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.quarto/idx/index.qmd.json

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-{"title":"Preface","markdown":{"yaml":{"description":"An introductory book built upon several lectures about computational biology.\n","citation":{"type":"book","doi":"10.5281/zenodo.6468280","url":"https://camilogarciabotero.github.io/biocomp-book/"}},"headingText":"Preface","headingAttr":{"id":"","classes":["unnumbered"],"keyvalue":[]},"containsRefs":false,"markdown":"\n\nWe started this book with the aim of compiling the lectures of the course Fundamentals of Computational Biology offered at EAFIT University for undergrad students in Biology. The course has been taught from different perspectives from its creation. All main units are depicted in this book, although the course is mainly composed from at least four of them. We suggest to cover the first three units/parts and vary the last. Units in this book are partitioned as follows: i) Unix, ii) sequence analysis, iii) genomics, iii) metagenomics iv) RNA seq v) structural biology.\n\nLectures are focused on a theoretical-practical approach where basic concepts from biology, bioinformatics and computer science and interleave with the practice to solve challenges. Exercises or challenges are designed to improve students' abilities that are likely to be involved in real-life problems in computational biology.\n\n::: { .callout-important appearance=\"minimal\"}\n#  {{< fa solid biohazard >}}\nThis book is a work in progress. If you find issues, typos or relevant information to share with, anything is welcome and appreciated.\n:::\n\n## Learning features {.unnumbered}\n\n::: callout-note\nSometimes other fields might add interested value to the understanding of the computational biology area. This feature remarks some of them and aim to explain these intersections.\n:::\n\n:::{.callout-tip}\nAs you move forward in the computational biology field you will find that there are several tips and tricks (mainly from the command line) as well as some random CLI programs that can leverage your daily workflow as a researcher. Using this feature we highlight some of those that appeared to linger on the field.\n:::\n\n:::{.callout-important}\nTo help you consolidate your understanding we end most chapters with important messages or concepts that help you evaluate yourself as you move forward on the lessons.\n:::\n\n:::{.callout-caution}\n## Caution\nWhen experimenting with the CLI and many other computational tools it is common to face several known errors and drawbacks. Then, we present some of them and how to sort them out.\n:::\n\n:::{.callout-warning}\n## Challenges\n\nSince focused on a competences learning approach we have highlighted several real-life (but basic) *challenges* a researcher faces when approaching computational biology problem (from tool selection, usage and result analysis). Therefore the book section *challenges* presents a selection of these problems that will later be approached by a computational biology strategy (mainly from the CLI).\n:::\n\n:::{.callout}\n## {{< fa file >}} File format\n\nAs many analysis specialize on data analysis, many formats arise that optimize the processing steps or the data storing steps. Some of these formats are keystones of bioinformatic analyses. We present examples of some formats an describe its main elements.\n:::\n\n## Notation\n\n### Mathematical notaions\n\n"},"formats":{"html":{"identifier":{"display-name":"HTML","target-format":"html"},"execute":{"fig-width":7,"fig-height":5,"fig-format":"retina","fig-dpi":96,"df-print":"paged","error":false,"eval":true,"cache":true,"freeze":false,"echo":true,"output":true,"warning":true,"include":true,"keep-md":false,"keep-ipynb":false,"ipynb":null,"enabled":null,"daemon":null,"daemon-restart":false,"debug":false,"ipynb-filters":[],"engine":"markdown"},"render":{"keep-tex":false,"keep-source":false,"keep-hidden":false,"prefer-html":false,"output-divs":true,"output-ext":"html","fig-align":"center","fig-pos":null,"fig-env":null,"code-fold":"none","code-overflow":"scroll","code-link":true,"code-line-numbers":false,"code-tools":false,"tbl-colwidths":"auto","merge-includes":true,"latex-auto-mk":true,"latex-auto-install":true,"latex-clean":true,"latex-max-runs":10,"latex-makeindex":"makeindex","latex-makeindex-opts":[],"latex-tlmgr-opts":[],"latex-input-paths":[],"latex-output-dir":null,"link-external-icon":false,"link-external-newwindow":false,"self-contained-math":false,"format-resources":[],"notebook-links":true,"format-links":true},"pandoc":{"standalone":true,"wrap":"none","default-image-extension":"png","to":"html","reference-location":"margin","highlight-style":"ayu","output-file":"index.html"},"language":{},"metadata":{"lang":"en","fig-responsive":true,"quarto-version":"1.3.26","bibliography":["references.bib"],"crossref":{"lst-title":"Code"},"comments":{"hypothesis":true,"giscus":{"repo":"camilogarciabotero/biocomp-book","theme":"transparent_dark"}},"google-scholar":true,"theme":{"light":["flatly","style/fonts.scss"],"dark":["darkly","style/fonts.scss"]},"code-copy":"hover","mainfont":"Atkinson Hyperlegible","monofont":"JetBrains","description":"An introductory book built upon several lectures about computational biology.\n","citation":{"type":"book","doi":"10.5281/zenodo.6468280","url":"https://camilogarciabotero.github.io/biocomp-book/"}},"extensions":{"book":{"multiFile":true}}}}}
