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* Create link-check.yml

* Update .github/workflows/link-check.yml

Co-authored-by: Bert Droesbeke <[email protected]>

* Update link-check.yml

* Update link-check.yml

* Update link-check.yml

* Update link-check.yml

* marine_metagenomics_assembly.md

* Update no_resources.md

* tool_and_resource_list.yml

---------

Co-authored-by: Bert Droesbeke <[email protected]>
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korbinib and bedroesb authored Dec 6, 2024
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10 changes: 5 additions & 5 deletions _data/tool_and_resource_list.yml
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name: MarDB
registry:
biotools: mardb
url: https://mmp2.sfb.uit.no/mardb/
url: https://sfb.mmp2.sigma2.no/mardb/
- description: MarFun is a manually curated marine fungi genome database.
id: marfun
name: MarFun
url: https://mmp2.sfb.uit.no/marfun/
url: https://sfb.mmp2.sigma2.no/marfun/
- description: High-quality curated and freely accessible microbial genomics and metagenomics resources for the marine scientific community
id: marine-metagenomics-portal
name: Marine Metagenomics Portal (MMP)
registry:
biotools: mmp
url: https://mmp2.sfb.uit.no/
url: https://sfb.mmp2.sigma2.no
- description: MarRef is a manually curated marine microbial reference genome database that equenced genomes. Each entry contains 120 metadata fields including information about sampling environment or host, organism and taxonomy, phenotype, pathogenicity, assembly and annotation information
id: marref
name: MarRef
registry:
biotools: marref
url: https://mmp2.sfb.uit.no/marref/
url: https://sfb.mmp2.sigma2.no/marref/
- description: Powerful search engine which uses mass spectrometry data to identify proteins from DNA, RNA and protein sequence databases as well as spectral libraries.
id: mascot
name: Mascot
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- description: SalDB is a salmon specific database of genome sequenced prokaryotes representing the microbiota of fishes found in the taxonomic family of Salmonidae.
id: saldb
name: salDB
url: https://mmp.sfb.uit.no/databases/saldb/
url: https://sfb.mmp2.sigma2.no/databases/saldb/
- description: Small Angle Scattering Biological Data Bank
id: sasbdb
name: SASBDB
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2 changes: 1 addition & 1 deletion pages/national_resources/no_resources.md
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related_pages:
your_tasks: [data_analysis]
tool_assembly: [marine_assembly]
url: https://mmp2.sfb.uit.no/metapipe/
url: https://sfb.mmp2.sigma2.no/metapipe/
- name: Norwegian COVID-19 Data Portal
description: The Norwegian COVID-19 Data Portal aims to bundle the Norwegian research efforts and offers guidelines, tools, databases and services to support Norwegian COVID-19 researchers.
related_pages:
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6 changes: 3 additions & 3 deletions pages/tool_assembly/marine_metagenomics_assembly.md
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---

## What is the Norwegian tool assembly for marine metagenomics data management?
The Norwegian tool assembly for marine metagenomics aims to provide a comprehensive toolkit for management of marine genomic research data throughout a project's data life cycle. The toolkit, developed by students and researchers in Norway, contains resources and software tools for both data management ([Planning](planning), [Processing](processing), [Storing](storage) and [Sharing](sharing)), data [analysis](analysing) and training. It is built on the [Norwegian e-Infrastructure for Life Sciences (NeLS)](nels_assembly) tool assembly of [ELIXIR Norway](https://elixir.no/) and the [Marine Metagenomics Platform (MMP)](https://mmp2.sfb.uit.no/).
The Norwegian tool assembly for marine metagenomics aims to provide a comprehensive toolkit for management of marine genomic research data throughout a project's data life cycle. The toolkit, developed by students and researchers in Norway, contains resources and software tools for both data management ([Planning](planning), [Processing](processing), [Storing](storage) and [Sharing](sharing)), data [analysis](analysing) and training. It is built on the [Norwegian e-Infrastructure for Life Sciences (NeLS)](nels_assembly) tool assembly of [ELIXIR Norway](https://elixir.no/) and the [Marine Metagenomics Platform (MMP)](https://sfb.mmp2.sigma2.no).

