Below you will find pages that utilize the taxonomy term “2013”
Blog
How to Get Transcripts (also Exons & Introns) of a Gene using Ensembl API
As a part of my project, I need to obtain exons and introns of certain genes. These genes are actually human genes that are determined for a specific reason that I will describe later when I explain my project. But for now, I want to share the way to obtain this information using (Perl) Ensembl API. Note that Ensembl has started a beautiful way (Ensembl REST API) of getting data but it is beta and it doesn’t provide exons / introns information.
Blog
Geany Color Schemes Ubuntu
There is a collection of color schemes for Geany as well.
Download it on GitHub and follow the instructions.
You’ll need to extract and copy all the files in colorschemes directory to ~/.config/geany/colorschemes/
Then, restart Geany and go to View -> Editor -> Color Schemes and choose your style.
I’m using Tango.
Source
Blog
Install Geany 1.23 on Ubuntu
Geany is a really nice text editor for Ubuntu. I would recommend it with TreeBrowser and some interface coding are color schemes.
But you’ll need the latest version which is 1.23 for now.
To install this version you need to add PPA, also this will keep it updated when you update your system.
Execute following lines one by one:
sudo add-apt-repository ppa:geany-dev/ppa sudo apt-get update sudo apt-get install geany Then, when you start Geany you’ll see “This is Geany 1.
Blog
Install Apache2, PHP5, MySQL & phpMyAdmin on Ubuntu 12.04
First, install apache2:
sudo apt-get install apache2 Then, for it to work: sudo service apache2 restart
For custom www folder:
sudo cp /etc/apache2/sites-available/default /etc/apache2/sites-available/www gksudo gedit /etc/apache2/sites-available/www Change DocumentRoot and Directory directive to point to new location. For example, /home/user/www/
Save and see (link here clean URLs not working Laravel 4)
Make www default and disable default:
sudo a2dissite default && sudo a2ensite www sudo service apache2 restart Create new file in www
Blog
Install Perl DBI Module on Ubuntu 12.04
On Terminal, run:
sudo apt-get install libdbi-perl Source
Blog
Start Ubuntu 12.04 Bluetooth Off
On Terminal:
sudo gedit /etc/rc.local Add following before the line “exit 0”
rfkill block bluetooth Save
Source
Blog
Install Steam on Ubuntu 12.04
Download steam_latest.deb at:
http://repo.steampowered.com/steam/archive/precise/steam_latest.deb Double click and open it on Ubuntu Software Center and click Install
It’ll start Terminal and ask password for sudo because there are some packages required, enter your password and continue
Next it’ll update itself
Done
Source
Blog
Enable Hibernation for Lenovo Z500 on Ubuntu 12.04
Using Terminal add this file:
sudo gedit /etc/polkit-1/localauthority/50-local.d/com.ubuntu.enable-hibernate.pkla This:
[Re-enable hibernate by default] Identity=unix-user:* Action=org.freedesktop.upower.hibernate ResultActive=yes Save & reboot
Source
Blog
Install Spotify on Ubuntu 12.04
Start Software Sources from Dash Home
Add following in Other Sources tab:
deb http://repository.spotify.com stable non-free Close Software Sources
Add Spotify repo key on Terminal:
sudo apt-key adv –keyserver keyserver.ubuntu.com –recv-keys 94558F59 Install Spotify on Terminal:
sudo apt-get update && sudo apt-get install spotify-client Find Spotify in Dash Home
Source
Blog
Enable Software Sources in Dash Home Ubuntu 12.04
First copy the software sources desktop file to your local applications folder:
mkdir -p ~/.local/share/applications cp /usr/share/applications/software-properties-gtk.desktop ~/.local/share/applications/ Edit the file & change the line NoDisplay=true to NoDisplay=false:
gedit ~/.local/share/applications/software-properties-gtk.desktop Save, logout and login
Source
Blog
Save Brightness Settings Ubuntu 12.04 LTS
If your laptop starts with minimized or maximized brightness and you want to have a fixed default value for that do following:
Run terminal and type to get maximum brightness:
cat /sys/class/backlight/acpi_video0/max_brightness Now set the brightness as you want and run following which give you the value for current setting:
cat /sys/class/backlight/acpi_video0/brightness Edit /etc/rc.local to have that value as default after each reboot / start:
sudo gedit /etc/rc.local Add this line before exit 0:
Blog
Hotkeys (special keys) Volume/Brightness Controls Don't Work After Suspend
What seems to solve this problem on Ubuntu 12.04 LTS (Lenovo Z500):
Open this file:
sudo gedit /etc/default/grub Modify the line as this:
GRUB_CMDLINE_LINUX="noapic" Close it and run the following:
sudo update-grub Restart your computer
Source
Blog
session_start() Permission denied (13) Laravel 4
Solve it by running following lines:
chmod -R 755 /path/to/your/laravel/directory chmod -R o+w /path/to/your/laravel/directory And/or maybe:
sudo chown -R www-data:user /path/to/your/laravel/directory
Blog
How To Make A File or Script Executable in Ubuntu
Start terminal CTRL + Alt + T can be used (or just go to Dash Home and type Terminal):
Run this command below:
sudo chmod +x /path/to/your/file Source
Blog
Suspend Laptop When Lid Closed Ubuntu 12.04 LTS in Lenovo Z500
I guess this is a bug. Although suspend is set in Power settings, it doesn’t suspend the laptop when its lid is closed.
