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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/43008?offset=50</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/45316/from-genes-to-algorithms-the-ai-revolution-in-bioinformatics</guid>
	<pubDate>Wed, 16 Sep 2026 02:23:40 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/45316/from-genes-to-algorithms-the-ai-revolution-in-bioinformatics</link>
	<title><![CDATA[From Genes to Algorithms: The AI Revolution in Bioinformatics]]></title>
	<description><![CDATA[<p>Imagine waking up to a message from your doctor saying your genetic profile has been analyzed and a small change in your DNA has been found that could raise your risk for a certain disease. Instead of being alarmed, you learn that the condition was caught early and your genetic information can help doctors find treatments that might work better for you. Not long ago, this would have seemed like science fiction. But thanks to the rapid progress of artificial intelligence (AI) and bioinformatics, it is becoming more realistic. Bioinformatics brings together biology, computer science, mathematics, and statistics to collect, manage, and analyze biological data. As new technologies produce huge amounts of genomic, transcriptomic, proteomic, and clinical data, traditional methods often cannot keep up. AI is now playing a bigger role in bioinformatics, helping researchers find patterns, make predictions, and understand biological systems in ways that were once out of reach.</p><p>Modern sequencing technologies have turned biology into a data-heavy science. The human genome has about three billion DNA base pairs, and sequencing can produce massive datasets quickly. Bioinformatics helps organize and interpret this information, allowing scientists to compare genomes, find genes, spot genetic differences, study gene expression, and understand diseases at the molecular level. Now, AI is changing how these datasets are analyzed. Machine learning and deep learning can find complex patterns in biological data and make predictions using large datasets. Rather than following only set rules, AI systems can learn from data and help researchers solve tough biological problems.</p><p>A key example of AI in bioinformatics is predicting protein structures. Proteins are vital for many functions in living things, and their three-dimensional shapes are closely tied to what they do. For a long time, figuring out these structures in the lab was slow and difficult. AI-based tools like AlphaFold have shown that deep learning can predict protein structures with impressive accuracy. These advances help speed up biological research and give scientists useful predictions to support their experiments. This shift means bioinformatics is moving from just analyzing biological data to predicting how biology works and designing new solutions.</p><p>AI is also expected to greatly influence drug discovery. Traditionally, developing a new drug is a long and costly process that involves finding biological targets, searching for possible drug molecules, testing how well they work, studying their properties, and running many experiments. AI can help researchers analyze large chemical and biological datasets, predict how molecules might interact with targets, find promising compounds, and estimate properties of drug candidates. Generative AI can even help design new molecules to test in the lab. This does not mean lab experiments will go away, but AI can help researchers focus on the best options and possibly speed up some parts of drug development.</p><p>Personalized medicine is another area where AI-driven bioinformatics could make a big difference. Each person has a unique mix of genetic, molecular, environmental, and lifestyle factors, so people with the same disease might respond differently to the same treatment. Bioinformatics lets researchers study individual biological data, and AI can combine many types of information, like genetic data, gene expression, protein levels, medical images, clinical records, and drug responses. In the future, this could help doctors look beyond just the disease and focus on the specific biology of each patient. This would support more personalized ways to diagnose, assess risk, and choose treatments.</p><p>As AI becomes more common, the job of bioinformaticians will likely change. Instead of spending most of their time on repetitive computer tasks, they may focus more on creating research questions, understanding AI results, checking predictions, and linking computer findings to lab experiments. Future professionals will need to know about molecular biology, genetics, statistics, programming, machine learning, data science, databases, and computational biology. But technical skills alone will not be enough. Being able to ask good scientific questions and carefully judge computer results will be even more important, since AI can make predictions, but scientists must decide if those predictions make sense and can be proven in the lab.</p><p>Even with its great potential, using AI in bioinformatics comes with big challenges. AI systems rely on the quality and variety of the data they are trained on. Biological and clinical datasets can have missing information, technical errors, inconsistent measurements, and may not represent all groups equally. A model that works well on one dataset might not work as well on another group or in a different setting. That is why data quality, proper validation, transparency, reproducibility, and careful model development are crucial for the future of AI in bioinformatics. Researchers also need to think about genetic privacy, data ownership, security, and using personal biological information responsibly. These concerns are especially important when AI predictions are used in healthcare.</p><p>The lab of the future may look very different from today&rsquo;s. Researchers might use AI to review scientific papers, find research questions, analyze large datasets, come up with ideas, and predict which experiments will be most helpful. Automated lab systems could then run these experiments, create new data, and send the results back to computer models. This would create a cycle of making guesses, predicting, experimenting, collecting data, and learning. This approach could speed up scientific discovery by helping researchers explore questions more efficiently. Bioinformatics could become a key link between computer predictions and real lab experiments.</p><p>In the end, the future of bioinformatics with AI will not be about replacing people with machines. It will be about humans and AI working together. Computers can handle huge amounts of biological data and spot patterns that a single person could not. But humans bring scientific understanding, creativity, critical thinking, ethical judgment, and the ability to see the bigger picture. AI might find a pattern in millions of genomes, but scientists need to figure out why it matters. An AI model could suggest a new drug, but researchers must check if it is safe and works well. A computer might find a genetic change, but doctors have to decide what it means for a real patient.</p><p>The future of bioinformatics is closely tied to the future of AI. As biological data grows and AI models get better, bioinformatics may shift from mainly analyzing data to predicting biological processes, designing new molecules, speeding up experiments, and supporting personalized healthcare. For students and researchers, this is an exciting chance to work where biology and technology meet. The most successful people will not just be those who use the latest AI tools, but those who understand biology well enough to ask good questions and judge the answers carefully. The future will not be about AI versus humans, but about people and AI working together to understand life in ways we never could before. The next big discovery may come from this partnership between a biological question, a computer model, a lab experiment, and human curiosity.</p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/21703/coding-ground</guid>
	<pubDate>Tue, 17 Mar 2015 00:47:20 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/21703/coding-ground</link>
	<title><![CDATA[Coding Ground]]></title>
	<description><![CDATA[<p>Online coding group for most of the programming languages.</p>
<p>Code in almost all popular languages using Coding Ground.&nbsp;Edit, compile, execute and share your projects, 100% cloud.</p>
<p>http://www.tutorialspoint.com/codingground.htm</p><p>Address of the bookmark: <a href="http://www.tutorialspoint.com/codingground.htm" rel="nofollow">http://www.tutorialspoint.com/codingground.htm</a></p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/33398/tiny-python36-notebook</guid>
	<pubDate>Sat, 03 Jun 2017 03:16:28 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/33398/tiny-python36-notebook</link>
	<title><![CDATA[Tiny Python3.6 Notebook]]></title>
	<description><![CDATA[<p><span>This is not so much an instructional manual, but rather notes, tables, and examples for Python syntax. It was created by the author as an additional resource during training, meant to be distributed as a physical notebook. Participants (who favor the physical characteristics of dead tree material) could add their own notes, thoughts, and have a valuable reference of curated examples.</span></p><p>Address of the bookmark: <a href="https://github.com/mattharrison/Tiny-Python-3.6-Notebook/blob/master/python.rst" rel="nofollow">https://github.com/mattharrison/Tiny-Python-3.6-Notebook/blob/master/python.rst</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/39307/awk-for-beginners</guid>
	<pubDate>Fri, 26 Apr 2019 16:19:41 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/39307/awk-for-beginners</link>
	<title><![CDATA[AWK for beginners !]]></title>
	<description><![CDATA[<p>AWK is a standard tool on every POSIX-compliant UNIX system. It&rsquo;s like flex/lex, from the command-line, perfect for text-processing tasks and other scripting needs. It has a C-like syntax, but without mandatory semicolons (although, you should use them anyway, because they are required when you&rsquo;re writing one-liners, something AWK excels at), manual memory management, or static typing. It excels at text processing. You can call to it from a shell script, or you can use it as a stand-alone scripting language.</p><p>Why use AWK instead of Perl? Readability. AWK is easier to read than Perl. For simple text-processing scripts, particularly ones that read files line by line and split on delimiters, AWK is probably the right tool for the job.</p><div><pre><span>#!/usr/bin/awk -f</span>

