Argh...was schreib ich denn? » working tipps

SAGM: preservation for RBC

schmart — Fri, 02 Mar 2007 14:47:43 +0000

Just starting to write my diploma thesis I was searching for a recipe of SAGM. After searching about 30 minutes in the Internet I decided to ask Noemi. Thanks to Noemi I can publish this recipe for SAGM solution.

For 100 ml of SAGM take

0.900 g Dextrose (monohydrate)
0.877 g NaCl
0.0169 g Adenine
0.525 g D-Mannitol

and dissolve it in water.

But for what are these additives good for?
In SAGM RBCs can be stored up to 42 days. It contains S = saline, A = adenine, G = glucose or dextrose, M = Mannitol. NaCl is responsible for the right osmolarity. Adenin iinfluences the ATP level in RBCs. Glucose or dextrose is essentialy for the nutrition of RBCs. Mannitol decreases the lysing rate of RBCs by supporting the integrity of the cell membrane.

Technorati Tags: SAGM SAG-M S.A.G.M. biology blood RBC

Putting sequences together

schmart — Sat, 17 Feb 2007 12:39:46 +0000

Sometimes it is a problem to open many seqeunces in one worksheet to analyse them. For examlple you have sequence data and try to open them in one worksheet in Bioedit. You can copy every sequence by copy&paste in one file or one worksheet or you can use a little helper who will do it for you. Here is one very simple helper written in Perl.
Basicaly you invoke it with an argument defining a file pattern, *.seq defines all files ending on .seq. The files should be text files. The script now reads the file contents and put the contents together in a file called sequences.fasta.
Let say you have the files 1.seq and 2.seq in one directory:

1.seq:

aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
cccccccccccccccccccccccccccccccccccccc

2.seq:

ttttttttttttttttttttttttttttttttttttt
ggggggggggggggggggggggggggggggggggggg

Invoking appendseq.pl with *.seq as argument will produce the file sequences.fasta containing:

>1.seq
aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
cccccccccccccccccccccccccccccccccccccc

>2.seq
ttttttttttttttttttttttttttttttttttttt
ggggggggggggggggggggggggggggggggggggg

The original filenames are at the beginning of the sequence behind > and define the name of the sequnce. The resulting file should be FASTA compatible.

You can download appendseq.pl here.

Freeware for the Lab!

schmart — Thu, 08 Feb 2007 20:00:12 +0000

Just reading in a StudiVZ-Group about freeware for biochemistry brings me to the idea to post this:

Biobar Add-On für Mozilla Firefox:
Search in Pubmed, NCBI-Databases, EBI-Databases right from your Browser. No need to surf to the webfrontend of the service.

Labplot für Linux (KDE):
Like Origin. You can use Labplot for regression analysis, creating graphs from data and many more. Only for Linux!

LaTex and Lyx:
Textprocessing another way. Not WYSIWYG but WYSIWYM. Get information at http://www.lyx.org/ and here LaTeX@Wikipedia
Give it a try, it’s easier than you think!

BioEdit:
I guess one of the most used sequence alignment editor for Windows. It works also with Linux, just run it with wine.

Gimp:
Not as good as Adobe Photoshop but Gimp is free Software. Maybe it doesn’t look like a Windows Application you are used to but give it a try. The new version should be great, you can try it if you use the 2.3.x Development Release and not the 2.2.x Release.

If you knew other freeware for the lab post a comment.

Technorati Tags: freeware scientific biology

Styles, Formats and Indexes in Open Office 2.1

schmart — Fri, 02 Feb 2007 13:03:01 +0000

Ever got fed up with changeing every headline in your document by hand? Ever got fed up with update your table of content by hand? Yes? So here is a (very) short howto use OpenOffice.org Writer for doing this for you.
I decided to write this only for OpenOffice for two reasons. First OpenOffice ist OpenSource and works with more than one Operating System (for me I can’t use MS Office because I’m using Linux). Second the idea behind Styles and Formats are the same for the most Office-Software.
The first thing you have to do is to install OpenOffice on your system. Download it here.

Styles and Formats

Now lets start. At the beginning there is an empty text document. If you don’t have already one create it with [ctrl+n] or with the file-menu file->new. Everytime you have to open an entry in a menu I will write it like this menu->entry.

