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diff --git a/joss.06474/10.21105.joss.06474.crossref.xml b/joss.06474/10.21105.joss.06474.crossref.xml
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+    <timestamp>20240604125143</timestamp>
+    <depositor>
+      <depositor_name>JOSS Admin</depositor_name>
+      <email_address>[email protected]</email_address>
+    </depositor>
+    <registrant>The Open Journal</registrant>
+  </head>
+  <body>
+    <journal>
+      <journal_metadata>
+        <full_title>Journal of Open Source Software</full_title>
+        <abbrev_title>JOSS</abbrev_title>
+        <issn media_type="electronic">2475-9066</issn>
+        <doi_data>
+          <doi>10.21105/joss</doi>
+          <resource>https://joss.theoj.org</resource>
+        </doi_data>
+      </journal_metadata>
+      <journal_issue>
+        <publication_date media_type="online">
+          <month>06</month>
+          <year>2024</year>
+        </publication_date>
+        <journal_volume>
+          <volume>9</volume>
+        </journal_volume>
+        <issue>98</issue>
+      </journal_issue>
+      <journal_article publication_type="full_text">
+        <titles>
+          <title>MousebreedeR: A novel software to assist in the design
+of breeding schema for complex genotypes of experimental
+organisms</title>
+        </titles>
+        <contributors>
+          <person_name sequence="first" contributor_role="author">
+            <given_name>Mike</given_name>
+            <surname>Sportiello</surname>
+            <ORCID>https://orcid.org/0000-0003-1690-8702</ORCID>
+          </person_name>
+          <person_name sequence="additional"
+                       contributor_role="author">
+            <given_name>David J.</given_name>
+            <surname>Topham</surname>
+            <ORCID>https://orcid.org/0000-0002-9435-8673</ORCID>
+          </person_name>
+        </contributors>
+        <publication_date>
+          <month>06</month>
+          <day>04</day>
+          <year>2024</year>
+        </publication_date>
+        <pages>
+          <first_page>6474</first_page>
+        </pages>
+        <publisher_item>
+          <identifier id_type="doi">10.21105/joss.06474</identifier>
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+          <ai:license_ref applies_to="tdm">http://creativecommons.org/licenses/by/4.0/</ai:license_ref>
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+        <rel:program>
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+            <rel:inter_work_relation relationship-type="references" identifier-type="doi">10.5281/zenodo.11405147</rel:inter_work_relation>
+          </rel:related_item>
+          <rel:related_item>
+            <rel:description>GitHub review issue</rel:description>
+            <rel:inter_work_relation relationship-type="hasReview" identifier-type="uri">https://github.com/openjournals/joss-reviews/issues/6474</rel:inter_work_relation>
+          </rel:related_item>
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+        <doi_data>
+          <doi>10.21105/joss.06474</doi>
+          <resource>https://joss.theoj.org/papers/10.21105/joss.06474</resource>
+          <collection property="text-mining">
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+              <resource mime_type="application/pdf">https://joss.theoj.org/papers/10.21105/joss.06474.pdf</resource>
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+          </collection>
+        </doi_data>
+        <citation_list>
+          <citation key="RN204">
+            <article_title>Simplified method to measure mouse
+fertility</article_title>
+            <author>Handelsman</author>
+            <journal_title>Endocrinology</journal_title>
+            <issue>8</issue>
+            <volume>161</volume>
+            <doi>10.1210/endocr/bqaa114</doi>
+            <issn>1945-7170</issn>
+            <cYear>2020</cYear>
+            <unstructured_citation>Handelsman, D. J., Walters, K. A.,
+&amp; Ly, L. P. (2020). Simplified method to measure mouse fertility.
+Endocrinology, 161(8).
+https://doi.org/10.1210/endocr/bqaa114</unstructured_citation>
+          </citation>
+          <citation key="RN203">
+            <article_title>Mouse gestation length is genetically
+determined</article_title>
+            <author>Murray</author>
+            <journal_title>PLoS One</journal_title>
+            <issue>8</issue>
+            <volume>5</volume>
+            <doi>10.1371/journal.pone.0012418</doi>
+            <issn>1932-6203</issn>
+            <cYear>2010</cYear>
+            <unstructured_citation>Murray, S. A., Morgan, J. L., Kane,
+C., Sharma, Y., Heffner, C. S., Lake, J., &amp; Donahue, L. R. (2010).
+Mouse gestation length is genetically determined. PLoS One, 5(8),
+e12418.
