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| Language: | English |
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2026
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| Online Access: | https://doi.org/10.5281/zenodo.20081075 |
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| _version_ | 1866901601602502656 |
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| author | Narita, Akihiro |
| author_facet | Narita, Akihiro |
| contents | <p class="MsoNormal">These programs were developed more than 10 years ago and were used in the following studies:</p> <p class="EndNoteBibliography">1. M. Vinzenz<em> et al.</em>, Actin branching in the initiation and maintenance of lamellipodia. <em>J Cell Sci</em> <strong>125</strong>, 2775-2785 (2012).</p> <p class="EndNoteBibliography">2. A. Narita<em> et al.</em>, Direct determination of actin polarity in the cell. <em>Journal of molecular biology</em> <strong>419</strong>, 359-368 (2012).</p> <p class="EndNoteBibliography">3. J. Mueller<em> et al.</em>, Electron tomography and simulation of baculovirus actin comet tails support a tethered filament model of pathogen propulsion. <em>PLoS biology</em> <strong>12</strong>, e1001765 (2014).</p> <p class="MsoNormal">They may not be suitable for new projects.</p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong>1: Requirement</strong></p> <p class="MsoNormal">We use openSUSE, but Red Hat–based operating systems should also work.</p> <p class="MsoNormal">The following software packages are required:</p> <ul> <li class="MsoNormal">IMOD</li> <li class="MsoNormal">Chimera</li> <li class="MsoNormal">bsoft ([bsoft](https://cbiit.github.io/Bsoft/?utm_source=chatgpt.com))</li> </ul> <p class="MsoNormal">For parallel calculations, you should be able to log in to localhost via SSH without a password. Please refer to:</p> <p class="MsoNormal">[SSH login without password guide]</p> <p class="MsoNormal">(http://www.linuxproblem.org/art_9.html?utm_source=chatgpt.com)</p> <p class="MsoNormal"> </p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong>2: Installation</strong></p> <p class="MsoNormal">programs.tar.gz contains programs required for the analysis. It has 4 directories.</p> <p class="MsoNormal">Eos </p> <p class="MsoNormal">Binary programs from EOS, including additional programs added to the original EOS package<br>([EOS project page] (<a href="http://sourceforge.jp/projects/eos/?utm_source=chatgpt.com">http://sourceforge.jp/projects/eos/?utm_source=chatgpt.com</a>);</p> <p class="MsoNormal"> Yasunaga and Wakabayashi, <em>J. Struct. Biol.</em>, 1996, 116, 155–160)</p> <p class="MsoNormal"> </p> <p class="MsoNormal">shells </p> <p class="MsoNormal">Programs written in Perl, Python, and shell scripts.</p> <p class="MsoNormal"> </p> <p class="MsoNormal">perlmodules </p> <p class="MsoNormal">Perl modules required by the programs.</p> <p class="MsoNormal"> </p> <p class="MsoNormal">refs </p> <p class="MsoNormal">Reference actin maps</p> <p class="MsoNormal"> </p> <p class="MsoNormal">If you use bash and place the directories in your home directory, add the following lines to .bashrc:</p> <p class="MsoNormal"> </p> <p class="MsoNormal">If you place the directories elsewhere, replace $HOME with the appropriate path.</p> <p>export PATH=\$HOME/shells:\$HOME/Eos:$PATH</p> <p>SPFPERLLIBRARY=$HOME/perlmodules</p> <p> </p> <p class="MsoNormal">examples.tar.gz contains examples of setting.</p> <p class="MsoNormal"> </p> <p class="MsoNormal">EosBase.tar.gz, lib.x86.tar.gz, bin.x86.tar.gz, util.x86.tar.gz:</p> <p class="MsoNormal">Source files of EOS including the additional programs and libraries added to the original EOS package.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_20081075 |
| institution | Zenodo |
| language | eng |
| publishDate | 2026 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Programs for polarity determination of the actin filament in tomograms Narita, Akihiro actin electron tomography polarity <p class="MsoNormal">These programs were developed more than 10 years ago and were used in the following studies:</p> <p class="EndNoteBibliography">1. M. Vinzenz<em> et al.</em>, Actin branching in the initiation and maintenance of lamellipodia. <em>J Cell Sci</em> <strong>125</strong>, 2775-2785 (2012).</p> <p class="EndNoteBibliography">2. A. Narita<em> et al.</em>, Direct determination of actin polarity in the cell. <em>Journal of molecular biology</em> <strong>419</strong>, 359-368 (2012).</p> <p class="EndNoteBibliography">3. J. Mueller<em> et al.</em>, Electron tomography and simulation of baculovirus actin comet tails support a tethered filament model of pathogen propulsion. <em>PLoS biology</em> <strong>12</strong>, e1001765 (2014).</p> <p class="MsoNormal">They may not be suitable for new projects.</p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong>1: Requirement</strong></p> <p class="MsoNormal">We use openSUSE, but Red Hat–based operating systems should also work.</p> <p class="MsoNormal">The following software packages are required:</p> <ul> <li class="MsoNormal">IMOD</li> <li class="MsoNormal">Chimera</li> <li class="MsoNormal">bsoft ([bsoft](https://cbiit.github.io/Bsoft/?utm_source=chatgpt.com))</li> </ul> <p class="MsoNormal">For parallel calculations, you should be able to log in to localhost via SSH without a password. Please refer to:</p> <p class="MsoNormal">[SSH login without password guide]</p> <p class="MsoNormal">(http://www.linuxproblem.org/art_9.html?utm_source=chatgpt.com)</p> <p class="MsoNormal"> </p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong>2: Installation</strong></p> <p class="MsoNormal">programs.tar.gz contains programs required for the analysis. It has 4 directories.</p> <p class="MsoNormal">Eos </p> <p class="MsoNormal">Binary programs from EOS, including additional programs added to the original EOS package<br>([EOS project page] (<a href="http://sourceforge.jp/projects/eos/?utm_source=chatgpt.com">http://sourceforge.jp/projects/eos/?utm_source=chatgpt.com</a>);</p> <p class="MsoNormal"> Yasunaga and Wakabayashi, <em>J. Struct. Biol.</em>, 1996, 116, 155–160)</p> <p class="MsoNormal"> </p> <p class="MsoNormal">shells </p> <p class="MsoNormal">Programs written in Perl, Python, and shell scripts.</p> <p class="MsoNormal"> </p> <p class="MsoNormal">perlmodules </p> <p class="MsoNormal">Perl modules required by the programs.</p> <p class="MsoNormal"> </p> <p class="MsoNormal">refs </p> <p class="MsoNormal">Reference actin maps</p> <p class="MsoNormal"> </p> <p class="MsoNormal">If you use bash and place the directories in your home directory, add the following lines to .bashrc:</p> <p class="MsoNormal"> </p> <p class="MsoNormal">If you place the directories elsewhere, replace $HOME with the appropriate path.</p> <p>export PATH=\$HOME/shells:\$HOME/Eos:$PATH</p> <p>SPFPERLLIBRARY=$HOME/perlmodules</p> <p> </p> <p class="MsoNormal">examples.tar.gz contains examples of setting.</p> <p class="MsoNormal"> </p> <p class="MsoNormal">EosBase.tar.gz, lib.x86.tar.gz, bin.x86.tar.gz, util.x86.tar.gz:</p> <p class="MsoNormal">Source files of EOS including the additional programs and libraries added to the original EOS package.</p> |
| title | Programs for polarity determination of the actin filament in tomograms |
| topic | actin electron tomography polarity |
| url | https://doi.org/10.5281/zenodo.20081075 |