Opera browser!

I recommend opera. It is easily to move from one system to another, All your staffs : E-mails, bookmarks, shortcuts, fast laucher, rss news.

Snapshot the screen.

install imagemagik

run
import xxx.png

Now, the mouse changed, you can select the region you want to take a snapshot, only a small region.

btw, window snapshot : Alt-PrintScreen

From Fedora to Ubuntu

Why have I transterred from Fedora to Ubuntu?
First, I can't fix the scim in QT program like opera, amsn, skype. I stand it for as long as more than half a year.
Secondly, I didn't install openafs properly.
Another reason is I can not login secure wireless network. I hope I can fix it in Ubuntu.

Why I did not transfer earlier?
I have already try it. But there were something I did not like.
1. The default vim do not have GUI. And I can not install it(long time ago)
2. Most important thing. I don't like the color and the themes. I like blue more.
3. There are even not l. and no default ll alias.

It took me one day to do the transfer. The chance come when I got a sencond hard disk bay adapter for Thinkpad T60 from eBay. Now I have two hard disk inside, and I prefer another system. I failed in hacking a MacOS on x86 first.
Since there is no more cdrom, I install Ubuntu from hard disk. Copying the system from existing system failed. Then I try to install it from hard disk. It took much time because I do not know it requires special iso image. Yes, you need alternate version.

The difference and difficulties:
I mount the home partition to ubuntu, so the configuration could be conserved.
1.fstab : ubuntu use UUID rather than /dev/sda(b). It identify the hard disk in different order every time. Google UUID you can get the solution.
2.gnome-terminal : No color theme of the text. It bother me a lot. I tried the gconf-editer first and even deleted the config folder in .gconf. It won't work. Finally, it because ls command don't have --color option. Do a alias in .bashrc can solve that.
3.Gvim : can open file from nautilus. E37 error. Config file problem. delete some terms.

The theme conserved from fedora. I use MacOS theme. And changed the login screen to blue ones and the background color the blue and splash pic to the one I like. Now you can not see ubuntu. It is fast, probably because it's new. I like it.

Partition table recovery

Use TestDisk.

http://www.cgsecurity.org/wiki/TestDisk_Download

You can backup the partiton table by dd. Google it to get the answer.

Flux balance Analysis(FBA) under linux

Considering you may find this page by google. I announce here my Software for FBA and MetaTOOL under frame of gtk.

Currently, the features are listed as following,
1. interface for linear programming
2. read reaction file in plain text
3. build model by hand in the form of work sheet
4. Layout the model and highlight the flux
i, generate network from model
ii, spring algorithm for layout
iii, highlight the modes and futile cycle
5. MetaTOOL
i, Output MetaTOOL input from FBA model
ii, run MetaTOOL
6. Other our utility unpublished for my poor English skills.
7. MOMA
8. Phaseplane
9. viability
10. subset of enzymes
11. Erase futile cycle

Go with a library handing FBA.

If you are interested, leave message here. I will read it some time.

Get the SBMLToolbox worked under the Linux

After several days work, I finally figured out the problem that the TranslateSBML function fail to work and you got a Segmentation violation.

The original aim for me is to install COBRAToolbox-1.1 in Linux and Matlab 2006b.

SBMLToolbox 2.0.2
libsbml 2.3.4
fedora core 6
gcc-4.1.1-51.fc6
matlab 7.3 (2006b)

1. Install libsbml-2.3.4 following the instructon in the package

2. Build the TranslateSBML.mexglx using the following arguments in the Makefile
Do not forget to change the matlab root directory.

MEX = /usr/local/Matlab74/bin/mex
XCFLAGS = $(CFLAGS) -g
XLDFLAGS = $(LDFLAGS) -L/usr/local/lib
XCPPFLAGS = $(CPPFLAGS) -I/usr/local/include -I/usr/local/include/sbml/
LIBS = -lsbml

3. sudo cp /usr/local/lib/libsbml.so /usr/local/Matlab74/bin/glnx86/
This is required by the matlab. But the glpkcc.mexglx worked without this operation. I don't know what happend.

Anyway, the TranslateSBML function should work now. Though I spent much time on the source code, it ends up only copying a file. :)

VPN connection in IUPUI

http://pptpclient.sourceforge.net/howto-fedora-core-6.phtml

First , install pptconfig as following,

# rpm -Uvh http://pptpclient.sourceforge.net/yum/stable/fc6/pptp-release-current.noarch.rpm
# yum --enablerepo=pptp-stable install pptpconfig

Yum will help you to install other programs.
1.
sudo route add -host 134.68.107.67 gw 10.235.96.100
2.
sudo pptconfig
name: any
server: pptp.iupui.edu
domain: ads
username: any
passwd: some

then add start
in log window 'connected' should be shown.

Finally,
3.
sudo route add default ppp0

It should be OK now!