There is a newer version of this record available.

Software Open Access

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


MARC21 XML Export

<?xml version='1.0' encoding='UTF-8'?>
<record xmlns="http://www.loc.gov/MARC21/slim">
  <leader>00000nmm##2200000uu#4500</leader>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">genome annotation</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">biocuration</subfield>
  </datafield>
  <controlfield tag="005">20190826215711.0</controlfield>
  <controlfield tag="001">2572932</controlfield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">UC Berkeley</subfield>
    <subfield code="a">Colin Diesh</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Lawrence Berkeley National Lab</subfield>
    <subfield code="a">Deepak Unni</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">UC Berkeley</subfield>
    <subfield code="a">Robert Buels</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">@BackofenLab</subfield>
    <subfield code="a">Helena Rasche</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">BIPAA/GenOuest</subfield>
    <subfield code="a">Anthony Bretaudeau</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">OHSU Computational Biology Department</subfield>
    <subfield code="a">Luke Sargent</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Curtin University</subfield>
    <subfield code="a">Robert Syme</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Wellcome Sanger Institute</subfield>
    <subfield code="a">Tim Stickland</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">UC Berkeley</subfield>
    <subfield code="a">Eric Y</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">WormBase</subfield>
    <subfield code="a">Michael Paulini</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">UC Berkeley</subfield>
    <subfield code="a">Ian Holmes</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">89464126</subfield>
    <subfield code="z">md5:98fb71ed03fe9259749f39dc7b3712fc</subfield>
    <subfield code="u">https://zenodo.org/record/2572932/files/GMOD/Apollo-2.3.1.zip</subfield>
  </datafield>
  <datafield tag="542" ind1=" " ind2=" ">
    <subfield code="l">open</subfield>
  </datafield>
  <datafield tag="260" ind1=" " ind2=" ">
    <subfield code="c">2019-02-19</subfield>
  </datafield>
  <datafield tag="909" ind1="C" ind2="O">
    <subfield code="p">software</subfield>
    <subfield code="o">oai:zenodo.org:2572932</subfield>
  </datafield>
  <datafield tag="100" ind1=" " ind2=" ">
    <subfield code="u">Lawrence Berkeley National Lab</subfield>
    <subfield code="a">Nathan Dunn</subfield>
  </datafield>
  <datafield tag="245" ind1=" " ind2=" ">
    <subfield code="a">GMOD/Apollo: 2.3.1</subfield>
  </datafield>
  <datafield tag="540" ind1=" " ind2=" ">
    <subfield code="u">http://www.opensource.org/licenses/BSD-2-Clause</subfield>
    <subfield code="a">BSD 2-Clause "Simplified" License</subfield>
  </datafield>
  <datafield tag="650" ind1="1" ind2="7">
    <subfield code="a">cc-by</subfield>
    <subfield code="2">opendefinition.org</subfield>
  </datafield>
  <datafield tag="520" ind1=" " ind2=" ">
    <subfield code="a">&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;</subfield>
  </datafield>
  <datafield tag="773" ind1=" " ind2=" ">
    <subfield code="n">url</subfield>
    <subfield code="i">isSupplementTo</subfield>
    <subfield code="a">https://github.com/GMOD/Apollo/tree/2.3.1</subfield>
  </datafield>
  <datafield tag="773" ind1=" " ind2=" ">
    <subfield code="n">doi</subfield>
    <subfield code="i">isVersionOf</subfield>
    <subfield code="a">10.5281/zenodo.598056</subfield>
  </datafield>
  <datafield tag="024" ind1=" " ind2=" ">
    <subfield code="a">10.5281/zenodo.2572932</subfield>
    <subfield code="2">doi</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">software</subfield>
  </datafield>
</record>
1,006
247
views
downloads
All versions This version
Views 1,00616
Downloads 2474
Data volume 21.8 GB357.9 MB
Unique views 75213
Unique downloads 463

Share

Cite as