Programming in the Life Sciences #9: APIs and Web Services

Continuing on the theory covered in this course, this part will talk about application programming interfaces (APIs) and web services. 2 minute read

Programming in the Life Sciences #11: HTML

HTML (HyperText Markup Language), the language of the web, is no longer the only language of the web. But it still is the primary language in which source code of webpages is shared. Originally, HTML pages were always static: the only HTML source of a web page was that was downloaded from a website. Nowadays, much HTML the is visualized in your web browser, is generated on the fly with JavaScript. In fact, that is exactly what you will learn to do in this course. 5 minute read

Programming in the Life Sciences #10: JavaScript Object Notation (JSON)

As said, JSON is the format we will use as serialization format for answers given by the Open PHACTS LDA. The API actually supports XML, RDF, HTML, and TSV too, but I think JSON is a good balance between expressiveness and compactness. Moreover, and perhaps a much better argument, JSON works very well in a JavaScript environment: it is very easy to convert the serialization into a data model: 1 minute read

Programming in the Life Sciences #8: coding standards

Never underestimate the power of lack of coding standards in code obfuscation. Just try randomly to read code you wrote a year ago or four years ago. You’ll be surprised with what you find. Coding standards are like the grammar in writing: they ensure that our message gets understood. Of course, the primary goal is that the CPU understands what you mean, but because programming languages are not your native language, you may not always say what you think you are saying. 4 minute read

Programming in the Life Sciences #7: theory

No course, with some good theory. In this six-day course, I plan to cover this computing theory. It’s very practice oriented: 9 minute read

Programming in the Life Sciences #6: functions

One key feature of programming languages is the following: first, there is linearity. This is an important point that is not always clear to students who just start to program. In fact, ask yourself what the algorithm is for counting the chairs in the room where you are now sitting. Could a computer do that in the same way? How should your algorithm change? A key point is, is that the program is run step by step, in a linear way. 2 minute read

Programming in the Life Sciences #5: converting the results into HTML

Now that we have the communication working with the Open PHACTS LDA, it is time to make a nice GUI. I will not go into details, but we can use basic JavaScript to iterate over the JSON results, and, for example, create a HTML table: less than 1 minute read