Open course ware

PROFESSOR: OK. So I need to move on a little bit now, and I want to talk about in fact, the earlier way that nature developed to make energy using proton gradients. And this part actually preceded the development of respiration as you'll see. It's what I somewhat flippantly refer to as photosynthesis release 1. In my first lecture, when I was giving you a sketch of evolution. Who knows, I mean these are very rough numbers, but may have evolved about $3.4 billion years ago and early life had begun to exhaust this sea of chemicals that had been produced. And it's known as cyclic photophosphorylation. And it's a way of taking the energy in sunlight and making ATP. So whatever organism figured this out, this was a really big deal. Because now instead of having to use the sort of natural reserves like the way the food around is a depleting resource just like our petroleum reserves, this was able to take the abundantly-available sunlight and use it to make energ...

User-mode programs need to communicate with the OS to request service or get access to useful OS data like the time of day. But if they're running in a different MMU context than the OS, they don't have direct access to OS code and data. And that might be bad idea in any case: the OS is usually responsible for implementing security and access policies and other users of the system would be upset if any random user program could circumvent those protections. What's needed is the ability for user-mode programs to call OS code at specific entry points, using registers or the user-mode virtual memory to send or receive information. We'd use these "supervisor calls" to access a well-documented and secure OS application programming interface (API). An example of such an interface is POSIX (https://en.wikipedia.org/wiki/POSIX), a standard interface implemented by many Unix-like operating systems. As it turns out, we have a way of transferring control fr...

The problem we need to solve is where to store the values needed by procedure: its arguments, its return address, its return value. The procedure may also need storage for its local variables and space to save the values of the caller's registers before they get overwritten by the procedure. We'd like to avoid any limitations on the number of arguments, the number of local variables, etc. So we'll need a block of storage for each active procedure call, what we'll call the "activation record". As we saw in the factorial example, we can't statically allocate a single block of storage for a particular procedure since recursive calls mean we'll have many active calls to that procedure at points during the execution. What we need is a way to dynamically allocate storage for an activation record when the procedure is called, which can then be reclaimed when the procedure returns. Let's see how activation records come and go as execution pro...

Often, you will need to load an external data file into R to do some analysis and modeling. In this class, we'll be working with csv files, or comma separated value files. This is a common format for data files and is easy to work with in R. The first thing you need to do to read in a data file is to navigate to the directory on your computer where the data file is saved. On a Mac, go to the Misc menu, then select "Change Working Directory...". On a PC, go to the File menu and select "Change dir...". This should pop up a browsing or navigation window. Navigate to the folder where you saved the data file WHO.csv that you've downloaded for this class, and then select that folder. Nothing should have happened in R, but if you type getwd, and then empty parentheses and hit Enter, you should see the path to the folder containing the data set that you just selected. Now, read in the data file by typing WHO = read.csv("WHO.csv") the name of ...