MartinsM - Personal blog

How to install COBRApy in Lubuntu 15.10

2016-02-06T16:00:00+02:00

sudo su
aptitude install python-pip
aptitude install python-dev

Install libSBML

The next step failed for me, but one can try:

pip install python-libsbml

This method worked for me:

sh -c "echo 'deb http://download.opensuse.org/repositories/home:/fbergman:/libsbml/xUbuntu_15.10/ /' >> /etc/apt/sources.list.d/python-libsbml.list"
apt-get update
apt-get install python-libsbml

Install COBRApy dependencies

apt-get install python-glpk
apt-get install python-numpy
apt-get install python-scipy
apt-get install glpk-utils
apt-get install libglpk-dev

Install COBRApy

pip install cobra
apt-get install ipython

Test COBRApy

In python console run:

from cobra.test import test_all
test_all()

Ran 83 tests in 66.987s
OK (skipped=1)

As it is noted in the title these instructions work on Ubuntu. Unfortunately I couldn't get COBRApy to pass tests on Fedora 23 because it can't locate glpk. Any help in comments is appreciated.

Python Pandas reindex and new index

2016-01-19T00:55:00+02:00

The answer comes from stackoverflow.com:

So if you have a DataFrame with index [0, 1, 2], then doing a reindex([2, 1, 0]) will return the rows in reverse order. Doing something like reindex([8, 9, 10]) does not make a new index for the rows; rather, it will return a DataFrame with NaN values, since there are no rows with indices 8, 9, or 10.

To generate new index for existing rows try this:

df.index = range(len(df))

How to manage printers in Fedora

2016-01-15T09:00:00+02:00

In browser open http://localhost:631

How to install LaTeX and XeLaTeX in Fedora 23

2016-01-10T18:00:00+02:00

XeLaTeX requires a number packages. First become root, then run this command:

dnf -y install texlive
    texlive-latex
    texlive-xetex
    texlive-collection-latex
    texlive-collection-latexrecommended
    texlive-xetex-def
    texlive-collection-xetex

Total download size: 182 M

Installed size: 307 M

Only if needed:

dnf -y install texlive-collection-latexextra

How to disable SElinux on Fedora 23

2015-12-15T10:00:00+02:00

Use the getenforce or sestatus commands to check the status of SELinux.

On systems with SELinux disabled, the SELINUX=disabled option is configured in /etc/selinux/config

As root open the file /etc/selinux/config

su -
gedit /etc/selinux/config

Change the line SELINUX=enforcing to SELINUX=disabled

Reboot your system. After reboot, confirm that the getenforce command returns Disabled.

Sources: docs.fedoraproject.org.

Things to do after fresh Fedora 23 installation

2015-12-02T13:51:00+02:00

Become root and run update

su -
dnf update

RPM Fusion repository

http://rpmfusion.org/Configuration

Install the missing software

dnf install gnome-tweak-tool gimp inkscape thunderbird bluefish filezilla vlc python-openoffice epiphany

dnf install VirtualBox
dnf install dconf-editor

Software for development

dnf groupinstall "Development Tools"

Scientific software

dnf install numpy scipy python-matplotlib python-pandas python-ipython

Upgrade SciPy

dnf install python-pip blas-devel lapack-devel gcc-c++ rpm-build
dnf groupinstall "Development Tools"
pip install --upgrade scipy

Install scikit-learn

pip install -U scikit-learn

How to upgrade SciPy on Fedora 23

2015-10-19T12:58:00+03:00

As it was with Fedora 22, the Fedora 23 still ships with SciPy version 0.14.1. To upgrade SciPy please run the following commands as root:

dnf install python-pip
dnf install blas-devel
dnf install lapack-devel
dnf install gcc-c++
dnf groupinstall "Development Tools"

If you now try to upgrade scipy you will get the following error

g++: error: /usr/lib/rpm/redhat/redhat-hardened-cc1: No such file or directory

On Fedora 23 one has also to install rpm-build to avoid errors during compilation of scipy:

dnf search rpm-build

Finally uninstall scipy 0.14.1, download 0.16.0, compile it and install. All with the following command:

pip install --upgrade scipy

How to play encrypted DVDs on Fedora 22

2015-09-08T19:27:00+03:00

Solution found here: http://forums.fedoraforum.org/showthread.php?t=304745

First become root:

su -

Then execute these 7 commands:

dnf install dh-autoreconf
git clone git://git.videolan.org/libdvdcss
cd libdvdcss/
autoreconf -i
./configure --prefix=/usr
make
make install

htaccess allow IP addresses

2013-09-10T15:52:00+03:00

If your website is under construction, you can simply edit .htaccess file to disallow visits to your website. Here is the code :

&lt;Limit GET POST PUT&gt;
order deny,allow
deny from all
allow from 12.245.67.190
&lt;/Limit&gt;

allow from 12.245.67.190 command allows access to your server only from 12.245.67.190 IP address.

You can allow more IP’s to access your website : <Limit GET POST PUT> order deny,allow deny from all allow from 12.245.67.190 allow from 12.245.67.192 </Limit> This practice is good in case you are modifying your website (performing a new joomla installation) and don’t want others to see the process.

Original source: http://htaccessfile.com/htaccess-allow-ip-addresses

How to add manual entries to Gnome Shell Launcher

2013-06-01T14:45:00+03:00

With gnome-shell, you'll need to create a .desktop file in '~/.local/share/applications/' which will then allow you to add the application to the gnome-shell dash.

