Merge pull request #71 from rasools/OMICSINT_H24

Omicsint h24

Gemfile

@@ -0,0 +1,28 @@
+source "https://rubygems.org"
+
+# Hello! This is where you manage which Jekyll version is used to run.
+# When you want to use a different version, change it below, save the
+# file and run `bundle install`. Run Jekyll with `bundle exec`, like so:
+#
+#     bundle exec jekyll serve
+#
+# This will help ensure the proper Jekyll version is running.
+# Happy Jekylling!
+gem "jekyll"
+
+# This is the default theme for new Jekyll sites. You may change this to anything you like.
+#gem "minima", "~> 2.0"
+
+# If you want to use GitHub Pages, remove the "gem "jekyll"" above and
+# uncomment the line below. To upgrade, run `bundle update github-pages`.
+# gem "github-pages", group: :jekyll_plugins
+
+# If you have any plugins, put them here!
+group :jekyll_plugins do
+  gem "github-pages"
+end
+
+gem "jemoji"
+
+# Windows does not include zoneinfo files, so bundle the tzinfo-data gem
+gem "tzinfo-data", platforms: [:mingw, :mswin, :x64_mingw, :jruby]

README.md

@@ -1,7 +1,8 @@
+[![DOI](https://zenodo.org/badge/172930292.svg)](https://zenodo.org/badge/latestdoi/172930292)
 =========================================
 # Omics Integration and Systems Biology 
 
-[Course homepage](https://uppsala.instructure.com/courses/96642)
+[Course homepage](https://uppsala.instructure.com/courses/52162)
 
 Past editions:
 - [Online 8 February - 10 February 2023][8]
@@ -20,26 +21,3 @@ Past editions:
 [3]: https://github.com/NBISweden/workshop_omics_integration/tree/course2104
 [2]: https://github.com/NBISweden/workshop_omics_integration/tree/course2010
 [1]: https://github.com/NBISweden/workshop_omics_integration/tree/c60abb4579849bb8a0acd756d1aa9e71125265ac
-
-
-# Contributions
-In this branch we have all different sessions. Each session usually have only one main lab but in some sessions like session_ml we have more than one (main labs are those that we need for the course and should make proper docker for each of them).
-
-In each of these folder we have this pattern:
-- lab (folder)
-- Dockerfile
-- [lab_name]_env.yml
-- run.sh
-- [lab_name].ipynb or [lab_name].rmd
-- slides for the lab
-
-Using the dockerfile you can make the desired docker. It copies all other files inside the docker and makes a conda env inside the docker based on [lab_name]_env.yml file.
-
-## For contribution:
-
-
-1. First either create an issue or pick one of the currently available issues.
-2. Create a branch based on the issue from OMICSINT_H24 brnach.
-3. Make your changes on the lab, Dockerfile, [lab_name]_env.yml, [lab_name].ipynb or [lab_name].rmd
-4. Make sure that the docker works properly by testing it on your local machine.
-5. Make a PR to OMICSINT_H24 brnach and assign it to one of the reviewers.

_config.yml

@@ -0,0 +1,30 @@
+title: "Omics Integration and Systems Biology"
+baseurl: /workshop_omics_integration
+
+# where things are
+# where things are
+layouts_dir: ./workshop-common/layouts
+includes_dir: ./workshop-common/includes
+sass:
+  sass_dir: ./workshop-common/sass
+
+plugins:
+  - jemoji
+
+defaults:
+  - values:
+      logosnav: true
+
+# menu:
+#   - title: Overview
+#     url:
+#   - title: Schedule
+#     url: schedule
+#   - title: Labs
+#     url: labs
+#   - title: Reading materials
+#     url: reading_materials
+#   - title: Pre-course
+#     url: precourse
+#   - title: Contact
+#     url: contact

