Blog

How to Download hg38/GRCh38 FASTA Human Reference Genome

hg38/GRCh38 is the latest human reference genome as of today which was released December, 2013. There are multiple sources for downloading it and also it comes in different versions. The most well-known databases to use for downloading the human reference genomes are UCSC Genome Browser, Ensembl and NCBI. The naming convention hg38 is used by UCSC Genome Browser, while Ensembl and NCBI use GRCh38 to refer to the latest human reference genome.

Blog

How to Install Valgrind on macOS High Sierra

Valgrind is a programming tool for memory debugging, memory leak detection and profiling. Its installation for macOS High Sierra seems problematic and I wanted to write this post to tell the solution that worked for me. I use Homebrew to install it which is the recommended way and the solution also uses it. So, when you try installing right away, you may get the following error: 1brew install valgrind 2valgrind: This formula either does not compile or function as expected on macOS 3versions newer than Sierra due to an upstream incompatibility.

Blog

Jupyter Notebook ile R Programlama - R Kernel Kurulumu

Daha önceki bir yazımda [Jupyter’in kurulumundan ve Jupyter Notebook]({% post_url 2018-03-31-jupyter-python-nedir-nasil-kurulur %})’tan bahsetmiştim. Jupyter’in kurulumu Jupyter Notebook’a Python kernelini direkt kuruyor ve Python ile programlamayı mümkün kılıyor ancak biyoenformatikte sıkça kullanılacak bir diğer programlama dili olan R programlama için ilgili kerneli ekstra kurmak gerekiyor. Bu yazımda bu kernelin kurulumundan bahsedeceğim. Öncelikle [Jupyter kurulumu]({% post_url 2018-03-31-jupyter-python-nedir-nasil-kurulur %}) ve R kurulumu yapılmış olması gerekiyor. Daha sonra Terminal’den aşağıdaki komutu kullanarak bir R oturumu başlatın:

Blog

Jupyter / Python Nedir, Nasıl Kurulur?

Jupyter çeşitli programlama dilleri için etkileşimli bir ortam sağlayan yazılımdır. Orijinal olarak IPython (interactive python) adıyla, Python programlama dili için geliştirildi ancak daha sonra kurucuları Jupyter projesini başlatıp IPython’ın birçok tarafını Jupyter’e kaydırdı. IPython, sadece Jupyter’in kerneli olarak devam ediyor. Jupyter’in özellikleri; Etkileşimli bir shell sunması, Komut İstemi/Terminal’den jupyter console komutu ile başlatılır ve orijinal Python shell’ine göre otomatik tamamlama gibi kullanıcı dostu özellikleri barındırır. Tarayıcı tabanlı defter (notebook) sunması, Komut İstemi/Terminal’den jupyter notebook komutu ile başlatılır, açılan tarayıcı penceresinden yeni defter oluşturularak çeşitli programlama dillerinde kodlar yazılabilir ve bu kodlar çalıştırılarak çıktıları (metin, grafik, vs) etkileşimli olarak direkt tarayıcıda görüntülenebilir.

Blog

Tags Cloud Sorted by Post Count for Jekyll Blogs without Plugins

Recently, I have been trying to transfer my old posts in a Blogger blog to my new Jekyll blog since I really liked this way of blogging. But there were some features that I like in Blogger and wasn’t supported in Jekyll by default. I did some research and found a very nice way of generating tags cloud the my blog. Although I build my blog locally and then push to GitHub pages, I still try not to use a custom plugin.

Blog

How to Generate Database EER Diagrams from SQL Scripts using MySQL Workbench

MySQL Workbench makes it really easy to generate EER diagrams from SQL scripts. Follow below steps to make one for yourself. Download and install MySQL Workbench for your system. See below simple SQL commands, later I’ll use them to generate a sample diagram. 1create table country ( 2 id integer primary key, 3 name CHAR(55)); 4 5create table city ( 6 id integer primary key, 7 country_id integer, 8 name CHAR(55), 9 foreign key (country_id) references country(id)); Open MySQL Workbench and create a new model (File -> New Model).

Blog

Get Size of MySQL Databases

Use below query in MySQL command prompt to get a table of databases and their sizes in MB. SELECT table_schema "DB Name", Round(Sum(data_length + index_length) / 1024 / 1024, 1) "DB Size in MB" FROM information_schema.tables GROUP BY table_schema;

Blog

Replace Entire Column with a Number in Bash

Use below awk one-liner to replace all values in a column (5th column in example) with a value (1 in example). awk "{$5=1} {print}" filename > filename.replaced

Blog

Make a Shortcut for SSH Connections

It could be really annoying to reenter the host name again and again if you are working over ssh and the host name is really long (i.e. mistral.ii.metu.edu.tr). Using this method, you can set a shorcut for the host name (i.e. mistral) and use it whenever you connect. Open ~/.ssh/config for editing: subl ~/.ssh/config Add your host definition as follows: Host mistral HostName mistral.ii.metu.edu.tr User gbudak