<span># Comments are like this</span>


<span># AWK programs consist of a collection of patterns and actions.</span>
<span>pattern1</span> <span>{</span> <span>action</span><span>;</span> <span>}</span> <span># just like lex</span>
<span>pattern2</span> <span>{</span> <span>action</span><span>;</span> <span>}</span>

<span># There is an implied loop and AWK automatically reads and parses each</span>
<span># record of each file supplied. Each record is split by the FS delimiter,</span>
<span># which defaults to white-space (multiple spaces,tabs count as one)</span>
<span># You can assign FS either on the command line (-F C) or in your BEGIN</span>
<span># pattern</span>

<span># One of the special patterns is BEGIN. The BEGIN pattern is true</span>
<span># BEFORE any of the files are read. The END pattern is true after</span>
<span># an End-of-file from the last file (or standard-in if no files specified)</span>
<span># There is also an output field separator (OFS) that you can assign, which</span>
<span># defaults to a single space</span>

<span>BEGIN</span> <span>{</span>

    <span># BEGIN will run at the beginning of the program. It's where you put all</span>
    <span># the preliminary set-up code, before you process any text files. If you</span>
    <span># have no text files, then think of BEGIN as the main entry point.</span>

    <span># Variables are global. Just set them or use them, no need to declare..</span>
    <span>count</span> <span>=</span> <span>0</span><span>;</span>

    <span># Operators just like in C and friends</span>
    <span>a</span> <span>=</span> <span>count</span> <span>+</span> <span>1</span><span>;</span>
    <span>b</span> <span>=</span> <span>count</span> <span>-</span> <span>1</span><span>;</span>
    <span>c</span> <span>=</span> <span>count</span> <span>*</span> <span>1</span><span>;</span>
    <span>d</span> <span>=</span> <span>count</span> <span>/</span> <span>1</span><span>;</span> <span># integer division</span>
    <span>e</span> <span>=</span> <span>count</span> <span>%</span> <span>1</span><span>;</span> <span># modulus</span>
    <span>f</span> <span>=</span> <span>count</span> <span>^</span> <span>1</span><span>;</span> <span># exponentiation</span>

    <span>a</span> <span>+=</span> <span>1</span><span>;</span>
    <span>b</span> <span>-=</span> <span>1</span><span>;</span>
    <span>c</span> <span>*=</span> <span>1</span><span>;</span>
    <span>d</span> <span>/=</span> <span>1</span><span>;</span>
    <span>e</span> <span>%=</span> <span>1</span><span>;</span>
    <span>f</span> <span>^=</span> <span>1</span><span>;</span>

    <span># Incrementing and decrementing by one</span>
    <span>a</span><span>++</span><span>;</span>
    <span>b</span><span>--</span><span>;</span>

    <span># As a prefix operator, it returns the incremented value</span>
    <span>++</span><span>a</span><span>;</span>
    <span>--</span><span>b</span><span>;</span>

    <span># Notice, also, no punctuation such as semicolons to terminate statements</span>

    <span># Control statements</span>
    <span>if</span> <span>(</span><span>count</span> <span>==</span> <span>0</span><span>)</span>
        <span>print</span> <span>"Starting with count of 0"</span><span>;</span>
    <span>else</span>
        <span>print</span> <span>"Huh?"</span><span>;</span>

    <span># Or you could use the ternary operator</span>
    <span>print</span> <span>(</span><span>count</span> <span>==</span> <span>0</span><span>)</span> <span>?</span> <span>"Starting with count of 0"</span> <span>:</span> <span>"Huh?"</span><span>;</span>

    <span># Blocks consisting of multiple lines use braces</span>
    <span>while</span> <span>(</span><span>a</span> <span>&lt;</span> <span>10</span><span>)</span> <span>{</span>
        <span>print</span> <span>"String concatenation is done"</span> <span>" with a series"</span> <span>" of"</span>
            <span>" space-separated strings"</span><span>;</span>
        <span>print</span> <span>a</span><span>;</span>

