From 97a7799deb6bb39a8fadd919065a94d776c7caa9 Mon Sep 17 00:00:00 2001 From: Elizabeth Humphries Date: Thu, 25 Jan 2024 07:50:52 -0500 Subject: [PATCH] cleaning up anvil modules language --- 01-BioDIGS_project_overview.Rmd | 3 +- 02-research_team.Rmd | 2 +- 03-data_tour.Rmd | 4 +- 04-billing_modules.Rmd | 2 +- 05-anvil_onboarding.Rmd | 2 +- 06-using_platforms_modules.Rmd | 4 +- 07-using_platforms_modules.Rmd | 124 -------------------------------- index.Rmd | 2 +- 8 files changed, 11 insertions(+), 132 deletions(-) delete mode 100644 07-using_platforms_modules.Rmd diff --git a/01-BioDIGS_project_overview.Rmd b/01-BioDIGS_project_overview.Rmd index 71ca3e4..6fd7779 100644 --- a/01-BioDIGS_project_overview.Rmd +++ b/01-BioDIGS_project_overview.Rmd @@ -3,9 +3,10 @@ # Background +One critical aspect of an undergraduate STEM education is hands-on research. Undergraduate research experiences enhance what students learn in the classroom as well as increase a student's interest in pursuing STEM careers ^1. It can also lead to improved scientific reasoning and increased academic performance overall ^2. However, many students at underresourced institutions like community colleges, Historically Black Colleges and Universities (HBCUs), tribal colleges and universities, and Hispanic-serving institutions have limited access to research opportunities compared to their cohorts at larger four-year colleges and R1 institutions. These students are also more likely to belong to groups that are already under-represented in STEM disciplines, particularly genomics and data science ^3 ^4. + The BioDIGS Project aims to be at the intersection of genomics, data science, cloud computing, and education. -One critical aspect of an undergraduate STEM education is hands-on research. Undergraduate research experiences enhance what students learn in the classroom as well as increase a student's interest in pursuing STEM careers ^1. It can also lead to improved scientific reasoning and increased academic performance overall ^2. However, many students at underresourced institutions like community colleges, Historically Black Colleges and Universities (HBCUs), tribal colleges and universities, and Hispanic-serving institutions have limited access to research opportunities compared to their cohorts at larger four-year colleges and R1 institutions. These students are also more likely to belong to groups that are already under-represented in STEM disciplines, particularly genomics and data science ^3 ^4. ## What is genomics? diff --git a/02-research_team.Rmd b/02-research_team.Rmd index 4c6d8ca..b3942e3 100644 --- a/02-research_team.Rmd +++ b/02-research_team.Rmd @@ -1,6 +1,6 @@ # Research Team -This project is coordinated by the Genomics Data Science Community Network (GDSCN). You can read more about the GDSCN and its mission at the network's [website](https://www.gdscn.org/home). +This project is coordinated by the Genomics Data Science Community Network (GDSCN). You can read more about the GDSCN and its mission at the network [website](https://www.gdscn.org/home). ## Soil sampling diff --git a/03-data_tour.Rmd b/03-data_tour.Rmd index 9ff6f64..a8d166a 100644 --- a/03-data_tour.Rmd +++ b/03-data_tour.Rmd @@ -12,10 +12,12 @@ You can also see images of each sampling site and soil characteristics at the [s This dataset includes basic information about the soil itself like pH, percentage of organic matter, variety of soil metal concentrations. The complete data dictionary is available [here](https://docs.google.com/spreadsheets/d/109xYUM48rjj33B76hZ3bNlrm8u-_S6uyoE_3wSCp0r0/edit#gid=188448677). The dataset is available at the [BioDIGS website](https://biodigs.org/#soil_data). +This dataset was generated by the [Delaware Soil Testing Program](https://www.udel.edu/canr/cooperative-extension/environmental-stewardship/soil-testing/) at the University of Delaware. + ## Genomics and Metagenomics Data You can access this data in both raw and processed forms. -The Illumina and Nanopore sequence data was generated at the [Johns Hopkins University Genetic Resources Core Facility](https://grcf.jhmi.edu/). PacBio sequencing was done by [PacBio](https://www.pacb.com/) directly. +The Illumina and Nanopore sequences were generated at the [Johns Hopkins University Genetic Resources Core Facility](https://grcf.jhmi.edu/). PacBio sequencing was done by [PacBio](https://www.pacb.com/) directly. More information coming soon! \ No newline at end of file diff --git a/04-billing_modules.Rmd b/04-billing_modules.Rmd index ef6aca4..fdbcdf7 100644 --- a/04-billing_modules.Rmd +++ b/04-billing_modules.Rmd @@ -5,7 +5,7 @@ knitr::opts_chunk$set(out.width = "100%") # Billing on AnVIL -Modules about billing and Billing Projects on Google Cloud Platform and Terra. +In order to use AnVIL, you will need to set up a billing account and add members to it. These sections guide you through that process.
