From 72bb4b1c0891d965925aea37d6a10e692f7165b7 Mon Sep 17 00:00:00 2001 From: avahoffman Date: Wed, 16 Oct 2024 09:22:36 -0400 Subject: [PATCH 1/6] skills --- index.Rmd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/index.Rmd b/index.Rmd index 4c1b838..e390411 100644 --- a/index.Rmd +++ b/index.Rmd @@ -27,10 +27,10 @@ The activities in this guide are written for undergraduate students and beginnin ::: {.notice} _Genetics_ - +**Beginner**: some genetics knowledge needed _Programming skills_ - +**Novice**: no programming experience needed ::: ## Platform From e5c748bf75b2cdd08c58a95ecdb382c2a2016f5f Mon Sep 17 00:00:00 2001 From: avahoffman Date: Wed, 16 Oct 2024 09:31:28 -0400 Subject: [PATCH 2/6] Polish details --- 06-using_galaxy.Rmd | 2 +- 08-student_guide.Rmd | 2 ++ index.Rmd | 2 +- 3 files changed, 4 insertions(+), 2 deletions(-) diff --git a/06-using_galaxy.Rmd b/06-using_galaxy.Rmd index 24c40b4..afd105e 100644 --- a/06-using_galaxy.Rmd +++ b/06-using_galaxy.Rmd @@ -2,7 +2,7 @@ knitr::opts_chunk$set(out.width = "100%") ``` -# Programming Platforms +# Using Galaxy This section provide a general overview of how to use Galaxy on AnVIL. diff --git a/08-student_guide.Rmd b/08-student_guide.Rmd index faa2113..95b8157 100644 --- a/08-student_guide.Rmd +++ b/08-student_guide.Rmd @@ -31,3 +31,5 @@ cow::borrow_chapter( ) ``` :::: + +More details coming soon! diff --git a/index.Rmd b/index.Rmd index 318a19d..9e91de6 100644 --- a/index.Rmd +++ b/index.Rmd @@ -13,7 +13,7 @@ favicon: assets/GDSCN_style/gdscn_favicon.ico # About this Book {-} -This is a companion training guide for BioDIGS, a GDSCN project that brings a research experience into the classroom. In this module, students will investigate whether metagenomic samples from the BioDIGS project contain either antimicrobial resistance genes or biosynthesis genes. They will run analyses using ABRicate as implemented on Galaxy. Visit the BioDIGS (BioDiversity and Informatics for Genomics Scholars) website [here](https://biodigs.org/) for more information about this collaborative, distributed research project, including how you can get involved! +This is a companion training guide for BioDIGS, a GDSCN project that brings a research experience into the classroom. In this module, students will investigate **whether metagenomic samples from the BioDIGS project contain antimicrobial resistance genes**. They will run analyses using **ABRicate as implemented on Galaxy**. Visit the BioDIGS (BioDiversity and Informatics for Genomics Scholars) website [here](https://biodigs.org/) for more information about this collaborative, distributed research project, including how you can get involved! The GDSCN (Genomics Data Science Community Network) is a consortium of educators who aim to create a world where researchers, educators, and students from diverse backgrounds are able to fully participate in genomic data science research. You can find more information about its mission and initiatives [here](https://www.gdscn.org/home). From 2cd301365db227c0d435aea6fc9351a46d1a96ce Mon Sep 17 00:00:00 2001 From: avahoffman Date: Wed, 16 Oct 2024 09:42:10 -0400 Subject: [PATCH 3/6] Add header --- 08-student_guide.Rmd | 2 ++ 1 file changed, 2 insertions(+) diff --git a/08-student_guide.Rmd b/08-student_guide.Rmd index 95b8157..f8eb14f 100644 --- a/08-student_guide.Rmd +++ b/08-student_guide.Rmd @@ -4,6 +4,8 @@ ottrpal::set_knitr_image_path() ``` +# AMR Resistance with Galaxy + ## AnVIL Account Setup :::: {.borrowed_chunk} From faeea9fe2fea8417e987dc1ca444919fb2f86e2b Mon Sep 17 00:00:00 2001 From: avahoffman Date: Wed, 16 Oct 2024 10:07:07 -0400 Subject: [PATCH 4/6] Add img --- index.Rmd | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/index.Rmd b/index.Rmd index 9e91de6..7b5a1f6 100644 --- a/index.Rmd +++ b/index.Rmd @@ -13,7 +13,13 @@ favicon: assets/GDSCN_style/gdscn_favicon.ico # About this Book {-} -This is a companion training guide for BioDIGS, a GDSCN project that brings a research experience