Below you will find pages that utilize the taxonomy term “2018”
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Bootstrap 4 Search Box with Search Icon
Bootstrap 4 is a very handy library to generate quick web user interfaces for web pages and web applications. Search box is a very fundamental UI element if the web page is providing some content and in this post I’ll describe some styles that make a nice text input for search box.
To accomplish this, I’ll make use of the default way of form validations in Bootstrap 3 which was removed in Bootstrap 4 because it doesn’t support font icons anymore.
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How to Install Sambamba on Linux
Sambamba is a great utility to work with alignment file formats in bioinformatics such as BAM and CRAM. Follow below steps on any 64-bit Linux machine to install (this guide installs version 0.6.8 go to Sambamba releases page for the most up-to-date version):
Create a softwares directory (optional but recommended)
cd ~/ mkdir softwares cd softwares/ Download the static executable
wget https://github.com/biod/sambamba/releases/download/v0.6.8/sambamba-0.6.8-linux-static.gz Unzip the package and rename the executable unpacked
Blog
Easy and Free Method to Compress Images on macOS with GUI and Terminal
Image compression is mostly needed if you are short of storage on your devices or if you want to serve your images online and you want to optimize them in a way that we load fast which greatly affects how search engines evaluates your content and how users will enjoy your website.
This is especially important if you are also aiming to support for mobile devices and internet connections that are relatively slow.
Blog
MongoDB Listing Database Collections/Tables with Number of Records/Rows
Use following script and command to quickly get the number of records/rows in the collections/tables in a database.
mongo-ls.js script:
1var collections = db.getCollectionNames(); 2for (var i = 0; i < collections.length; ++i) { 3 print(collections[i] + ' - ' + db[collections[i]].count() + ' records'); 4} So, copy-paste this script in to text file and save as mongo-ls.js.
Finally, use the following command to query the database. Make sure you change HOSTNAME, DBNAME, USERNAME and PASSWORD with your own.
Blog
Convert Gene Symbols to Entrez IDs in R
Bioinformatics studies usually includes gene symbols as identifiers (IDs) as they are more recognizable comparing to other IDs such as Entrez IDs. However, certain analyses (tools) may not use gene symbols as there are usually more than one symbol so it is more difficult to implement a method to work with gene symbols. In such cases, you may need to do a conversion which is very common thing to do in bioinformatics.
Blog
Correct Installation and Configuration of pip2 and pip3
You may have to keep both Python version, the old 2 and 3, at the same time due to your projects and they will require corresponding pip installation so you can separately install and maintain packages for both version.
There are multiple ways of installing pip to a system but the version configuration and setting the default version for pip executable can be tricky.
Below is the easiest solution I’ve found.
Blog
Capture Full Size Screenshot on Chrome without Extension
Chrome’s new Developer Tools has a way to capture high quality full size screenshot of the page so you don’t have to have an extension for it anymore!
Update for latest Chrome versions: Chrome DevTools was slightly changed so here are the new steps (tested in Version 71.0.3578.98 (Official Build) (64-bit) on macOS).
Open the website that you want to capture Use Ctrl + Shift + J shortcut on Windows/Linux or Cmd + Opt + J on Mac to open Developer Tools.
Blog
Memory Leak Testing with Valgrind on macOS using Docker Containers
I had some issues installing Valgrind on macOS High Sierra and [posted some tips to successfully install it to the system]({% post_url 2018-04-28-how-to-install-valgrind-on-macos-high-sierra %}). Although I could install the software this way, it didn’t work correctly after testing with with several real and dummy C++ codes. It was giving me a memory leak error even with an empty code. So, then I decided to use an Ubuntu 16.04 based Docker container to test the code within the container using the Ubuntu version of Valgrind.
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.