        <span>a</span><span>++</span><span>;</span>
    <span>}</span>

    <span>for</span> <span>(</span><span>i</span> <span>=</span> <span>0</span><span>;</span> <span>i</span> <span>&lt;</span> <span>10</span><span>;</span> <span>i</span><span>++</span><span>)</span>
        <span>print</span> <span>"Good ol' for loop"</span><span>;</span>

    <span># As for comparisons, they're the standards:</span>
    <span># a &lt; b   # Less than</span>
    <span># a &lt;= b  # Less than or equal</span>
    <span># a != b  # Not equal</span>
    <span># a == b  # Equal</span>
    <span># a &gt; b   # Greater than</span>
    <span># a &gt;= b  # Greater than or equal</span>

    <span># Logical operators as well</span>
    <span># a &amp;&amp; b  # AND</span>
    <span># a || b  # OR</span>

    <span># In addition, there's the super useful regular expression match</span>
    <span>if</span> <span>(</span><span>"foo"</span> <span>~</span> <span>"^fo+$"</span><span>)</span>
        <span>print</span> <span>"Fooey!"</span><span>;</span>
    <span>if</span> <span>(</span><span>"boo"</span> <span>!~</span> <span>"^fo+$"</span><span>)</span>
        <span>print</span> <span>"Boo!"</span><span>;</span>

    <span># Arrays</span>
    <span>arr</span><span>[</span><span>0</span><span>]</span> <span>=</span> <span>"foo"</span><span>;</span>
    <span>arr</span><span>[</span><span>1</span><span>]</span> <span>=</span> <span>"bar"</span><span>;</span>

    <span># You can also initialize an array with the built-in function split()</span>

    <span>n</span> <span>=</span> <span>split</span><span>(</span><span>"foo:bar:baz"</span><span>,</span> <span>arr</span><span>,</span> <span>":"</span><span>);</span>

    <span># You also have associative arrays (actually, they're all associative arrays)</span>
    <span>assoc</span><span>[</span><span>"foo"</span><span>]</span> <span>=</span> <span>"bar"</span><span>;</span>
    <span>assoc</span><span>[</span><span>"bar"</span><span>]</span> <span>=</span> <span>"baz"</span><span>;</span>

    <span># And multi-dimensional arrays, with some limitations I won't mention here</span>
    <span>multidim</span><span>[</span><span>0</span><span>,</span><span>0</span><span>]</span> <span>=</span> <span>"foo"</span><span>;</span>
    <span>multidim</span><span>[</span><span>0</span><span>,</span><span>1</span><span>]</span> <span>=</span> <span>"bar"</span><span>;</span>
    <span>multidim</span><span>[</span><span>1</span><span>,</span><span>0</span><span>]</span> <span>=</span> <span>"baz"</span><span>;</span>
    <span>multidim</span><span>[</span><span>1</span><span>,</span><span>1</span><span>]</span> <span>=</span> <span>"boo"</span><span>;</span>

    <span># You can test for array membership</span>
    <span>if</span> <span>(</span><span>"foo"</span> <span>in</span> <span>assoc</span><span>)</span>
        <span>print</span> <span>"Fooey!"</span><span>;</span>

    <span># You can also use the 'in' operator to traverse the keys of an array</span>
    <span>for</span> <span>(</span><span>key</span> <span>in</span> <span>assoc</span><span>)</span>
        <span>print</span> <span>assoc</span><span>[</span><span>key</span><span>];</span>

    <span># The command line is in a special array called ARGV</span>
    <span>for</span> <span>(</span><span>argnum</span> <span>in</span> <span>ARGV</span><span>)</span>
        <span>print</span> <span>ARGV</span><span>[</span><span>argnum</span><span>];</span>

    <span># You can remove elements of an array</span>
    <span># This is particularly useful to prevent AWK from assuming the arguments</span>
    <span># are files for it to process</span>
    <span>delete</span> <span>ARGV</span><span>[</span><span>1</span><span>];</span>

    <span># The number of command line arguments is in a variable called ARGC</span>
    <span>print</span> <span>ARGC</span><span>;</span>

    <span># AWK has several built-in functions. They fall into three categories. I'll</span>
    <span># demonstrate each of them in their own functions, defined later.</span>

    <span>return_value</span> <span>=</span> <span>arithmetic_functions</span><span>(</span><span>a</span><span>,</span> <span>b</span><span>,</span> <span>c</span><span>);</span>
    <span>string_functions</span><span>();</span>
    <span>io_functions</span><span>();</span>
<span>}</span>

<span># Here's how you define a function</span>
<span>function</span> <span>arithmetic_functions</span><span>(</span><span>a</span><span>,</span> <span>b</span><span>,</span> <span>c</span><span>,</span>     <span>d</span><span>)</span> <span>{</span>

    <span># Probably the most annoying part of AWK is that there are no local</span>
    <span># variables. Everything is global. For short scripts, this is fine, even</span>
    <span># useful, but for longer scripts, this can be a problem.</span>

    <span># There is a work-around (ahem, hack). Function arguments are local to the</span>
    <span># function, and AWK allows you to define more function arguments than it</span>
    <span># needs. So just stick local variable in the function declaration, like I</span>
    <span># did above. As a convention, stick in some extra whitespace to distinguish</span>
    <span># between actual function parameters and local variables. In this example,</span>
    <span># a, b, and c are actual parameters, while d is merely a local variable.</span>

    <span># Now, to demonstrate the arithmetic functions</span>

    <span># Most AWK implementations have some standard trig functions</span>
    <span>localvar</span> <span>=</span> <span>sin</span><span>(</span><span>a</span><span>);</span>
    <span>localvar</span> <span>=</span> <span>cos</span><span>(</span><span>a</span><span>);</span>
    <span>localvar</span> <span>=</span> <span>atan2</span><span>(</span><span>b</span><span>,</span> <span>a</span><span>);</span> <span># arc tangent of b / a</span>

    <span># And logarithmic stuff</span>
    <span>localvar</span> <span>=</span> <span>exp</span><span>(</span><span>a</span><span>);</span>
    <span>localvar</span> <span>=</span> <span>log</span><span>(</span><span>a</span><span>);</span>

    <span># Square root</span>
    <span>localvar</span> <span>=</span> <span>sqrt</span><span>(</span><span>a</span><span>);</span>

