From 9fb5c20fb8ab3887f00653902585288dee42bdbb Mon Sep 17 00:00:00 2001 From: Katherine Heal Date: Tue, 9 Jul 2024 09:01:05 -0700 Subject: [PATCH 1/2] Fixes 50 by updating links in readmes --- NEON_soil_metadata/README.md | 8 ++++---- README.md | 6 +++--- bioscales_biogeochemical_metadata/README.md | 8 ++++---- taxonomic_dist_by_soil_layer/README.md | 10 +++++----- 4 files changed, 16 insertions(+), 16 deletions(-) diff --git a/NEON_soil_metadata/README.md b/NEON_soil_metadata/README.md index ed050a22..b4956fb5 100644 --- a/NEON_soil_metadata/README.md +++ b/NEON_soil_metadata/README.md @@ -3,9 +3,9 @@ This folder includes two notebooks, in R and Python, that explore various ways of analyzing and visualizing the metadata the NEON soil metagenomes study using the [NMDC-runtime API](https://api.microbiomedata.org/docs#). More documentation on the NMDC-runtime API can be found [here](https://github.com/microbiomedata/NMDC_documentation/blob/main/docs/howto_guides/api_gui.md). ## R -- [Static rendered Jupyter notebook](https://nbviewer.org/github/microbiomedata/notebook_hackathons/blob/main/NEON_soil_metadata/R/NEON_data_exploration.ipynb). _Viewing only, not editable_ -- [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/microbiomedata/notebook_hackathons/blob/main/NEON_soil_metadata/R/NEON_data_exploration.ipynb). This is the recommended way to interact with the notebook. _You need a google account to use this option_ +- [Static rendered Jupyter notebook](https://nbviewer.org/github/microbiomedata/nmdc_notebooks/blob/main/NEON_soil_metadata/R/NEON_data_exploration.ipynb). _Viewing only, not editable_ +- [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/microbiomedata/nmdc_notebooks/blob/main/NEON_soil_metadata/R/NEON_data_exploration.ipynb). This is the recommended way to interact with the notebook. _You need a google account to use this option_ ## Python -- [Static rendered Jupyter notebook](https://nbviewer.org/github/microbiomedata/notebook_hackathons/blob/main/NEON_soil_metadata/python/neon_soil_metadata_visual_exploration.ipynb). _Viewing only, not editable_ -- [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/microbiomedata/notebook_hackathons/blob/main/NEON_soil_metadata/python/neon_soil_metadata_visual_exploration.ipynb).This is the recommended way to interact with the notebook. _You need a google account to use this option_ \ No newline at end of file +- [Static rendered Jupyter notebook](https://nbviewer.org/github/microbiomedata/nmdc_notebooks/blob/main/NEON_soil_metadata/python/neon_soil_metadata_visual_exploration.ipynb). _Viewing only, not editable_ +- [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/microbiomedata/nmdc_notebooks/blob/main/NEON_soil_metadata/python/neon_soil_metadata_visual_exploration.ipynb).This is the recommended way to interact with the notebook. _You need a google account to use this option_ \ No newline at end of file diff --git a/README.md b/README.md index 94c40f06..98a7f085 100644 --- a/README.md +++ b/README.md @@ -3,9 +3,9 @@ ## Quick Start Notebooks that are ready for use and exploration. -- [NEON Soil MetaData](https://github.com/microbiomedata/notebook_hackathons/tree/main/NEON_soil_metadata) -- [Bio-Scales Biogeochemical MetaData](https://github.com/microbiomedata/notebook_hackathons/tree/main/bioscales_biogeochemical_metadata) -- [NEON Soil Microbial Community Composition](https://github.com/microbiomedata/notebook_hackathons/tree/main/taxonomic_dist_by_soil_layer) +- [NEON Soil MetaData](https://github.com/microbiomedata/nmdc_notebooks/tree/main/NEON_soil_metadata) +- [Bio-Scales Biogeochemical MetaData](https://github.com/microbiomedata/nmdc_notebooks/tree/main/bioscales_biogeochemical_metadata) +- [NEON Soil Microbial Community Composition](https://github.com/microbiomedata/nmdc_notebooks/tree/main/taxonomic_dist_by_soil_layer) ## Overview diff --git a/bioscales_biogeochemical_metadata/README.md b/bioscales_biogeochemical_metadata/README.md index