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GMOD/Apollo: 2.3.1

Nathan Dunn; Colin Diesh; Deepak Unni; Robert Buels; Helena Rasche; Anthony Bretaudeau; Luke Sargent; Robert Syme; Tim Stickland; Eric Y; Michael Paulini; Ian Holmes


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  <identifier identifierType="DOI">10.5281/zenodo.2572932</identifier>
  <creators>
    <creator>
      <creatorName>Nathan Dunn</creatorName>
      <affiliation>Lawrence Berkeley National Lab</affiliation>
    </creator>
    <creator>
      <creatorName>Colin Diesh</creatorName>
      <affiliation>UC Berkeley</affiliation>
    </creator>
    <creator>
      <creatorName>Deepak Unni</creatorName>
      <affiliation>Lawrence Berkeley National Lab</affiliation>
    </creator>
    <creator>
      <creatorName>Robert Buels</creatorName>
      <affiliation>UC Berkeley</affiliation>
    </creator>
    <creator>
      <creatorName>Helena Rasche</creatorName>
      <affiliation>@BackofenLab</affiliation>
    </creator>
    <creator>
      <creatorName>Anthony Bretaudeau</creatorName>
      <affiliation>BIPAA/GenOuest</affiliation>
    </creator>
    <creator>
      <creatorName>Luke Sargent</creatorName>
      <affiliation>OHSU Computational Biology Department</affiliation>
    </creator>
    <creator>
      <creatorName>Robert Syme</creatorName>
      <affiliation>Curtin University</affiliation>
    </creator>
    <creator>
      <creatorName>Tim Stickland</creatorName>
      <affiliation>Wellcome Sanger Institute</affiliation>
    </creator>
    <creator>
      <creatorName>Eric Y</creatorName>
      <affiliation>UC Berkeley</affiliation>
    </creator>
    <creator>
      <creatorName>Michael Paulini</creatorName>
      <affiliation>WormBase</affiliation>
    </creator>
    <creator>
      <creatorName>Ian Holmes</creatorName>
      <affiliation>UC Berkeley</affiliation>
    </creator>
  </creators>
  <titles>
    <title>GMOD/Apollo: 2.3.1</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2019</publicationYear>
  <subjects>
    <subject>genome annotation</subject>
    <subject>biocuration</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2019-02-19</date>
  </dates>
  <resourceType resourceTypeGeneral="Software"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/2572932</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsSupplementTo">https://github.com/GMOD/Apollo/tree/2.3.1</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.598056</relatedIdentifier>
  </relatedIdentifiers>
  <version>2.3.1</version>
  <rightsList>
    <rights rightsURI="http://www.opensource.org/licenses/BSD-2-Clause">BSD 2-Clause "Simplified" License</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;2.3.1 &lt;strong&gt;Official Release&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;Many bug fixes and some minor enhancements. Many thanks to the community for reporting, testing, and fixing these issues.&lt;/p&gt;

&lt;p&gt;&lt;a href="https://github.com/GMOD/Apollo/blob/master/ChangeLog.md#231"&gt;https://github.com/GMOD/Apollo/blob/master/ChangeLog.md#231&lt;/a&gt;&lt;/p&gt;

&lt;p&gt;Bug Fixes&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;Fixed issue when dragging features to resize was not providing an indicator box &lt;a href="https://github.com/GMOD/Apollo/pull/1988"&gt;1988&lt;/a&gt;&lt;/li&gt;
	&lt;li&gt;Fixed issue when sequence alterations were not rendering the full height of the sequence track &lt;a href="https://github.com/GMOD/Apollo/pull/2049"&gt;2049&lt;/a&gt;&lt;/li&gt;
	&lt;li&gt;Making organisms obsolete should remove associated permissions &lt;a href="https://github.com/GMOD/Apollo/pull/2043"&gt;2043&lt;/a&gt;&lt;/li&gt;
	&lt;li&gt;User-created features taken from split reads should create features with introns &lt;a href="https://github.com/GMOD/Apollo/pull/2036"&gt;2036&lt;/a&gt;&lt;/li&gt;
	&lt;li&gt;Should indicate split reads properly in evidence &lt;a href="https://github.com/GMOD/Apollo/pull/2034"&gt;2034&lt;/a&gt;&lt;a href="https://github.com/GMOD/Apollo/pull/2054"&gt;2054&lt;/a&gt;&lt;/li&gt;
	&lt;li&gt;Temporary files not removed during export of GFF3 or other file types &lt;a href="https://github.com/GMOD/Apollo/pull/1966"&gt;1966&lt;/a&gt;&lt;/li&gt;
	&lt;li&gt;Fixed issue where you could not alter an isoform after deleting a gene name &lt;a href="https://github.com/GMOD/Apollo/pull/1961"&gt;1961&lt;/a&gt;&lt;/li&gt;
	&lt;li&gt;Fixed some minor issues associated with sequence alterations &lt;a href="https://github.com/GMOD/Apollo/pull/1497"&gt;1497&lt;/a&gt;&lt;/li&gt;
	&lt;li&gt;Multiple owners tagged on GFF3 export &lt;a href="https://github.com/GMOD/Apollo/pull/29"&gt;29&lt;/a&gt;&lt;/li&gt;
	&lt;li&gt;Setting gene description puts UcA into a bad state &lt;a href="https://github.com/GMOD/Apollo/issues/2056"&gt;2056&lt;/a&gt;&lt;/li&gt;
	&lt;li&gt;Fixes plugin inclusion error by reverting prior fix &lt;a href="https://github.com/GMOD/Apollo/issues/2055"&gt;2055&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;Minor Features&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;Allowed duplication of organism from the Organism Panel &lt;a href="https://github.com/GMOD/Apollo/pull/1968"&gt;1968&lt;/a&gt;&lt;/li&gt;
	&lt;li&gt;Allows making an organism obsolete &lt;a href="https://github.com/GMOD/Apollo/pull/1967"&gt;1967&lt;/a&gt;&lt;/li&gt;
	&lt;li&gt;Create a filter and flag for inactive users &lt;a href="https://github.com/GMOD/Apollo/pull/1937"&gt;1937&lt;/a&gt;&lt;/li&gt;
	&lt;li&gt;Allowed deletion of feature from the Sequence and Annotator Panels &lt;a href="https://github.com/GMOD/Apollo/pull/2040"&gt;2040&lt;/a&gt;&lt;/li&gt;
	&lt;li&gt;Allow export of orig_id as an optional attribute &lt;a href="https://github.com/GMOD/Apollo/pull/2002"&gt;2002&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;</description>
  </descriptions>
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