    <span># Truncate floating point to integer</span>
    <span>localvar</span> <span>=</span> <span>int</span><span>(</span><span>5.34</span><span>);</span> <span># localvar =&gt; 5</span>

    <span># Random numbers</span>
    <span>srand</span><span>();</span> <span># Supply a seed as an argument. By default, it uses the time of day</span>
    <span>localvar</span> <span>=</span> <span>rand</span><span>();</span> <span># Random number between 0 and 1.</span>

    <span># Here's how to return a value</span>
    <span>return</span> <span>localvar</span><span>;</span>
<span>}</span>

<span>function</span> <span>string_functions</span><span>(</span>    <span>localvar</span><span>,</span> <span>arr</span><span>)</span> <span>{</span>

    <span># AWK, being a string-processing language, has several string-related</span>
    <span># functions, many of which rely heavily on regular expressions.</span>

    <span># Search and replace, first instance (sub) or all instances (gsub)</span>
    <span># Both return number of matches replaced</span>
    <span>localvar</span> <span>=</span> <span>"fooooobar"</span><span>;</span>
    <span>sub</span><span>(</span><span>"fo+"</span><span>,</span> <span>"Meet me at the "</span><span>,</span> <span>localvar</span><span>);</span> <span># localvar =&gt; "Meet me at the bar"</span>
    <span>gsub</span><span>(</span><span>"e+"</span><span>,</span> <span>"."</span><span>,</span> <span>localvar</span><span>);</span> <span># localvar =&gt; "m..t m. at th. bar"</span>

    <span># Search for a string that matches a regular expression</span>
    <span># index() does the same thing, but doesn't allow a regular expression</span>
    <span>match</span><span>(</span><span>localvar</span><span>,</span> <span>"t"</span><span>);</span> <span># =&gt; 4, since the 't' is the fourth character</span>

    <span># Split on a delimiter</span>
    <span>n</span> <span>=</span> <span>split</span><span>(</span><span>"foo-bar-baz"</span><span>,</span> <span>arr</span><span>,</span> <span>"-"</span><span>);</span> <span># a[1] = "foo"; a[2] = "bar"; a[3] = "baz"; n = 3</span>

    <span># Other useful stuff</span>
    <span>sprintf</span><span>(</span><span>"%s %d %d %d"</span><span>,</span> <span>"Testing"</span><span>,</span> <span>1</span><span>,</span> <span>2</span><span>,</span> <span>3</span><span>);</span> <span># =&gt; "Testing 1 2 3"</span>
    <span>substr</span><span>(</span><span>"foobar"</span><span>,</span> <span>2</span><span>,</span> <span>3</span><span>);</span> <span># =&gt; "oob"</span>
    <span>substr</span><span>(</span><span>"foobar"</span><span>,</span> <span>4</span><span>);</span> <span># =&gt; "bar"</span>
    <span>length</span><span>(</span><span>"foo"</span><span>);</span> <span># =&gt; 3</span>
    <span>tolower</span><span>(</span><span>"FOO"</span><span>);</span> <span># =&gt; "foo"</span>
    <span>toupper</span><span>(</span><span>"foo"</span><span>);</span> <span># =&gt; "FOO"</span>
<span>}</span>

<span>function</span> <span>io_functions</span><span>(</span>    <span>localvar</span><span>)</span> <span>{</span>

    <span># You've already seen print</span>
    <span>print</span> <span>"Hello world"</span><span>;</span>

    <span># There's also printf</span>
    <span>printf</span><span>(</span><span>"%s %d %d %d\n"</span><span>,</span> <span>"Testing"</span><span>,</span> <span>1</span><span>,</span> <span>2</span><span>,</span> <span>3</span><span>);</span>

    <span># AWK doesn't have file handles, per se. It will automatically open a file</span>
    <span># handle for you when you use something that needs one. The string you used</span>
    <span># for this can be treated as a file handle, for purposes of I/O. This makes</span>
    <span># it feel sort of like shell scripting, but to get the same output, the string</span>
    <span># must match exactly, so use a variable:</span>

    <span>outfile</span> <span>=</span> <span>"/tmp/foobar.txt"</span><span>;</span>

    <span>print</span> <span>"foobar"</span> <span>&gt;</span> <span>outfile</span><span>;</span>

    <span># Now the string outfile is a file handle. You can close it:</span>
    <span>close</span><span>(</span><span>outfile</span><span>);</span>

    <span># Here's how you run something in the shell</span>
    <span>system</span><span>(</span><span>"echo foobar"</span><span>);</span> <span># =&gt; prints foobar</span>

    <span># Reads a line from standard input and stores in localvar</span>
    <span>getline</span> <span>localvar</span><span>;</span>

    <span># Reads a line from a pipe (again, use a string so you close it properly)</span>
    <span>cmd</span> <span>=</span> <span>"echo foobar"</span><span>;</span>
    <span>cmd</span> <span>|</span> <span>getline</span> <span>localvar</span><span>;</span> <span># localvar =&gt; "foobar"</span>
    <span>close</span><span>(</span><span>cmd</span><span>);</span>

    <span># Reads a line from a file and stores in localvar</span>
    <span>infile</span> <span>=</span> <span>"/tmp/foobar.txt"</span><span>;</span>
    <span>getline</span> <span>localvar</span> <span>&lt;</span> <span>infile</span><span>;</span> 
    <span>close</span><span>(</span><span>infile</span><span>);</span>
<span>}</span>

<span># As I said at the beginning, AWK programs consist of a collection of patterns</span>
<span># and actions. You've already seen the BEGIN pattern. Other</span>
<span># patterns are used only if you're processing lines from files or standard</span>
<span># input.</span>
<span>#</span>
<span># When you pass arguments to AWK, they are treated as file names to process.</span>
<span># It will process them all, in order. Think of it like an implicit for loop,</span>
<span># iterating over the lines in these files. these patterns and actions are like</span>
<span># switch statements inside the loop. </span>

<span>/^fo+bar$/</span> <span>{</span>

    <span># This action will execute for every line that matches the regular</span>
    <span># expression, /^fo+bar$/, and will be skipped for any line that fails to</span>
    <span># match it. Let's just print the line:</span>

