Merge pull request #77 from plantbreeding/edits_by_patrick

[ci skip] This build is based on 1d3e3a1. This commit was created by the following CI build and job: https://github.com/plantbreeding/BrAPI-Manuscript2/commit/1d3e3a1526b0f6215dabf65bfeb018efbb9db827/checks https://github.com/plantbreeding/BrAPI-Manuscript2/actions/runs/10460189828
plantbreeding · Aug 19, 2024 · 5cc9e94 · 5cc9e94
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diff --git a/citations.tsv b/citations.tsv
@@ -16,7 +16,8 @@ doi:10.1093/database/bax046	doi:10.1093/database/bax046	doi:10.1093/database/bax
 doi:10.1093/bioinformatics/btr330	doi:10.1093/bioinformatics/btr330	doi:10.1093/bioinformatics/btr330	PzHxvkzH
 https://github.com/ga4gh-metadata/SchemaBlocks	https://github.com/ga4gh-metadata/SchemaBlocks	url:https://github.com/ga4gh-metadata/SchemaBlocks	186zclKvK
 doi:10.1093/gigascience/giad025	doi:10.1093/gigascience/giad025	doi:10.1093/gigascience/giad025	9fRbvOj2
-doi:10.1016/S0022-2836	doi:10.1016/S0022-2836	doi:10.1016/s0022-2836	1DwGXrhur
+doi:10.1186/1471-2105-10-421	doi:10.1186/1471-2105-10-421	doi:10.1186/1471-2105-10-421	nEsJGUWa
+doi:10.1186/s13742-015-0080-7	doi:10.1186/s13742-015-0080-7	doi:10.1186/s13742-015-0080-7	1HIbyz3rL
 doi:10.1093/bioinformatics/btq580	doi:10.1093/bioinformatics/btq580	doi:10.1093/bioinformatics/btq580	Wz8l0HlN
 doi:10.1093/gigascience/giz051	doi:10.1093/gigascience/giz051	doi:10.1093/gigascience/giz051	AVjkjraw
 doi:10.1002/ppp3.10187	doi:10.1002/ppp3.10187	doi:10.1002/ppp3.10187	bvSFyrtt

diff --git a/manuscript.docx b/manuscript.docx
diff --git a/manuscript.html b/manuscript.html
diff --git a/manuscript.md b/manuscript.md
@@ -100,8 +100,8 @@ header-includes: |
   <meta name="dc.date" content="2024-08-19" />
   <meta name="citation_publication_date" content="2024-08-19" />
   <meta property="article:published_time" content="2024-08-19" />
-  <meta name="dc.modified" content="2024-08-19T16:50:36+00:00" />
-  <meta property="article:modified_time" content="2024-08-19T16:50:36+00:00" />
+  <meta name="dc.modified" content="2024-08-19T20:08:37+00:00" />
+  <meta property="article:modified_time" content="2024-08-19T20:08:37+00:00" />
   <meta name="dc.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -339,9 +339,9 @@ header-includes: |
   <meta name="citation_fulltext_html_url" content="https://plantbreeding.github.io/BrAPI-Manuscript2/" />
   <meta name="citation_pdf_url" content="https://plantbreeding.github.io/BrAPI-Manuscript2/manuscript.pdf" />
   <link rel="alternate" type="application/pdf" href="https://plantbreeding.github.io/BrAPI-Manuscript2/manuscript.pdf" />
-  <link rel="alternate" type="text/html" href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/dab19d16cde75b4702f4d6bcc35796de67310c51/" />
-  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/dab19d16cde75b4702f4d6bcc35796de67310c51/" />
-  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/dab19d16cde75b4702f4d6bcc35796de67310c51/manuscript.pdf" />
+  <link rel="alternate" type="text/html" href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/1d3e3a1526b0f6215dabf65bfeb018efbb9db827/" />
+  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/1d3e3a1526b0f6215dabf65bfeb018efbb9db827/" />
+  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/1d3e3a1526b0f6215dabf65bfeb018efbb9db827/manuscript.pdf" />
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@@ -363,9 +363,9 @@ manubot-clear-requests-cache: false
 