a2ecce0c..c643e6cf 100644 --- a/bioscales_biogeochemical_metadata/README.md +++ b/bioscales_biogeochemical_metadata/README.md @@ -5,9 +5,9 @@ This folder includes two notebooks, in R and Python, that explore the chemical m More documentation on the NMDC-runtime API can be found [here](https://github.com/microbiomedata/NMDC_documentation/blob/main/docs/howto_guides/api_gui.md). ## R -- [Static rendered Jupyter notebook](https://nbviewer.org/github/microbiomedata/notebook_hackathons/blob/main/bioscales_biogeochemical_metadata/R/bioscales_metadata.ipynb). _Viewing only, not editable_ -- [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/microbiomedata/notebook_hackathons/blob/main/bioscales_biogeochemical_metadata/R/bioscales_metadata.ipynb). This is the recommended way to interact with the notebook. _You need a google account to use this option_ +- [Static rendered Jupyter notebook](https://nbviewer.org/github/microbiomedata/nmdc_notebooks/blob/main/bioscales_biogeochemical_metadata/R/bioscales_metadata.ipynb). _Viewing only, not editable_ +- [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/microbiomedata/nmdc_notebooks/blob/main/bioscales_biogeochemical_metadata/R/bioscales_metadata.ipynb). This is the recommended way to interact with the notebook. _You need a google account to use this option_ ## Python -- [Static rendered Jupyter notebook](https://nbviewer.org/github/microbiomedata/notebook_hackathons/blob/main/bioscales_biogeochemical_metadata/python/bioscales.ipynb). _Viewing only, not editable_ -- [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/microbiomedata/notebook_hackathons/blob/main/bioscales_biogeochemical_metadata/python/bioscales.ipynb).This is the recommended way to interact with the notebook. _You need a google account to use this option_ +- [Static rendered Jupyter notebook](https://nbviewer.org/github/microbiomedata/nmdc_notebooks/blob/main/bioscales_biogeochemical_metadata/python/bioscales.ipynb). _Viewing only, not editable_ +- [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/microbiomedata/nmdc_notebooks/blob/main/bioscales_biogeochemical_metadata/python/bioscales.ipynb).This is the recommended way to interact with the notebook. _You need a google account to use this option_ diff --git a/taxonomic_dist_by_soil_layer/README.md b/taxonomic_dist_by_soil_layer/README.md index d474186c..5a581223 100644 --- a/taxonomic_dist_by_soil_layer/README.md +++ b/taxonomic_dist_by_soil_layer/README.md @@ -1,11 +1,11 @@ # Taxonomic Distribution of Contigs by Soil Layer in Colorado -This folder includes one notebook (in Python) that explores how the taxonomic distribution of contigs differs by soil layer (M or O horizon) in Colorado using the [NMDC-runtime API](https://api.microbiomedata.org/docs#). More documentation on the NMDC-runtime API can be found [here](https://github.com/microbiomedata/NMDC_documentation/blob/main/docs/howto_guides/api_gui.md). This notebook is an example of using the NMDC metadata to access processed metagenome data that describes the taxa present. +This folder includes two notebooks, in R and Python that explore how the taxonomic distribution of contigs differs by soil layer (M or O horizon) in Colorado using the [NMDC-runtime API](https://api.microbiomedata.org/docs#). More documentation on the NMDC-runtime API can be found [here](https://github.com/microbiomedata/NMDC_documentation/blob/main/docs/howto_guides/api_gui.md). This notebook is an example of using the NMDC metadata to access processed metagenome data that describes the taxa present. ## R -- [Static rendered Jupyter notebook](https://nbviewer.org/github/microbiomedata/notebook_hackathons/blob/main/taxonomic_dist_by_soil_layer/R/taxonomic_dist_by_soil_layer_R.ipynb). _Viewing only, not editable_ -- [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/microbiomedata/notebook_hackathons/blob/main/taxonomic_dist_by_soil_layer/R/taxonomic_dist_by_soil_layer_R.ipynb). **Running this notebook in the