# ABI OMICSS Guide 2021 ## ABI OMICSS Guide 2021 - [Welcome](https://docs.abi.am/abi-omicss-guide-2021/master.md): This guide is created by the Armenian Bioinformatics Institute (ABI) and is the curriculum of the OMICSS summer school. - [Molecular Biology](https://docs.abi.am/abi-omicss-guide-2021/week-1/molecular-biology.md): We begin Week 1 with the basics of molecular biology. This module takes an estimated 5 hours to complete. - [Introduction to Biology](https://docs.abi.am/abi-omicss-guide-2021/week-1/molecular-biology/introduction-to-biology.md): This section takes an estimated 40 minutes to complete. - [Macromolecules](https://docs.abi.am/abi-omicss-guide-2021/week-1/molecular-biology/macromolecules.md): This page takes an estimated 2.5 hours to complete. - [DNA & RNA](https://docs.abi.am/abi-omicss-guide-2021/week-1/molecular-biology/dna-and-rna.md): This page takes an estimated 1.5 hours to complete. - [Cell Division](https://docs.abi.am/abi-omicss-guide-2021/week-1/molecular-biology/cell-division.md): This page takes an estimated 30 minutes to complete - [Command-Line](https://docs.abi.am/abi-omicss-guide-2021/week-1/command-line.md): We continue with an introduction to Command-Line. This module takes an estimated 2 hours to complete. - [Connecting to the Server](https://docs.abi.am/abi-omicss-guide-2021/week-1/command-line/connecting-to-the-server.md): This page takes an estimated 15 minutes to complete. - [The Linux Command-Line For Beginners](https://docs.abi.am/abi-omicss-guide-2021/week-1/command-line/the-linux-command-line-for-beginners.md): This page takes an estimated 1 hour to complete. - [The Bash Terminal](https://docs.abi.am/abi-omicss-guide-2021/week-1/command-line/the-bash-terminal.md): This page takes an estimated 1 hour to complete. - [R Programming](https://docs.abi.am/abi-omicss-guide-2021/week-1/r-programming.md): We conclude Week 1 with introduction to R Programming. This module takes an estimated 1.5 hours to complete. - [Getting Started](https://docs.abi.am/abi-omicss-guide-2021/week-1/r-programming/getting-started.md): This page takes an estimated 40 minutes to complete. - [The Basics](https://docs.abi.am/abi-omicss-guide-2021/week-1/r-programming/the-basics.md): This page takes an estimated 45 minutes to complete. - [Data Types](https://docs.abi.am/abi-omicss-guide-2021/week-1/r-programming/data-types.md): This page takes an estimated 25 minutes to complete. - [Week 1 Exam](https://docs.abi.am/abi-omicss-guide-2021/week-1/week-1-exam.md): Complete this exam after you finish Week 1 course material. - [Molecular Biology](https://docs.abi.am/abi-omicss-guide-2021/week-2/molecular-biology.md): We begin Week 2 with molecular biology and pick up where we left off. This module takes an estimated 3 hours to complete. - [DNA Proofreading And Repair](https://docs.abi.am/abi-omicss-guide-2021/week-2/molecular-biology/dna-proofreading-and-repair.md): This page takes an estimated 20 minutes to complete. - [Telomeres and Telomerase](https://docs.abi.am/abi-omicss-guide-2021/week-2/molecular-biology/telomeres-and-telomerase.md): This page takes an estimated 15 minutes to complete. - [Genes](https://docs.abi.am/abi-omicss-guide-2021/week-2/molecular-biology/genes.md): This page takes an estimated 45 minutes to complete. - [The One Gene, One Enzyme Hypothesis](https://docs.abi.am/abi-omicss-guide-2021/week-2/molecular-biology/the-one-gene-one-enzyme-hypothesis.md): This page takes an estimated 15 minutes to complete. - [Transcription](https://docs.abi.am/abi-omicss-guide-2021/week-2/molecular-biology/untitled.md): This page takes an estimated 1 hour to complete - [Translation](https://docs.abi.am/abi-omicss-guide-2021/week-2/molecular-biology/translation.md): This page takes an estimated 