 <small><em>
 This manuscript
-([permalink](https://plantbreeding.github.io/BrAPI-Manuscript2/v/dab19d16cde75b4702f4d6bcc35796de67310c51/))
+([permalink](https://plantbreeding.github.io/BrAPI-Manuscript2/v/1d3e3a1526b0f6215dabf65bfeb018efbb9db827/))
 was automatically generated
-from [plantbreeding/BrAPI-Manuscript2@dab19d1](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/dab19d16cde75b4702f4d6bcc35796de67310c51)
+from [plantbreeding/BrAPI-Manuscript2@1d3e3a1](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/1d3e3a1526b0f6215dabf65bfeb018efbb9db827)
 on August 19, 2024.
 </em></small>
 
@@ -741,7 +741,7 @@ on August 19, 2024.
     <br>
   <small>
      Leibniz Institute of Plant Genetics and Crop Plant Research
-     · Funded by The AGENT project is funded by the European Union's Horizon 2020 research and innovation programme under grant agreement no. 862613.
+     · Funded by The SHAPE3 project is funded by a grant from the German Ministry of Research and Education (BMBF, FKZ 031B1302A).
   </small>
 
 + **Suman Kumar**
@@ -1339,17 +1339,15 @@ Initially developed by DArT, the tool is gaining popularity within the breeding
 
 #### DivBrowse
 
-<!-- Sebastian B -->
+<!-- Sebastian B and Patrick K -->
 [DivBrowse](https://divbrowse.ipk-gatersleben.de/) [@doi:10.1093/gigascience/giad025] is a web platform for exploratory data analysis of large genotyping studies. 
 The software can be run standalone or integrated as a plugin into existing web portals. 
 At its core, DivBrowse combines the convenience of a genome browser with features tailored to germplasm diversity analysis. 
 DivBrowse provides visual access to VCF files obtained through genotyping experiments and can handle hundreds of millions of variants across thousands of samples.
 It is able to display genomic features such as nucleotide sequence, associated gene models, and short genomic variants. DivBrowse also calculates and displays variant statistics such as minor allele frequencies, the proportion of heterozygous calls, and the proportion of missing variant calls. 
 Dynamic principal component analyses can be performed on a user-specified genomic area to provide information on local genomic diversity. 
-
-DivBrowse employs the BrAPI-Genotyping module to access genotypic data from external BrAPI endpoints. 
-DivBrowse also has an interface to [BLAST](https://blast.ncbi.nlm.nih.gov/blast/Blast.cgi) [@doi:10.1016/S0022-2836(05)80360-2], which can be used to directly access genes or other genomic features. 
-The modular structure of DivBrowse allows developers to configure and easily embed links to other external information systems.
+DivBrowse also has an interface to BLAST+ tools [@doi:10.1186/1471-2105-10-421] installed on Galaxy servers [@doi:10.1186/s13742-015-0080-7], which can be used to directly access genes or other genomic features from results of custom BLAST query. 
+DivBrowse employs the BrAPI-Genotyping module to serve genotypic data as a BrAPI endpoint and to get genotypic data from other BrAPI endpoints.
 
 
 #### Flapjack
@@ -1654,6 +1652,7 @@ The authors would like to acknowledge the following funding sources:
 + The French Networks of Biological Resource Centres for Agricultural, Environmental and Life Sciences, doi: 10.15454/b4ec-tf49
 + The work was supported by the German Research Foundation DFG under the grant agreement number 442032008 (NFDI4Biodiversity). NFDI4Biodiversity is part of NFDI, the National Research Data Infrastructure in Germany ([www.nfdi.de](www.nfdi.de)).
 + The Bill and Malinda Gates Foundation in cooperation with the Excellence in Breeding Platform of the CGIAR
++ The development of DivBrowse is funded by a grant from the German Ministry of Research and Education (BMBF, FKZ 031B1302A).
 
