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.
As a bioinformatics analyst, you just need to know about different software or tools, how to execute them via a pipeline or bash scripting, and how to filter your results, analyze them, and extract some useful information. Generally, all the software packages that are used in Bioinformatics always come with a manual explaining their usage and different features. So, there is no need to learn any specific language for them. Users can easily follow the tutorial and get the results but of course, they have to have a basic understanding of what they are doing and why, whereas, for some analyses such as component analysis using MATLAB (The MathWorks, Inc., Natick, Massachusetts, United States.) may require the knowledge of some specific languages, for example, R.
In the other case, if you are in an algorithm-driven lab which is more focussed on developing software, pipelines, and so on, then definitely, you need to have a knowledge of programming languages. At first, you should understand the algorithm development and then a few programming languages to amend it. The circumstances to develop new software are when there is no simple, easy-to-use solution is available to a certain problem.
In the field of bioinformatics, some commonly used computer languages include Python, R, MySql, PHP, and Perl. Its always better to know more advanced languages such as Java. In conclusion, it is better to learn some programming languages to pursue your career in bioinformatics but if you want to be an expert in bioinformatics analysis, then not knowing these languages would not be a problem.
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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…)
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. (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…)
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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