30 minutes to complete. - [R Programming](https://docs.abi.am/abi-omicss-guide-2021/week-2/r-programming.md): We pick up where we left off in week 2 of R Programming. This module takes an estimated 4 hours to complete. - [Data Types (continuation)](https://docs.abi.am/abi-omicss-guide-2021/week-2/r-programming/data-types-continuation.md): This page takes an estimated 45 minutes to complete. - [Reading Data](https://docs.abi.am/abi-omicss-guide-2021/week-2/r-programming/reading-data.md): This page takes an estimated 20 minutes to complete. - [Subsetting](https://docs.abi.am/abi-omicss-guide-2021/week-2/r-programming/subsetting.md): This page takes an estimated 35 minutes to complete. - [Control Structures](https://docs.abi.am/abi-omicss-guide-2021/week-2/r-programming/control-structures.md): This page takes an estimated 30 minutes to complete. - [Functions](https://docs.abi.am/abi-omicss-guide-2021/week-2/r-programming/functions.md): This section takes an estimated 45 minutes to complete. - [Scoping Rules](https://docs.abi.am/abi-omicss-guide-2021/week-2/r-programming/scoping-rules.md): This page takes an estimated 1 hour to complete. - [Week 2 Exam](https://docs.abi.am/abi-omicss-guide-2021/week-2/week-2-exam.md): Complete this exam after you finish Week 2 course material. - [Molecular Biology](https://docs.abi.am/abi-omicss-guide-2021/week-3/molecular-biology.md): We begin week 3 with molecular biology and pick up where we left off. This module takes an estimated 3 hours to complete. - [tRNA and Ribosomes](https://docs.abi.am/abi-omicss-guide-2021/week-3/molecular-biology/trna-and-ribosomes.md): This page takes an estimated 15 minutes to complete. - [Stages of Translation & Protein Targeting](https://docs.abi.am/abi-omicss-guide-2021/week-3/molecular-biology/stages-of-translation-and-protein-targeting.md): This page takes an estimated 15 minutes to complete. - [Heredity](https://docs.abi.am/abi-omicss-guide-2021/week-3/molecular-biology/heredity.md): This page takes an estimated 1.5 hours to complete. - [Probabilities In Genetics](https://docs.abi.am/abi-omicss-guide-2021/week-3/molecular-biology/probabilities-in-genetics.md): This page takes an estimated 45 minutes to complete. - [R Programming](https://docs.abi.am/abi-omicss-guide-2021/week-3/r-programming.md): We continue exploring the possibilities of R in Week 3. This module takes an estimated 2.5 hours to complete. - [Loop Functions](https://docs.abi.am/abi-omicss-guide-2021/week-3/r-programming/loop-functions.md): This page takes an estimated 1 hour to complete. - [Base Graphics](https://docs.abi.am/abi-omicss-guide-2021/week-3/r-programming/base-graphics.md): This page takes an estimated 30 minutes to complete. - [Statistics and R](https://docs.abi.am/abi-omicss-guide-2021/week-3/statistics-and-r.md): Lastly, we begin studying Statistics and R. This module takes an estimated 1 hour to complete. - [The Basics](https://docs.abi.am/abi-omicss-guide-2021/week-3/statistics-and-r/the-basics.md): This page takes an estimated 1 hour to complete. - [Week 3 Exam](https://docs.abi.am/abi-omicss-guide-2021/week-3/week-3-exam.md): Complete this exam after you finish Week 3 course material. - [Molecular Biology](https://docs.abi.am/abi-omicss-guide-2021/week-4/untitled.md): This is the final week of studying molecular biology. This module takes an estimated 1.5 hours to complete. - [Interesting Cases of Genes](https://docs.abi.am/abi-omicss-guide-2021/week-4/untitled/interesting-cases-of-genes.md): This page takes an estimated 35 minutes to complete - [The Chromosomal Basis of Inheritance](https://docs.abi.am/abi-omicss-guide-2021/week-4/untitled/the-chromosomal-basis-of-inheritance.md): This page takes an estimated 30 minutes to complete - [Variation in