colab interactive environment is not recommended due to long API calls**. _You need a google account to use this option_. +- [Static rendered Jupyter notebook](https://nbviewer.org/github/microbiomedata/nmdc_notebooks/blob/main/taxonomic_dist_by_soil_layer/R/taxonomic_dist_by_soil_layer_R.ipynb). _Viewing only, not editable_ +- [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/microbiomedata/nmdc_notebooks/blob/main/taxonomic_dist_by_soil_layer/R/taxonomic_dist_by_soil_layer_R.ipynb). **Running this notebook in the colab interactive environment is not recommended due to long API calls**. _You need a google account to use this option_. ## Python -- [Static rendered Jupyter notebook](https://nbviewer.org/github/microbiomedata/notebook_hackathons/blob/main/taxonomic_dist_by_soil_layer/python/taxonomic_dist_soil_layer.ipynb). _Viewing only, not editable_ -- [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/microbiomedata/notebook_hackathons/blob/main/taxonomic_dist_by_soil_layer/python/taxonomic_dist_soil_layer.ipynb). **Running this notebook in the colab interactive environment is not recommended due to long API calls**. _You need a google account to use this option_. +- [Static rendered Jupyter notebook](https://nbviewer.org/github/microbiomedata/nmdc_notebooks/blob/main/taxonomic_dist_by_soil_layer/python/taxonomic_dist_soil_layer.ipynb). _Viewing only, not editable_ +- [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/microbiomedata/nmdc_notebooks/blob/main/taxonomic_dist_by_soil_layer/python/taxonomic_dist_soil_layer.ipynb). **Running this notebook in the colab interactive environment is not recommended due to long API calls**. _You need a google account to use this option_. From d37f62d1d16f04a538c467d3540e5a92ac8f4155 Mon Sep 17 00:00:00 2001 From: Katherine Heal Date: Tue, 9 Jul 2024 10:12:46 -0700 Subject: [PATCH 2/2] Fix typo in R taxon notebook link --- taxonomic_dist_by_soil_layer/README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/taxonomic_dist_by_soil_layer/README.md b/taxonomic_dist_by_soil_layer/README.md index 5a581223..7130c2d8 100644 --- a/taxonomic_dist_by_soil_layer/README.md +++ b/taxonomic_dist_by_soil_layer/README.md @@ -3,8 +3,8 @@ This folder includes two notebooks, in R and Python that explore how the taxonomic distribution of contigs differs by soil layer (M or O horizon) in Colorado using the [NMDC-runtime API](https://api.microbiomedata.org/docs#). More documentation on the NMDC-runtime API can be found [here](https://github.com/microbiomedata/NMDC_documentation/blob/main/docs/howto_guides/api_gui.md). This notebook is an example of using the NMDC metadata to access processed metagenome data that describes the taxa present. ## R -- [Static rendered Jupyter notebook](https://nbviewer.org/github/microbiomedata/nmdc_notebooks/blob/main/taxonomic_dist_by_soil_layer/R/taxonomic_dist_by_soil_layer_R.ipynb). _Viewing only, not editable_ -- [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/microbiomedata/nmdc_notebooks/blob/main/taxonomic_dist_by_soil_layer/R/taxonomic_dist_by_soil_layer_R.ipynb). **Running this notebook in the colab interactive environment is not recommended due to long API calls**. _You need a google account to use this option_. +- [Static rendered Jupyter notebook](https://nbviewer.org/github/microbiomedata/nmdc_notebooks/blob/main/taxonomic_dist_by_soil_layer/R/taxonomic_dist_soil_layer_R.ipynb). _Viewing only, not editable_ +- [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/microbiomedata/nmdc_notebooks/blob/main/taxonomic_dist_by_soil_layer/R/taxonomic_dist_soil_layer_R.ipynb). **Running this notebook in the colab interactive environment is not recommended due to long API calls**. _You need a google account to use this option_. ## Python - [Static rendered Jupyter notebook](https://nbviewer.org/github/microbiomedata/nmdc_notebooks/blob/main/taxonomic_dist_by_soil_layer/python/taxonomic_dist_soil_layer.ipynb). _Viewing only, not editable_