From 4f3354c8e44bdba38153afd325fe5b9cb39aa13e Mon Sep 17 00:00:00 2001
From: Alexander <38151284+abotzki@users.noreply.github.com>
Date: Wed, 9 Jun 2021 16:48:39 +0200
Subject: [PATCH 1/3] first version of RSE subject guide for biology

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From 2c407c2e7a8a8c93b5c90a6d24a35b21c03bfd41 Mon Sep 17 00:00:00 2001
From: Alexander <38151284+abotzki@users.noreply.github.com>
Date: Wed, 9 Jun 2021 16:56:23 +0200
Subject: [PATCH 2/3] input for #10 update bioimaging informatics

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 docs/_pages/subjectguide/biology.md | 129 ++++++++++++++++++++++++++++
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diff --git a/docs/_pages/subjectguide/biology.md b/docs/_pages/subjectguide/biology.md
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+# Biology
+
+## Bioinformatics
+
+Major languages:
+
+for tools and also web-development efforts
+* Python
+* R
+* Java
+* minor c++
+* lately some poeple are big advocats of Rust
+
+for web development,a lot of different web technology stacks are used ranging for older stacks to the latest and greatest with React.js, Vue, etc
+Q: should we try to get some ideas on what is used most? I'll check if I can find some overview publication (eWorkbench?)
+
+A lot of emphasis is put on enabling Reproducible Research lately. This includes container technologies like Docker and workflow systems like Nextflow, snakemake which are the most popular ones.
+
+### Typical journals
+
+A lot of work is published in the following journals:
+
+* Bioinformatics
+* NAR
+* PLoS
+* eLife
+* JOSS
+
+Furthermore, an enormeous amount of articles about bioinformatics software are published on bioarxiv before actual publication via the said journals.
+
+
+### Resources
+
+* https://github.com/danielecook/Awesome-Bioinformatics
+* https://www.reddit.com/r/bioinformatics/
+* https://global.oup.com/academic/product/introduction-to-protein-science-9780198716846
+* https://web.stanford.edu/~hastie/ElemStatLearn/
+* https://www.biostars.org/
+* an overview of curated tools from the literature https://bio.tools/
+
+#### Python
+- pypi
+- (bio)conda
+- https://biopython.org/
+
+#### R
+- CRAN/MRAN
+- Bioconductor
+
+#### Java
+- mvn
+- https://biojava.org/
+
+#### C++
+- conan.io
+- http://biocpp.sourceforge.net/
+
+#### Rust
+
+
+### Introductory books
+- https://global.oup.com/academic/product/introduction-to-bioinformatics-9780198794141
+
+### Communities
+- ELIXIR
+
+### commercial companies
+- Qiagen
+- 10X Genomics
+- https://en.wikipedia.org/wiki/List_of_bioinformatics_companies
+
+
+## Bioimaging
+
+Major languages:
+
+for tools and also web-development efforts
+
+* Java
+* Python, more specifically Machine Learning and Deeplearning
+
+* web development
+
+### Typical journal
+
+- Nature Methods
+- Journal of Microscopy
+- computer science journals for algorithmic approaches
+
+### main topics and challenges
+        
+- big data and performance
+
+- bioformats / open and closed source image file formats
+
+- open-source tools centered around ImageJ (Fiji)
+    - plugins
+    - centralised repo
+
+### specific skill sets
+
+- image processing
+- image analyis
+- general algoritms for Machine Learning and Deeplearning
+
+### specific tools list
+
+- Cell Profiler
+- cytomine
+- qpath
+- ilastik
+- imageJ/Fiji
+
+        commerical tools imaris,
+
+        microscope vender software
+
+### communities
+
+- Euro BioImaging
+- Global Bioimaging
+- Neubias http://eubias.org/NEUBIAS/ or follow-up conference series
+- https://www.youtube.com/channel/UC-oy7UpEhRfHQ-5ePCviKFg
+- https://forum.image.sc/about
+
+### general tips
+
+- not scared if you do not have biology background
+- strong need for RSEs in the field at the moment

From 3c8ad196adfbbd8eefdabf0b021b182703d37441 Mon Sep 17 00:00:00 2001
From: Alexander <38151284+abotzki@users.noreply.github.com>
Date: Wed, 9 Jun 2021 17:22:02 +0200
Subject: [PATCH 3/3] #10 update yml file'

---
 docs/_pages/subjectguide/biology.md | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/docs/_pages/subjectguide/biology.md b/docs/_pages/subjectguide/biology.md
index 9825ef8..a40c794 100644
--- a/docs/_pages/subjectguide/biology.md
+++ b/docs/_pages/subjectguide/biology.md
@@ -1,3 +1,10 @@
+---
+permalink: /subject-guide/biology/
+title: RSE Toolkit - Subject Guide
+breadcrumb: Subject Guide
+layout: single
+---
+
 # Biology
 
 ## Bioinformatics