Tips & Tricks
Bioinformatics- Where & How to Start?
Bioinformatics being an interdisciplinary area of biological science and computer science may sound complicated to beginners in this field. However, it is quite simple. The only thing you need is knowledge in both areas. Here is a way for the beginners to start with bioinformatics.
Getting started with Bioinformatics:
1. Learn basic computer languages
Start with learning basic computer languages such as C or C++. Learn to develop algorithm and write simple programs, then you can move on to writing complex programs. Don’t get disappointed while you see multiple errors while executing your code. Solve these errors and you will learn more of it so that you will not make that mistake again.
2. Basic bioinformatics tools
Try hands-on over basic bioinformatics tools such as alignment tools, structure prediction tools, docking, and so on. Read about their algorithms and complete mechanism in their research papers to understand how they work. It will help you in gaining interest in the next programming language you will want to learn. Besides, learn to interpret their output. Using bioinformatics tools is not only about getting results but also about the conclusion. It is important to analyze results to know what information you get after clicking or running commands.
3. Practice more computer languages
Programming is a very important part of bioinformatics. After learning about algorithm development and basic computer languages, practice more languages such as JAVA, PHP, Python, and so on.
4. Work on Linux-based environment
Get command on a Linux-based environment. You can start with Ubuntu. Start with some basic command lines. Read tutorials and install the software in Linux. It will help you to understand how Linux works. Perform some bash commands such as awk, sed, grep, etc., on FASTA files.
5. Write programs
Occasionally, write some programs as they come up in your research. For example, convert file formats using your generated scripts. Try to build some simple tools.
6. Keep yourself updated
Keep yourself updated regarding new tools and techniques in bioinformatics. Read as many research papers as you can. That way you can learn new techniques and biological problems as well. Read about current biological problems and how to solve them.
7. Do simple projects
Start doing some small projects where you can use some tools and write small programs. You can develop tools as well. It will also help you in conducting a research and may add to your skills.
8. Familiarize yourself with web development
Learn to develop and manage databases on servers. Develop a web front for your database and query the database in back-end to display output at the user-front. Google is always at your service. You will find several similar queries on several platforms.
These are the basic steps that can help beginners in getting started with bioinformatics. Try to be proficient in programming. You can always add more.
Software
CMake installation and upgrade: What worked & what didn’t?!
CMake is a widely used cross-platform build system that automates the process of compiling and linking software projects. In bioinformatics, CMake can be utilized to manage the build process of software tools and pipelines used for data analysis, algorithm implementation, and other computational tasks. However, managing the versions of CMake or upgrading it on Ubuntu (Linux) can be a trivial task for beginners. In this article, we provide methods for installing and upgrading CMake on Ubuntu.
Tips & Tricks
Common mistakes made during computational docking.
Computational docking is not a trivial task once we avoid making some mistakes. In this section, let’s learn about some important points that we should keep in mind while performing computational docking.
Tips & Tricks
How to download FASTA sequences from PDB for multiple structures?
In this article, we are going to download FASTA sequences for multiple structures from PDB [1]. We need to have PDB IDs only for input. (more…)
Software
How to install the LigAlign plugin on Pymol on Ubuntu (Linux)?
Few errors appear when we try to run the LigAlign plugin [1] in Pymol [2]. For example, if you try to run the ligand_alignment plugin, it will give you multiple errors including “Unable to initialize LigAlign v1.00“, or “can’t run LigAlign v1.00” or “incorrect Python syntax” or “Plugin has been installed but initialization failed“. In this article, we explain the reason for this issue and how you can rectify these errors. (more…)
Tips & Tricks
How to make an impactful science presentation?
After your hard work, it is time to showcase your study and the methods of your study to an audience. You must make every point useful and informative. Here, in this article, we are going to share some tips to make your scientific presentation impactful. (more…)
Tips & Tricks
Basic bioinformatics concepts to learn for beginners
This article is for beginners who are stepping into the field of bioinformatics. We will discuss some basic concepts that you need to learn while trying to enter the field of bioinformatics. (more…)
Tips & Tricks
A Beginner’s Guide on How to Write Good Manuscripts
Drafting a manuscript could be a difficult task for beginners in the field of research. In this article, we will provide a few tips for how can you write a good manuscript being a research scholar. (more…)
Tips & Tricks
How to remove HETATMS and chains from PDB file?