## Who can use the marine metagenomics data management tool assembly?
This tool assembly is useful for students and researchers, in Norway, who are interested in analysing marine datasets (e.g. genomes, metagenomes, and transcriptomes). Parts of the assembly, such as data storage, are based on national infrastructures, laws and regulations, and consequently limited to Norwegian users, while other parts, such as data analysis tools and data repositories, are globally accessible.

## How can you access the marine metagenomics data management tool assembly?
To be able to use resources and tools that are mentioned here, you are recommended to have a [Feide account](https://www.feide.no/). In addition, it is important for you to have a NeLs account in order to access [usegalaxy.no](https://usegalaxy.no/). In case your institution does not use the national Feide secure login service, you can apply for a NeLs IDP through the [ELIXIR Norway help desk](mailto:[email protected]?subject=marine%20metagenomics). Note, that Marine Metagenomics Platform (MMP) is an open-access platform that can be accessed without a Feide account at [https://mmp2.sfb.uit.no/](https://mmp2.sfb.uit.no/).
To be able to use resources and tools that are mentioned here, you are recommended to have a [Feide account](https://www.feide.no/). In addition, it is important for you to have a NeLs account in order to access [usegalaxy.no](https://usegalaxy.no/). In case your institution does not use the national Feide secure login service, you can apply for a NeLs IDP through the [ELIXIR Norway help desk](mailto:[email protected]?subject=marine%20metagenomics). Note, that Marine Metagenomics Platform (MMP) is an open-access platform that can be accessed without a Feide account at [https://mmp2.sfb.uit.no/](https://sfb.mmp2.sigma2.no).

## For what purpose can you use the marine metagenomics data management tool assembly?

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The solutions for data storage, sharing and computation are built on the services and infrastructure delivered by ELIXIR Norway described in the Norwegian e-Infrastructure for Life Sciences (NeLS) [tool assembly](nels_assembly).

### Data processing and analysis
The {% tool "marine-metagenomics-portal" %} provides a complete service for analysis of marine metagenomic data through the tool [META-pipe](https://mmp2.sfb.uit.no/metapipe/). META-pipe is a pipeline that can assemble your high-throughput sequence data, functionally annotate the predicted genes, and taxonomically profile your marine metagenomics samples, helping you to gain insight into the phylogenetic diversity, metabolic and functional potential of environmental communities. You can read more [details about META-pipe in the publication](https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC6480938/). Norwegian users with Feide access can access the online version of META-pipe. For other users META-pipe is [downloadable](https://gitlab.com/uit-sfb/metapipe) and can easily be run on any computing environment (e.g. any Linux workstation, SLURM cluster or Kubernetes).
The {% tool "marine-metagenomics-portal" %} provides a complete service for analysis of marine metagenomic data through the tool [META-pipe](https://sfb.mmp2.sigma2.no/metapipe/). META-pipe is a pipeline that can assemble your high-throughput sequence data, functionally annotate the predicted genes, and taxonomically profile your marine metagenomics samples, helping you to gain insight into the phylogenetic diversity, metabolic and functional potential of environmental communities. You can read more [details about META-pipe in the publication](https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC6480938/). Norwegian users with Feide access can access the online version of META-pipe. For other users META-pipe is [downloadable](https://gitlab.com/uit-sfb/metapipe) and can easily be run on any computing environment (e.g. any Linux workstation, SLURM cluster or Kubernetes).

[Usegalaxy.no](https://usegalaxy.no/) is a Norwegian instance of the {% tool "galaxy" %} web-based platform for data intensive life science research that provides users with a unified, easy-to-use graphical interface to a host of more than 200 different analysis tools. Here, you can find tools for a wide variety of analysis for your marine metagenomic and genomic data. The tools are publicly available in the [Galaxy Toolshed](https://toolshed.g2.bx.psu.edu/) which serves as an "appstore" so you can easily transfer them to your favourite Galaxy instance anywhere. You can run the tools interactively, one by one, or combine them into multi-step workflows that can be executed as a single analysis. Premade workflows (i.e for Taxonomic classification of metagenomic sequences) are provided, and you can request installation of your favourite tool by contacting the [ELIXIR Norway help desk](mailto:[email protected]?subject=marine metagenomics).

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