<div dir="ltr"><span style="font-size:12.8px"><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap">Dear EM-community,</span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap">We are proud to announce the release of Scipion v1.0.0 </span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap">(</span><a href="http://scipion.cnb.csic.es/" target="_blank" style="text-decoration:none"><span style="font-size:14.6667px;font-family:Arial;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">http://scipion.cnb.csic.es</span></a><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap">), our software workflow framework to obtain 3D maps </span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap">of </span><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">macromolecular complexes that integrates multiple EM software packages.</span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">Scipion is open-source software and can be freely downloaded from:</span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><a href="http://scipion.cnb.csic.es/m/download_form/" target="_blank" style="text-decoration:none"><span style="font-size:14.6667px;font-family:Arial;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">http://scipion.cnb.csic.es/m/download_form/</span></a></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">Installation instructions can be found at:</span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><a href="https://github.com/I2PC/scipion/wiki/How-to-Install" target="_blank" style="text-decoration:none"><span style="font-size:14.6667px;font-family:Arial;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">http://github.com/I2PC/scipion/wiki/How-to-Install</span></a></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">Scipion's main features (while we wait for the paper describing it  to be out) are:</span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">1. Integration and Interoperability</span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">Scipion transparently integrates several software packages such as: </span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">Xmipp, Relion, Spider, Eman, Sparx, Frealign and Ctffind, among others.</span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">The system  allows users to easily combine different programs in the same project</span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">in the form of a graphical workflow.  All required format conversions are done automatically. More than 100 protocols are currently implemented, see the full list at: </span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><a href="https://github.com/I2PC/scipion/wiki/Integrated-Protocols" target="_blank" style="text-decoration:none"><span style="font-size:14.6667px;font-family:Arial;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">http://github.com/I2PC/scipion/wiki/Integrated-Protocols</span></a></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">2. Traceability and Reproducibility</span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">All parameters used and steps performed are stored! The entire workflow </span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">is presented as a workflow tree or as a list. Several steps can be copied and re-executed </span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">with different parameters. The workflow, or part of it, can be exported to </span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">a template that can imported into a different project. The workflow template</span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">is a text file that can be easily shared (email, http, etc)</span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">3. Graphical tools</span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">Scipion comes with several built-in graphical tools. All protocols are </span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">executed from a form that contains validations and help messages for each </span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">parameter. A data viewer is provided that can visualize images, volumes, </span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">micrographs and their related metadata (shifts, angles, weights, etc). </span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">The data viewer is very useful for sets manipulation, also stored as steps </span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">in the project history.</span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">4. Automation and API</span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">All the operations that can be done from the GUI can also be done from </span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">Python scripts. This includes creating a new project, launching runs and </span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">repeating previous runs, among others. Developers also have Python libraries </span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">to operate with images and metadata files. </span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">5. Extensibility</span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">Scipion is designed with extensibility in mind. As a result, new algorithms </span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">and visualization tools can be added with relative small effort. Everyone </span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">is welcome to contribute.</span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">A good starting point is the tutorials page: </span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><a href="https://github.com/I2PC/scipion/wiki/User-Documentation" target="_blank" style="text-decoration:none"><span style="font-size:14.6667px;font-family:Arial;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">http://github.com/I2PC/scipion/wiki/User-Documentation</span></a></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent">During this year we will have multiple Scipion workshops. Do not miss your next one at:</span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><a href="http://github.com/I2PC/scipion/wiki/News-and-events" target="_blank" style="font-size:12.8px;line-height:normal">http://github.com/I2PC/scipion/wiki/News-and-events</a><br></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">We hope Scipion will be a useful tool for the whole community, for novice as well as experienced users.</span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent"><br></span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">Any feedback is welcome.</span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">Bests,</span></p><span style="font-size:14.6667px;font-family:Arial;vertical-align:baseline;white-space:pre-wrap;background-color:transparent">Scipion Development Team</span></span><div class="" style="font-size:12.8px"><div id=":o6v" class="" tabindex="0"><img class="" src="https://ssl.gstatic.com/ui/v1/icons/mail/images/cleardot.gif"></div></div><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr"><div>Prof. Jose-Maria Carazo<br>Biocomputing Unit, Head, CNB-CSIC<br>Spanish National Center for Biotechnology</div><div>Darwin 3, Universidad Autonoma de Madrid</div><div>28049 Madrid, Spain</div><div><p style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif"><br></p>Cell: +34639197980<br></div></div></div>
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