+{"title":"Preface","markdown":{"yaml":{"description":"An introductory book built upon several lectures about computational biology.\n","citation":{"type":"book","doi":"10.5281/zenodo.6468280","url":"https://camilogarciabotero.github.io/biocomp-book/"}},"headingText":"Preface","headingAttr":{"id":"","classes":["unnumbered"],"keyvalue":[]},"containsRefs":false,"markdown":"\n\nWe started this book with the aim of compiling the lectures of the course Fundamentals of Computational Biology offered at EAFIT University for undergrad students in Biology. The course has been taught from different perspectives from its creation. All main units are depicted in this book, although the course is mainly composed from at least four of them. We suggest to cover the first three units/parts and vary the last. Units in this book are partitioned as follows: i) Unix, ii) sequence analysis, iii) genomics, iii) metagenomics iv) RNA seq v) structural biology.\n\nLectures are focused on a theoretical-practical approach where basic concepts from biology, bioinformatics and computer science and interleave with the practice to solve challenges. Exercises or challenges are designed to improve students' abilities that are likely to be involved in real-life problems in computational biology.\n\n::: { .callout-important appearance=\"minimal\"}\n#  {{< fa solid biohazard >}}\nThis book is a work in progress. If you find issues, typos or relevant information to share with, anything is welcome and appreciated.\n:::\n\n## Learning features {.unnumbered}\n\n::: callout-note\nSometimes other fields might add interested value to the understanding of the computational biology area. This feature remarks some of them and aim to explain these intersections.\n:::\n\n:::{.callout-tip}\nAs you move forward in the computational biology field you will find that there are several tips and tricks (mainly from the command line) as well as some random CLI programs that can leverage your daily workflow as a researcher. Using this feature we highlight some of those that appeared to linger on the field.\n:::\n\n:::{.callout-important}\nTo help you consolidate your understanding we end most chapters with important messages or concepts that help you evaluate yourself as you move forward on the lessons.\n:::\n\n:::{.callout-caution}\n## Caution\nWhen experimenting with the CLI and many other computational tools it is common to face several known errors and drawbacks. Then, we present some of them and how to sort them out.\n:::\n\n:::{.callout-warning}\n## Challenges\n\nSince focused on a competences learning approach we have highlighted several real-life (but basic) *challenges* a researcher faces when approaching computational biology problem (from tool selection, usage and result analysis). Therefore the book section *challenges* presents a selection of these problems that will later be approached by a computational biology strategy (mainly from the CLI).\n:::\n\n:::{.callout}\n## {{< fa file >}} File format\n\nAs many analysis specialize on data analysis, many formats arise that optimize the processing steps or the data storing steps. Some of these formats are keystones of bioinformatic analyses. We present examples of some formats an describe its main elements.\n:::\n\n## Notation\n\n### Mathematical notaions\n\n"},"formats":{"html":{"identifier":{"display-name":"HTML","target-format":"html"},"execute":{"fig-width":7,"fig-height":5,"fig-format":"retina","fig-dpi":96,"df-print":"paged","error":false,"eval":true,"cache":true,"freeze":false,"echo":true,"output":true,"warning":true,"include":true,"keep-md":false,"keep-ipynb":false,"ipynb":null,"enabled":null,"daemon":null,"daemon-restart":false,"debug":false,"ipynb-filters":[],"engine":"markdown"},"render":{"keep-tex":false,"keep-source":false,"keep-hidden":false,"prefer-html":false,"output-divs":true,"output-ext":"html","fig-align":"center","fig-pos":null,"fig-env":null,"code-fold":"none","code-overflow":"scroll","code-link":true,"code-line-numbers":false,"code-tools":false,"tbl-colwidths":"auto","merge-includes":true,"latex-auto-mk":true,"latex-auto-install":true,"latex-clean":true,"latex-max-runs":10,"latex-makeindex":"makeindex","latex-makeindex-opts":[],"latex-tlmgr-opts":[],"latex-input-paths":[],"latex-output-dir":null,"link-external-icon":false,"link-external-newwindow":false,"self-contained-math":false,"format-resources":[],"notebook-links":true,"format-links":true},"pandoc":{"standalone":true,"wrap":"none","default-image-extension":"png","to":"html","reference-location":"margin","highlight-style":"ayu","output-file":"index.html"},"language":{},"metadata":{"lang":"en","fig-responsive":true,"quarto-version":"1.3.56","bibliography":["references.bib"],"crossref":{"lst-title":"Code"},"comments":{"hypothesis":true,"giscus":{"repo":"camilogarciabotero/biocomp-book","theme":"transparent_dark"}},"google-scholar":true,"theme":{"light":["flatly","style/fonts.scss"],"dark":["darkly","style/fonts.scss"]},"code-copy":"hover","mainfont":"Atkinson Hyperlegible","monofont":"JetBrains","description":"An introductory book built upon several lectures about computational biology.