Bioinformatics is an interdisciplinary field that lies at the junction of biological data and computational analysis techniques. The pace at which biological data is being generated in current times strictly requires high-quality data ‘storage, filtering, analytical and visualization’ tools. Bioinformatics comprises all these tools, techniques and methods; all being computational in nature!
Where it is the identification of a novel biological organism or screening of a new gene to increase the productivity of a certain crop plant, bioinformatics helps in bringing sense to the heavy biological data files generated in the 21st century.
Ranging from medicine, agriculture, genetic engineering, synthetic biology, evolutionary biology, pharmaceutical science, biotechnology, and many more fields, bioinformatics has changed the way Biology used to work before the 1960s. And as Science advances toward AI, ML, and data science, even scientists in this field have made humongous leaps by applying the same approach.
Since the range of tools is very wide, students find it confusing and baffling to choose a starting point from where they can dive into this deep sea of knowledge.
Educators dealing with bioinformatics courses often face the same issue. This article can provide real help as it highlights the blocks encountered by students and lists practical solutions to resolve them. By the end, we’ll share why a virtual lab simulation will prove useful not only for your students but also for you as an educator to deliver concepts more efficiently.
There are 3 reasons why students dread and confuse the topic of Bioinformatics. Acknowledging these blocks is the first step toward making the topic more approachable.
Usually the classroom teaching at school and university level incorporates a lot of usual biology subject knowledge but curricula around the world haven’t unanimously updated much to include bioinformatics as a core course. It is usually provided as one of the electives or optional courses. Due to less guidance and exposure, the learning path for bioinformatics feels new, lonely, and less-guided. Educators, even though aware about the different scopes (research-wise, job-wise and innovation-wise) of the same, don’t get the opportunity to introduce the concepts in classroom teaching.
For many students who have the option to study Bioinformatics from an early career stage, there’s another story. Many biologists are for no reason hesitant to deal with algorithms, softwares, analytical tools and anything that pertains to computational involvement in their courses and research. Some rationalize it saying it requires a computer science background, which obviously isn’t true. While some others dodge it stating it is useless for their work (even this isn’t true when looked at from a larger perspective)! Adding to all this, a poor understanding of the central dogma concept (DNA, RNA, protein) further aggravates the situation as the student swings like a pendulum between core biology and bioinformatics; knowing nothing about both!
Since the bioinformatics domain is an ever-evolving one, the older versions of some softwares and tools keep updating with time. While on the other hand, students are usually taught some very basic features for a limited type of bioinformatics analysis. The dearth of dynamic teaching and updates in the Bioinfo-tech by educators to their students deprives them of knowing the plethora of applications of this field. Uninformed students stay oblivious to more than 50-60% tools in the different softwares they are trained to use at their institute level.
In order to address the blocks encountered while teaching Bioinformatics, educators can engage the under-listed solutions in their classes. These can clarify many instrumental aspects of Bioinformatics. Not only can they make teaching easier for educators like you but will also make lessons clearer and easier to assimilate for your students.
Learning alignment tools, protein modelling tools, molecular docking tools, etc without knowing when to apply them in education and research turns monotonous for students. It would be advisable to teach your students different aspects of the subject with relevant examples. We provide one for you to begin with.
Bio-prospection and ethno-botany are gaining particular interest of governments and industries across the world. Scientists are being encouraged to utilize modern techniques to discover active molecules and compounds from different plant sources. This is mostly working at the interface of ‘ethnobotanical leads from tribal, ethnic and indigenous groups’ and ‘rapidly advancing technology and bioinformatics tools’.
You can engage the example as used in Bioinformatics simulation by Labster. Let’s say a report of an “anti-malarial drug” from a plant used by the tribal people of a region surfaced in the media recently. Now, we have to find the gene responsible for the production of the enzyme that catalyzes the synthesis of this antimalarial compound in plants. But will this help us??? The elucidation of the gene can help us in “setting up industrial production of the anti-malarial molecule in bacterial or yeast systems' ' (which are the biological factories)!
