diff --git a/Sujet_Mblum_masterMSIAM_20172018.pdf b/Sujet_Mblum_masterMSIAM_20172018.pdf new file mode 100644 index 0000000..c912a00 Binary files /dev/null and b/Sujet_Mblum_masterMSIAM_20172018.pdf differ diff --git a/Washington_case.jpg b/Washington_case.jpg new file mode 100644 index 0000000..be4e2d2 Binary files /dev/null and b/Washington_case.jpg differ diff --git a/agglo_clustering.jpg b/agglo_clustering.jpg new file mode 100644 index 0000000..3ded06f Binary files /dev/null and b/agglo_clustering.jpg differ diff --git a/gitcompbiol.Rproj b/gitcompbiol.Rproj new file mode 100644 index 0000000..8e3c2eb --- /dev/null +++ b/gitcompbiol.Rproj @@ -0,0 +1,13 @@ +Version: 1.0 + +RestoreWorkspace: Default +SaveWorkspace: Default +AlwaysSaveHistory: Default + +EnableCodeIndexing: Yes +UseSpacesForTab: Yes +NumSpacesForTab: 2 +Encoding: UTF-8 + +RnwWeave: Sweave +LaTeX: pdfLaTeX diff --git a/intro_ComBiol_20172018.Rmd b/intro_ComBiol_20172018.Rmd new file mode 100644 index 0000000..4ef7d8a --- /dev/null +++ b/intro_ComBiol_20172018.Rmd @@ -0,0 +1,72 @@ +--- +title: "Computational Biology" +author: "michael.blum@univ-grenoble-alpes.fr" +date: "`r Sys.Date()`" +output: + ioslides_presentation: + css: style.css +--- + + +```{r setup, include=FALSE} +knitr::opts_chunk$set(fig.align="center",echo = TRUE) +options(Encoding="UTF-8") +``` + +## Schedule +###First part of the course (michael.blum@univ-grenoble-alpes.fr) is about how to build phylogenetic trees based on DNA sequences. You will have to work, not me! + +- October 3, 09h45-12h45, D208: Introduction and mathematical computations +- October 10, 09h45-12h45, E300: Mathematical computations, practical in R, and report writing +- October 17, 09h45-12h45, E300: Practical in R, and report writing +- October 20: Deadline to submit your report + + +###Second part of the course (Olivier François) + +## An example of Phylogeny: Hominidae +```{r, echo=FALSE,out.width = "500px"} +knitr::include_graphics("tree_primates.jpg") +``` + +## A second example of phylogeny: US criminal case: State of Washington v Anthony Eugene Whitfield +```{r, echo=FALSE,out.width = "400px"} +knitr::include_graphics("Washington_case.jpg") +``` + +## A third example of phylogeny: Tracking SARS back to its source +```{r, echo=FALSE,out.width = "800px"} +knitr::include_graphics("sars.jpg") +``` + +*** +### There are different methods to reconstruct phylogeny. +- Distance-based methods (this course). +- Parcimonious approach (old school). +- Maximum likelihood (computer intensive). + +###What are you going to learn about data science (methods) if you are moderately interested in phylogeny. +- Agglomerative hierarchical clustering: how to make clusters. +- Bootstrap methods: how to evaluate uncertainty. + +##Agglomerative hierarchical clustering +```{r, echo=FALSE,out.width = "800px"} +knitr::include_graphics("agglo_clustering.jpg") +``` + +##Hierarchical clustering + +###Cluster dissimilarity +A measure of dissimilarity between sets of observations (Euclidean distance,…). + +###Linkage criteria +Distance between sets of observations as a function of the pairwise distances between observations (see [Wikipedia webpage about Hierarchical hierarchical clustering](https://en.wikipedia.org/wiki/Hierarchical_clustering) for examples). + +##What are you going to learn about data science (software) if you are moderately interested in phylogeny. +- How to use [R](https://cran.r-project.org/). +- How to use [RStudio](https://www.rstudio.com/). +- Perform dynamic reporting with [R Markdown](http://rmarkdown.rstudio.com/) documents. + +This presentation has been written in .Rmd. + + diff --git a/intro_ComBiol_20172018.html b/intro_ComBiol_20172018.html new file mode 100644 index 0000000..17950ae --- /dev/null +++ b/intro_ComBiol_20172018.html @@ -0,0 +1,198 @@ + + + + Computational Biology + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+

+

+

+

2017-10-02

+
+ + +

Schedule

+ +

First part of the course (michael.blum@univ-grenoble-alpes.fr) is about how to build phylogenetic trees based on DNA sequences. You will have to work, not me!

+ +
    +
  • October 3, 09h45-12h45, D208: Introduction and mathematical computations
    • +
  • October 10, 09h45-12h45, E300: Mathematical computations, practical in R, and report writing
    • +
  • October 17, 09h45-12h45, E300: Practical in R, and report writing
    • +
  • October 20: Deadline to submit your report
    • +
+ +

Second part of the course (Olivier François)

+ +

An example of Phylogeny: Hominidae

+ +

+ +

A second example of phylogeny: US criminal case: State of Washington v Anthony Eugene Whitfield

+ +

+ +

A third example of phylogeny: Tracking SARS back to its source

+ +

+ +

+ +

There are different methods to reconstruct phylogeny.

+ +
    +
  • Distance-based methods (this course).
    • +
  • Parcimonious approach (old school).
    • +
  • Maximum likelihood (computer intensive).
    • +
+ +

What are you going to learn about data science (methods) if you are moderately interested in phylogeny.

+ +
    +
  • Agglomerative hierarchical clustering: how to make clusters.
    • +
  • Bootstrap methods: how to evaluate uncertainty.
    • +
+ +

Agglomerative hierarchical clustering

+ +

+ +

Hierarchical clustering

+ +

Cluster dissimilarity

+ +

A measure of dissimilarity between sets of observations (Euclidean distance,…).

+ +

Linkage criteria

+ +

Distance between sets of observations as a function of the pairwise distances between observations (see Wikipedia webpage about Hierarchical hierarchical clustering for examples).

+ +

What are you going to learn about data science (software) if you are moderately interested in phylogeny.

+ +
    +
  • How to use R.
    • +
  • How to use RStudio.
    • +
  • Perform dynamic reporting with R Markdown documents.
    • +
+ +

This presentation has been written in .Rmd.

 + + + + + + + + + + + + + + diff --git a/sars.jpg b/sars.jpg new file mode 100644 index 0000000..4624ab0 Binary files /dev/null and b/sars.jpg differ diff --git a/style.css b/style.css new file mode 100644 index 0000000..0132f9a --- /dev/null +++ b/style.css @@ -0,0 +1,6 @@ +pre { + width: 100%; /* 106%; */ + left: 0; /* -60px; */ + padding: 10px 15px 10px 15px; /* 10px 0 10px 60px; */ + border-radius: 10px; +} \ No newline at end of file diff --git a/tree_primates.jpg b/tree_primates.jpg new file mode 100644 index 0000000..ad8b2ae Binary files /dev/null and b/tree_primates.jpg differ