Blog

How to Make a Customizable Google Custom Search Engine Box

Google Custom Search Engine (CSE) is a great service when you need to implement a search functionality to a website and do not spend too much time. However, the default way of implementing it restricting us to have a certain search box design that might not blend well to our website. In this post, I’ll show how I found a workaround solution and actually implement on this very blog. To see the solution in action, feel free to search anything on the search box at the top of the right sidebar.

Blog

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.

Blog

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.