http://wiki.docking.org/index.php?action=history&feed=atom&title=JupyterNotebook 2026-04-07T17:23:32Z Revision history for this page on the wiki MediaWiki 1.39.1 http://wiki.docking.org/index.php?title=JupyterNotebook&diff=15555&oldid=prev 2023-10-19T21:05:17Z

<p>asdf</p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 21:05, 19 October 2023</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l35">Line 35:</td> <td colspan="2" class="diff-lineno">Line 35:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     # on a laptop outside the lab network</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     # on a laptop outside the lab network</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     JUPYTER_PORT=5048</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     JUPYTER_PORT=5048</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; 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>     ssh -N -p 22 -D 1080 momeara@<del style="font-weight: bold; text-decoration: none;">portal</del>.ucsf.<del style="font-weight: bold; text-decoration: none;">bkslab.org </del>-L $JUPYTER_PORT:gimel:$JUPYTER_PORT</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; 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>     ssh -N -p 22 -D 1080 momeara@<ins style="font-weight: bold; text-decoration: none;">portal3.combpio</ins>.ucsf.<ins style="font-weight: bold; text-decoration: none;">edu </ins>-L $JUPYTER_PORT:gimel:$JUPYTER_PORT</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     # open a web browser and navigate to localhost:JUPYTER_PORT/lab and enter the token</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     # open a web browser and navigate to localhost:JUPYTER_PORT/lab and enter the token</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Tips ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Tips ==</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* use localhost:JUPYTER_PORT/&#039;&#039;&#039;lab&#039;&#039;&#039; to get the JuypterLab interface, its much better but for some reason not the default yet</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* use localhost:JUPYTER_PORT/&#039;&#039;&#039;lab&#039;&#039;&#039; to get the JuypterLab interface, its much better but for some reason not the default yet</div></td></tr> </table>

Frodo http://wiki.docking.org/index.php?title=JupyterNotebook&diff=11602&oldid=prev 2019-03-28T19:12:49Z

<p>Basics for setting up Jupyter Notebook</p> <p><b>New page</b></p><div><br /> = Using Jupyter Notebooks =<br /> <br /> == jupyter ports ==<br /> Talk to Ben about getting a port range set up for you<br /> {| class=&quot;wikitable&quot;<br /> |-<br /> ! Lab Member<br /> ! Port range<br /> |-<br /> | Matthew O&#039;Meara<br /> | 5040-5049<br /> |-<br /> |}<br /> <br /> <br /> == install dependencies ==<br /> Install conda environment for python, typically I use<br /> <br /> <br /> conda create -n main anaconda<br /> source activate main<br /> <br /> Start the notebook server<br /> <br /> # set the jupyter port (see above)<br /> JUPYTER_PORT=5048<br /> <br /> # on gimel in the bkslab cluster<br /> jupyter notebook --ip=0.0.0.0 --port=$JUPYTER_PORT<br /> # copy the token e.g. &#039;e0593317037148392cb9b0489a5f376ca950f3a14d37e371&#039; to the clipboard<br /> <br /> log in to the notebook server from a client<br /> <br /> # on a laptop outside the lab network<br /> JUPYTER_PORT=5048<br /> ssh -N -p 22 -D 1080 momeara@portal.ucsf.bkslab.org -L $JUPYTER_PORT:gimel:$JUPYTER_PORT<br /> # open a web browser and navigate to localhost:JUPYTER_PORT/lab and enter the token<br /> <br /> == Tips ==<br /> * use localhost:JUPYTER_PORT/&#039;&#039;&#039;lab&#039;&#039;&#039; to get the JuypterLab interface, its much better but for some reason not the default yet</div>

Matthew O'Meara