Check if you have the “Styles and Formats”-Toolbox open. If not, go to Format->Styles and Formats or press [F11]. Click into Headline 1 (don’t select it).

Write those lines in your document:
Styles and Formats
a short how to use them with Open Office 2.1
Headline 1
Headline 2
Headline 4
normal text

Now double-click on Headline 1 in your “Styles and Formats”-Toolbox. Do this for the other headlines as for headline 1 but select the matching type.
To format the first two lines select “Chaptertemplates” from the pull down menu you can see on the upper picture. There you set the first line to “Title” and the second line to “subtitle”.
Now you should have something like this:

Maybe you ask why to do this in that way. What would happen if you have to change the format of your headlines? If you use Styles and Formats you only have to change the template and every text with the according type will use the new parameters. In the upper picture you can see a dialog for changing the style and format for the Heading 1 template. You can open this dialog by right-clicking on “Headline 1″ in you “Styles and Formats”-Toolbox and selct “change”. Now you can change the font-type, size, familily, style, the alignment and much more.
This should make the work with large documents much easier.

And here is another reason to use “Styles and Formats”. If you have to make a Table of content now the programme do the work for you!

Creating a TOC

Use the document from above and try to create a TOC. First open Insert->Indexes and Tables. Now a dialog like this should appear:

The left part of the dialog shows you am preview of the TOC. The right part allows you to change the appear of the appearance of you TOC. For the fist time just use the standard options — later you can play with them arround to get used to the dialog. Click on OK. OpenOffice will insert the TOC at the cursors position.

As you can see here the TOC is gray. The gray color stands for special fields inside a text. Now just right click into the gray text. A context menu will open. One option is: “Update Index”. So if you have written new text or changed the structure of your document just click on “Update Index” and the TOC should be up to date.

I hope this short howto helped you a little bit. For MS Office it is nearly the same (I guess and hope). Maybe the names of the dialogs and menus are different. If you wan’t to know more or if you habe ideas for other topics just post a question (after registering).

Have fun!

RSS-Feeds

schmart — Tue, 30 Jan 2007 11:15:15 +0000

What is a RSS-Feed? RSS stands for Really Simple Syndication. But what is the use of RSS-Feeds? RSS-Feeds are something like a mailing list. But not the same. You can’t post to RSS-Feeds. You only can read RSS-Feeds. RSS-Feeds are XML-Documents, you can read them with a normal editor with is really silly. Or you can use a RSS-Reader. If you use a RSS-Reader you can organize your feeds. The feeds could be something like the Table Of Content from PLOS Biology, Nature, Science or Malaria Journal.
Nerly every journal has RSS-Feeds. But sometimes they are hard to find. For the most sites you can use your browsers find function and search for rss.
Now I will show you an example of a RSS-Reader. As for me I’m working mostly with Linux it is most important to use something with work under nearly every Operating System (like Windows and Mac OS). So I will show you how to use Mozilla Firefox and Sage (an extension for Firefox) as RSS-Reader.

1. Step

Download and install Mozilla Firefox.

Start Mozilla Firefox.

2. Step

Open Extra -> Add-Ons

Now you should have something like this on your Desktop:

In the lower right corner of the new window is a link (get more extensions — or something similar to this). Click it!
After clicking it Firefox will open a new window with the URL: https://addons.mozilla.org/firefox/extensions/

3. Step
Now you can download and install Sage (and many more other plugins).

You will get something like this:

Open the link to Sage and install it by clicking on the install button on the next page. Before installing you have to wait a few seconds to make sure you read the content of the installation window. But after a few seconds it will look like this:

After installation you have to restart Firefox (close all windows of Firefox).

Using Sage
You can use Sage by pressing alt+z or by open the menu Extras and click on Sage. After doing this Sage will open in the Sidebar. You can add Feeds with drag&drop and delete feeds by marking them and pressing del. Below a short explanation for using Sage (click image for lager image).

Now try and add the RSS-Feeds of PLOS Biology, Malria Journal, Nature. Hint: Try the search feed button in Sage.

Have fun! For questions post a comment (after registering).

Technorati Tags: rss sage firefox howto