diff --git a/05-anvil_onboarding.Rmd b/05-anvil_onboarding.Rmd index 82a30a7..a21fc15 100644 --- a/05-anvil_onboarding.Rmd +++ b/05-anvil_onboarding.Rmd @@ -5,7 +5,7 @@ ottrpal::set_knitr_image_path() ``` -You can easily access the data on AnVIL by cloning the dedicated workspace. +You can easily access the data on AnVIL by cloning the dedicated workspace. These sections guide you through creating an AnVIL account and accessing the workspace. ## Create Google Account diff --git a/06-using_platforms_modules.Rmd b/06-using_platforms_modules.Rmd index c1cab54..47dae24 100644 --- a/06-using_platforms_modules.Rmd +++ b/06-using_platforms_modules.Rmd @@ -2,9 +2,9 @@ knitr::opts_chunk$set(out.width = "100%") ``` -# Using programming platforms on AnVIL +# Using Programming Platforms -Modules about opening, touring, and closing AnVIL platforms +These sections provide a general overview of how to use RStudio and Galaxy on AnVIL.
diff --git a/07-using_platforms_modules.Rmd b/07-using_platforms_modules.Rmd deleted file mode 100644 index d53cf5c..0000000 --- a/07-using_platforms_modules.Rmd +++ /dev/null @@ -1,124 +0,0 @@ -```{r echo = FALSE} -knitr::opts_chunk$set(out.width = "100%") -``` - -# Programming Platforms - -Modules about opening, touring, and closing AnVIL platforms - -
- -## Video overview on using Jupyter Notebooks - -```{r, echo = FALSE, results='asis'} -cow::borrow_chapter( - doc_path = "child/_child_jupyter_video.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` - -## Launching Jupyter - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -cow::borrow_chapter( - doc_path = "child/_child_jupyter_launch.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: - -## Video overview on using Galaxy - -```{r, echo = FALSE, results='asis'} -cow::borrow_chapter( - doc_path = "child/_child_galaxy_video.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` - -## Starting Galaxy - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -cow::borrow_chapter( - doc_path = "child/_child_galaxy_start.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: - -## Navigating Galaxy - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -cow::borrow_chapter( - doc_path = "child/_child_galaxy_navigate.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: - -## Deleting Galaxy - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -cow::borrow_chapter( - doc_path = "child/_child_galaxy_delete.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: - -## Video overview on using RStudio - -```{r, echo = FALSE, results='asis'} -cow::borrow_chapter( - doc_path = "child/_child_rstudio_video.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` - -## Launching RStudio - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -cow::borrow_chapter( - doc_path = "child/_child_rstudio_launch.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: - -## Touring RStudio - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -cow::borrow_chapter( - doc_path = "child/_child_rstudio_tour.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: - -## Pausing RStudio - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -cow::borrow_chapter( - doc_path = "child/_child_rstudio_pause.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: - -## Deleting RStudio - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -cow::borrow_chapter( - doc_path = "child/_child_rstudio_delete.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: diff --git a/index.Rmd b/index.Rmd index ab2ff1d..44d36c6 100644 --- a/index.Rmd +++ b/index.Rmd @@ -30,4 +30,4 @@ The activities in this guide are demonstrated on NHGRI's [AnVIL](https://anvilpr The data generated by the BioDIGS project is available through the [BioDIGS website](biodigs.org), as well as through an [AnVIL workspace](https://anvilproject.org). -Data about the soil itself as well as soil metal content was generated by the [Delaware Soil Testing Program](https://www.udel.edu/canr/cooperative-extension/environmental-stewardship/soil-testing/) at the University of Delaware. Short-read and long-read sequences were generated by the [Johns Hopkins University Genetic Resources Core Facility](https://grcf.jhmi.edu/). +Data about the soil itself as well as soil metal content was generated by the [Delaware Soil Testing Program](https://www.udel.edu/canr/cooperative-extension/environmental-stewardship/soil-testing/) at the University of Delaware. Sequences were generated by the [Johns Hopkins University Genetic Resources Core Facility](https://grcf.jhmi.edu/) and by [PacBio](https://www.pacb.com/).