contact.md

@@ -0,0 +1,15 @@
+---
+layout: default
+title: contact
+---
+
+#### <img border="0" src="https://www.svgrepo.com/show/35048/email.svg" width="25" height="25"> Contact
+
+For information about this course please contact [Rui Benfeitas][1] or through the email `edu.omics-integration[ at ]nbis.se`.
+
+For further information about NBIS support, training and infrastructure, see our [webpage][2].
+
+
+
+[1]: https://nbis.se/about/staff/rui-benfeitas/
+[2]: https://nbis.se/

custom.css

@@ -0,0 +1,56 @@
+
+/* Images side by side */
+/* Three image containers (use 25% for four, and 50% for two, etc) */
+.column3 {
+  float: left;
+  width: 33.33%;
+  padding: 5px;
+}
+
+.column2 {
+  float: left;
+  width: 50%;
+  padding: 5px;
+}
+
+.column4{
+    float:left;
+    width: 25%;
+    padding: 5px;
+}
+
+
+/* Clear floats after image containers */
+.row::after {
+  content: "";
+  clear: both;
+  display: table;
+} 
+
+/* Images side by side */
+/* Three image containers (use 25% for four, and 50% for two, etc) */
+.column3 {
+  float: left;
+  width: 33.33%;
+  padding: 5px;
+}
+
+.column2 {
+  float: left;
+  width: 50%;
+  padding: 5px;
+}
+
+.column4{
+    float:left;
+    width: 25%;
+    padding: 5px;
+}
+
+
+/* Clear floats after image containers */
+.row::after {
+  content: "";
+  clear: both;
+  display: table;
+} 

index.md

@@ -0,0 +1,40 @@
+---
+layout: default
+title: Omics Integration and Systems Biology
+---
+
+#### <img border="0" src="https://s3-us-west-2.amazonaws.com/slack-files2/avatars/2019-09-12/751389607265_d59c0d58846bb2db7123_132.jpg" width="50" height="50"> Omics Integration and Systems Biology
+[![DOI](https://zenodo.org/badge/172930292.svg)](https://zenodo.org/badge/latestdoi/172930292) <img border="0" src="https://www.svgrepo.com/show/305241/github.svg" width="20" height="20"> [Github repository](https://github.com/NBISweden/workshop_omics_integration)  
+
+Please refer to [the new homepage](https://uppsala.instructure.com/courses/52162) for updated information.
+
+Contact `edu.omics-integration [at] nbis.se` for questions.
+
+<hr>
+
+Legacy information (April 2021) can be found under the following pages:
+- [schedule][1]
+- [reading materials][2]
+- [pre-course preparation][3]
+
+
+=========================================
+
+
+[Course homepage](https://uppsala.instructure.com/courses/52162)
+
+Past editions:
+- [Online 22 - 23 July 2021, as part of the ICMB / ECCB][4]
+- [Online 19 - 23 April 2021][3]
+- [Lund 5 - 9 October 2020][2]
+- [Stockholm 9 - 12 Sep 2019][1]
+
+[4]: https://github.com/NBISweden/workshop_omicsint_ISMBECCB/
+[3]: https://github.com/NBISweden/workshop_omics_integration/tree/course2104
+[2]: https://github.com/NBISweden/workshop_omics_integration/tree/course2010
+[1]: https://github.com/NBISweden/workshop_omics_integration/tree/c60abb4579849bb8a0acd756d1aa9e71125265ac
+
+
+[1]: schedule.html
+[2]: reading_materials.html
+[3]: precourse.html