 ## Author Contributions {.page_break_before}
 
@@ -1667,7 +1666,7 @@ The authors would like to acknowledge the following funding sources:
 + **Johan Steven Aparicio**: Johan wrote the section on the Mr.Bean project, and has made significant contributions to the BrAPI compatibility of the Mr.Bean project. 
 + **Jan Erik Backlund**: Jan Erik has made significant contributions to the BMS project. 
 + **Aldrin Batac**: Aldrin has made significant contributions to the BMS project. 
-+ **Sebastian Beier**: Sebastian wrote the section on the DivBrowse project, and has made significant contributions to the BrAPI compatibility of the DivBrowse project. 
++ **Sebastian Beier**: Sebastian wrote the section about the DivBrowse tool. 
 + **Gabriel Besombes**: Gabriel has made significant contributions to the PHIS project. 
 + **Alice Boizet**: Alice wrote the section on the Florilège projects, and has made significant contributions to the BrAPI compatibility of the Florilège, Gigwa and ShinyBrAPPs projects. 
 + **Matthijs Brouwer**: Matthijs has made significant contributions to the AGENT project. 
@@ -1694,7 +1693,7 @@ The authors would like to acknowledge the following funding sources:
 + **Sook Jung**: Sook wrote the section on the BIMS project, and has made significant contributions to the BrAPI compatibility of the BIMS project. 
 + **Paul Kersey**: Paul has made significant contributions to the AGENT project. 
 + **Andrzej Kilian**: Andrzej has made significant contributions to the DArT Sample Submission and DArTView projects. 
-+ **Patrick König**: Patrick has made significant contributions to the AGENT project. 
++ **Patrick König**: Patrick contributed to the section about the DivBrowse tool, and has made significant contributions to the BrAPI compatibility of the DivBrowse tool, and has made significant contributions to the BrAPI compatibility of the AGENT project.
 + **Suman Kumar**: Suman has made significant contributions to the AGENT project. 
 + **Josh Lamos-Sweeney**: Josh wrote the section on the G-Crunch project, and has made significant contributions to the BrAPI compatibility of the G-Crunch project. 
 + **Laszlo Lang**: Laszlo has made significant contributions to the Zendro project. 

