005265.</li>
<li><a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003542">Goodman A, Pepe A, Blocker AW, Borgman CL, Cranmer K, Crosas M, et al. Ten Simple Rules for the Care and Feeding of Scientific Data. Bourne PE, editor. PLoS Computational Biology. 2014 Apr 24;10(4):e1003542.</a></li>
</ul>
<h4> Recommended Courses and Tutorials and useful links</h4>
<a href="https://query.wikidata.org/">WikiData</a>
<a href="https://www.codecademy.com/learn/learn-html">Code Academy</a>
<a href ="https://www.codecademy.com/learn/introduction-to-javascript">Code Aca JS</a>
<a href="https://www.w3schools.com/sql/default.asp">w3schools</a>
<a href="https://www.datacamp.com/courses/intro-to-sql-for-data-science">DataCamp Intro to SQL</a>
<h1>html</h1>
<p>Collection of useful html things.</p>
<a href="https://ballsofwool.wordpress.com/">Blog link</a>
<button>Click me</button>
<h4> html pointers </h4>
<ul>
<li>Think of screen readers</li>
<li>Think of search engines</li>
<li>Always close tags</li>
<li>Use lower case for tags, attributes,</li>
<li>Always "" values</li>
</ul>
<img src="img_typo.jpg" alt="Girl with a jacket">
<p>If we try to display an image that does not exist, the value of the alt attribute will be displayed instead. </p>
<h4> Some specialised html vocabulary </h4>
<p>Tag (start/end), attribute, body, nested, element, <br/>"empty element", content, name-value pairs, source (filename), style, <br/>title provides tooltip; body/head (of an html page); invoke
</p>
<h1>JavaScript</h1>
<p>You will find JavaScript between script tags. JavaScript is now the default scripting language in html. Javascript can change attribute values; change styles of or hide/show html elements. Placing scripts at the bottom of the <body> element improves the display speed, because script interpretation slows down the display. </p>
<a href="https://www.w3schools.com/jsref/default.asp">JavaScript reference</a>
<h4> Some specialised JavaScript vocabulary </h4>
<p> method (a function), id, element content, event, <br/> external files, extension .js, <br/> file paths: full url vs. specified folder on the current website <br/>
</p>
<h4> Some JavaScript methods </h4>
<ol>
<li>getElementById</li>
</body>
</html>
<h1>SQL</h1>
<p>"field" means column , think of columns as describing a single attribute belonging to the things in the rows. <br/> "record" means row , think of rows as entities. <br/>
"keywords" means eg "SELECT" and "FROM" (not case sensitive) </p>
<h1>Results of mouse query </h1>
<iframe style="width: 80vw; height: 50vh; border: none;" src="https://query.wikidata.org/embed.html#%23Task%20%3A%20find%20the%20top%2010%20or%20so%20genes%20in%20Mus%20musculus%20taxon%0A%23%28chosen%20to%20replace%20E%20coli%20in%20original%20question%29%0A%23which%20code%20for%20the%20most%20proteins.%0A%23Chose%20top%2014%20genes%20which%20code%20for%20%3E%3D%205%20proteins%20each%2C%20beyond%20that%204%20proteins%20or%20fewer%0A%23with%20many%20genes%20coding%20for%204%20proteins%0ASELECT%20%3Fgene%20%28COUNT%28DISTINCT%20%3Fprotein%29%20AS%20%3Fcount%29%0AWHERE%20%7B%20%20%3Fprotein%20wdt%3AP702%20%3Fgene%20.%0A%20%20%20%20%20%20%20%20%3Fgene%20wdt%3AP31%20wd%3AQ7187%20%3B%0A%20%20%20%20%20%20%20%20%20%20%20%20%20%20wdt%3AP703%20wd%3AQ83310%20.%0ASERVICE%20wikibase%3Alabel%20%7B%20bd%3AserviceParam%20wikibase%3Alanguage%20%22%5BAUTO_LANGUAGE%5D%2Cen%22.%20%7D%0A%7D%20%0A%23Q83310%20is%20mus%20musculus%20taxon%20%22mouse%22%0AGROUP%20BY%20%3Fgene%0AORDER%20BY%20DESC%28%3Fcount%29%0ALIMIT%2014" referrerpolicy="origin" sandbox="allow-scripts allow-same-origin allow-popups" ></iframe>