labs.md

@@ -0,0 +1,123 @@
+---
+layout: default
+title:  'Labs'
+---
+
+### <img border="0" src="https://www.svgrepo.com/show/7421/computer.svg" width="25" height="25"> Lab instructions
+
+#### Clone the course repository
+
+Retrieve the entire repository including all datasets and notebooks.
+```
+cd ~/Desktop/course
+git clone [email protected]:NBISweden/workshop_omics_integration.git .
+```
+
+Inside you will find the following folders:
+- `environments/` - all conda environments necessary for running notebooks
+- `session_preprocessing/` - data pre-processing, prior to course start
+- `session_ml/` - the machine learning sessions, days 1 and 2
+- `session_topology/` - the network topology analysis, day 3 morning
+- `session_meta/` - network meta-analysis, day 3 afternoon
+- `session_nmf/` - session on matrix factorization, SNF and recommender systems, day 4 morning
+- `session_gems/` - the genome-scale modeling session, day 4 afternoon
+- `session_gsa/` - gene set and reporter feature, day 5 morning
+- `.../` - remaining folders not necessary for running any of the contents
+
+You will need to create specific [conda environments as indicated below](#environments).
+
+***Environments*** 
+See the [pre-course installation](./precourse.md), specifically [**3. Create and activate the environment**](./precourse.md#3-create-and-activate-the-environment).  
+***Environments*** - we merged the environments for many notebooks down to 4 environments. 
+- **Data pre-processing** (linux: `env-preprocessing_linux.yaml`, macOS: `env-preprocessing.yaml`)
+- **Supervised Integration & Feature selection&** (linux: `env-ml_linux.yaml` | macOS: `env-ml.yaml`)
+- **Meta analysis** (linux | macOS `/session_meta/renv.lock`)
+- **All remaining notebooks** (linux `env-ml_nets_linux.yaml` | MacOS `env-ml_nets.yaml`)
+
+Alternatively, you can find smaller environments below.
+
+##### Before the course: data pre-processing
+
+- **Data pre-processing:**
+    - environment macOS: `/environments/env-preprocessing.yaml` 
+    - environment linux: `/environments/env-preprocessing_linux.yaml`
+    - notebook ([html](https://nbisweden.github.io/workshop_omics_integration/session_preprocessing/preprocessing.html)): `/session_preprocessing/preprocessing.ipynb`
+
+
+##### Day 1: Supervised and Unsupervised integration
+In MacOSX you need to install [XQuartz](https://www.xquartz.org/) if you get errors related with `rgl`:
+```
+install.packages('session_ml/rgl_0.100.54.tgz', repos = NULL, type="source", dependencies = TRUE)
+```
+
+- **Supervised integration:**
+    - environment macOS: `/environments/env-ml.yaml`
+    - environment linux: `/environments/env-ml_linux.yaml`
+    - notebook ([html](https://nbisweden.github.io/workshop_omics_integration/session_ml/SupervisedOMICsIntegration/supervised_omics_integr_CLL.html)): `/session_ml/SupervisedOMICsIntegration/supervised_omics_integr_CLL/supervised_omics_integr_CLL.Rmd`
+
+- **Feature selection:**
+    - environment macOS: `/environments/env-ml.yaml`
+    - environment linux: `/environments/env-ml_linux.yaml`
+    - notebook ([html](https://nbisweden.github.io/workshop_omics_integration/session_ml/FeatureSelectionIntegrOMICs/OmicsIntegration_FeatureSelection.html)): `session_ml/FeatureSelectionIntegrOMICs/OmicsIntegration_FeatureSelection.Rmd`
+
+
+- **Unsupervised integration:**
+    - environment macOS: `/environments/env-ml_day2.yaml`
+    - environment linux: `/environments/env-ml_day2_linux.yaml`
+    - notebook ([html](https://nbisweden.github.io/workshop_omics_integration/session_ml/UnsupervisedOMICsIntegration/UnsupervisedOMICsIntegration.html)): `session_ml/UnsupervisedOMICsIntegration/UnsupervisedOMICsIntegration.Rmd`
+
+
+
+##### Day 2: Dimensionality reduction, deep learning, single-cell omics integration
