The programming course accompanies the lectures. In the first half of the semester, computer assignments will be distributed weekly, and the given problems can be solved in the Computer Pool. I will provide help during the regular course hours. At the beginning of the second half of the semester, a set of more advanced problems will be distributed. A group of two or three students can sign up for a specific project, and they should work together on a solution for several weeks. Help will again be provided during the regular course hours.
To obtain a Course Certificate (“Schein”), an oral presentation of the results of the project together with a one-page written summary of the results is required. The presentations will take place on Monday, July 12, 2004, instead of the lecture.
The computer pool consists of one server and 12 client computers (mostly Intel Pentium 4 CPUs) running GNU/Linux (Fedora Core 1).
All machines are equipped with ssh (Secure Shell), this means you can securely connect and remotely work on them using “ssh user@host” on UNIX, PuTTY on Windows or MacSSH on a Mac.
If you are on a publicly available terminal and can not install the software, then point a JAVA capable browser to http://itb1.biologie.hu-berlin.de/ssh.html or to http://sdf.lonestar.org/ssh/.
Go and see a list of the IP addresses.
If you still don't have an account, drop a line to 
.
For those of you who are not familiar with UNIX, I wrote a little UNIX Commands Reference Card.
We will write our programs using the Python programming language. You can find Python documentation online or locally under /home/cns4tut/docs/html/python2.2.3/index.html .
Additionally the SciPy (Scientific Python) module, an open source library of scientific tools for Python, is installed. It includes modules for graphics and plotting, optimization, integration, special functions, signal and image processing, genetic algorithms, ODE solvers, and others. You can find a SciPy tutorial online or locally under /home/cns4tut/docs/pdf/scipy.pdf .
Anyway the best way of getting help is within the Python interpreter itself. Launch the interpreter with:
[user@biopoolsrv user]$ python
You will get something like this:
Python 2.2.3 (#1, Oct 15 2003, 23:33:35)
[GCC 3.3.1 20030930 (Red Hat Linux 3.3.1-6)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>>
Type help() at the prompt and don't be shy! You can ask for help about the function foo typing help(foo).
| Remember: To obtain the Course Certificate (“Schein”), you need to sign up for a specific project. You are going to present the results of your work on Monday, July 12, 2004. The time required to tackle the advanced problems presented in the projects is far longer than two hours a week (actually we estimated something around 40 hours). I will provide help on Fridays (17:00-19:00) in the computer pool, but you must work more than that. If you wuold like to work at home you could either do it remotely (look into the Hardware section of this page to know how) or installing the necessary software on your computer (I will try to help you in this case). The best option is to work on the computers that are available in the computer pool: They are fast machines and the software is correctly installed. It is also easier for me to help you if I have direct access to your files. In case of urgent need, I am available in my office: |
Institute for Theoretical Biology
Humboldt-Universität zu Berlin
Invalidenstraße, 43
D-10115 Berlin, Germany
room: 1306
phone: +49 30 2093-8630
fax: +49 30 2093-8801