better links

Author: afrendeiro

source/communication_and_meetings.md

@@ -56,10 +56,10 @@
 ### Strategic collaborative projects (SCPs)
 
 - Everyone is encouraged to participate in more than one depending on interest/relevance
-- SCP2: Aging & longevity:
+- SCP2: "Tissue biology in health, aging, and disease":
   - One meeting per month
   - Two organizers (generally from De Rooij and Rendeiro labs)
-  - Mailing list: scp2@cemmat.onmicrosoft.com
+  - Mailing list: [scp2@cemmat.onmicrosoft.com](mailto:scp2@cemmat.onmicrosoft.com)
   - Send papers with the usual format/tag in subject: `[paper] <title>`, and body: `<title> \n <url> \n <comment>`
 
 ### Hackatons
@@ -95,7 +95,7 @@ See also the "asking questions" section on [the learning note](learning.md).
 
 ## Messaging
 
-Use the lab's mailing list (rendeirogroup@int.cemm.at) for searchable, archivable content (announcements, scheduling, papers).
+Use the lab's mailing list ([rendeirogroup@int.cemm.at](rendeirogroup@int.cemm.at)) for searchable, archivable content (announcements, scheduling, papers).
 
 Use Microsoft Teams for non-archival content (curiosities, non-urgent questions, fun stuff).
 
@@ -121,4 +121,5 @@ Fields with `<>` should be replaced with content.
 ## Social meetings and celebrations
 
 Social gatherins for example in celebrations of personal and professional achievements are welcome and encouraged.
+
 They should however follow the guidelines and rules from CeMM.

source/getting_started.md

@@ -2,6 +2,8 @@
 
 Welcome to the Rendeiro lab at CeMM!
 
+This page is meant to help new members get started with the lab and for the PI and team to make sure onboarding is smooth.
+
 You are at the start of an adventure, don’t forget to enjoy the journey.
 
 ## Get informed

source/learning.md

@@ -43,7 +43,7 @@ As a member of the lab you are responsible to be aware, understand, and eventual
   - Feature extraction
   - Graph neural networks
   - Self-supervised learning
-  - Federated learning (https://federated.withgoogle.com/)
+  - Federated learning ([https://federated.withgoogle.com/](https://federated.withgoogle.com/))
 - Image analysis:
   - Common data formats
   - Storing and manipulating images in a computer
@@ -190,129 +190,129 @@ Note that learning is a iterative and continuous process. You will need to revis
 
 ## Tutorials
 
-- Gradient descent and backpropagation: https://www.youtube.com/watch?v=VMj-3S1tku0
-- Transformers from scratch: https://e2eml.school/transformers.html
-- Data visualization / figure making with Python: https://github.com/frankligy/python_visualization_tutorial
-- Histology @ Yale: http://medcell.org/histology/histology.php
-- Systems Cell Biology @ Yale: http://medcell.med.yale.edu/systems_cell_biology/systems_cell_biology.php
-- Immunology: https://www.youtube.com/watch?v=iwB8kKdNgdQ
-- Software development: many paths to learning: https://www.youtube.com/watch?v=66tfvFeALBQ
+- Gradient descent and backpropagation: [https://www.youtube.com/watch?v=VMj-3S1tku0](https://www.youtube.com/watch?v=VMj-3S1tku0)
+- Transformers from scratch: [https://e2eml.school/transformers.html](https://e2eml.school/transformers.html)
+- Data visualization / figure making with Python: [https://github.com/frankligy/python_visualization_tutorial](https://github.com/frankligy/python_visualization_tutorial)
+- Histology @ Yale: [http://medcell.org/histology/histology.php](http://medcell.org/histology/histology.php)
+- Systems Cell Biology @ Yale: [http://medcell.med.yale.edu/systems_cell_biology/systems_cell_biology.php](http://medcell.med.yale.edu/systems_cell_biology/systems_cell_biology.php)
+- Immunology: [https://www.youtube.com/watch?v=iwB8kKdNgdQ](https://www.youtube.com/watch?v=iwB8kKdNgdQ)
+- Software development: many paths to learning: [https://www.youtube.com/watch?v=66tfvFeALBQ](https://www.youtube.com/watch?v=66tfvFeALBQ)
 
 ## Software packages
 
 These are some of the software packages we use often in the lab. You can more easily be aware of the direction of their development and new versions by subscribing to their releases on Github (bell sign -> custom -> releases).
 
