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A huge amount of work, data and knowledge is lost in academic environment because of lack of organization and communication. The infrastructure and organization that help researchers make their work available/accessible to their group members is very often missing or not known or relying on private/external services.
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A huge amount of work, data and knowledge is lost in academic environment because of lack of organisation and communication. The infrastructure and organisation that help researchers make their work accessible to their group members is very often missing or not known or relying on private or external services.
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>We want to respect WUR data management policies.
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Sharing code and documentation among researchers working at microbiology is key to create and spread common knowledge and create an environment in which lab members may get a head start in analyzing data, learn about methods and get new ideas for their research.
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Sharing code and documentation among researchers working at microbiology is key to create and spread common knowledge and create an environment in which lab members may get a head start in analysing data, learn about methods and get new ideas for their research.
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Within Microbiology we encounter the use of multiple types of repositories to store and share code. Often scientists use their private repositories such as a public Github or their local disks. Such practice leads to use and spread of not up-to date or errornous code (it should be considered bad practice). With such practice it is also not easy to find out about existing scripts and it prevents the development of general pipelines, which is needed (Also no distinction between different version).
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Within Microbiology we encounter the use of multiple types of repositories to store and share code. Often scientists use their private repositories such as a public Github or their local disks. Such practice leads to use and spread of not up-to date or erroneous code (it should be considered bad practice). With such practice it is also not easy to find out about existing scripts and it prevents the development of general pipelines, which is needed (Also no distinction between different version).
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Members of one research group may not know of repositories or scripts used by other group members and we encountered several situations where people experience difficulty to find useful utility scripts or methods even though someone else might have already tackled the problem. Relying on private repositories will lead to data/code loss since nobody have knowlegde of their existence and such practice does not align with WUR data policies.
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Members of one research group may not know of repositories or scripts used by other group members and we encountered several situations where people experience difficulty to find useful utility scripts or methods even though someone else might have already tackled the problem. Relying on private repositories will lead to data/code loss since nobody have knowledge of their existence and such practice does not align with WUR data policies.
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Wageningen University & Research has created an environment for researchers to store and collaborate on their source code and statistical models, along with documentation how those models and code should be used. Managed by FT-IT, a centralized GIT repository is available at https://git.wur.nl with full support.
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Wageningen University & Research has created an environment for researchers to store and collaborate on their source code and statistical models, along with documentation how those models and code should be used. Managed by FT-IT, a centralised GIT repository is available at https://git.wur.nl with full support.
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... | ... | @@ -20,7 +20,9 @@ By using this infrastructure we ensure code is stored in a shared and safe envir |
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>>>>>To enhance and stimulate sharing across our research groups we propose to organize the repository, not by research group, but by project and general data analysis themes, e.g. scripts and. pipelines for metagenomics, scripts for phylogenetics, visualization, etc.etc.
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>>>>>
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TOREMOVE?
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To enhance and stimulate sharing across our research groups we propose to organise the repository, not by research group, but by project and general data analysis themes, e.g. scripts and. pipelines for _metagenomics_, scripts for _phylogenetics_, _visualization_, etc.etc.
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Ownership will be maintained by the bioinformatics staff ensuring proper succession for the future.
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<<<<<
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... | ... | @@ -35,10 +37,10 @@ Who has access to it? |
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---------------------
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The WUR git (https://git.wur.nl) is open to all WUR members by default. If you do not use it yet, we recommend you do so and request access to <MIB repository>. An account can be arranged for external collaborators if needed.
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This git space is maintained and administered by MIB Bioinfo. By default the locations reserved for papers and teaching documents are opened world-wide (anyone can see and download them), the space reserved to code is restricted by default but could be made public on request or depending on the license strategy. MIB users can request write acces rights by email to bioinfo.mib@wur.nl.
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This git space is maintained and administered by MIB Bioinfo. By default the locations reserved for papers and teaching documents are opened world-wide (anyone can see and download them), the space reserved to code is restricted by default but could be made public on request or depending on the license strategy. MIB users can request write access rights by email to bioinfo.mib@wur.nl.
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Preferrably, development should be made in your personal space on gitlab then make a pull request to the correct repository on MIB gitlab. The bioinfo will make sure the code is usable and well described.
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Preferably, development should be made in your personal space on gitlab then make a pull request to the correct repository on MIB gitlab. The bioinfo will make sure the code is usable and well described.
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Organisation and accessibility
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------------------------------
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... | ... | @@ -52,8 +54,8 @@ The environment consists of 4 directories, see below for explanations. More dire |
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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 emaill 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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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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This folder is visible world-wide, MIB members can request write access.
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*Scripts:*
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... | ... | @@ -75,7 +77,7 @@ This folder is visible world-wide, mib members can request write access. |
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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 knowlegde 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 writting 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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... | ... | |