add preambel draft

Signed-off-by: zethson <[email protected]>

.gitignore

@@ -29,3 +29,7 @@ doc/_build
 .idea
 *.code-workspace
 .vscode
+
+jupyter-book/data
+*.h5ad
+*.h5mu

jupyter-book/_toc.yml

@@ -1,6 +1,15 @@
+root: preamble
 format: jb-book
-root: intro
-chapters:
-- file: markdown
-- file: notebooks
-- file: scanpy_demo
+defaults:
+  numbered: true
+parts:
+- caption: Introduction
+  chapters:
+  - file: introduction/prior_art
+  - file: introduction/experimental_data_collection
+  - file: introduction/raw_data_processing
+  - file: introduction/data_infrastructure
+  - file: introduction/interoperability
+- caption: Demo
+  chapters:
+  - file: scanpy_demo

jupyter-book/introduction/data_infrastructure.md

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+# Data infrastructure

jupyter-book/introduction/experimental_data_collection.md

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+# Experimental data collection

jupyter-book/introduction/interoperability.md

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+# Interoperability

jupyter-book/introduction/prior_art.md

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+# Prior art

jupyter-book/introduction/raw_data_processing.md

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+# Raw data processing

jupyter-book/preamble.md

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+# Extended Single-cell Best-practices
+
+## Overview
+
+You are on the landing page of the Extended Single-cell Best-practices book.
+The goal of this book is to teach newcomers and advanced professionals alike the **best-practices** of single-cell sequencing analysis.
+This book will teach you about the most common analysis steps ranging from preprocessing over visualization to statistical evaluation.
+After having worked through this book you will be able to analyze multimodal sequencing data on your own.
+
+## Motivation
+
+As once newcomers ourselves in the field we noticed that while teaching materials exist they are often scattered in various places.
+Furthermore, in a rapidly developing research area like single-cell, many tools exist and get published every day.
+It is difficult to know which tool to use for which steps and why.
+Hence, we committed to writing our guidelines on not only how to do things, but how to do things right.
+These suggestions are based on external benchmarks and reviews whereever possible.
+Finally, we consider this book to be a living book which can easily be updated when the recommendations change.
+
+## What this book covers
+
+This book aims to be comprehensive and to cover as many analysis steps as possible. 
+We cover all steps entailed in the publication TBD while adding additional information for situations that an analyst may encounter regularly.
+A simple example might be converting between analysis ecosystems and data formats.
+
+## What this book does not cover
+
+This book does not cover the fundamental basics of biology or computer science including programming.
+Moreover, this book does not cover all possible tools to approach a specific issue and only focuses on the tools, which ideally were externally verified to work best.
+Whenever this is not possible and we cannot cover the explicit community verified best-practices, we only recommend a workflow based on our extensive experiences.
+
+## Prerequisites
+
+Trying to get into bioinformatician is difficult since a background is required in not only biology, but also computer science.
+Single-cell especially combines many subfields making it challenging to get into it.
+This book cannot cover all prerequisites for computation single-cell analysis. The book would simply explode.
+
+We therefore recommend to have a coarse overview over the following topics:
+
+* Basic Python programming. You should be familiar with control flow (loops, conditional statements, ...), basic data structures (lists, dictionaries, sets) and core functionality of the most used libraries such as Pandas and Numpy.
+* Basics of scanpy and AnnData. If interested in multimodal data analysis the basics of muon and MuData are recommended.
+* Basics R programming. Familiarity with control flow and basic data structures suffices.
+* Basics of biology. While we roughly introduce the generation of the data, we will not cover the fundamentals of DNA, RNA and proteins.
+
+## Acknowledgements
+
+This book would not have been possible without the help of all members of the Theislab and external experts.
+Furthermore we thank all developers and maintainers of all displayed tools and projects without whom none of this would be possible.