Bioinformatics has always used computer programs for determining gene and protein functions and establishing evolutionary relationships. Programming languages are useful in bioinformatics for several reasons. If you want to stand out as a bioinformatics specialist, having programming knowledge and skills in Python can be highly beneficial.
In this article, you will learn about the benefits of using Python in bioinformatics, available educational paths, and Python bioinformatics libraries. There’s also a step-by-step learning guide to help get you started. You will gain all the information required to become an expert when it comes to Python and bioinformatics.
What Is Python?
Python is a general-purpose programming language that is used for website and software development, automation, and data analysis. It is one of the most popular programming languages in the world due to its high-level, accessible, and easy-to-understand design which makes it adequate for many projects.
Python has been used to write several popular software applications like YouTube, Google, Instagram, Spotify, Reddit, and Quora. It is preferred by programmers because it is more intuitive than other programming languages. It is also one of the common tools used in bioinformatics because of its emphasis on code readability.
What Is Python Used for in Bioinformatics?
Python is used for several tasks in bioinformatics including academic research, data manipulation, protein sequencing, data analysis, data visualization, accessing databases, and statistical learning. It is also used for macromolecular structure analysis, DNA sequence analysis, and microarray data analysis.
Most bioinformatics specialists or biologists do not know how to program and prefer to spend their time on other tasks. This makes Python ideal for them because of the numerous libraries available that streamline the programming process. These professionals also find it useful for faster prototyping, easier debugging, and more fruitful results.
How Long Will It Take to Learn Python for Bioinformatics?
It will take between a few weeks and a few months. This depends on your educational path, learning format, and previous knowledge or programming experience. There are different educational paths for you to learn Python such as a coding bootcamp or an online class.
Coding bootcamps typically take between four weeks to nine months depending on your choice of bootcamp and learning format. Part-time and online programs typically last longer than full-time and in-person programs. Online courses are mostly self-paced and depend solely on you.
Why Should You Learn Python for Bioinformatics?
Python is the preferred programming language for bioinformatics for many reasons. This section will cover brief details on a few of those reasons including its easy-to-use design, vast community and libraries, consistency and reliability, easy data manipulation, and compatibility with existing tools.
Ease of Use
Python is designed for beginners to be able to take advantage of its benefits with the help of numerous libraries that are freely available. It has a syntax that is similar to the English language making it easy to find your way around programming and web or software development.
As a bioinformatics specialist, you will have other tasks to focus on and need an easy programming language that won’t take too much of your time to master.
Large Community
Python is a very popular language with a large community which has led to the creation of several libraries to support the bioinformatics field. The Python community is made up of millions of software developers willing to help you.
Some of the most popular Python communities include Full Stack Python, PySlackers, Real Python, and Python Discord. As someone willing to learn and use Python, joining any of these communities will come in handy as you can easily reach out to any of the experts available for help.
Versatile, Reliable, and Efficient
Python can work efficiently in many environments. Whether you’re working with a web or desktop application, you can expect the same results. This is one of the reasons why Python is so popular among programmers. It is also much faster than many other programming languages.
Easy Data Manipulation and Visualization
As a bioinformatics specialist, you will regularly work with data manipulation. Pandas, an open-source library under Python, allows for easy, high-performance data structures and data analysis which is necessary for data manipulation.
Python is also good for data visualization because it is open-source, easily accessible, and has a library for numerous tasks. Many Python data visualization libraries can be used to create live, personalized plots, and interactive presentations.
Compatibility With Existing Tools
One of the best things about Python is its ability to integrate with existing technologies. When working on a task with Python, REST APIs can help you with integration. Python can also run on almost all platforms.
How Can I Learn Python for Bioinformatics?
You can choose different educational paths to learn Python for bioinformatics. You can join a coding bootcamp, enroll in an online course, or read and practice with Python textbooks. They each have their advantages and the decision depends on what aligns with your career goals and path.
Coding Bootcamps
Coding bootcamps are designed to equip students with the relevant skills needed to start a career in technology. They typically offer programs in different technology fields from specific programming languages like Python to tech specializations like data science.
