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The environment consists of 4 directories at the moment, more directories & sub-directories can be added.
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**Documentation:**
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This repository will be used to share all documentation and template about the MIB git.
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Wiki can be found via the following [link](https://git.wur.nl/afsg-microbiology/documentation/-/wikis/home)
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templates can be found at [https://git.wur.nl/afsg-microbiology/documentation/-/tree/main](https://git.wur.nl/afsg-microbiology/documentation/-/tree/main)
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This repository will be used to share all documentation and templates about the MIB git. This page is part of the wiki of this repository.
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**Education:**
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This folder is meant to host material dedicated to education such as courses presentations or tutorials.
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The subject does not matter, in principle molecular biology and hardcore linux tutorials can be part of this folder. Making subfolders can help organising the documents, you can request subfolders via email to bioinfo.mib@wur.nl.
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The subject does not matter, in principle molecular biology and hardcore linux tutorials can be part of this folder. Making subfolders can help organising the documents, you can request subfolders or repositories via email to bioinfo.mib@wur.nl.
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This folder is visible world-wide, MIB members can request write access.
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**Scripts:**
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Any specialised script or utility script will be placed in this repository. Take a look at [templates] folder and good coding practices to get ideas on how to make your code publishable. The development phase is always made in your personal repositories then shared via a "pull request" to this repository or take contact with bioinfo.mib@wur.nl by email.
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Any specialised script or utility script will be placed in this folder. Take a look at the [templates] folder and good coding practices to get ideas on how to make your code publishable. The development phase is always made in your personal repositories then your work is shared via a "pull request" to this repository or by contacting with bioinfo.mib@wur.nl by email.
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**Pipelines:**
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This part of the space is reserved for more complex scripts that full processing of data. Also use "pull request" to have your pipeline published here.
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This part of the space is reserved for more complex scripts that accomplish full data processing. Same rules as for scripts, see above.
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**Publication Supplementary Material:**
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Each publications should have a repository here, The abstract can be copied to the README file.
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The name of the repository should follow this format, DATE_FirstAuthorName_...
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Supplementary materials could be placed in the repository, make sure all "big" files are compressed.
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In case the supplementary data are already published no need to add them here, simply give a link where to find them in the README file.
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This folder will be visible by anybody on the internet.
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This folder and subfolders will be visible by anybody on the internet.
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Where to start?
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---------------
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If you have scripts/pipeline that are widely used within your group. You have made tutorials for yourself to maybe describe a lab process or a method on data processing or on a specific tool. You have been part of a course and you want to centralise the material for the next course... all of that is a valuable knowledge to share with all MIB, if you are in that case please send an email to bioinfo.mib@wur.nl. You can also format your documents or code to make them usable by other MIB members. This could mean writing documentation for code (see templates) or...
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If you have scripts/pipeline that are widely used within your group. You have made tutorials for yourself to maybe describe a lab process or a method on data processing or on a specific tool. You have been part of a course and you want to centralise the material for the next course... all of that is a valuable knowledge to share with all MIB, if you are in that case please send an email to bioinfo.mib@wur.nl. You can also format your documents or code to make them usable by other MIB members. This could mean writing documentation for code (see templates) or...
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How do I share/collaborate my code/stuff!
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