Update adopters.md

- fixed various broken links
- removed section of RDP which no longer exists

pages/about/adopters.md

@@ -16,31 +16,32 @@ ENA also offers customizable MIxS templates for downloads in their login-based s
 
 ### The GOLD Database
 
-The Genomes Online Database ([GOLD](https://gold.jgi-psf.org/)) displays a wide range of metadata for complete and ongoing genome and metagenome projects. It now also accepts [submission](https://gold.jgi-psf.org/goldlogin) of new entries and metadata.
-
-### MG-RAST
-
-MG-RAST has implemented the use of MIxS by using simple spreadsheets to capture metadata, with a minimal number of required fields (in red in the spreadsheets) and a number of optional fields. The spreadsheet is separated into multiple tabs representing the different metadata categories. A more detailed explanation can be found in the [MG-RAST blog](http://blog.metagenomics.anl.gov/metadata-in-mg-rast/).
+The Genomes Online Database ([GOLD](https://gold.jgi.doe.gov/)) displays a wide range of metadata for complete and ongoing genome and metagenome projects. It now also accepts [submission](https://signon.jgi.doe.gov/signon) of new entries and metadata.
 
 ### NMDC
 The National Microbiome Data Collaborative ([NMDC](https://microbiomedata.org/)) supports the long-term advancement of microbiome science, and is building an agile, integrated data ecosystem, utilising the GSC MIxS standards.
 
 ### GigaDB
 
-The GigaScience Press database, [GigaDB](http://gigadb.org) hosts datasets linked to manuscripts published in <i>[GigaScience](https://www.gigasciencejournal.com)</i> and <i>[GigaByte](https://www.gigabytejournal.com)</i> journals. Where appropriate the sample metadata is curated using the MIxS checklists.
+The GigaScience Press database, [GigaDB](http://gigadb.org) hosts datasets linked to manuscripts published in <i>[GigaScience](https://academic.oup.com/gigascience)</i> and <i>[GigaByte](https://www.gigabytejournal.com)</i> journals. Where appropriate the sample metadata is curated using the MIxS checklists.
+
+### MG-RAST 
+This project is no longer actively supported by any organization, but continues to provide access to historic data with a voluntary Helpdesk.
+
+MG-RAST had implemented the use of MIxS by using simple spreadsheets to capture metadata, with a minimal number of required fields (in red in the spreadsheets) and a number of optional fields. The spreadsheet is separated into multiple tabs representing the different metadata categories.
 
 
 ## Tools
 
 ### ISA infrastructure
 
-The [Investigation/Study/Assay (ISA) Infrastructure](http://isatab.sourceforge.net/) is a freely available software suite that:
+The [Investigation/Study/Assay (ISA) Infrastructure](https://isa-tools.org/) is a freely available software suite that:
 
 1.  assists in the **curation**, **reporting** and **local management** of experimental metadata (i.e. sample characteristics, technologies used, type of measurements) from studies employing one or a combination of technologies;
-2.  empowers communities to **uptake GSC community-defined standards**: minimum information checklists (MIGS/MIMS/MIMARKS) and ontologies (e.g, [EnvO](http://www.environmentontology.org/), [OBI](http://obi-ontology.org/page/Main_Page) etc);
+2.  empowers communities to **uptake GSC community-defined standards**: minimum information checklists (MIGS/MIMS/MIMARKS) and ontologies (e.g, [EnvO](http://www.environmentontology.org/), [OBI](http://obi-ontology.org) etc);
 3.  facilitates **submission to international public repositories** of genomics studies (e.g. [ENA](http://www.ebi.ac.uk/ena/) and [SRA](http://www.ncbi.nlm.nih.gov/sra) databases), but also of transcriptomics and proteomics studies ([ArrayExpress](http://www.ebi.ac.uk/arrayexpress) and [Pride](http://www.ebi.ac.uk/pride)).
 