 ### Data science
 
-- Numpy (https://numpy.org/)
-- Pandas (https://pandas.pydata.org/)
-- Scipy (https://scipy.org/)
-- Scanpy (https://scanpy.readthedocs.io/en/stable/)
-- Squidpy (https://squidpy.readthedocs.io/en/stable/)
-- Networkx (https://networkx.org/)
-- Scikit-networks (https://scikit-network.readthedocs.io/)
+- Numpy ([https://numpy.org/](https://numpy.org/))
+- Pandas ([https://pandas.pydata.org/](https://pandas.pydata.org/))
+- Scipy ([https://scipy.org/](https://scipy.org/))
+- Scanpy ([https://scanpy.readthedocs.io/en/stable/](https://scanpy.readthedocs.io/en/stable/))
+- Squidpy ([https://squidpy.readthedocs.io/en/stable/](https://squidpy.readthedocs.io/en/stable/))
+- Networkx ([https://networkx.org/](https://networkx.org/))
+- Scikit-networks ([https://scikit-network.readthedocs.io/](https://scikit-network.readthedocs.io/))
 
 ### Statistics / machine learning
 
-- pingouin (https://pingouin-stats.org/)
-- statsmodels (https://www.statsmodels.org/stable/index.html)
-- sklearn (https://scikit-learn.org/stable/)
-- imbalanced-learn (https://imbalanced-learn.org/)
-- pymer4 (https://eshinjolly.com/pymer4/)
-- PyMC (https://www.pymc.io/welcome.html, https://www.pymc.io/projects/docs/en/stable/learn.html)
+- pingouin ([https://pingouin-stats.org/](https://pingouin-stats.org/))
+- statsmodels ([https://www.statsmodels.org/stable/index.html](https://www.statsmodels.org/stable/index.html))
+- sklearn ([https://scikit-learn.org/stable/](https://scikit-learn.org/stable/))
+- imbalanced-learn ([https://imbalanced-learn.org/](https://imbalanced-learn.org/))
+- pymer4 ([https://eshinjolly.com/pymer4/](https://eshinjolly.com/pymer4/))
+- PyMC ([https://www.pymc.io/welcome.html, https://www.pymc.io/projects/docs/en/stable/learn.html](https://www.pymc.io/welcome.html, https://www.pymc.io/)projects/docs/en/stable/learn.html)
 
 ### Tensor-specific
 
-- einops (https://github.com/arogozhnikov/einops)
-- tensorly (https://tensorly.org/)
+- einops ([https://github.com/arogozhnikov/einops](https://github.com/arogozhnikov/einops))
+- tensorly ([https://tensorly.org/](https://tensorly.org/))
 
 ### Deep learning
 
-- weightsandbiases (https://wandb.ai/site) \<- join the lab's team at https://wandb.ai/rendeiro-group
-- pytorch (https://pytorch.org/)
-- pytorch-lightning (https://www.pytorchlightning.ai/)
-- pytorch-geometric (https://pytorch-geometric.readthedocs.io/en/latest/)
-- captum (https://captum.ai/)
-- fastai (https://docs.fast.ai/)
-- timm, pytorch-image-models (https://github.com/rwightman/pytorch-image-models)
-- TabPFN (https://github.com/automl/TabPFN)
-- fiftyone (https://voxel51.com/docs/fiftyone/)
-- transformers (https://github.com/huggingface/transformers)
+- weightsandbiases ([https://wandb.ai/site](https://wandb.ai/site)) \<- join the lab's team at [https://wandb.ai/rendeiro-group](https://wandb.ai/rendeiro-group)
+- pytorch ([https://pytorch.org/](https://pytorch.org/))
+- pytorch-lightning ([https://www.pytorchlightning.ai/](https://www.pytorchlightning.ai/))
+- pytorch-geometric ([https://pytorch-geometric.readthedocs.io/en/latest/](https://pytorch-geometric.readthedocs.io/en/latest/))
+- captum ([https://captum.ai/](https://captum.ai/))
+- fastai ([https://docs.fast.ai/](https://docs.fast.ai/))
+- timm, pytorch-image-models ([https://github.com/rwightman/pytorch-image-models](https://github.com/rwightman/pytorch-image-models))
+- TabPFN ([https://github.com/automl/TabPFN](https://github.com/automl/TabPFN))
+- fiftyone ([https://voxel51.com/docs/fiftyone/](https://voxel51.com/docs/fiftyone/))
+- transformers ([https://github.com/huggingface/transformers](https://github.com/huggingface/transformers))
 
 ### Visualization
 
-- matplotlib (https://matplotlib.org/)
-- seaborn (https://seaborn.pydata.org/)
-- scikit-yb (https://www.scikit-yb.org/en/latest)
-- inkscape (https://inkscape.org/):
+- matplotlib ([https://matplotlib.org/](https://matplotlib.org/))
+- seaborn ([https://seaborn.pydata.org/](https://seaborn.pydata.org/))
+- scikit-yb ([https://www.scikit-yb.org/en/latest](https://www.scikit-yb.org/en/latest))
+- inkscape ([https://inkscape.org/)](https://inkscape.org/):)
   - https://www.inkscapeforstem.com/Inkscape-For-STEM-ee6dacb7a2e543218f87a29f69177fee
   - https://bioicons.com/
-- napari (https://napari.org/)
-- bokeh (https://docs.bokeh.org/en/latest/)
-- plotly (https://plotly.com/)
-- D3.js (https://d3js.org/)
+- napari ([https://napari.org/](https://napari.org/))
+- bokeh ([https://docs.bokeh.org/en/latest/](https://docs.bokeh.org/en/latest/))
+- plotly ([https://plotly.com/](https://plotly.com/))
+- D3.js ([https://d3js.org/](https://d3js.org/))
 
