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<p></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;' lang='en'> <td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td> <td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 18:06, 1 February 2021</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l7" >Line 7:</td> <td colspan="2" class="diff-lineno">Line 7:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== Full document ==</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== Full document ==</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&lt;pdf&gt;Media:<del class="diffchange diffchange-inline">Draft_Content_128849419</del>-beopen2063-<del class="diffchange diffchange-inline">5834</del>-document.pdf&lt;/pdf&gt;</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&lt;pdf&gt;Media:<ins class="diffchange diffchange-inline">Lampa_et_al_2018a</ins>-beopen2063-<ins class="diffchange diffchange-inline">6128</ins>-document.pdf&lt;/pdf&gt;</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr> <!-- diff cache key mw_drafts_scipedia-sc_mwd_:diff:version:1.11a:oldid:196284:newid:196467 --> </table>

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<p>Scipediacontent moved page <a href="/public/Draft_Content_128849419" class="mw-redirect" title="Draft Content 128849419">Draft Content 128849419</a> to <a href="/public/Lampa_et_al_2018a" title="Lampa et al 2018a">Lampa et al 2018a</a></p> <table class="diff diff-contentalign-left" data-mw="interface"> <tr style='vertical-align: top;' lang='en'> <td colspan='1' style="background-color: white; color:black; text-align: center;">← Older revision</td> <td colspan='1' style="background-color: white; color:black; text-align: center;">Revision as of 15:16, 1 February 2021</td> </tr><tr><td colspan='2' style='text-align: center;' lang='en'><div class="mw-diff-empty">(No difference)</div> </td></tr></table>

Scipediacontent https://www.scipedia.com/wd/index.php?title=Lampa_et_al_2018a&diff=196283&oldid=prev 2021-02-01T15:16:08Z

<p>Created page with &quot; == Abstract == Background&lt;/jats:title&gt;&lt;jats:p&gt;The complex nature of biological data has driven the development of specialized software tools. Scientific workflow management...&quot;</p> <p><b>New page</b></p><div><br /> == Abstract ==<br /> <br /> Background&lt;/jats:title&gt;&lt;jats:p&gt;The complex nature of biological data has driven the development of specialized software tools. Scientific workflow management systems simplify the assembly of such tools into pipelines, assist with job automation and aid reproducibility of analyses. Many contemporary workflow tools are specialized and not designed for highly complex workflows, such as with nested loops, dynamic scheduling and parametriza-tion, which is common in e.g. machine learning.&lt;/jats:p&gt;&lt;/jats:sec&gt;&lt;jats:sec&gt;&lt;jats:title&gt;Findings&lt;/jats:title&gt;&lt;jats:p&gt;SciPipe is a workflow programming library implemented in the programming language Go, for managing complex and dynamic pipelines in bioinformatics, cheminformatics and other fields. SciPipe helps in particular with workflow constructs common in machine learning, such as extensive branching, parameter sweeps and dynamic scheduling and parametrization of downstream tasks. SciPipe builds on Flow-based programming principles to support agile development of workflows based on a library of self-contained, reusable components. It supports running subsets of workflows for improved iterative development, and provides a data-centric audit logging feature that saves a full audit trace for every output file of a workflow, which can be converted to other formats such as HTML, TeX and PDF on-demand. The utility of SciPipe is demonstrated with a machine learning pipeline, a genomics, and a transcriptomics pipeline.&lt;/jats:p&gt;&lt;/jats:sec&gt;&lt;jats:sec&gt;&lt;jats:title&gt;Conclusions&lt;/jats:title&gt;&lt;jats:p&gt;SciPipe provides a solution for agile development of complex and dynamic pipelines, espe-cially in machine leaning, through a flexible programming API suitable for scientists used to programming or scripting.&lt;/jats:p&gt;&lt;/jats:sec<br /> <br /> Document type: Article<br /> <br /> == Full document ==<br /> &lt;pdf&gt;Media:Draft_Content_128849419-beopen2063-5834-document.pdf&lt;/pdf&gt;<br /> <br /> <br /> == Original document ==<br /> <br /> The different versions of the original document can be found in:<br /> <br /> * [http://dx.doi.org/10.1093/gigascience/giz044 http://dx.doi.org/10.1093/gigascience/giz044] under the license https://creativecommons.org/licenses/by<br /> <br /> * [http://dx.doi.org/10.1101/380808 http://dx.doi.org/10.1101/380808] under the license http://creativecommons.org/licenses/by/4.0<br /> <br /> * [http://europepmc.org/articles/PMC6486472 http://europepmc.org/articles/PMC6486472]<br /> <br /> * [http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-358347 http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-358347]<br /> <br /> * [https://academic.oup.com/gigascience/article-pdf/8/5/giz044/28538382/giz044.pdf https://academic.oup.com/gigascience/article-pdf/8/5/giz044/28538382/giz044.pdf]<br /> <br /> * [https://www.biorxiv.org/content/biorxiv/early/2018/10/06/380808.full.pdf https://www.biorxiv.org/content/biorxiv/early/2018/10/06/380808.full.pdf] under the license cc-by<br /> <br /> * [http://academic.oup.com/gigascience/article-pdf/8/5/giz044/28538382/giz044.pdf http://academic.oup.com/gigascience/article-pdf/8/5/giz044/28538382/giz044.pdf],<br /> : [http://dx.doi.org/10.1093/gigascience/giz044 http://dx.doi.org/10.1093/gigascience/giz044] under the license cc-by<br /> <br /> * [https://academic.oup.com/gigascience/article/8/5/giz044/5480570 https://academic.oup.com/gigascience/article/8/5/giz044/5480570],<br /> : [https://www.ncbi.nlm.nih.gov/pubmed/31029061 https://www.ncbi.nlm.nih.gov/pubmed/31029061],<br /> : [http://www.diva-portal.org/smash/record.jsf?pid=diva2:1242254 http://www.diva-portal.org/smash/record.jsf?pid=diva2:1242254],<br /> : [http://uu.diva-portal.org/smash/record.jsf?pid=diva2:1242254 http://uu.diva-portal.org/smash/record.jsf?pid=diva2:1242254],<br /> : [https://academic.microsoft.com/#/detail/2949297597 https://academic.microsoft.com/#/detail/2949297597] under the license http://creativecommons.org/licenses/by/4.0/<br /> <br /> * [https://syndication.highwire.org/content/doi/10.1101/380808 https://syndication.highwire.org/content/doi/10.1101/380808],<br /> : [http://dx.doi.org/10.1101/380808 http://dx.doi.org/10.1101/380808]<br /> <br /> * [https://www.biorxiv.org/content/10.1101/380808v1 https://www.biorxiv.org/content/10.1101/380808v1],<br /> : [https://www.biorxiv.org/content/early/2018/08/01/380808 https://www.biorxiv.org/content/early/2018/08/01/380808],<br /> : [https://www.biorxiv.org/content/biorxiv/early/2018/10/06/380808.full.pdf https://www.biorxiv.org/content/biorxiv/early/2018/10/06/380808.full.pdf],<br /> : [https://academic.microsoft.com/#/detail/2887206084 https://academic.microsoft.com/#/detail/2887206084]<br /> <br /> * [ ]<br /> <br /> <br /> <br /> <br /> <br /> DOIS: 10.1093/gigascience/giz044 10.1101/380808</div>

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