Species](https://docs.abi.am/abi-omicss-guide-2021/week-4/untitled/variation-in-species.md): This page takes an estimated 20 minutes to complete. - [Phenotype plasticity](https://docs.abi.am/abi-omicss-guide-2021/week-4/untitled/phenotype-plasticity.md): This page takes an estimated 5 minutes to complete. - [R Programming](https://docs.abi.am/abi-omicss-guide-2021/week-4/r-programming.md): In the final week of learning R Programming, we focus on practice exercises. This module takes an estimated 40 minutes to complete. - [Practice 2](https://docs.abi.am/abi-omicss-guide-2021/week-4/r-programming/practice-2.md): This page takes an estimated 20 minutes to complete. - [Practice 3](https://docs.abi.am/abi-omicss-guide-2021/week-4/r-programming/practice-3.md): This page takes an estimated 20 minutes to complete. - [Statistics and R](https://docs.abi.am/abi-omicss-guide-2021/week-4/statistics-and-r.md): This module takes an estimated 3 hours to complete. - [Random Variables and Probability Distributions](https://docs.abi.am/abi-omicss-guide-2021/week-4/statistics-and-r/random-variables-and-probability-distributions.md): This page takes an estimated 55 minutes to complete. - [Central Limit Theorem](https://docs.abi.am/abi-omicss-guide-2021/week-4/statistics-and-r/central-limit-theorem.md): This page takes an estimated 2 hours to complete - [Week 4 Exam](https://docs.abi.am/abi-omicss-guide-2021/week-4/week-4-exam.md): Complete this exam after you finish Week 4 course material. - [Statistics and R](https://docs.abi.am/abi-omicss-guide-2021/week-5/untitled.md): We pick up where we left off in week 5 of statistics. This module takes an estimated 2.5 hours to complete. - [Confidence Interval](https://docs.abi.am/abi-omicss-guide-2021/week-5/untitled/confidence-interval.md): This page takes an estimated 45 minutes to complete. - [Introduction to Inference](https://docs.abi.am/abi-omicss-guide-2021/week-5/untitled/introduction-to-inference.md): This page takes an estimated 1 hour to complete. - [t-distribution and Comparing Means](https://docs.abi.am/abi-omicss-guide-2021/week-5/untitled/t-distribution-and-comparing-means.md): This page takes an estimated 20 minutes to complete. - [Linear Models](https://docs.abi.am/abi-omicss-guide-2021/week-5/untitled/linear-models.md): This page takes an estimated 15 minutes to complete. - [Experimental Techniques](https://docs.abi.am/abi-omicss-guide-2021/week-5/experimental-techniques.md): This module takes an estimated 1.5 hours to complete. - [Polymerase Chain Reaction (PCR)](https://docs.abi.am/abi-omicss-guide-2021/week-5/experimental-techniques/polymerase-chain-reaction-pcr.md): This page takes an estimated 35 minutes to complete. - [Gel Electrophoresis](https://docs.abi.am/abi-omicss-guide-2021/week-5/experimental-techniques/gel-electrophoresis.md): This page takes an estimated 40 minutes to complete. - [Sanger Sequencing](https://docs.abi.am/abi-omicss-guide-2021/week-5/experimental-techniques/sanger-sequencing.md): This page takes an estimated 20 minutes to complete. - [NGS Sequencing](https://docs.abi.am/abi-omicss-guide-2021/week-5/experimental-techniques/ngs-sequencing.md): This page takes an estimated 30 minutes to complete. - [Week 5 Exam](https://docs.abi.am/abi-omicss-guide-2021/week-5/week-5-exam.md): Complete this exam after you finish Week 5 course material. - [Statistics and R](https://docs.abi.am/abi-omicss-guide-2021/week-6/untitled.md): We pick up where we left off in week 6 of statistics. This module takes an estimated 2 hours to complete. - [Power](https://docs.abi.am/abi-omicss-guide-2021/week-6/untitled/power.md): This page takes an estimated 25 minutes to complete. - [ANOVA](https://docs.abi.am/abi-omicss-guide-2021/week-6/untitled/anova.md): This page takes