 ### Data-specific
 
 #### Imaging:
 
-- skimage (https://scikit-image.org/)
-- Deformetrica (https://gitlab.com/icm-institute/aramislab/deformetrica, http://www.deformetrica.org/)
+- skimage ([https://scikit-image.org/](https://scikit-image.org/))
+- Deformetrica ([https://gitlab.com/icm-institute/aramislab/deformetrica, http://www.deformetrica.org/](https://gitlab.com/icm-institute/aramislab/)deformetrica, http://www.deformetrica.org/)
 
 #### Survival data:
 
-- Lifelines (https://lifelines.readthedocs.io/en/latest/)
-- Auton-survival (https://github.com/autonlab/auton-survival)
+- Lifelines ([https://lifelines.readthedocs.io/en/latest/](https://lifelines.readthedocs.io/en/latest/))
+- Auton-survival ([https://github.com/autonlab/auton-survival](https://github.com/autonlab/auton-survival))
 
 #### Computational Pathology:
 
-- QuPath (https://qupath.github.io/)
-- Cytomine (https://doc.cytomine.org/, https://cytomine.com/)
-- PathML (https://github.com/Dana-Farber-AIOS/pathml)
-- HistomicsTK (https://digitalslidearchive.github.io/HistomicsTK)
-- CLAM (https://github.com/mahmoodlab/CLAM)
-- ASAP (https://github.com/GeertLitjens/ASAP)
+- QuPath ([https://qupath.github.io/](https://qupath.github.io/))
+- Cytomine ([https://doc.cytomine.org/, https://cytomine.com/](https://doc.cytomine.org/, https://cytomine.com/))
+- PathML ([https://github.com/Dana-Farber-AIOS/pathml](https://github.com/Dana-Farber-AIOS/pathml))
+- HistomicsTK ([https://digitalslidearchive.github.io/HistomicsTK](https://digitalslidearchive.github.io/HistomicsTK))
+- CLAM ([https://github.com/mahmoodlab/CLAM](https://github.com/mahmoodlab/CLAM))
+- ASAP ([https://github.com/GeertLitjens/ASAP](https://github.com/GeertLitjens/ASAP))
 
 ### Web
 
-- Flask (https://flask.palletsprojects.com/en/2.1.x/)
-- fastapi (https://fastapi.tiangolo.com/)
-- nativefier (https://github.com/nativefier/nativefier)
+- Flask ([https://flask.palletsprojects.com/en/2.1.x/](https://flask.palletsprojects.com/en/2.1.x/))
+- fastapi ([https://fastapi.tiangolo.com/](https://fastapi.tiangolo.com/))
+- nativefier ([https://github.com/nativefier/nativefier](https://github.com/nativefier/nativefier))
 
 ### Productivity and logistics
 
 - Note taking:
-  - obsidian (https://obsidian.md/, https://github.com/obsidianmd)
+  - obsidian ([https://obsidian.md/, https://github.com/obsidianmd](https://obsidian.md/, https://github.com/obsidianmd))
 - Integrated development environment (IDE):
-  - sublimetext (https://www.sublimetext.com/)
-  - vscode (https://code.visualstudio.com/)
+  - sublimetext ([https://www.sublimetext.com/](https://www.sublimetext.com/))
+  - vscode ([https://code.visualstudio.com/](https://code.visualstudio.com/))
 - Figure editing:
-  - inkscape (https://inkscape.org/)
+  - inkscape ([https://inkscape.org/](https://inkscape.org/))
 - Software management:
-  - pip (https://pip.pypa.io/en/stable/)
-  - poetry (https://python-poetry.org/)
-  - uv (https://github.com/astral-sh/uv)
-  - conda (https://docs.conda.io/en/latest/)
-  - docker (https://www.docker.com/)
+  - pip ([https://pip.pypa.io/en/stable/](https://pip.pypa.io/en/stable/))
+  - poetry ([https://python-poetry.org/](https://python-poetry.org/))
+  - uv ([https://github.com/astral-sh/uv](https://github.com/astral-sh/uv))
+  - conda ([https://docs.conda.io/en/latest/](https://docs.conda.io/en/latest/))
+  - docker ([https://www.docker.com/](https://www.docker.com/))
 - Code improvement:
-  - ruff (https://github.com/astral-sh/ruff)
-  - mypy (https://mypy-lang.org/)
-  - pre-commit (https://pre-commit.com/)
-  - sublimemerge (https://www.sublimemerge.com/)
+  - ruff ([https://github.com/astral-sh/ruff](https://github.com/astral-sh/ruff))
+  - mypy ([https://mypy-lang.org/](https://mypy-lang.org/))
+  - pre-commit ([https://pre-commit.com/](https://pre-commit.com/))
+  - sublimemerge ([https://www.sublimemerge.com/](https://www.sublimemerge.com/))
 - Documentation:
-  - sphinx (https://www.sphinx-doc.org/en/master/)
-  - pandoc (https://pandoc.org/)
+  - sphinx ([https://www.sphinx-doc.org/en/master/](https://www.sphinx-doc.org/en/master/))
+  - pandoc ([https://pandoc.org/](https://pandoc.org/))
 - Interactive and environment management:
-  - IPython (https://ipython.org/)
-  - virtualenv (https://virtualenv.pypa.io/en/latest/)
-  - jupyter-notebook (https://jupyter.org/)
+  - IPython ([https://ipython.org/](https://ipython.org/))
+  - virtualenv ([https://virtualenv.pypa.io/en/latest/](https://virtualenv.pypa.io/en/latest/))
+  - jupyter-notebook ([https://jupyter.org/](https://jupyter.org/))
 
