First steps with Darwin

Starting Darwin in the student computer rooms at ETH

Log-in to one of the PC's in IFW D31 or CAB E37 under linux. Open a terminal window and enter the following commands at the command line:

/home/darwin/bin/darwin

Using Darwin on your private PC or notebook

Darwin is free available and can be downloaded. After you get Darwin for your operating system, decompress the file and start Darwin with the following command:

darwinfolder/darwin -l darwinfolder/lib

darwinfolder is the path to the Darwin executable file. The essential library files are located in the subfolder lib.

Now you should be able to type in Darwin commands at the prompt '>'.

Loading the SwissProt database

We created a protein database with around 2000 entries which should be sufficent for first try outs in Darwin. Save the downloaded file in your darwin folder.

To load the small databas enter at the darwin-prompt:

> ReadDb('/home/darwin/DB/Problem2.db');

When the database is successfully loaded, you will see some information about the database similar to this one:

Peptide file(/home/darwin/DB/Problem2.db(1828388), 2159 entries, 919543
 aminoacids)

If using the databases causes a segmentation fault, you have to unlimit the stacksize of your linux system, see " Frequently asked questions" below.

To learn the basic syntax, you may want to go through this biorecipe.

Happy Darwin'ing

Darwin Help

On the Darwin Help Webpage you find all Darwin functions with explanation and examples.

In Darwin, you can enter ? followed by a text about which you want to have information. As an example ?tree gives you a list of all procedures and data structures involved in tree construction and visualisation.

Frequently asked questions

"Segmentation fault" with Darwin alignments

If you want to align sequences with Darwin you have to adjust the stacksize limit on your linux system. Before starting Darwin type in your shell the following command. You maybe want to write this command in the .tcshrc file in order to be automatically applied when you log in.

unlimit stacksize