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

Programming in the Life Sciences #4: communication from within HTML

The purpose of a web service is that you give it a question or task, and that it returns an answer. For example, we can ask the Open PHACTS platform what compounds it knows with aspirin in the name. We pass the question (with the API key) and get a list of matching compounds. Now, this communication is complex: it happens at many levels, which are spelled out in the Internet Model. There are various variants of the stack of communication layers, but we are interested mostly in the top layers, at the application layer. In fact, for this course this model only serves as supporting information for those who want to learn more. 2 minute read

Programming in the Life Sciences #3: the assessment

Now that I have wrote out the goals, what they students will practically do, and how to get started with the Open PHACTS platform, I will list how we will assess the students: less than 1 minute read