diff --git a/manuscript.pdf b/manuscript.pdf
diff --git a/references.json b/references.json
@@ -2795,6 +2795,62 @@
     "id": "kWLsm7g6",
     "note": "This CSL Item was generated by Manubot v0.5.6 from its persistent identifier (standard_id).\nstandard_id: doi:10.1111/nph.16544"
   },
+  {
+    "publisher": "Springer Science and Business Media LLC",
+    "issue": "1",
+    "abstract": "<jats:title>Abstract</jats:title>\n          <jats:sec>\n            <jats:title>Background</jats:title>\n            <jats:p>Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences. There are also some shortcomings in the user-interface of the current command-line applications.</jats:p>\n          </jats:sec>\n          <jats:sec>\n            <jats:title>Results</jats:title>\n            <jats:p>We describe features and improvements of rewritten BLAST software and introduce new command-line applications. Long query sequences are broken into chunks for processing, in some cases leading to dramatically shorter run times. For long database sequences, it is possible to retrieve only the relevant parts of the sequence, reducing CPU time and memory usage for searches of short queries against databases of contigs or chromosomes. The program can now retrieve masking information for database sequences from the BLAST databases. A new modular software library can now access subject sequence data from arbitrary data sources. We introduce several new features, including strategy files that allow a user to save and reuse their favorite set of options. The strategy files can be uploaded to and downloaded from the NCBI BLAST web site.</jats:p>\n          </jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion</jats:title>\n            <jats:p>The new BLAST command-line applications, compared to the current BLAST tools, demonstrate substantial speed improvements for long queries as well as chromosome length database sequences. We have also improved the user interface of the command-line applications.</jats:p>\n          </jats:sec>",
+    "DOI": "10.1186/1471-2105-10-421",
+    "type": "article-journal",
+    "source": "Crossref",
+    "title": "BLAST+: architecture and applications",
+    "volume": "10",
+    "author": [
+      {
+        "given": "Christiam",
+        "family": "Camacho"
+      },
+      {
+        "given": "George",
+        "family": "Coulouris"
+      },
+      {
+        "given": "Vahram",
+        "family": "Avagyan"
+      },
+      {
+        "given": "Ning",
+        "family": "Ma"
+      },
+      {
+        "given": "Jason",
+        "family": "Papadopoulos"
+      },
+      {
+        "given": "Kevin",
+        "family": "Bealer"
+      },
+      {
+        "given": "Thomas L",
+        "family": "Madden"
+      }
+    ],
+    "container-title": "BMC Bioinformatics",
+    "language": "en",
+    "issued": {
+      "date-parts": [
+        [
+          2009,
+          12
+        ]
+      ]
+    },
+    "URL": "https://doi.org/cnjxgz",
+    "container-title-short": "BMC Bioinformatics",
+    "PMCID": "PMC2803857",
+    "PMID": "20003500",
+    "id": "nEsJGUWa",
+    "note": "This CSL Item was generated by Manubot v0.5.6 from its persistent identifier (standard_id).\nstandard_id: doi:10.1186/1471-2105-10-421"
+  },
   {
     "publisher": "Springer Science and Business Media LLC",
     "issue": "1",
@@ -2884,6 +2940,54 @@
     "id": "Ne0E9HbC",
     "note": "This CSL Item was generated by Manubot v0.5.6 from its persistent identifier (standard_id).\nstandard_id: doi:10.1186/s12859-022-04755-2"
   },
+  {
+    "publisher": "Oxford University Press (OUP)",
+    "issue": "1",
+    "DOI": "10.1186/s13742-015-0080-7",
+    "type": "article-journal",
+    "source": "Crossref",
+    "title": "NCBI BLAST+ integrated into Galaxy",
+    "volume": "4",
+    "author": [
+      {
+        "given": "Peter J. A.",
+        "family": "Cock"
+      },
+      {
+        "given": "John M.",
+        "family": "Chilton"
+      },
+      {
+        "given": "Björn",
+        "family": "Grüning"
+      },
+      {
+        "given": "James E.",
+        "family": "Johnson"
+      },
+      {
+        "given": "Nicola",
+        "family": "Soranzo"
+      }
+    ],
+    "container-title": "GigaScience",
+    "language": "en",
+    "issued": {
+      "date-parts": [
+        [
+          2015,
+          8,
+          25
+        ]
+      ]
+    },
+    "URL": "https://doi.org/gt7dv7",
+    "container-title-short": "GigaSci",
+    "PMCID": "PMC4557756",
+    "PMID": "26336600",
+    "id": "1HIbyz3rL",
+    "note": "This CSL Item was generated by Manubot v0.5.6 from its persistent identifier (standard_id).\nstandard_id: doi:10.1186/s13742-015-0080-7"
+  },
   {
     "publisher": "Springer Science and Business Media LLC",
     "issue": "1",

diff --git a/spelling-error-locations.txt b/spelling-error-locations.txt
@@ -82,72 +82,74 @@ content/90.back-matter.md:26:DFG
 content/90.back-matter.md:26:nfdi
 content/90.back-matter.md:26:nfdi
 content/90.back-matter.md:26:NFDI
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-content/90.back-matter.md:103:Grzegorz
-content/90.back-matter.md:103:Uszynski
-content/90.back-matter.md:106:Yarnes
+content/90.back-matter.md:28:BMBF
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+content/90.back-matter.md:88:Palladino
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+content/90.back-matter.md:104:Grzegorz
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diff --git a/spelling-errors.txt b/spelling-errors.txt
@@ -18,6 +18,7 @@ barcodes
 Berlinstraße
 Besombes
 BioinfOmics
+BMBF
 Boizet
 boxplot
 breedwithbims
@@ -45,6 +46,7 @@ DSBrAPP
 EE
 erlefloch
 FFAR
+FKZ
 Florilège
 François
 GBS
@@ -53,7 +55,7 @@ georeferencing
 GeoTIFF
 GH
 Gigwa’s
-Grzegorz
+grzegorz
 Hershberger
 Hok
 Hulse

diff --git a/variables.json b/variables.json