-The [Java-based ISA software components and a relational database](http://isatab.sourceforge.net/tools.html) are based on the ISA-Tab format and designed for local use and can work independently, or as unified system:
+The [Java-based ISA software components and a relational database](https://isa-tools.org/) are based on the ISA-Tab format and designed for local use and can work independently, or as unified system:
 
 *   ISAcreatorConfig, for curators or power users to regulate the fields displayed in the ISAcreator; i.e., declaring certain fields mandatory or mandating the use of a specific set of ontology terms (accessed via [BioPortal](http://bioportal.bioontology.org/) and [OLS](http://www.ebi.ac.uk/ontology-lookup/) public portal).
     *   Download **ISA creator configuration files** for the MIMARKS environmental packages from [sourceforge](https://sourceforge.net/projects/isatab/files/release20100520/ISAcreator_v1.2/custom-ISAconfigurations/MIMARKS-configurations-alpha/MIMARKS-ISA-configurations-alpha.zip/download). Please note these are alpha versions to be further evaluated and these should not be used in a production environment. MIGS/MIMS configuration files will follow.
@@ -65,11 +66,15 @@ CDinFusion (Contextual Data and FASTA infusion) is a submission-preparation-tool
 
 Qiita (_canonically pronounced cheetah_) is an entirely open-source microbiome storage and analysis resource that can run on everything from your laptop to a supercomputer. It is built on top of the widely used [QIIME](http://qiime.org/) package, and enables the exploration of -omics data. The resource ([http://qiita.microbio.me/](http://qiita.microbio.me/)) currently supports the MIMARKS specification, allowing users to generate and validate MIMARKS-compliant templates. These templates can be viewed and completed in the users’ spreadsheet editor of choice (e.g. Microsoft Excel). The Qiita web-platform also offers an ontology lookup and georeferencing tool to aid users when completing the MIMARKS templates. Additional tools for processing and analyzing MIMARKS-compliant microbial communities using this platform will be made available to the public on an ongoing basis.
 
-### RDP Googlesheets and SRA services
-
-[RDP’s Google Sheets](http://rdp.cme.msu.edu/misc/googleSheetsHelp.jsp) assist researchers by providing easy online accessible data entry and storage for metadata conforming to the MIxS and the MIMARKS specifications for all 14 current environments. After you collect your metadata, you can export your MIMARKS-compliant data by selecting the menu item “MIMARKS Export” and choose your desired output: WebIN or Sequin. The RDP SRA Prepkit is no longer available. Please use the new SRA prep/submission tools hosted by ENA or NCBI to complete data submission. RDP users should contact RDP Staff if you have questions or need assistance to begin the process involved in preparing metadata documents that are required for submission to the Sequence Read Archive (SRA).
 
 ### EBI Metagenomics Portal (MGNify)
 
 The [EBI Metagenomics](http://www.ebi.ac.uk/metagenomics/) service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the functional and metabolic potential of a sample. Until October 2012, the EBI Metagenomics service offered a manually-assisted submission route, with help available to ensure data and metadata formatting complied with the Sequence Read Archive (SRA) data schema and the Genomic Standards Consortium (GSC) sample metadata guidelines respectively, allowing harmonisation of analysis efforts across the wider genomics community. From October 2012, submitters of metagenomic datasets are encouraged to make use of [ENA’s SRA Webin submission service](https://www.ebi.ac.uk/ena/about/submit_and_update), which supports all of the MIxS checklists.
 
+
+<!---
+The RDP project no longer exists...
+
+### RDP Googlesheets and SRA services
+
+[RDP’s Google Sheets](http://rdp.cme.msu.edu/misc/googleSheetsHelp.jsp) assist researchers by providing easy online accessible data entry and storage for metadata conforming to the MIxS and the MIMARKS specifications for all 14 current environments. After you collect your metadata, you can export your MIMARKS-compliant data by selecting the menu item “MIMARKS Export” and choose your desired output: WebIN or Sequin. The RDP SRA Prepkit is no longer available. Please use the new SRA prep/submission tools hosted by ENA or NCBI to complete data submission. RDP users should contact RDP Staff if you have questions or need assistance to begin the process involved in preparing metadata documents that are required for submission to the Sequence Read Archive (SRA). --->