Biocybernetics and Systems Biology Course

by András Aszódi

CoCalc basics

The CoCalc site provides access to the SAGE computer algebra system. We will use it for online demonstrations and homework assignments.

First steps

Please create a (free) account for yourself on CoCalc with the e-mail address you used to communicate with the AIT staff. Based on this e-mail address I will be able to find you on CoCalc and enroll you into the BioCybernetics course.

CoCalc course management

Your homework assignments are short SAGE scripts containing comments that explain the task. You are usually required to write a few Python functions yourself. You see the current assignment when you log in to the SAGE cloud; new assignments arrive on the day after class. The assignments have deadlines. Somewhat surprisingly you are not supposed to "submit" your homework, rather the teacher "collects" the assignment from you instead. After grading the homework is returned to you. My SAGE/CoCalc primer (PDF) summarises the procedure.

Help

The CoCalc Web interface is relatively easy to use. For more details please refer to the CoCalc online help. Or download the SAGE for Undergraduates PDF (obtained from Gregory V Bard's website).

Linear algebra basics

For an easy introduction, consult my CoCalc linear algebra primer (PDF).

The SAGE documentation provides a SAGE linear algebra tutorial. The reference manual is mainly for mathematicians, enjoy it with moderation.

Solving differential equations

My CoCalc differential equation primer (PDF) explains the basics of how to solve differential equations in SAGE. If you are interested in the details, the SAGE differential solver reference page covers both symbolic and numerical solvers.

Plotting

Most of the time we will draw 2D plots.