Bytes and Molecules - A curious beginner’s journey into bioinformatics

The pandemic brought to light the tremendous efforts of scientists who work hard to find a cure for COVID-19. These fast-paced scientific advancements gave hope for a better world and a curiosity to know and learn more. It also encouraged us to be a part of the science community, as we can do wonders together. To fulfill my curiosity to learn and make an impact, I did a lot of searching. OmicsLogic platform was the answer, equipped with multiple courses, and enabled anyone to make an impact in science.

Bytes and Molecules

Molecules are the fundamental blocks of living organisms, that help them survive and sustain. The major molecules are nucleic acids (DNA and RNA), proteins, carbohydrates, lipids, and metabolites. The hard drive of life is the nucleic acid, which has all the information required for life to continue. The CPU is the protein that runs the life machine using sequences of amino acids. These sequences are bytes of data that can be gathered, analyzed, and interpreted using statistics and information technology. The field analyzing this biological data is called Bioinformatics. The study of each molecular data is Omics. The ‘Bytes and Molecule’ course has 11 lessons that cover all the omics currently being studied. . The ‘Bytes and Molecules’ course gives a brief look into the data used from living organisms, the types of data collected, the methods, and the ways used to improve human health, agriculture, wildlife conservation, etc.

Code of Life and Molecules, Data, and Life:

I often think, “What did my ancestors do?” and my knowledge of ancestors stops with my grandparents. Genealogy services like Ancestry and 23andMe use our DNA data to find out these answers. The lesson ‘Molecules, Data, and Life’ gives an insight into how our ancestry is mapped or looked into using the DNA’s code. The DNA code called the genotype can determine the physical characteristics called the phenotype. The data is reanalyzed for drug discovery, effects on smoking, etc. 

The lesson ‘Code of Life’ explains the structure of DNA, how the DNA packages information using nucleotides, how the nucleotide information is transferred into proteins and is passed on to generations.  

Introduction to Omics:

Omics is the study of molecular data that determines the phenotype of organisms. The study of DNA data is called Genomics, RNA is called Transcriptomics, microbial data from a sample is called Metagenomics, and the data collected from space is called Space Omics.

  • Genomics

Genomics

Organisms are made of cells that keep reproducing to continue life. The DNA, or in some cases RNA has the blueprint to divide and reproduce. The genomics lesson describes the structure of DNA and the nucleotide base pairing. It gives a glimpse of how and why DNA is folded into a chromatin structure and how it folds and unfolds. It shows how the genetic information is passed on to produce proteins and sustain the cell. It also details why a change in this sequence called mutations can affect us and cause diseases. It highlights the Human Genome Project which was done to sequence the entire genome of humans. It briefs about the technologies used in getting the sequences, analyzing the sequences, and the use of analysis in medicine, agriculture, disease control, etc.

  • Transcriptomics

Transcriptomics

The lesson describes the microarray and sequencing techniques required to analyze RNA data. RNA has the functional gene part and the lesson discusses how it can be used to analyze the expression of genes. The lesson explains how the data can be used to find trends and research based on the data called Data-driven research. It introduces us to machine learning aspects that can be used to simulate, analyze, process and annotate these data.

  • Metagenomics

OL Metagenomics

The human body has 10 to 100 trillion microbial cells and micro-organisms that interact with their surrounding environment having both positive and negative impacts. The disease-causing microbes disrupt life and the gut microbes help with digestion. The microbes of an environment co-exist and studying them helps in identifying the normal situation. Abnormalities in the environment can cause disastrous effects. Thus metagenomics is used to find solutions for better disease control, plant growth, etc. The lesson briefly goes through the history of microbiology, the technique of shotgun metagenome sequencing and 16s rRNA sequencing, and the methods to analyze these data. The lesson also goes through the current Human Microbiome Project and American Gut Project. 

  • Protein Structure

Proteins are the machinery of life that carry out the tasks in our cells. This lesson explains the translation of DNA to amino acids, and how they are arranged into primary and secondary structures. The lesson briefs the different types of proteins found in our body and how different structures have different functions. The lesson discusses how sequence similarity, structure similarity play a role in the function of the protein and how two proteins with the same structure can have different sequences and vice versa.

  • Space Omics and Astronaut health

Space Omics - Overview.001 (1)

Many of us have dreamt of being astronauts. But the conditions in space can affect the health conditions of astronauts. The data collected from space can enable us to reduce these adverse effects and make space travel safer. This lesson addresses the problems faced in space that cause adverse health effects. The lesson highlights the Human Research Program by NASA and how the data for studying space omics is collected and the databases available now. One such study is the twin study to identify the aging difference between astronauts in space and earth.

  • Precision Medicine and Bioinformatics:

OL Precision Medicine

Precision medicine’s motto is “One size doesn’t fit all”. Every human has a different genetic makeup. Same drug treatment for a particular disease helps only a very few people. Sequencing techniques generate huge amounts of omics data. The big data can be used to identify precise biomarkers, tailored treatments for each patient, and further improvements in drug discovery. The lesson discusses the prospects of big data analysis in precision medicine. It highlights the number of problems big data still faces and how it can be reduced. It introduces the study of pharmacogenomics that deals with the study of DNA and drug response.

  • Citizen Science and Introduction to R:

R

The ‘Citizen Science’ lesson describes how common people can contribute to science with their visual abilities and language recognition. It highlights projects and research works that are currently done using the help of people.

Figure: Interactive R console in OmicsLogic

The ‘Introduction to R’ lesson has basic R commands for data analysis. R codes can run in an interactive platform. In Figure-6, it can be seen that a terminal is present to run codes in the OmicsLogic platform. 

Highlights of the Course:

  • A biology student, researcher, or anyone can understand and navigate the lesson easily through its guided topics
  • Every lesson has a detailed history, the ongoing research, and the future aspects of each topic
  • Every lesson had multiple external links for reference
  • Quizzes for each lesson is fun to solve 
  • The lesson breaks down every complex term
  • A glossary is present for each lesson 
  • Multiple projects for a particular lesson is linked and they can be immediately analyzed using the T-bioinfo server

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