 ### Data repositories
 
 - Generic:
-  - Zenodo (https://zenodo.org/)
-  - GigaDB (http://gigadb.org/)
-  - Synapse (https://www.synapse.org/)
+  - Zenodo ([https://zenodo.org/](https://zenodo.org/))
+  - GigaDB ([http://gigadb.org/](http://gigadb.org/))
+  - Synapse ([https://www.synapse.org/](https://www.synapse.org/))
 - Transcriptomics:
   - GEO
   - ArrayExpress

source/research.md

@@ -5,11 +5,11 @@
 ### Initializing a project
 
 1. Register your project in the lab's project register:
-   1. Go to https://cemmat.sharepoint.com/sites/rendeirolab and find the 'Lab project register.xlsx' or directly at https://cemmat.sharepoint.com/:x:/r/sites/rendeirolab/\_layouts/15/Doc.aspx?sourcedoc=%7B4c72f84b-f33b-4162-a5e8-f05556fdf66b%7D&action=editnew
+   1. Go to [https://cemmat.sharepoint.com/sites/rendeirolab](https://cemmat.sharepoint.com/sites/rendeirolab) and find the 'Lab project register.xlsx' or directly [here](https://cemmat.sharepoint.com/:x:/r/sites/rendeirolab/\_layouts/15/Doc.aspx?sourcedoc=%7B4c72f84b-f33b-4162-a5e8-f05556fdf66b%7D&action=editnew).
    1. Start a new row for your project and increment the `Project ID` by one.
    1. Choose an intuitive name for the project, avoiding adding personal information e.g. collaborator names.
 1. Create a project directory structure from the lab's template: `cookiecutter gh:rendeirolab/_project_template`
-1. Create a git repository on GitHub (https://github.com/rendeirolab) with the same name as the project, make a first commit and push to Github.
+1. Create a git repository on GitHub ([https://github.com/rendeirolab](https://github.com/rendeirolab)) with the same name as the project, make a first commit and push to Github.
 1. Create a directory for the project in the CeMM cluster at: `/research/groups/lab_rendeiro/projects/`
    1. Create a directory inside called `data` to store raw data.
 1. Create a directory for the project in the CeMM cluster at: `/nobackup/groups/lab_rendeiro/projects/`
@@ -69,7 +69,7 @@ Below are the preferred types of technology to be used in the lab:
 
 ## Meta-science
 
-- The Night Science Series (https://night-science.org/genome-biology-miniseries/)
-- The Night Science Podcast (https://night-science.org/the-night-science-podcast/)
-- The importance of stupidity in scientific research (https://doi.org/10.1242/jcs.033340)
-- Parachute use to prevent death and major trauma when jumping from aircraft: randomized controlled trial (http://dx.doi.org/10.1136/bmj.k5094)
+- The Night Science Series ([https://night-science.org/genome-biology-miniseries/](https://night-science.org/genome-biology-miniseries/))
+- The Night Science Podcast ([https://night-science.org/the-night-science-podcast/](https://night-science.org/the-night-science-podcast/))
+- The importance of stupidity in scientific research ([https://doi.org/10.1242/jcs.033340](https://doi.org/10.1242/jcs.033340))
+- Parachute use to prevent death and major trauma when jumping from aircraft: randomized controlled trial ([http://dx.doi.org/10.1136/bmj.k5094](http://dx.doi.org/10.1136/bmj.k5094))