+After activating the environment as above, open the `.Rmd` below by launching Rstudio with `rstudio &` or the jupyter notebooks with `jupyter-notebook`.
+
+- **Dimensionality reduction:**
+    - environment macOS: `/environments/env-ml_day2.yaml`
+    - environment linux: `/environments/env-ml_day2_linux.yaml`
+    - notebook ([html](https://nbisweden.github.io/workshop_omics_integration/session_ml/DimReductSingleCell/OmicsIntegration_DimensionReduction.html)): `session_ml/DimReductSingleCell/OmicsIntegration_DimensionReduction.Rmd`
+
+
+- **UMAP for data integration:**
+    - Note that the data needs to be decompressed before running the notebook `gunzip scRNAseq.csv.gz; gunzip scProteomics.csv.gz`
+    - environment macOS: `/environments/env-ml_day2.yaml`
+    - environment linux: `/environments/env-ml_day2_linux.yaml`
+    - notebook ([html](https://nbisweden.github.io/workshop_omics_integration/session_ml/UMAP_DataIntegration/UMAP_DataIntegration.html)): `session_ml/UMAP_DataIntegration/UMAP_DataIntegration.ipynb`
+
+
+- **Deep learning:**
+    - environment macOS: `/environments/env-ml_day2.yaml`
+    - environment linux: `/environments/env-ml_day2_linux.yaml`
+    - notebook ([html](https://nbisweden.github.io/workshop_omics_integration/session_ml/DeepLearningDataIntegration/DeepLearningDataIntegration.html)): `session_ml/DeepLearningDataIntegration/DeepLearningDataIntegration.ipynb`
+
+
+- **Single cell:**
+    - environment macOS: `/environments/env-ml_day2.yaml`
+    - environment linux: `/environments/env-ml_day2_linux.yaml`
+    - notebook ([html](https://nbisweden.github.io/workshop_omics_integration/session_ml/SingleCell/SingleCell_OmicsIntegration.html)): `session_ml/SingleCell/SingleCell_OmicsIntegration.Rmd`
+
+
+##### Day 3: Network topology
+- **Network topology:**
+    - environment macOS: `/environments/env-merged_nets.yaml`
+    - environment linux: `/environments/env-merged_nets_linux.yaml`
+    - notebook ([html](https://nbisweden.github.io/workshop_omics_integration/session_topology/lab.html)): `/session_topology/lab.ipynb`
+
+
+- **Meta analyses:**
+    - environment macOS:`/session_meta/renv.lock`
+    - environment linux:`/session_meta/renv.lock`
+    - notebook ([html](https://nbisweden.github.io/workshop_omics_integration/session_meta/lab_meta-analayses-v2.html)): `/session_meta/lab_meta-analayses-v2.Rmd`
+
+
+##### Day 4: GEM structure and simulation with Cobrapy
+- **Genome-scale metabolic modeling:**
+    - environment macOS: `/environments/env-merged_nets.yaml`
+    - environment linux: `/environments/env-merged_nets_linux.yaml`
+    - notebook ([html](https://nbisweden.github.io/workshop_omics_integration/session_gems/lab.html)): `/session_gems/lab.ipynb`
+
+
+##### Day 5: Gene set and reporter analysis
+- **Gene set analysis and reporter features:**
+    - environment macOS: `/environments/env-merged_nets.yaml`
+    - environment linux: `/environments/env-merged_nets_linux.yaml`
+    - notebook: ([html](https://nbisweden.github.io/workshop_omics_integration/session_gsa/GEM_GSA.html)): `/session_gsa/GEM_GSA.Rmd`

precourse.md

@@ -5,8 +5,6 @@ title:  Pre-course
 
 {::options parse_block_html="true" /}
 
-// todo: #46 edit precourse.md to include the pre-course content for the workshop omicsint_h24
-
 #### <img border="0" src="https://www.svgrepo.com/show/26916/book.svg" width="15" height="15"> Preparation for the tutorial
 ***
 

reading_materials.md

@@ -3,8 +3,6 @@ layout: default
 title:  Reading materials
 ---
 
-// todo: #45 edit this file to include the reading materials for the workshop omicsint_h24
-
 #### <img border="0" src="https://www.svgrepo.com/show/26916/book.svg" width="25" height="25"> Reading materials  
 This page contains recommended reading materials in addition to the [pre-course content][1].