To solve it, I’ve found a workaround on web. Here is how you implement it:
Generate folder if it’s not present:
sudo mkdir /etc/acpi/local Set its permissions:
sudo chmod 755 /etc/acpi/local Generate the script:
sudo gedit /etc/acpi/local/lid.sh.post Copy-paste the following:
#!/bin/bash grep -q closed /proc/acpi/button/lid/*/state if [ $?
Blog
Install Ensembl API and BioPerl 1.2.3 on Your System
I’m going to work on a project that requires lots of queries on Ensembl databases so I wanted to install Ensembl API to begin with. Since it’s programmed in Perl, I will be using Perl in this project.
There is a nice tutorial on Ensembl website for API installation. Here I will describe some steps.
1. Download the API and BioPerl
Go to Ensembl FTP ftp://ftp.ensembl.org/pub/ and download “ensembl-api.tar.gz” or click here
Blog
If clean URLs don't work in Laravel 4 on Ubuntu 12.04 LTS
.htaccess directions are correct, mod_rewrite is enabled but still you are getting 404 Not Found errors…
You need to change AllowOverride None to AllowOverride All in /etc/apache2/sites-available/default.
Modified section in the file:
<Directory /home/user/www/> Options Indexes FollowSymLinks MultiViews AllowOverride All Order allow,deny allow from all </Directory>
Blog
A Nice File Browser for Geany 1.23 on Ubuntu 12.04 LTS
If you’re looking for a file browser for Geany, check out TreeBrowser plugin on its page (see the page for screenshots).
To install and enable, just run following o Terminal:
sudo apt-get install geany-plugin-treebrowser And go to “Tools” -> “Plugin Manager”, check “TreeBrowser”
Source
Blog
Permission Issues develop Laravel 4 on Ubuntu 12.04 LTS
If your CSS or JS files don’t seem to load or you get 403 Forbidden or Permissions denied, all you need to do is to run following on terminal:
sudo chmod -R 755 /path/to/your/laravel/directory
Blog
Base URL for Your Laravel 4 Website
To get base URL of your website to generate links to your content or assets do following:
Set $url in app/config/app.php to your base URL:
1'url' => 'http://localhost/example', Use it everywhere with URL::to(), for example:
1echo URL::to('assets/css/general.css'); 2/* outputs http://localhost/example/assets/css/general.css */
Blog
Remove public from URL Laravel 4
Move all content of (files in) public/ folder one level above (to the base)
Fix paths in index.php:
1require __DIR__.'/bootstrap/autoload.php'; 2$app = require_once __DIR__.'/bootstrap/start.php'; Fix path in bootstrap/paths.php:
1'public' => __DIR__.'/..', Done
Source
Blog
Last Submissions to the Challenge
Today, I submitted in silico and experimental data network inference results on Synapse for the next leaderboard on this Wednesday.
For experimental part, I had to exclude edges with FGFR1 and FGFR3 because the data lacks phosphorylated forms of these proteins and networks must be constructed using only phosphoproteins in the data.
Since there was an update for in silico part, I had to modify the script and resubmit the results.
Blog
Network Visualization Using Cytoscape
Cytoscape is a nice tool to visualize network for better understanding and delivery. I used it for in silico data network visualization and the result was really pretty. Now, I have networks constructed using experimental data from HPN-DREAM Challenge.