    <span>print</span><span>;</span>

    <span># Whoa, no argument! That's because print has a default argument: $0.</span>
    <span># $0 is the name of the current line being processed. It is created</span>
    <span># automatically for you.</span>

    <span># You can probably guess there are other $ variables. Every line is</span>
    <span># implicitly split before every action is called, much like the shell</span>
    <span># does. And, like the shell, each field can be access with a dollar sign</span>

    <span># This will print the second and fourth fields in the line</span>
    <span>print</span> <span>$</span><span>2</span><span>,</span> <span>$</span><span>4</span><span>;</span>

    <span># AWK automatically defines many other variables to help you inspect and</span>
    <span># process each line. The most important one is NF</span>

    <span># Prints the number of fields on this line</span>
    <span>print</span> <span>NF</span><span>;</span>

    <span># Print the last field on this line</span>
    <span>print</span> <span>$</span><span>NF</span><span>;</span>
<span>}</span>

<span># Every pattern is actually a true/false test. The regular expression in the</span>
<span># last pattern is also a true/false test, but part of it was hidden. If you</span>
<span># don't give it a string to test, it will assume $0, the line that it's</span>
<span># currently processing. Thus, the complete version of it is this:</span>

<span>$</span><span>0</span> <span>~</span> <span>/^fo+bar$/</span> <span>{</span>
    <span>print</span> <span>"Equivalent to the last pattern"</span><span>;</span>
<span>}</span>

<span>a</span> <span>&gt;</span> <span>0</span> <span>{</span>
    <span># This will execute once for each line, as long as a is positive</span>
<span>}</span>

<span># You get the idea. Processing text files, reading in a line at a time, and</span>
<span># doing something with it, particularly splitting on a delimiter, is so common</span>
<span># in UNIX that AWK is a scripting language that does all of it for you, without</span>
<span># you needing to ask. All you have to do is write the patterns and actions</span>
<span># based on what you expect of the input, and what you want to do with it.</span>

<span># Here's a quick example of a simple script, the sort of thing AWK is perfect</span>
<span># for. It will read a name from standard input and then will print the average</span>
<span># age of everyone with that first name. Let's say you supply as an argument the</span>
<span># name of a this data file:</span>
<span>#</span>
<span># Bob Jones 32</span>
<span># Jane Doe 22</span>
<span># Steve Stevens 83</span>
<span># Bob Smith 29</span>
<span># Bob Barker 72</span>
<span>#</span>
<span># Here's the script:</span>

<span>BEGIN</span> <span>{</span>

    <span># First, ask the user for the name</span>
    <span>print</span> <span>"What name would you like the average age for?"</span><span>;</span>

    <span># Get a line from standard input, not from files on the command line</span>
    <span>getline</span> <span>name</span> <span>&lt;</span> <span>"/dev/stdin"</span><span>;</span>
<span>}</span>

<span># Now, match every line whose first field is the given name</span>
<span>$</span><span>1</span> <span>==</span> <span>name</span> <span>{</span>

    <span># Inside here, we have access to a number of useful variables, already</span>
    <span># pre-loaded for us:</span>
    <span># $0 is the entire line</span>
    <span># $3 is the third field, the age, which is what we're interested in here</span>
    <span># NF is the number of fields, which should be 3</span>
    <span># NR is the number of records (lines) seen so far</span>
    <span># FILENAME is the name of the file being processed</span>
    <span># FS is the field separator being used, which is " " here</span>
    <span># ...etc. There are plenty more, documented in the man page.</span>

    <span># Keep track of a running total and how many lines matched</span>
    <span>sum</span> <span>+=</span> <span>$</span><span>3</span><span>;</span>
    <span>nlines</span><span>++</span><span>;</span>
<span>}</span>

<span># Another special pattern is called END. It will run after processing all the</span>
<span># text files. Unlike BEGIN, it will only run if you've given it input to</span>
<span># process. It will run after all the files have been read and processed</span>
<span># according to the rules and actions you've provided. The purpose of it is</span>
<span># usually to output some kind of final report, or do something with the</span>
<span># aggregate of the data you've accumulated over the course of the script.</span>

