Because I don't have Netscape installed on my computer, the help function of Staden doesn't work automatically. During the staden course James told be to look into /usr/local/staden-linux-rel-1-4/lib/tk_utils/help_netscape.tcl I might do so, but as a quick fix I made a symbolic link to mozilla: sudo ln -s /usr/bin/mozilla /usr/bin/netscape And this really works. I also tried it succesfully with Konqueror: sudo ln -sf /opt/kde3/bin/konqueror /usr/bin/netscape

I want to store all sequence traces of a sequencing project (using Staden) in one file. You can do that if you simply tar all the *.ztr files: tar -cvf ./test.tar *.ztr Then you have to specify in gap4 Options -> Configure menus -> Expert And then you need to specify Options -> Trace file location -> TAR=./test.tar

To make one sequence a reference sequence, just select its name from the gap4 Edit Contig window and right click and select as reference sequence. If the file is in embl format, the features will show up as Staden tags in the alignment.

KMail has always problems with multiple smtp servers. As a solution I installed sendmail. Then I just created a new outgoing mailserver and selected the sendmail option. No further configuration was necessary and it seems to work.

I am trying to use EMBOSS for the assembly of vector sequences. Long time ago, I used the CGC seqed program for this purpose and at the moment I use the Gene Construction Kit. EMBOSS doesn't have a straight equivalent for seqed and one has to use a bunch of other tools to replace its functionality. Look at this comparison between CGC and EMBOSS.

Today I installed the Staden Package on Tanja's Macintosh G4 computer (MacOS 10.3). I recommend using the ebiotools package made by Anders Nister. It includes other useful software such as EMBOSS, Blast, etc.). Installation instructions are available in the embnet news issues 9/1, 9/2, 9/3 and 10/1 or gathered into one pdf file from here.

The perl script /usr/local/backuppc/bin/BackupPC_zcat does it, but you need BackupPC installed for this purpose. There is a standalone frontend for the compression libraries available called Zzzz... made by the same guy who is behind mplayer.

Serves 4 300g paglia e fieno ('flattened spaghetti') 2 tablespoons butter 1 teaspoon finely chopped fresh sage or 1/2 teaspoon dried sage, plus fresh sage leaves to garnish (optional) 120 g gorgonzola 3 tablespoons mascarpone cheese 5 tablespoons milk 1/2 cup walnut halves, ground 2 tablespoons freshly grated Parmesan cheese freshly ground black pepper Cook the pasta in a large pot of salted boiling water, according to the instructions on the package. Meanwhile, melt the butter in a large skillet or saucepan over low heat, add the sage and stir it around.

Serves 4 3 cups farfale ('motylki') 180 g gorgonzola cheese, any rind removed, diced 2/3 cup of heavy cream pinch of granulated sugar 2 teaspoons finely chopped fresh sage, plus fresh sage leaves to garnish salt and ground balck pepper Cook the pasta until al dente: 8-10 minutes or according to the instructions on the package. Meanwhile, put the gorgonzola and cream in a medium saucepan. Add the sugar and plenty of ground black pepper and heat gently, stirring frequently, until the cheese has melted. Remove the pan from heat.

Serves 4 1 tbsp corn oil 2 garlic cloves, crushed 1 red pepper & 1 green pepper, deseeded and diced 1 celery stalk, diced 1 tsp hot chilli poeder 400g can chopped tomatoes, 325g can sweetcorn, drained 215g can kidney beans, drained and rinsed 2 tbsp chopped freshed coriander salt and pepper tomato and avocado salad, to serve Topping: 125g cornmeal 1 tbsp plain flower 1/2 tsp salt 2 tsp baking powder 1 egg, beaten 100ml milk 1 tbsp corn oil 125g grated mature Cheddar Heat the oil in a large frying pan and gently fry the garlic, peppers and celery for 5-6 minutes or until just softened.