My .desktop file for Sublime Text looks like this:

#!/usr/bin/env xdg-open
[Desktop Entry]
Version=1.0
Type=Application
Name=Sublime Text
GenericName=Text Editor
Comment=Sophisticated text editor for code, markup and prose
#Exec=/opt/sublime_text/sublime_text %F
Exec=/home/username/workspace/sublime_text_3/sublime_text %F
Terminal=false
MimeType=text/plain;
Icon=/home/username/workspace/sublime_text_3/Icon/48x48/sublime-text.png
Categories=TextEditor;Development;
StartupNotify=true
Actions=Window;Document;
[Desktop Action Window]
Name=New Window
Exec=/home/username/workspace/sublime_text_3/sublime_text -n
[Desktop Action Document]
Name=New File
Exec=/home/username/workspace/sublime_text_3/sublime_text --command new_file

Original source here.

How to download a complete website

2013-05-28T09:43:00+03:00

If you ever need to download an entire Web site, wget can do the job:

wget \
     --recursive \
     --no-clobber \
     --page-requisites \
     --adjust-extension \
     --convert-links \
     --restrict-file-names=windows \
     --domains example.com \
     --no-parent http://example.com.lv/thefolder/

The options are: --recursivedownload the entire Web site.

--domains example.com don't follow links outside example.com.

--no-parent don't follow links outside the directory thefolder/.

--page-requisites get all the elements that compose the page (images, CSS and so on).

--html-extension save files with the .html extension.

--convert-links convert links so that they work locally, off-line.

--restrict-file-names=windows modify filenames so that they will work in Windows as well.

--no-clobber don't overwrite any existing files (used in case the download is interrupted and resumed).

Also note that in wget 1.12, –html-extension is renamed to –adjust-extension

The orignal resource: http://www.linuxjournal.com/...

Mendeley's LibreOffice Plugin

2013-05-14T22:29:00+03:00

Got this error:

(com.sun.start.lang.DisposedException) {{{Message="Binary URP bridge disposed during call", Context=(com.sun.star.uno.XInterface) @7f9191447838}}}

I solved this by installing Python support for LibreOffice.

yum install python-openoffice

Enable Dell Latitude WiFi on Debian

2013-04-08T11:28:00+03:00

I partly followed instructions on this page: http://wiki.debian.org/wl.

In terminal (as root):

aptitude install broadcom-sta-dkms
modprobe -r b44 b43 b43legacy ssb brcmsmac
modprobe wl

Run this command to verify:

iwconfig

How to create an SBML file using libSBML in Python

2012-09-25T16:31:00+03:00

This tutorial is intended as a quick introduction on how to create an SBML file using libSBML. For a full developer's guide, please see libSBML Python API has no title attribute.

from libsbml import *
document = SBMLDocument()
model = document.createModel(2, 4) # SBML level and version

First you have to create compartments

c1 = model.createCompartment()
c1.setName('Forest')
c1.setId('comp_FOREST')

Set the volume of compartments

c1.setVolume(1000)

Continue with other compartments

c2 = model.createCompartment()
c2.setName('Meadow')
c2.setId('comp_Meadow')
c2.setVolume(1000)

When you have finished with compartments, proceed with species.

s1 = model.createSpecies()
s1.setName('Foxes')
s1.setId('spec_FOXES')
s1.setCompartment('comp_FOREST')
s1.setInitialAmount(10)

s2 = model.createSpecies()
s2.setName('Rabbits')
s2.setId('spec_RABBITS')
s2.setCompartment('comp_FOREST')
s2.setInitialAmount(50)

s3 = model.createSpecies()
s3.setName('Snakes')
s3.setId('spec_Snakes')
s3.setCompartment('comp_Meadow')
s3.setInitialAmount(100)

When you are done with compartments and species, create reactions.

r1 = model.createReaction()
r1.setName('Foxes eat rabbits')
r1.setId('R1')

Create reactants and products

reac1 = r1.createReactant()
reac1.setSpecies('spec_RABBITS')
prod1 = r1.createProduct()
prod1.setSpecies('spec_FOXES')

if necessary, set Stoichiometry

reac1.setStoichiometry(2) # 2 rabbits
prod1.setStoichiometry(1) # 1 fox

Notice that we create seemingly independent objects for comprartments, reaction, reactant and product. We set some values to the properties of these objects and never actually add these elements to the model. Thats because they are automatically added. You can try this inside a loop and it will still work.

Now when you have done whith your model you have to add it to the document. document.setModel(model)

If you wish you can add optional information.

model.setName('My test model')
model.setId('MyModelID')

Save to file.

writeSBMLToFile(document,'name_of_your_model.xml')

That's it! Copy&paste this code and try it yourself! Please note that this tutorial is really basic. For more comprehensive examples, please see the examples/ folder in the libSBML source tree.

How to install libSBML in Ubuntu 12.04 with Python bindings

2012-01-13T12:41:00+02:00

Install compiler

apt-get install build-essential

On a fresh ubuntu 12.04 setup you will need to install some additional packages

apt-get install python2.7-dev
apt-get install libxml2-dev
apt-get install swig

Compile and install libSBML

Go to the directory where you have exctracted libsbml source and run these 3 commands

./configure --with-python
make
make install