<span>END</span> <span>{</span>
    <span>if</span> <span>(</span><span>nlines</span><span>)</span>
        <span>print</span> <span>"The average age for "</span> <span>name</span> <span>" is "</span> <span>sum</span> <span>/</span> <span>nlines</span><span>;</span>
<span>}</span>
</pre><p><span>&nbsp;</span></p></div>]]></description>
	<dc:creator>BioJoker</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/42813/bioinformatics-in-africa-part5-nigeria</guid>
	<pubDate>Sat, 06 Feb 2021 21:13:47 -0600</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/42813/bioinformatics-in-africa-part5-nigeria</link>
	<title><![CDATA[Bioinformatics in Africa: Part5 - Nigeria]]></title>
	<description><![CDATA[<p>Covenant University (CU)&shy;Ota:<br />Covenant University (with her enriching and growing state&shy;of&shy;the&shy;art laboratories in the area of &nbsp;science and technology, arts, business and social sciences) is presently the Best University in &nbsp;Nigeria (Private University category), based on the recent over&shy;all rating just concluded by the &nbsp;Nigeria &nbsp; University &nbsp; Commission &nbsp; (NUC). &nbsp; Recently, &nbsp; Covenant &nbsp; University &nbsp; has &nbsp; initiated &nbsp; the &nbsp;establishment of a Centre for Applied Biotech, Bio&shy;Informatics and Microbiology (CBBM) to be &nbsp;situated at the University. The institute has been designed to be a Public&shy;Private Partnership for a productive synergy b/w Academia, Industry and Government. The whole concept is still evolving &nbsp;and more details will be release soon. As regards CBBM, a dedicated computing lab is in plan, but even our computing capacity is &nbsp;presently enormous. In the department of Computer and Information Sciences, we have more than &nbsp;250 Pentium 4 PCs set aside for teaching and research purposes. Furthermore, we have several &nbsp;moderate speed PCs at the Postgraduate research lab and our engineering departments and units. &nbsp;Our wet lab facilities is presently minimal (basic for teaching), the Centre requirement as it touches &nbsp;the wet&shy;laboratories is also set to upgrade this to basic tools expected at an international centre of learning.</p><p>University&nbsp;of&nbsp;Ibadan&nbsp;(UIB)&shy;Ibadan:<br />There&nbsp;has&nbsp;been&nbsp;significant&nbsp;increase&nbsp;in&nbsp;the&nbsp;number&nbsp;of&nbsp;bioinformatics&nbsp;activities&nbsp;in&nbsp;Nigeria&nbsp;(and&nbsp;West Africa)&nbsp;since&nbsp;2003&nbsp;when&nbsp;the&nbsp;program&nbsp;was&nbsp;initiated&nbsp;by&nbsp;the&nbsp;West&nbsp;African&nbsp;Biotechnology&nbsp;Workshops Series&nbsp;(WABWS,&nbsp;http://www.wabw.org)&nbsp;at&nbsp;the&nbsp;University&nbsp;of&nbsp;Ibadan,&nbsp;Nigeria&nbsp;(in&nbsp;collaboration&nbsp;with&nbsp; the&nbsp;South&nbsp;African&nbsp;National&nbsp;Bioinformatics&nbsp;Institute&nbsp;(SANBI,&nbsp;http:/www.sanbi.ac.za).&nbsp;Workshops&nbsp; that&nbsp;were&nbsp;open&nbsp;to&nbsp;scientists&nbsp;from&nbsp;all&nbsp;African&nbsp;countries&nbsp;have&nbsp;seen&nbsp;a&nbsp;very&nbsp;high&nbsp;number&nbsp;of&nbsp;applications&nbsp; from&nbsp;scientists&nbsp;based&nbsp;in&nbsp;West&nbsp;Africa.&nbsp;The&nbsp;encouraging&nbsp;desire&nbsp;to&nbsp;acquire&nbsp;cutting&shy;edge&nbsp;skills&nbsp;to&nbsp; computational&nbsp;process&nbsp;data&nbsp;and&nbsp;extract&nbsp;useful&nbsp;knowledge&nbsp;from&nbsp;genome&nbsp;projects&nbsp;led&nbsp;to&nbsp;the&nbsp;interest&nbsp;of&nbsp; the&nbsp;West&nbsp;African&nbsp;Biotechnology&nbsp;Workshops&nbsp;(WABW)&nbsp;to&nbsp;develop&nbsp;an&nbsp;agenda&nbsp;to&nbsp;address&nbsp;the&nbsp; bioinformatics&nbsp;skills&nbsp;gap&nbsp;among&nbsp;scientists&nbsp;in&nbsp;West&nbsp;Africa.&nbsp;An&nbsp;increased&nbsp;commitment&nbsp;from&nbsp;agencies&nbsp; like&nbsp;NEPAD&nbsp;would&nbsp;be&nbsp;required&nbsp;in&nbsp;the&nbsp;provision&nbsp;of&nbsp;infrastructure&nbsp;to&nbsp;establish&nbsp;and&nbsp;sustain&nbsp;regional&nbsp; and&nbsp;national&nbsp;networks.</p><p>University&nbsp;of&nbsp;Ilorin&nbsp;(UIL)&shy;Ilorin:<br />The&nbsp;University&nbsp;of&nbsp;Ilorin&nbsp;was&nbsp;established&nbsp;in&nbsp;1976&nbsp;by&nbsp;the&nbsp;Federal&nbsp;Government&nbsp;of&nbsp;Nigeria.&nbsp; Bioinformatics&nbsp;activities&nbsp;started&nbsp;at&nbsp;the&nbsp;University&nbsp;in&nbsp;February&nbsp;2003&nbsp;with&nbsp;the&nbsp;establishment&nbsp;of&nbsp;the&nbsp; West&nbsp;African&nbsp;Bioinformatics&nbsp;Research&nbsp;Initiative&nbsp;(WABRI).&nbsp;However,&nbsp;progress&nbsp;has&nbsp;been&nbsp;rather&nbsp;slow&nbsp; due&nbsp;to&nbsp;inadequate&nbsp;funding.&nbsp;We&nbsp;are&nbsp;mainly&nbsp;engaged&nbsp;in&nbsp;Bioinformatics&nbsp;training&nbsp;at&nbsp;the&nbsp;introductory&nbsp; level&nbsp;and&nbsp;proteomics&nbsp;studies&nbsp;on&nbsp;various&nbsp;species&nbsp;of&nbsp;malaria&nbsp;parasites.&nbsp;Recently,&nbsp;we&nbsp;became&nbsp;interested&nbsp; in&nbsp;comparative&nbsp;genome&nbsp;analysis&nbsp;of&nbsp;various&nbsp;species&nbsp;of &nbsp;Plasmodium&nbsp; and&nbsp;the&nbsp;comparison&nbsp;of&nbsp; chloroquine&nbsp;sensitive&nbsp;and&nbsp;chloroquine&nbsp;resistant&nbsp;strains&nbsp;of&nbsp;Plasmodium&nbsp;falciparum.&nbsp;Other&nbsp;activities&nbsp; and&nbsp;areas&nbsp;of&nbsp;interest&nbsp;can&nbsp;be&nbsp;seen&nbsp;on&nbsp;our&nbsp;website,&nbsp;http://www.wabri.org,&nbsp;although&nbsp;not&nbsp;all&nbsp;our&nbsp; proposed&nbsp;interests&nbsp;have&nbsp;been&nbsp;fully&nbsp;implemented&nbsp;due&nbsp;to&nbsp;our&nbsp;level&nbsp;of&nbsp;funding.</p><p>Training:<br />The&nbsp;University&nbsp;of&nbsp;Ilorin&nbsp;has&nbsp;introduced&nbsp;M.Sc.&nbsp;and&nbsp;Ph.D.&nbsp;programmes&nbsp;in&nbsp;Computer&nbsp;Science&nbsp;(with&nbsp; options&nbsp;in&nbsp;Bioinformatics).&nbsp;The&nbsp;programme&nbsp;is&nbsp;based&nbsp;in&nbsp;the&nbsp;Department&nbsp;of&nbsp;Computer&nbsp;Science&nbsp;and&nbsp; emphasis&nbsp;is&nbsp;on&nbsp;the&nbsp;development&nbsp;of&nbsp;algorithms&nbsp;to&nbsp;solve&nbsp;problems&nbsp;in&nbsp;bioinformatics. The&nbsp;Covenant&nbsp;University&nbsp;offers&nbsp;M.Sc.&nbsp;and&nbsp;Ph.D&nbsp;in&nbsp;Computer&nbsp;Science&nbsp;with&nbsp;option&nbsp;in&nbsp;Bioinformatics&nbsp; (Computational&nbsp;Biology).&nbsp;Furthermore,&nbsp;through&nbsp;affiliated&nbsp;departments,&nbsp;the&nbsp;CBBM&nbsp;is&nbsp;been&nbsp;design&nbsp;to&nbsp;award&nbsp;Diploma&nbsp;and&nbsp;Degree&nbsp;certificates&nbsp;in&nbsp;Biotechnology.</p><p>Web&nbsp;sites&nbsp;and&nbsp;links: http://www.covenantuniversity.com http://www.run.edu.ng http://www.uniben.edu http://www.wabri.org http://www.wabw.org http://www.unilorin.edu.ng http://www.wabri.org http://www.asopah.org</p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43431/code-golf</guid>