They are short-term and immersive and can teach you the skills needed in several weeks or months depending on your learning format and bootcamp choice. Thinkful is a top coding bootcamp that offers multiple programs including the data science program that teaches Python in its curriculum. It offers a part-time online schedule that lasts for six months.
Online Courses
Online courses are a good way to become a self-taught programmer. There are several online learning platforms that you can use to your advantage today and gain the skills you need in your own time. The great thing about online programs is the fact they are typically self-paced and may also offer hands-on training.
For those who are on a budget, you can also find several free courses that offer the same curriculum as the paid courses. An example of this is Coursera’s Biology Meets Programming: Bioinformatics for Beginners that allows you to enroll for free and also get a shareable certificate at the end of the program.
Books
While you may be able to learn all the necessary details and steps through books, it may not be enough. However, it can help you get started in the field if you engage in regular hands-on projects to practice the skills you learn.
There are several books available to those who would like to learn about or increase their knowledge in Python for bioinformatics. Some of them include Python for Bioinformatics by Sebastian Bassi, Bioinformatics Programming Using Python by Mitchell L. Model, and Mastering Python for Bioinformatics by Ken Youens-Clark.
Top Python for Bioinformatics Libraries
Python has vast libraries that you will find useful as a beginner and expert in the field. For any task you may want to perform using Python, you can be almost guaranteed of finding a library for it. Listed below are some Python for bioinformatics libraries.
- BioPython. BioPython is an open-source tool in Python created by an international coalition of developers. It is a compilation of Python tools used for computational biology and bioinformatics. This is an ideal library to use when learning Python for bioinformatics and features documentation, sequence alignment, and source code.
- PyCogent. PyCogent is a software library for genomic biology that is used for making sense of biological and genome sequences.
- Biskit. Biskit is another open-source Python library that can be used for structural bioinformatics research, manipulation, and analysis of macromolecular structures, protein complexes, and molecular dynamics trajectories.
- Galaxy. Galaxy is an open, web-based platform for data-intensive biomedical research with a community of experts who like to share their findings. It is easy to use, reproducible, and transparent.
- PyMOL. PyMOL is open-source molecular visualization software that can be used to render and animate 3D molecular structures.
How to Learn Python for Bioinformatics: A Step-by-Step Guide
There are different steps that you can take to learn Python for bioinformatics depending on what works for you. The following step-by-step guide is recommended to make your learning journey easier and also help you become a professional.
Perfect Your Math Skills
To start learning Python as a bioinformatics tool, you need to ensure that you know important aspects of mathematics including algebra, calculus, probability, and statistics. These skills are essential to helping you understand the basics of Python and programming as a whole. You can do this by taking some online courses, reading relevant books, and practicing.
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Learn Algorithms and Data Structures
Data structures allow you to store and access data and having a good understanding of them will help you when working in Python. Python is designed so users can build their own data structures and control their functionality. Algorithms are used to provide solutions to data analysis problems that you may encounter while working.
Learn to Code with Python
Once you gain an understanding of data structures and algorithms, you can take any of the many courses available on the Internet to learn how to code with Python. Learning Python can be easy as its syntax is similar to the English language and beginner-friendly. If you run into any difficulty, you can seek help from Python’s large community and libraries.
Learn Bioinformatics
This is for those who aren’t already experts in bioinformatics. Those who are can easily proceed to the next stage and begin to work on projects. For those who aren’t, you should gather up as many resources as possible and utilize online resources to gain an in-depth understanding of bioinformatics. This should be easy, especially for those who already have biology experience.
Work on Python Bioinformatics Projects
The final stage involves you working on as many projects as you can, starting with easy ones. You can check online for Python bioinformatics projects for beginners and try to work on one code per day to perfect them. Once you have completed some beginner-level projects and have confidence in your skills, you can move to the next level and apply for entry-level roles.
Start Learning Python for Bioinformatics Today
According to the Bureau of Labor Statistics, computer and information research scientists, which includes bioinformatics professionals, have a job outlook of 22 percent. This rate is higher than most other occupations. Bioinformatics scientists have an average annual salary of $96,979 according to PayScale, which is also higher than most occupations.
Learning Python for bioinformatics will help you advance your career prospects in the industry. Whether you’re new to bioinformatics or a seasoned professional, having Python skills will increase your career prospects.
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