\n","citation":{"type":"book","doi":"10.5281/zenodo.6468280","url":"https://camilogarciabotero.github.io/biocomp-book/"}},"extensions":{"book":{"multiFile":true}}}}}

.quarto/idx/intro.qmd.json

@@ -1 +1 @@
-{"title":"Introduction","markdown":{"yaml":{"filters":["nutshell"]},"headingText":"Introduction","headingAttr":{"id":"","classes":["unnumbered"],"keyvalue":[]},"containsRefs":false,"markdown":"\n\n\nThe present book gathers the lecture notes of the undergrad course in Fundamentals of Computational Biology that takes place in EAFIT University. The first part will focus on how to use the the command line interface (aka CLI). It includes a long-format chapter about the Unix tools and concepts that is taught during the first four class lessons. The second chapter of covers the basics of git and the principal workflows to work daily on a collaborative manner this is actually the second lesson of the course. The third lessons, highlights the importance of package manager systems (such as homebrew and conda or scoop) and briefly introduce the main concepts and relevant commands. Later, in a fourth lesson, we introduce important concepts about how computers handle the tasks or jobs, and the parallelization of them. We talk about the computer architectures, the cluster architectures and the job scheduling software called Slurm, which is used on our local HPC cluster.\n\nThe second part is dedicated to sequence analysis and will cover several topics related to sequencing technologies, sequence alignments. All this topics are covered from the biological perspective, mathematical notions and the practical computing approach. Some of the main bioinformatics file extensions are covered and the git \n\nThird part is focused genomics. It will cover main algorithms for genome assembly and some relevant programs. Also the biological nuances of gene calling and gene annotation, and finally will variant calling analysis, which introduces the gene mapping concept and some of the most important bioinformatics file extensions.\n\nNext parts are currently optionals for the course per-se and some iterations may only include one of those or some combinations. They are mainly dedicated to introduce metagenomics, differential gene expression analysis and structural bioinformatics.\n\n<!-- Include a section, maybe an appendix about how to handle errors\nInclude s section about the windows subsystem for linux (WSL) and the ease of use for windows users -->\n\n## Bioinformatics vs. Computational biology\n\n## The extent of computational biology\n\nThere so many fields on bioinformarics [Fig. @fig-biofields], that sometimes its hard to focus on the fundamentals. But this is also an opportunity to discuss the main aspects and differences across the fields.\n\n![Different areas on bioinfomatics](chs-command-line/imgs-cli/biofields.png){#fig-biofields}"},"formats":{"html":{"identifier":{"display-name":"HTML","target-format":"html"},"execute":{"fig-width":7,"fig-height":5,"fig-format":"retina","fig-dpi":96,"df-print":"paged","error":false,"eval":true,"cache":true,"freeze":false,"echo":true,"output":true,"warning":true,"include":true,"keep-md":false,"keep-ipynb":false,"ipynb":null,"enabled":null,"daemon":null,"daemon-restart":false,"debug":false,"ipynb-filters":[],"engine":"markdown"},"render":{"keep-tex":false,"keep-source":false,"keep-hidden":false,"prefer-html":false,"output-divs":true,"output-ext":"html","fig-align":"center","fig-pos":null,"fig-env":null,"code-fold":"none","code-overflow":"scroll","code-link":true,"code-line-numbers":false,"code-tools":false,"tbl-colwidths":"auto","merge-includes":true,"latex-auto-mk":true,"latex-auto-install":true,"latex-clean":true,"latex-max-runs":10,"latex-makeindex":"makeindex","latex-makeindex-opts":[],"latex-tlmgr-opts":[],"latex-input-paths":[],"latex-output-dir":null,"link-external-icon":false,"link-external-newwindow":false,"self-contained-math":false,"format-resources":[],"notebook-links":true,"format-links":true},"pandoc":{"standalone":true,"wrap":"none","default-image-extension":"png","to":"html","reference-location":"margin","highlight-style":"ayu","filters":["nutshell"],"output-file":"intro.html"},"language":{},"metadata":{"lang":"en","fig-responsive":true,"quarto-version":"1.3.26","bibliography":["references.bib"],"crossref":{"lst-title":"Code"},"comments":{"hypothesis":true,"giscus":{"repo":"camilogarciabotero/biocomp-book","theme":"transparent_dark"}},"google-scholar":true,"theme":{"light":["flatly","style/fonts.scss"],"dark":["darkly","style/fonts.scss"]},"code-copy":"hover","mainfont":"Atkinson Hyperlegible","monofont":"JetBrains"},"extensions":{"book":{"multiFile":true}}}}}