In this post, I want to demonstrate how to visualize a network with scores. I’m using Cytoscape 2.8 on Ubuntu 12.
First, the network will be read from a SIF file which is default format of Cytoscape for networks.
Blog
Plotting Expression Curves for Experimental Data
As I can plot expression curves for in silico data. I moved on experimental data which is more complex and larger. This data is the result of RPPA experiments on different breast cancer cell lines and it includes protein abundance measurements for about 45 phophoproteins. These phosphoproteins are treated with different inhibitors and stimuli and by comparing their expressions, I will try to infer relations between them.
Before moving on inferring part, I want to have a script that can plot the graphs so that I can see particular results for specific cases.
Blog
Experimental Data Optimization for Network Inference
As I mentioned in my previous post, experimental data from the challenge has missing data values that create problems during analyses. To solve it, first thing I did was to optimize data, which includes detecting missing conditions and putting NAs for data values and sorting them if necessary.
I wrote two functions in the script. First one ranks the data according to the fashion and sorts it based on these ranks.
Blog
Working with Experimental Data from Network Inference Challenge
As I almost finished with in silico data, I moved on to analyses of experimental data using the same script. But since the characteristics of data is somehow different, before inferring network, I need to modify the script to be able to read experimental data files.
These differences include missing data values for some conditions. This makes analyses difficult because I have to estimate a value for them and this will decrease the confidence score of edges.
Blog
In silico Network Inference Last Improvements and Visualization of Result in Cytoscape
I’m almost done with the analysis of in silico data, although I need to decide if I need further analysis with the inhibiting parent nodes in the network. Last, I couldn’t filter out duplicate edges, which were scored differently. Now, with some improvements in the script, low scores duplicates are filtered and there is a better final list of edges which is ready to be visualized.
I also tried visualizing it on Cytoscape.
Blog
Some String Functions in R, String Manipulation in R
I have programmed with Perl, Python, and PHP before, and string manipulation was more direct and easier in them than in R. But still there are useful functions for string manipulation in R. I’m not an expert in R but I’ve been dealing with it for a while and I’ve learned some good functions for this purpose.
Concatenate strings
Concatenation is done with paste function. It gets concatenated strings as arguments separated bu comma and also separator character(s).
Blog
Latest Progress on Network Inference and Edge Scoring
I have improved network inference part of the script slightly by changing the way of comparing intervention (presence of inhibitor and stimulus) and no intervention (presence of stimulus) data from in silico part.
Now, I’m using a function (simp) from an R package called StreamMetabolism, which gets time points and data values and (does integration) calculates the area under the curve (Sefick, 2009). I do this integration for both condition and then I compare them.
Blog
Scoring Edges Network Inference HPN-DREAM Challenge
Yesterday, I managed to infer a network for some part of in silico data from the challenge. Since the challenge also asks for scoring the edges in networks, I developed the script further and add a function for that.
edgeScorer function gets data object of average time points for each curve in intervention/no-intervention sets and scores each edge for each set of conditions. For this, first, it looks for the largest difference among the sets and set it as maxDifference and later, it stores differences divided by maxDifference in another data object.
Blog
Determining Edges More Progress on Network Inference
Lately, I have been writing an R script to infer network using in silico data. Last version of the script was reading MIDAS file and plotting expression profiles. I have modified it and now it reads MIDAS file, does some analyses and prints causal relations to a file. This file is a SIF file as required.
This dataset is generated with 20 antibodies but only 3 of them are perturbed. Also, for one, stimulus is missing.
Blog
Plotting Expression Profiles Data Analysis for Network Inference
For in silico data network inference I decided to develop a script because the existing tools have bugs and they are not compatible with the data. At the same time, I will try to report bugs and the compatibility issues to developers.
in silico data has 660 experiment results of 20 antibodies, 4 kinds of stimuli and 3 kinds of inhibitors. Antibodies are treated with a stimulus, say at t_0 and in the case of inhibitors, say at t_i, antibodies are pre-incubated for some time (t_pre) and then, treated with a stimulus.
Blog
Webinar on HPN-DREAM Breast Cancer Network Inference Challenge
DREAM8 organizers plan a webinar about HPN-DREAM Breast Cancer Network Inference Challenge on July 19, at 10:30 - 11:30 (PDT / UTC -7). General setup of the challenge, demo submissions to the leaderboard will be discussed and also questions about the challenge will be accepted during webinar. The number of the participants to the challenge is also announced: 138.
