first draft Home page

index.md

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 title : Welcome
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+filename: index.md
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-Welcome to BIOP-desktop!
+# BIOP-desktop 
+
+# Acknoledgements 
+
+This whole project was possible thanks the previous work of the [renku](https://renkulab.io/) team ([renku-desktop](https://renkulab.io/projects/learn-renku/renku-desktop)) and the support of [RCP](https://www.epfl.ch/research/facilities/rcp/) and [SV IT](https://www.epfl.ch/schools/sv/it/) teams, [EPFL](https://www.epfl.ch/en/).
+
+
+# Introduction
+
+The BIOP-desktop is a **`Versioned Computer`** with [software]() pre-installed and pre-configured so you can focus on your analysis (and not on the installation).
+
+![desktop-screeshot](/resources/BIOP-desktop.png)
+
+The **BIOP-desktop** is 
+| Users Point of View | IT & Dev. Point of View |
+|---|---|
+| a **`Computer`** with "everything" installed and running! | a **`Docker`** image that you can simply pull and run |
+| [**START**]() | [**Installation**]() | 
+
+
+## What is a Versioned Computer?
+
+By **`Versioned Computer`**, we mean a computer in which every software is fixed, making it possible to reproduce the same environment at any time.
+
+Making use of the [Docker images](https://docs.docker.com/manuals/), we can create a **`Versioned Computer`** that is reproducible, shareable, and open.
+We make use of [multi-stage build](https://docs.docker.com/build/building/multi-stage/) to ease building and versionning. Indeed we can build a new image, changing a single component and keeping the rest of the image unchanged, if needed.
+
+## What is a Versioned Computer for?
+
+A **`Versioned Computer`** is useful for:
+- **Focusing on your analysis**: you don't have to worry about installing and configuring software.
+- **Reproducibility**: you can reproduce your analysis at any time, even years later.
+- **Collaboration**: you can share your analysis with your collaborators, and they can reproduce it.
+- **Teaching**: you can share your analysis with your students, and they can reproduce it.
+- **Publication**: you can share your analysis with the reviewers, and they can reproduce it.
+- **Open Science**: you can share your analysis with the world, and they can reproduce it.
+
+# BIOP-desktop installed software
+
+| Software | Description | Notes | 
+| --- | --- |
+| [Fiji](https://fiji.sc/) | a “batteries-included” ImageJ  with many update sites : clij, stardist, ptbiop , ilastik … |
+| [ilastik (GPU)](https://www.ilastik.org/) | interactive learning and segmentation toolkit | 
+| [QuPath](https://qupath.github.io/) | with extensions : cellpose, samapi extension , ABBA ... |
+| [cellprofiler](https://cellprofiler.org/) | |
+| [devbio-napari](https://github.com/haesleinhuepf/devbio-napari) | The Fijiest way to do image analysis in Python | 
+| [EMPanADA](https://empanada.readthedocs.io/en/latest/)| DNN to segment mitochondria in EM images | 
+| [stardist](https://github.com/stardist/stardist) | |
+| [ABBA](https://biop.github.io/ijp-imagetoatlas/) | including : elastix, transformix, DeepSlice, ... | | 
+| [inkscape](https://inkscape.org/) |  Vectoriel drawing (and more!) | 
+
+
+ | [Home](/index.md)| [Installation](/installation.md) | [Build](/build.md) | [Run](/run.md) |
+ |---|---|---|---|