an estimated 20 minutes to complete. - [Covariance and Correlation](https://docs.abi.am/abi-omicss-guide-2021/week-6/untitled/covariance-and-correlation.md): This page takes an estimated 1 hour to complete. - [NGS](https://docs.abi.am/abi-omicss-guide-2021/week-6/ngs.md): This module takes an estimated 3 hours to complete. - [Basic Unix Commands](https://docs.abi.am/abi-omicss-guide-2021/week-6/ngs/basic-unix-commands.md): This page takes an estimated 40 minutes to complete. - [Sequences and Genomic Features](https://docs.abi.am/abi-omicss-guide-2021/week-6/ngs/sequences-and-genomic-features.md): This page takes an estimated 1 hour to complete. - [FastQC](https://docs.abi.am/abi-omicss-guide-2021/week-6/ngs/fastqc.md): This page takes an estimated 1 hour to complete. - [Practice Exercises](https://docs.abi.am/abi-omicss-guide-2021/week-6/ngs/practice-exercises.md): This page takes an estimated 15 minutes to complete. - [Week 6 Exam](https://docs.abi.am/abi-omicss-guide-2021/week-6/week-6-exam.md): Complete this exam after you finish Week 6 course material. - [Statistics and R](https://docs.abi.am/abi-omicss-guide-2021/week-7/untitled.md): This is the final week of statistics. This module takes an estimated 2 hours to complete. - [Monte Carlo Simulation](https://docs.abi.am/abi-omicss-guide-2021/week-7/untitled/monte-carlo-simulation.md): This page takes an estimated 45 minutes to complete. - [Exploratory Data Analysis](https://docs.abi.am/abi-omicss-guide-2021/week-7/untitled/exploratory-data-analysis.md): This page takes an estimated 45 minutes to complete. - [Linear Regression](https://docs.abi.am/abi-omicss-guide-2021/week-7/untitled/linear-regression.md): This page takes an estimated 40 minutes to complete. - [NGS](https://docs.abi.am/abi-omicss-guide-2021/week-7/ngs.md): This module takes an estimated 2 hours to complete. - [BEDtools](https://docs.abi.am/abi-omicss-guide-2021/week-7/ngs/bedtools.md): This page takes an estimated 1 hour to complete. - [Alignment and Sequence Variation](https://docs.abi.am/abi-omicss-guide-2021/week-7/ngs/alignment-and-sequence-variation.md): This page takes an estimated 35 minutes to complete. - [Integrated Genomics Viewer](https://docs.abi.am/abi-omicss-guide-2021/week-7/ngs/integrated-genomics-viewer.md): This page takes an estimated 15 minutes to complete. - [Week 7 Exam](https://docs.abi.am/abi-omicss-guide-2021/week-7/week-7-exam.md): Complete this exam after you finish Week 7 course material. - [NGS](https://docs.abi.am/abi-omicss-guide-2021/week-8/untitled.md): In the final week of the guide, we focus on NGS. This module takes an estimated 1 hour to complete. - [Variant Calling With GATK](https://docs.abi.am/abi-omicss-guide-2021/week-8/untitled/variant-calling-with-gatk.md): This page takes an estimated 45 minutes to complete. - [Practice 1](https://docs.abi.am/abi-omicss-guide-2021/week-8/untitled/practice-1.md): This page takes an estimated 15 minutes to complete. - [Week 8 Exam](https://docs.abi.am/abi-omicss-guide-2021/week-8/week-8-exam.md): Complete this exam after you finish Week 8 course material. - [Module Syllabi](https://docs.abi.am/abi-omicss-guide-2021/syllabi.md): Here you can download the syllabi for all the modules in the guide. - [Additional Resources](https://docs.abi.am/abi-omicss-guide-2021/additional-resources.md): Here you can find additional materials to deeper explore data science. - [Conclusion](https://docs.abi.am/abi-omicss-guide-2021/conclusion.md): Congratulations! You have successfully completed the ABI OMICSS 2021 Guide. --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on a page URL with the `ask` query parameter: ``` GET https://docs.abi.am/abi-omicss-guide-2021/master.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.