Registration to the webinar is done using this form. There are limited number of “seats”, but later recordings will be published.
Blog
Network Inference Challenge in silico Data
I had a meeting with BiGCaT this week and we discussed DREAM Breast Cancer Challenge. I presented the challenge and also some ways that I have found to solve the first sub-challenge network inference. Tina, from BiGCaT, suggested starting with in silico data which is much simpler than breast cancer data. Later, I can use the methods I develop for in silico data in experimental data.
in silico data contains 20 antibodies, 3 inhibitors and 2 ligand stimuli with 2 different concentration for each.
Blog
First Impressions and Thoughts on Rosalind Project
Actually, I signed up Rosalind.info 8 months ago, I didn’t really play around with it. But last week, in a BiGCaT science cafe, after I learnt it, I was more interested than before and I just started solving problems.
In each problem, you have a description about the context and also about the problem. Also, there is a sample input and output. Sometimes there are hints about the solution. What I did was to write a solution that works for the sample and hopefully for the problem.
Blog
Playing around with CellNOptR Tool and MIDAS File
With CellNOptR, we will try to construct network models for the challenge. For this, the tool needs two inputs. First one is a special data object called CNOlist that stores vectors and matrices of data. Second one is a .SIF file that contains prior knowledge network which can be obtained from pathway database and analysis tools.
CNOlist contains following fields: namesSignals, namesCues, namesStimuli and namesInhibitors, which are vectors storing the names of measurements.
Blog
Progress on Network Inference Sub-Challenge
This sub-challenge has several requirements:
Directed and causal edges on the models (32 models - 4 cell lines × 8 stimuli) Edges should be scored (normalizing to range between 0 and 1) that will show confidence Nodes will be phosphoproteins from the data Prior knowledge network (that can be constructed using pathway databases) is allowed to be used (actually this is a must for some network inference tools) First thing was to look for existing tools.
Blog
Retrieving Data with AJAX using jQuery, PHP and MySQL
Last semester, I took a course from Informatics Institute at METU called “Biological Databases and Data Analysis Tools” where first we learned what is a database and how to do queries on it. Also, the technology behind databases are taught. Then, we learned many biological databases and data analysis tools available. These include gene, protein and pathway databases, tools for creating databases.
As a final project, we were asked to create an online tool that can search a database and get the data and display it on any web browsers.
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Using Online Tools for Teaching Bioinformatics
I attended one of science cafe meetings of BiGCaT group today and we discussed use of online tools for teaching bioinformatics.
Andra Waagmeester (PhD student form BiGCaT) introduced Rosalind Project as a teaching tool. This project mainly focuses on bioinformatics solutions. Various questions about bioinformatics are asked on the website. Actually, those are various problems that can be seen in any bioinformatics research and by solving them, it helps you learn bioinformatics.
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Network Inference DREAM Breast Cancer Challenge
The inference of causal edges are described as the change on a node seen after the intervention of another node. If the curves obtained over time overlap (under intervention or no intervention), then there is no relation. Otherwise, we can draw an edge between those nodes and according to the level, up or down, the edge will be activating or inhibiting. These causal edges are context-specific so in different cell line data, we may have different relations.
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DREAM Breast Cancer Sub-challenges
I have been going over the sub-challenges before attempting to solve them. As I mentioned, there are three sub-challenges and somehow they are connected.
First, using given data and other possible data sources such as pathway databases, the causal signaling network of the phosphoproteins. There are 4 cell lines and 8 stimulus so they make total 32 networks at the end. Nodes are phosphoproteins and edges should be directed and causal (activator or inhibitor).
Blog
HPN-DREAM Breast Cancer Network Inference Challenge
Understanding signaling networks might bring more insights on cancer treatment because cells respond to their environment by activating these networks and phosphorylation reactions play important roles in these networks.
The goal of this challenge is to advance our ability and knowledge on signaling networks inference and protein phosphorylation dynamics prediction. Also, we are asked to develop a visualization method for the data.
The dataset provided is extensive and a result of RPPA (reverse-phase protein array) experiments.
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Dream Challenge
This year, 8th Dream Challenge takes place and I will be working on this project as my internship job in BiGCaT, Bioinformatics, UM. The challenge brings scientists to catalyze the interaction between experiment and theory in the area of cellular network inference and quantitative model building in systems biology (as said on their webpage).
In this competition, I will work on a specific challenge about network modeling, dynamic response predictions and data visualization.