This is a basic tutorial on removing the hetero-atoms (HETATMS) and chains from PDB files. It is an essential step for computational and molecular dynamics simulation. (more…)
Tips & Tricks
Importance of Reasoning in Research
Research is considered complicated. As it involves reading multiple research articles and reviews, devising hypotheses and appropriate experiments, and last but not the least, getting a significant output. This seems difficult to read multiple research papers and then extract useful information regarding your project. It involves a methodology to read and understand research articles in one go. This is explained in our previous article “A guide on how to read the research articles”. This article explains the importance of thinking during your entire research. (more…)
Docking
How to Find Binding Pocket/ Binding Site for Docking?
Finding binding sites/pockets in a target protein is one of the important steps in docking studies. It is relatively easier to find a binding pocket in the proteins whose resolved structures are available in PDB than that of the predicted structures. In this article, we will discuss the ways to know a binding pocket or a binding site in a target protein. (more…)
Tips & Tricks
Careers in Bioinformatics and Computational Biology
Bioinformatics is an interesting field of research combining biological sciences and computer sciences. In this article, we will discuss making careers in bioinformatics for starters. (more…)
Tips & Tricks
Current Research Topics in Bioinformatics
Researchers working in the scientific area always want to explore new and hot topics to make informed choices. In this article, all new, current, and demanding research topics in bioinformatics are mentioned. This article is helpful for the researchers who are looking for trends in bioinformatics to select a research topic of broad-spectrum. (more…)
MD Simulation
MD Simulation using GROMACS: Things to remember
Molecular dynamics (MD) simulation is considered amongst the important methods in bioinformatics. Installation of MD simulation software and execution of their commands is critical. It requires several parameters to be considered before performing simulations. A single mistake may result in impractical outputs. In this article, we will discuss such important things to remember during the MD simulation and installation and execution of its software (GROMACS) [1,2]. (more…)
Bioinformatics Books
List of Bioinformatics Books for Beginners
It is difficult to decide which book to read to start learning bioinformatics. Beginners can read this article to know the basic steps involved in learning bioinformatics. A few books are suggested in this article to read for starters in bioinformatics. (more…)
Docking
Common mistakes made during Autodock Vina Installation and Execution
Several errors occur while installing MGLTools and Autodock Vina on Ubuntu. We have explained the complete process of Autodock Vina installation and docking in previous articles. Here are some common errors and mistakes that should be taken care of while installing and running Vina on Ubuntu. (more…)
Tips & Tricks
What does a bioinformatician do?
Bioinformaticians play an important part in data analysis and result interpretation in the field of bioinformatics. However, it is unclear to many what specific role bioinformaticians play day to day. We are often asked by many about what exactly a bioinformatician does. But first, who is a bioinformatician?
Software
MGL Tools & Autodock Vina installation: Frequently Asked Questions and Answers
I have received several e-mails from researchers and students alike regarding installing MGL Tools and Autodock Vina on Ubuntu. Most questions are similar in nature, so I thought of answering them once and for all. In this article, I have collected some frequently asked questions and provided the link to their answers in our question-answer section of Bioinformatics Review. (more…)
Tips & Tricks
A guide on how to read the research articles
Reading a research article could be a problem for students starting their careers in research. Research papers are sometimes difficult to understand especially when you are new to this field. In this article, we will discuss how to read and understand a research article. (more…)
Tips & Tricks
Bioinformatics and programming languages- what do you need to know!
There are various things which come to mind when someone is going to enter in the field of Bioinformatics and the topmost concern is “Do I need to learn computer languages to pursue my career in Bioinformatics?”. The answer is a bit tricky but it could be both “yes” and “no”. This article will describe the conditions where you need to learn programming languages in Bioinformatics. (more…)
Docking
Site-specific docking: Frequently Asked Questions & answers for starters
I have been getting several E-mails from researchers and students alike regarding in-silico docking. Most questions are similar in nature, so I thought of answering them once and for all. In this article, I have collected some frequently asked questions and provided the link to their answers present in our question-answer section of Bioinformatics Review.
It is good to have questions in mind and they can be solved in a way as quoted by Sir Einstein:
“We cannot solve our problems with the same thinking we used when we created them.”
In this article, I have collected some of the most Frequently Asked Questions while performing site-specific and/ or blind docking. You have to consider a lot of factors before performing an actual docking on a protein with a specific ligand.
Question: How do you predict protein’s binding sites?
Question: What is the difference between the blind docking and binding site based docking?
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