+https://doi.org/10.1371/journal.pone.0012418</unstructured_citation>
+          </citation>
+        </citation_list>
+      </journal_article>
+    </journal>
+  </body>
+</doi_batch>
diff --git a/joss.06474/10.21105.joss.06474.pdf b/joss.06474/10.21105.joss.06474.pdf
diff --git a/joss.06474/paper.jats/10.21105.joss.06474.jats b/joss.06474/paper.jats/10.21105.joss.06474.jats
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+<?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Publishing DTD v1.2 20190208//EN"
+                  "JATS-publishing1.dtd">
+<article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" dtd-version="1.2" article-type="other">
+<front>
+<journal-meta>
+<journal-id></journal-id>
+<journal-title-group>
+<journal-title>Journal of Open Source Software</journal-title>
+<abbrev-journal-title>JOSS</abbrev-journal-title>
+</journal-title-group>
+<issn publication-format="electronic">2475-9066</issn>
+<publisher>
+<publisher-name>Open Journals</publisher-name>
+</publisher>
+</journal-meta>
+<article-meta>
+<article-id pub-id-type="publisher-id">6474</article-id>
+<article-id pub-id-type="doi">10.21105/joss.06474</article-id>
+<title-group>
+<article-title>MousebreedeR: A novel software to assist in the design of
+breeding schema for complex genotypes of experimental
+organisms</article-title>
+</title-group>
+<contrib-group>
+<contrib contrib-type="author" corresp="yes">
+<contrib-id contrib-id-type="orcid">https://orcid.org/0000-0003-1690-8702</contrib-id>
+<name>
+<surname>Sportiello</surname>
+<given-names>Mike</given-names>
+</name>
+<xref ref-type="aff" rid="aff-1"/>
+<xref ref-type="aff" rid="aff-2"/>
+<xref ref-type="corresp" rid="cor-1"><sup>*</sup></xref>
+</contrib>
+<contrib contrib-type="author">
+<contrib-id contrib-id-type="orcid">https://orcid.org/0000-0002-9435-8673</contrib-id>
+<name>
+<surname>Topham</surname>
+<given-names>David J.</given-names>
+</name>
+<xref ref-type="aff" rid="aff-1"/>
+</contrib>
+<aff id="aff-1">
+<institution-wrap>
+<institution>Center for Vaccine Biology and Immunology, University of
+Rochester Medical Center, Rochester, NY 14642, United States of
+America</institution>
+</institution-wrap>
+</aff>
+<aff id="aff-2">
+<institution-wrap>
+<institution>Medical Scientist Training Program, University of Rochester
+Medical Center, Rochester, NY 14642, United States of
+America</institution>
+</institution-wrap>
+</aff>
+</contrib-group>
+<author-notes>
+<corresp id="cor-1">* E-mail: <email></email></corresp>
+</author-notes>
+<pub-date date-type="pub" publication-format="electronic" iso-8601-date="2023-12-28">
+<day>28</day>
+<month>12</month>
+<year>2023</year>
+</pub-date>
+<volume>9</volume>
+<issue>98</issue>
+<fpage>6474</fpage>
+<permissions>
+<copyright-statement>Authors of papers retain copyright and release the
+work under a Creative Commons Attribution 4.0 International License (CC
+BY 4.0)</copyright-statement>
+<copyright-year>2022</copyright-year>
+<copyright-holder>The article authors</copyright-holder>
+<license license-type="open-access" xlink:href="https://creativecommons.org/licenses/by/4.0/">
+<license-p>Authors of papers retain copyright and release the work under
+a Creative Commons Attribution 4.0 International License (CC BY
+4.0)</license-p>
+</license>
+</permissions>
+<kwd-group kwd-group-type="author">
+<kwd>breeding</kwd>
+<kwd>mouse</kwd>
+<kwd>experimental organism</kwd>
+<kwd>colony management</kwd>
+</kwd-group>
+</article-meta>
+</front>
+<body>
+<sec id="summary">
+  <title>Summary</title>
+  <p>With the advent of gene editing playing a regular role in producing
+  new experimental models, the need to get the appropriate allele at
+  each respective locus in a model organism is now common. Instead of
+  simple “knockout” vs “wildtype” mouse experiments, for example, it is
+  common for there to be a gene of interest that is either floxed
+  (surrounded by known genetic sequence that allow for a gene to be
+  knocked out when coexpression of the cre protein is expressed) or not
+  floxed depending on the experimental group, another gene that marks
+  cells of a certain phenotype such as a fluorescent reporter, a cre
+  expression cassette to flox the gene of interest out, and more. While
+  it is often obvious how to efficiently breed experimental organisms to
+  obtain one locus of interest, once three or more loci are involved
+  this becomes difficult to assess. MousebreedeR is a free and open
+  source web-based shiny app and command line R package that takes
+  desired mouse genotypes as well as the genotypes of potential mouse
+  breeders that the user already has on hand as inputs, and delivers
+  efficient breeding schema as the output. In addition, it supplies the
+  user with the probability of producing each potential pup, the
+  probability that no pups with the desired genotype are born in a
+  litter, and more. We have also supplied code that assists the user in