into the classroom. In this module, students will investigate **whether metagenomic samples from the BioDIGS project contain antimicrobial resistance genes**. They will run analyses using **ABRicate as implemented on Galaxy**. Visit the BioDIGS (BioDiversity and Informatics for Genomics Scholars) website [here](https://biodigs.org/) for more information about this collaborative, distributed research project, including how you can get involved! +This is a companion training guide for BioDIGS, a GDSCN project that brings a research experience into the classroom. In this module, students will investigate **whether metagenomic samples from the BioDIGS project contain antimicrobial resistance genes**. They will run analyses using **ABRicate as implemented on Galaxy**. + +```{r, echo=FALSE, fig.alt="Landing page for the AMR Activity."} +ottrpal::include_slide("https://docs.google.com/presentation/d/1Hb51t_aYJtY6u97-w6F8vnP1edPActzY3uYyG6AXtlY/edit#slide=id.g2d459dad204_0_16") +``` + +Visit the BioDIGS (BioDiversity and Informatics for Genomics Scholars) website [here](https://biodigs.org/) for more information about this collaborative, distributed research project, including how you can get involved! The GDSCN (Genomics Data Science Community Network) is a consortium of educators who aim to create a world where researchers, educators, and students from diverse backgrounds are able to fully participate in genomic data science research. You can find more information about its mission and initiatives [here](https://www.gdscn.org/home). From 3a6c4db03446853da68a5fbf659081807917d488 Mon Sep 17 00:00:00 2001 From: avahoffman Date: Wed, 16 Oct 2024 10:34:31 -0400 Subject: [PATCH 5/6] fix img --- index.Rmd | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/index.Rmd b/index.Rmd index 7b5a1f6..0b53bb8 100644 --- a/index.Rmd +++ b/index.Rmd @@ -15,7 +15,7 @@ favicon: assets/GDSCN_style/gdscn_favicon.ico This is a companion training guide for BioDIGS, a GDSCN project that brings a research experience into the classroom. In this module, students will investigate **whether metagenomic samples from the BioDIGS project contain antimicrobial resistance genes**. They will run analyses using **ABRicate as implemented on Galaxy**. -```{r, echo=FALSE, fig.alt="Landing page for the AMR Activity."} +```{r, echo=FALSE, fig.alt="Landing page for the AMR Activity.", fig.align='center', out.width='60%'} ottrpal::include_slide("https://docs.google.com/presentation/d/1Hb51t_aYJtY6u97-w6F8vnP1edPActzY3uYyG6AXtlY/edit#slide=id.g2d459dad204_0_16") ``` @@ -32,10 +32,10 @@ knitr::include_graphics("https://raw.githubusercontent.com/fhdsl/GDSCN_BioDIGS_B The activities in this guide are written for undergraduate students and beginning graduate students. ::: {.notice} -_Genetics_ +_Genetics_ **Beginner**: some genetics knowledge needed -_Programming skills_ +_Programming skills_ **Novice**: no programming experience needed ::: From 04e639a4131cd2cfb54e81ebc28199bed87bf515 Mon Sep 17 00:00:00 2001 From: avahoffman Date: Wed, 16 Oct 2024 10:43:04 -0400 Subject: [PATCH 6/6] Update index.Rmd --- index.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index.Rmd b/index.Rmd index 0b53bb8..4da1a6e 100644 --- a/index.Rmd +++ b/index.Rmd @@ -15,7 +15,7 @@ favicon: assets/GDSCN_style/gdscn_favicon.ico This is a companion training guide for BioDIGS, a GDSCN project that brings a research experience into the classroom. In this module, students will investigate **whether metagenomic samples from the BioDIGS project contain antimicrobial resistance genes**. They will run analyses using **ABRicate as implemented on Galaxy**. -```{r, echo=FALSE, fig.alt="Landing page for the AMR Activity.", fig.align='center', out.width='60%'} +```{r, echo=FALSE, fig.alt="Landing page for the AMR Activity.", fig.align='center', out.width = '80%'} ottrpal::include_slide("https://docs.google.com/presentation/d/1Hb51t_aYJtY6u97-w6F8vnP1edPActzY3uYyG6AXtlY/edit#slide=id.g2d459dad204_0_16") ```