	<pubDate>Wed, 06 Oct 2021 04:17:29 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43431/code-golf</link>
	<title><![CDATA[Code Golf]]></title>
	<description><![CDATA[<p>Code Golf is a game designed to let you show off your code-fu by solving problems in the least number of characters.</p>
<p>Since this is your first time here, I suggest starting with something simple like&nbsp;<a href="https://code.golf/fizz-buzz">Fizz Buzz</a>.</p><p>Address of the bookmark: <a href="https://code.golf/" rel="nofollow">https://code.golf/</a></p>]]></description>
	<dc:creator>Abhi</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44633/learn-python-with-example</guid>
	<pubDate>Tue, 06 Aug 2024 23:51:51 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44633/learn-python-with-example</link>
	<title><![CDATA[Learn python with example]]></title>
	<description><![CDATA[<div><div><div><p>There are over 21 unique&nbsp;Python project&nbsp;walkthroughs in this content that range from beginner to advanced. See below for the timestamps for these projects:</p><p><span>00:00:00 | How To Navigate These Projects</span><br /><span>---</span><br /><span>00:01:46 | #1 - Quiz Game (Easy)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F5-Python-Projects-For-Beginners%2Fblob%2Fmain%2Fquiz_game.py" target="_blank">https://github.com/techwithtim/5-Python-Projects-For-Beginners/blob/main/quiz_game.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>00:22:00 | #2 - Number Guessing Game (Easy)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F5-Python-Projects-For-Beginners%2Fblob%2Fmain%2Fnumber_guesser.py" target="_blank">https://github.com/techwithtim/5-Python-Projects-For-Beginners/blob/main/number_guesser.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>00:39:49 | #3 - Rock, Paper, Scissors (Easy)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F5-Python-Projects-For-Beginners%2Fblob%2Fmain%2Frock_paper_scissors.py" target="_blank">https://github.com/techwithtim/5-Python-Projects-For-Beginners/blob/main/rock_paper_scissors.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>00:54:40 | #4 - Choose Your Own Adventure Game (Easy)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F5-Python-Projects-For-Beginners%2Fblob%2Fmain%2Fchoose_your_own_adventure.py" target="_blank">https://github.com/techwithtim/5-Python-Projects-For-Beginners/blob/main/choose_your_own_adventure.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>01:06:47 | #5 - Password Manager (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F5-Python-Projects-For-Beginners%2F" target="_blank">https://github.com/techwithtim/5-Python-Projects-For-Beginners/</a><span>&nbsp;</span><br /><span>Fernet Cryptography Documentation:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fcryptography.io%2Fen%2Flatest%2Ffernet%2F" target="_blank">https://cryptography.io/en/latest/fernet/</a><span>&nbsp;</span><br /><span>---</span><br /><span>01:37:37 | #6 - PIG (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects%2Fblob%2Fmain%2Fproject1.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects/blob/main/project1.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>01:59:07 | #7 - Madlibs Generator (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects%2Fblob%2Fmain%2Fproject2.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects/blob/main/project2.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>02:15:04 | #8 - Timed Math Challenge (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects%2Fblob%2Fmain%2Fproject3.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects/blob/main/project3.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>02:28:02 | #9 - Slot Machine (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FPython-Slot-Machine" target="_blank">https://github.com/techwithtim/Python-Slot-Machine</a><span>&nbsp;</span><br /><span>---</span><br /><span>03:20:43 | #10 - Turtle Racing (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FTurtle-Racing-V2" target="_blank">https://github.com/techwithtim/Turtle-Racing-V2</a><span>&nbsp;</span><br /><span>Turtle Docs:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fdocs.python.org%2F3%2Flibrary%2Fturtle.html" target="_blank">https://docs.python.org/3/library/turtle.html</a><span>&nbsp;</span><br /><span>---</span><br /><span>04:13:09 | #11 - WPM Typing Test (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FWPM_Typing_Test" target="_blank">https://github.com/techwithtim/WPM_Typing_Test</a><span>&nbsp;</span><br /><span>Curses Docs:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fdocs.python.org%2F3%2Fhowto%2Fcurses.html" target="_blank">https://docs.python.org/3/howto/curses.html</a><span>&nbsp;</span><br /><span>05:09:43 | #12 - Alarm Clock (Easy)</span><br /><span>Python Project Idea Blog:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fhackr.io%2Fblog%2Fpython-projects" target="_blank">https://hackr.io/blog/python-projects</a><span>&nbsp;</span><br /><span>Sound Effects:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fwww.fesliyanstudios.com%2Froyalty-free-sound-effects-download%2Falarm-203" target="_blank">https://www.fesliyanstudios.com/royalty-free-sound-effects-download/alarm-203</a><span>&nbsp;</span><br /><span>---</span><br /><span>05:22:07 | #13 - Password Generator (Easy)</span><br /><span>Python Project Idea Blog:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fhackr.io%2Fblog%2Fpython-projects" target="_blank">https://hackr.io/blog/python-projects</a><span>&nbsp;</span><br /><span>---</span><br /><span>05:39:16 | #14 - Shortest Path Finder (Advanced)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects-For-Intermediates%2Fblob%2Fmain%2Fpath-finder.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects-For-Intermediates/blob/main/path-finder.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>06:14:53 | #15 - NBA Stats &amp; Current Scores (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects-For-Intermediates%2Fblob%2Fmain%2Fnba-scores.