+  plotting these tables to help them visualize crosses of interest and
+  make decisions in their breeding.</p>
+</sec>
+<sec id="statement-of-need">
+  <title>Statement of need</title>
+  <p>Efficient breeding is a scientific imperative: with a limited
+  period of fertility in experimental organisms, users may only have
+  limited attempts with organisms of desired genotypes
+  (<xref alt="Handelsman et al., 2020" rid="ref-RN204" ref-type="bibr">Handelsman
+  et al., 2020</xref>;
+  <xref alt="Murray et al., 2010" rid="ref-RN203" ref-type="bibr">Murray
+  et al., 2010</xref>). Taking into account both gestational time and
+  the necessary time it takes to wean pups off their mother’s milk, an
+  inefficient cross can set the user back months in the case of a female
+  pregnant with the non-optimal male’s offspring. Furthermore, as most
+  research centers pay <italic>per diem</italic> costs, inefficiency is
+  a large direct cost for many experimentalists. Individual cages often
+  cost hundreds of dollars per year just in maintenance fees, not even
+  accounting for the cost of extra rounds of genotyping (requiring PCR
+  primers, PCR mastermix, gels, dye, etc) or for the time dedicated to
+  the project by employees. Most importantly, ethical and animal welfare
+  concerns also arise as inefficient breeding results in the mass
+  euthanasia of non-desired animals as well as ear/tail-clipping
+  required for genotyping, which may cause animals pain and
+  distress.</p>
+  <p>While the breeding schema to obtain a litter of full knockout mice
+  from one wildtype/wildtype parent and one knockout/knockout parent is
+  straightforward, this is not the case for the situation where one has
+  4 alleles at 4 loci in 4 separate mice, which all need to co-occur in
+  the same mouse for a given planned experiment, for example.
+  Furthermore, to our knowledge, no current software exists that can
+  quantitatively assist the user in creating their breeding schema.
+  Indeed, if there are 2 alleles at each locus, when attempting to make
+  a genetically marked, inducible, cre-lox model with T cell specificity
+  as our lab was doing and which prompted us to create this software, 81
+  possible combinations exist (3 (AA, Aa, and aa) to the 4th power).
+  With 81 possible males and 81 possible females to mate, 6561 possible
+  pairings exist (81 * 81). Use of the mousebreedeR software to optimize
+  that breeding schema has been most helpful.</p>
+</sec>
+<sec id="acknowledgements">
+  <title>Acknowledgements</title>
+  <p>This work was supported by the National Institutes of Health (NIH)
+  National Institute of Allergy and Infectious Diseases Grant
+  P01-AI102851-10. M.S. was supported by the NIH/National Heart, Lung,
+  and Blood Institute Training Grant T32-HL066988-20, as well as by the
+  NIH Training Grant/National Institute of General Medical Sciences
+  Grant T32GM007356-48.</p>
+</sec>
+</body>
+<back>
+<ref-list>
+  <ref id="ref-RN204">
+    <element-citation publication-type="article-journal">
+      <person-group person-group-type="author">
+        <name><surname>Handelsman</surname><given-names>D. J.</given-names></name>
+        <name><surname>Walters</surname><given-names>K. A.</given-names></name>
+        <name><surname>Ly</surname><given-names>L. P.</given-names></name>
+      </person-group>
+      <article-title>Simplified method to measure mouse fertility</article-title>
+      <source>Endocrinology</source>
+      <year iso-8601-date="2020">2020</year>
+      <volume>161</volume>
+      <issue>8</issue>
+      <issn>1945-7170</issn>
+      <uri>https://www.ncbi.nlm.nih.gov/pubmed/32645712</uri>
+      <pub-id pub-id-type="doi">10.1210/endocr/bqaa114</pub-id>
+    </element-citation>
+  </ref>
+  <ref id="ref-RN203">
+    <element-citation publication-type="article-journal">
+      <person-group person-group-type="author">
+        <name><surname>Murray</surname><given-names>S. A.</given-names></name>
+        <name><surname>Morgan</surname><given-names>J. L.</given-names></name>
+        <name><surname>Kane</surname><given-names>C.</given-names></name>
+        <name><surname>Sharma</surname><given-names>Y.</given-names></name>
+        <name><surname>Heffner</surname><given-names>C. S.</given-names></name>
+        <name><surname>Lake</surname><given-names>J.</given-names></name>
+        <name><surname>Donahue</surname><given-names>L. R.</given-names></name>
+      </person-group>
+      <article-title>Mouse gestation length is genetically determined</article-title>
+      <source>PLoS One</source>
+      <year iso-8601-date="2010">2010</year>
+      <volume>5</volume>
+      <issue>8</issue>
+      <issn>1932-6203</issn>
+      <uri>https://www.ncbi.nlm.nih.gov/pubmed/20811634</uri>
+      <pub-id pub-id-type="doi">10.1371/journal.pone.0012418</pub-id>
+      <fpage>e12418</fpage>
+      <lpage></lpage>
+    </element-citation>
+  </ref>
+</ref-list>
+</back>
+</article>