Computer labs

Computer Labs of appbio145 This course has four labs consisting of sets of assignments and one larger programming project.

Preparations Be sure to issue the command

course join appbio13 before working on your first assignment (it is supposed to be "appbio145", but for some reason I can't get that working)! You will unfortunately also have to logout and log in again. This procedure makes sure that you have access to all the tools we need in this course.

Single or group? You are welcome to work in pairs. In fact, this is highly recommended, especially for beginners, since you will have someone to discuss problems with and simply have more fun.

Get in line! with SimaManagerQWait To make it easier for the lab tutors to find the next person in line, we will use the lab queuing system SimaManager. If yQWait. Check it ourt appbio12 environment is setup correctly, you type¶ sm in the terminal to start the queuing system. You get a list of courses and if you click "bioinfo", you will see the current list of people waiting. To get in line, click on the help button!t qwait.csc.kth.se where we will have a queue for this course. This is the first year we use this service (the old system, SIMA has been turned off), so there might be some hiccups.

Editing Python code Any Real Programmer will use a classic programming text editor such as Emacs! This editor has everything, including a steep learning curve! If you write programs, or know you will spend a lot of time editing code in the future, you might want to consider using Emacs for editing code in this course. Start it by writing:

emacs & The ampersand (&) ensures that you can continue to work in the terminal. Some people decide to use a lesser, yet popular, editor like VIM. Apparently, that works too.

Python actually has its own programming editor: start it by running "idle".

There are simplistic text editors without all the hard-to-use bells and whistles of Emacs, and a good alternativ choice is gedit. Write

gedit & to get a nice graphical user interface suitable for Python programming!

Many people, in particular with more experience, feel that Eclipse is the only way to go. This integrated development environment, IDE, have many and convenient features.

Mac users seems to like the editors Sublime and TextWrangler. ¶

The labs The actual lab assignments are found in the menu in the left margin! But you should read this page before starting on them!