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects-For-Intermediates/blob/main/nba-scores.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>06:38:22 | #16 - Currency Converter (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects-For-Intermediates%2Fblob%2Fmain%2Fcurrency-converter.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects-For-Intermediates/blob/main/currency-converter.py</a><span>&nbsp;</span><br /><span>API: https://free.currencyconverterapi.com/</span><br /><span>---</span><br /><span>06:58:51 | #17 - YouTube Video Downloader (Medium)</span><br /><span>Code: &nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FPython-Beginner-Automation-Projects%2Fblob%2Fmain%2Fyoutube.py" target="_blank">https://github.com/techwithtim/Python-Beginner-Automation-Projects/blob/main/youtube.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>07:09:50 | #18 - Automated File Backup (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FPython-Beginner-Automation-Projects%2Fblob%2Fmain%2Fbackup.py" target="_blank">https://github.com/techwithtim/Python-Beginner-Automation-Projects/blob/main/backup.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>07:21:18 | #19 - Mastermind/4 Color Match (Advanced)</span><br /><span>---</span><br /><span>07:48:20 | #20 - Aim Trainer (Advanced)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FPython-Aim-Trainer" target="_blank">https://github.com/techwithtim/Python-Aim-Trainer</a><span>&nbsp;</span><br /><span>---</span><br /><span>08:39:20 | #21 - Advanced Python Scripting (Advanced)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FPython-Scripting-Project" target="_blank">https://github.com/techwithtim/Python-Scripting-Project</a><span>&nbsp;</span></p></div></div></div>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44648/modern-statistics-with-r</guid>
	<pubDate>Thu, 22 Aug 2024 04:44:06 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44648/modern-statistics-with-r</link>
	<title><![CDATA[Modern Statistics with R]]></title>
	<description><![CDATA[<p>This is the online version of the second edition of&nbsp;<em>Modern Statistics with R</em>. It is free to use, and always will be.&nbsp;<a href="https://www.routledge.com/Modern-Statistics-with-R-From-Wrangling-and-Exploring-Data-to-Inference-and-Predictive-Modelling/Thulin/p/book/9781032512440">Printed copies</a>&nbsp;are available from CRC Press.</p>
<p><span>Live&nbsp;<a href="https://statistikakademin.se/in-english-r/">online courses on statistics with R</a></span>&nbsp;based on this book, led by the author, are offered regularly; see&nbsp;<a href="https://statistikakademin.se/in-english-r/">this page</a>&nbsp;for more information and dates.</p>
<p>The past decades have transformed the world of statistical data analysis, with new methods, new types of data, and new computational tools. The aim of&nbsp;<em>Modern Statistics with R</em>&nbsp;is to introduce you to key parts of the modern statistical toolkit. It teaches you:</p>
<ul>
<li><span>Data wrangling</span>&nbsp;- importing, formatting, reshaping, merging, and filtering data in R.</li>
<li><span>Exploratory data analysis</span>&nbsp;- using visualisations and multivariate techniques to explore datasets.</li>
<li><span>Statistical inference</span>&nbsp;- modern methods for testing hypotheses and computing confidence intervals.</li>
<li><span>Predictive modelling</span>&nbsp;- regression models and machine learning methods for prediction, classification, and forecasting.</li>
<li><span>Simulation</span>&nbsp;- using simulation techniques for sample size computations and evaluations of statistical methods.</li>
<li><span>Ethics in statistics</span>&nbsp;- ethical issues and good statistical practice.</li>
<li><span>R programming</span>&nbsp;- writing code that is fast, readable, and (hopefully!) free from bugs.</li>
</ul>
<p>The book includes plenty of examples and more than 200 exercises with worked solutions.&nbsp;<a href="http://www.modernstatisticswithr.com/data.zip">The datasets used for the examples and the exercises can be downloaded here.</a></p><p>Address of the bookmark: <a href="https://www.modernstatisticswithr.com/" rel="nofollow">https://www.modernstatisticswithr.com/</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40754/understanding-your-reads-and-mapping</guid>
	<pubDate>Wed, 29 Jan 2020 06:29:55 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40754/understanding-your-reads-and-mapping</link>
	<title><![CDATA[Understanding your reads and mapping !]]></title>
	<description><![CDATA[<p>One of the best tutorial for beginners ...</p>
<p>https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/Day1/Session4-seqIntro.html</p><p>Address of the bookmark: <a href="https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/Day1/Session4-seqIntro.html" rel="nofollow">https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/Day1/Session4-seqIntro.html</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43273/understanding-kmer</guid>
	<pubDate>Wed, 18 Aug 2021 04:27:51 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43273/understanding-kmer</link>
	<title><![CDATA[Understanding kmer !]]></title>
	<description><![CDATA[<p><a href="https://en.wikipedia.org/wiki/k-mer">What is a&nbsp;<em>k-mer</em>&nbsp;anyway?</a><span>&nbsp;A&nbsp;</span><em>k-mer</em><span>&nbsp;is just a sequence of&nbsp;</span><em>k</em><span>&nbsp;characters in a string (or nucleotides in a DNA sequence). Now, it is important to remember that to get&nbsp;</span><em>all k-mers</em><span>&nbsp;from a sequence you need to get the first&nbsp;</span><em>k</em><span>&nbsp;characters, then move just a single character for the start of the next&nbsp;</span><em>k-mer</em><span>&nbsp;and so on. Effectively, this will create sequences that overlap in&nbsp;</span><code>k-1</code><span>&nbsp;positions.</span></p><p>Address of the bookmark: <a href="https://bioinfologics.github.io/post/2018/09/17/k-mer-counting-part-i-introduction/" rel="nofollow">https://bioinfologics.github.io/post/2018/09/17/k-mer-counting-part-i-introduction/</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>

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