RNA-Seq is one such tool that can be helpful here. It is a sequencing technique that utilizes the next-generation sequencing (NGS) approach to identify, quantify and analyze the RNA in biological samples. It is used for several applied purposes like quantification of gene expression, novel mRNA (transcript) discovery and much more.
Explaining how RNA-Seq works can develop the interest of your students here. And then teaching the bioinformatics tools for the same can become more engaging and worthwhile.
This is one of the most underrated advice but most useful one too for educators. Since bioinformatics data works at the core of molecular biology concepts, students who don’t understand the central dogma of life and how that operates in the biological world can never understand the simple or complex analytical tools pertaining to them. We deal with data from different types of molecules like DNA, RNA, proteins, etc in bioinformatics.
Even when dealing with RNA-Seq, one needs to know how to answer some basic questions like differences between DNA and RNA, mRNA and cDNA, transcription and reverse transcription, etc. The basic rationale behind cDNA library preparation is the more stable nature of dsDNA than mRNA. This is the reason that the 1st step of RNA-Seq involves RNA isolation, followed by mRNA separation and then reverse transcription to generate cDNA. Explaining these little concepts can make lab handling as well as data analyses more logically driven.
Bioinformatics runs majorly on commands, syntaxes and stepwise usage of different databases and tools. Involving more visually engaging tools where students can actively follow these commands becomes primarily important.
Usually bioinformatics books list the different steps used to run a software or a tool. Let’s take an example of the BLAST tool available on NCBI.
In RNA-Seq protocol, after amplifying the cDNA and sequencing it using NGS, you’ll receive very heavy biological data files. Now in order to “screen the gene” coding for the enzyme that catalyzes the production of the antimalarial compound, we will have to use the BLAST tool. Rather than just telling your students to go to NCBI and use the BLAST, explaining the purpose and guiding them using a visually interactive video or flowchart might be more productive. You can also explain the purposes of the different types of BLAST tools that NCBI offers.
There are a number of phylogenetic analysis methods like maximum parsimony, maximum likelihood, Bayesian inference, etc. Teaching your students how each of these methods parses and uses that DNA/RNA data can help them in making informed choices when using phylogenetic tools. Stressing on the concepts of molecular evolution and how its rate varies from nuclear to chloroplast to mitochondrial DNA also become important.
Even for educating your students about the structural differences between mRNA and DNA, visually interactive videos would be a better option. Alternatively, you can use the Bioinformatics simulation by Labster for this purpose.
Figure: This snippet from the Bioinformatics simulation by Labster shows how visually interactive methods can help students in understanding the structures of 3-D molecules effectively. It is available for University / College classes.
Since the frequency of using this analysis method is rare in conventional labs, the hesitation and the air of sophistication around Bioinformatics have lived on for years now. Educators need to go beyond the curricula and teach as many bioinfo-tech tools as possible to their students starting from the school and college level. Usually the trend is opposite that harms the biologists in the long run. We usually teach or our PhD researchers learn Bioinformatics tools in their doctoral research works when they become the necessity of the time. The biologists of the next generation should be abundantly equipped in order to make the most of the rapidly-accumulating biological data!!
Also, educators and teachers should shoulder the responsibility of showing the magnanimous range of applications that this field offers. As the world transcends towards the Science of data analytics- ML, AI and Data Science, biologists should also be equipped well to use the biological data for quicker solution and product deliveries in the field of drug discovery, biomedical science, cancer research, genome editing and similar kinds.
Since Bioinformatics sometimes becomes a mechanical subject to teach in classroom setups, educators can gather more student indulgence using visualization tools. With virtual laboratory simulations from Labster, teachers can make more insightful points as students are rendered with better visual options. The 3-D simulations help them better understand how the steps of each analysis advance and results are delivered.
Your students don’t have to struggle to imagine different aspects of this topic themselves as our interactive Bioinformatics simulation along with gamification elements come to the rescue. By using this way of an active and immersive teaching, our virtual learning platform takes an advent in the field of Science to make the upcoming scientists thorough with the “basics of their respective subjects”.