+{"title":"Introduction","markdown":{"yaml":{"filters":["nutshell"]},"headingText":"Introduction","headingAttr":{"id":"","classes":["unnumbered"],"keyvalue":[]},"containsRefs":false,"markdown":"\n\n\nThe present book gathers the lecture notes of the undergrad course in Fundamentals of Computational Biology that takes place in EAFIT University. The first part will focus on how to use the the command line interface (aka CLI). It includes a long-format chapter about the Unix tools and concepts that is taught during the first four class lessons. The second chapter of covers the basics of git and the principal workflows to work daily on a collaborative manner this is actually the second lesson of the course. The third lessons, highlights the importance of package manager systems (such as homebrew and conda or scoop) and briefly introduce the main concepts and relevant commands. Later, in a fourth lesson, we introduce important concepts about how computers handle the tasks or jobs, and the parallelization of them. We talk about the computer architectures, the cluster architectures and the job scheduling software called Slurm, which is used on our local HPC cluster.\n\nThe second part is dedicated to sequence analysis and will cover several topics related to sequencing technologies, sequence alignments. All this topics are covered from the biological perspective, mathematical notions and the practical computing approach. Some of the main bioinformatics file extensions are covered and the git \n\nThird part is focused genomics. It will cover main algorithms for genome assembly and some relevant programs. Also the biological nuances of gene calling and gene annotation, and finally will variant calling analysis, which introduces the gene mapping concept and some of the most important bioinformatics file extensions.\n\nNext parts are currently optionals for the course per-se and some iterations may only include one of those or some combinations. They are mainly dedicated to introduce metagenomics, differential gene expression analysis and structural bioinformatics.\n\n<!-- Include a section, maybe an appendix about how to handle errors\nInclude s section about the windows subsystem for linux (WSL) and the ease of use for windows users -->\n\n## Bioinformatics vs. Computational biology\n\n## The extent of computational biology\n\nThere so many fields on bioinformarics [Fig. @fig-biofields], that sometimes its hard to focus on the fundamentals. But this is also an opportunity to discuss the main aspects and differences across the fields.\n\n![Different areas on bioinfomatics](chs-command-line/imgs-cli/biofields.png){#fig-biofields}"},"formats":{"html":{"identifier":{"display-name":"HTML","target-format":"html"},"execute":{"fig-width":7,"fig-height":5,"fig-format":"retina","fig-dpi":96,"df-print":"paged","error":false,"eval":true,"cache":true,"freeze":false,"echo":true,"output":true,"warning":true,"include":true,"keep-md":false,"keep-ipynb":false,"ipynb":null,"enabled":null,"daemon":null,"daemon-restart":false,"debug":false,"ipynb-filters":[],"engine":"markdown"},"render":{"keep-tex":false,"keep-source":false,"keep-hidden":false,"prefer-html":false,"output-divs":true,"output-ext":"html","fig-align":"center","fig-pos":null,"fig-env":null,"code-fold":"none","code-overflow":"scroll","code-link":true,"code-line-numbers":false,"code-tools":false,"tbl-colwidths":"auto","merge-includes":true,"latex-auto-mk":true,"latex-auto-install":true,"latex-clean":true,"latex-max-runs":10,"latex-makeindex":"makeindex","latex-makeindex-opts":[],"latex-tlmgr-opts":[],"latex-input-paths":[],"latex-output-dir":null,"link-external-icon":false,"link-external-newwindow":false,"self-contained-math":false,"format-resources":[],"notebook-links":true,"format-links":true},"pandoc":{"standalone":true,"wrap":"none","default-image-extension":"png","to":"html","reference-location":"margin","highlight-style":"ayu","filters":["nutshell"],"output-file":"intro.html"},"language":{},"metadata":{"lang":"en","fig-responsive":true,"quarto-version":"1.3.56","bibliography":["references.bib"],"crossref":{"lst-title":"Code"},"comments":{"hypothesis":true,"giscus":{"repo":"camilogarciabotero/biocomp-book","theme":"transparent_dark"}},"google-scholar":true,"theme":{"light":["flatly","style/fonts.scss"],"dark":["darkly","style/fonts.scss"]},"code-copy":"hover","mainfont":"Atkinson Hyperlegible","monofont":"JetBrains"},"extensions":{"book":{"multiFile":true}}}}}