<div dir="ltr">Hi Jacob,<div><br></div><div>That is pretty cool, what you are doing. I am helping NASA with JupyterHub and Dask Gateway, feel free to contact me directly if you want to see a demo or even get access to our Daskhub cluster for testing.</div><div><br></div><div>We have actually set up a system where you can deploy an HPC cluster on AWS straight from a Notebook though an integration of JupyterHub with AWS Parallel Cluster (<a href="https://aws.amazon.com/hpc/parallelcluster/">https://aws.amazon.com/hpc/parallelcluster/</a>).</div><div>In other words, from JupyterHub you can sbatch a job straigh to Slurm or similar and it will execute the job for you on a cluster of spot instances or on demand instances</div><div><br></div><div>If anyone is interested in seeing a demo let me know, I am using open source technology</div><div><br></div><div>Ramon</div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Jul 15, 2021 at 3:30 PM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com">jacob.barhak@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Greetings,<div><br></div><div>StartCluster was great - it allowed me to launch my disease modeling on the Amazon cloud in those days. Some of you mentioned some newer solutions, can you please elaborate?</div><div><br></div><div>I am curious to what are the newer tools that can create a cluster of nodes with a shared NFS directory,</div><div><br></div><div>I moved away from StarCluster towards using services like Rescale or other specialized solutions, on multiple clouds, Here are some recent results from COVID modeling:</div><div><ul><li><p style="margin-bottom:0in;line-height:0.15in;background:transparent"><span style="font-variant-numeric:normal;font-variant-east-asian:normal"><font color="#00000a"><font face="Times New Roman, serif"><font style="font-size:11pt">Jacob Barhak,</font></font></font></span><span style="font-variant-numeric:normal;font-variant-east-asian:normal"><font color="#00000a"><font face="Calibri, serif"><font style="font-size:11pt"> </font></font></font></span><span style="font-variant-numeric:normal;font-variant-east-asian:normal"><font color="#00000a"><font face="Times New Roman, serif"><font style="font-size:11pt">The Reference Model is a Multi-Scale Ensemble Model of COVID-19. Self Published Interactive Manuscript. Publication Date: 27-May-2021</font></font></font></span><span style="font-variant-numeric:normal;font-variant-east-asian:normal"><font color="#00000a"><font face="Times New Roman, serif"><font style="font-size:11pt"> </font></font></font></span><a href="http://doi.org/10.34235/b7eaa32b-1a6b-444f-9848-76f83f5a733c" style="color:rgb(0,0,128)" target="_blank"><span style="font-variant-numeric:normal;font-variant-east-asian:normal"><font color="#0000ff"><font face="Times New Roman, serif"><font style="font-size:11pt">http://doi.org/10.34235/b7eaa32b-1a6b-444f-9848-76f83f5a733c</font></font></font></span></a></p></li><li><p style="margin-bottom:0in;line-height:0.15in;background:transparent"><span style="font-variant-numeric:normal;font-variant-east-asian:normal"><font color="#00000a"><font face="Times New Roman, serif"><font style="font-size:11pt">Jacob Barhak: The Reference Model for COVID-19 - The First Multi-Scale Ensemble Disease Mode</font></font></font></span><span style="font-variant-numeric:normal;font-variant-east-asian:normal"><font color="#00000a"><font face="Times New Roman, serif"><font style="font-size:11pt">l</font></font></font></span><span style="font-variant-numeric:normal;font-variant-east-asian:normal"><font color="#00000a"><font face="Times New Roman, serif"><font style="font-size:11pt">, MIDAS Webinar - 28 May 2021,</font></font></font></span><span style="font-variant-numeric:normal;font-variant-east-asian:normal"><font color="#00000a"><font face="Times New Roman, serif"><font style="font-size:11pt"> </font></font></font></span><a href="https://jacob-barhak.github.io/COVID19_Ensemble_MIDAS_Webinar.html" style="color:rgb(0,0,128)" target="_blank"><span style="font-variant-numeric:normal;font-variant-east-asian:normal"><font color="#0000ff"><font face="Times New Roman, serif"><font style="font-size:11pt">https://jacob-barhak.github.io/COVID19_Ensemble_MIDAS_Webinar.html</font></font></font></span></a><span style="font-variant-numeric:normal;font-variant-east-asian:normal"><font color="#00000a"><font face="Calibri, serif"><font style="font-size:11pt"> </font></font></font></span><span style="font-variant-numeric:normal;font-variant-east-asian:normal"><font color="#00000a"><font face="Times New Roman, serif"><font style="font-size:11pt">Video:</font></font></font></span><span style="font-variant-numeric:normal;font-variant-east-asian:normal"><font color="#00000a"><font face="Times New Roman, serif"><font style="font-size:11pt"> </font></font></font></span><a href="https://youtu.be/-z8N40TdKDk?t=1860" style="color:rgb(0,0,128)" target="_blank"><span style="font-variant-numeric:normal;font-variant-east-asian:normal"><font color="#0000ff"><font face="Times New Roman, serif"><font style="font-size:11pt">https://youtu.be/-z8N40TdKDk?t=1860</font></font></font></span></a></p></li></ul><p style="margin-bottom:0in;line-height:14.95px;background:transparent">
</p><ul><li><p style="margin-bottom:0in;line-height:100%;font-family:Calibri,serif;font-size:11pt;direction:ltr;color:rgb(0,0,10);background:transparent"> Jacob Barhak. How Dask Helped Model Diseases and Specifically
COVID-19. Blog at Coiled. June 23, 2021
<font color="#0000ff"><u><a href="https://coiled.io/how-dask-helped-model-diseases-and-specifically-covid-19/" style="color:rgb(0,0,255)" target="_blank">https://coiled.io/how-dask-helped-model-diseases-and-specifically-covid-19/</a></u></font></p>
</li></ul></div><div><br></div><div>I will be happy to learn more about new techniques to do the same thing - and will be happy to learn people are still using StarCluster - I was great.</div><div><br></div><div> Jacob</div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Jul 14, 2021 at 10:27 AM Arman Eshaghi <<a href="mailto:arman.eshaghi@gmail.com" target="_blank">arman.eshaghi@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">StarCluster was a decade ahead of its time in 2010. But is it still relevant with AWS batch? <div><br></div><div>Arman</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Jul 14, 2021 at 4:00 PM Ramon Ramirez-Linan <<a href="mailto:rlinan@navteca.com" target="_blank">rlinan@navteca.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">That is a great use Ed.<div>We use Pcluster at everage Spot Instances too, from earth science to space science</div><div><br></div><div>Ramon</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Jul 14, 2021 at 10:15 AM Ed Gray <<a href="mailto:gray_ed@hotmail.com" target="_blank">gray_ed@hotmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
We used StarCluster to leverage spot instance pricing for bioinformatics. Many compute years over a weekend to chug through 40000 genes over 10 species.
<div><br>
</div>
<div><br>
</div>
<div>-------- Original message --------</div>
<div>From: Ramon Ramirez-Linan <<a href="mailto:rlinan@navteca.com" target="_blank">rlinan@navteca.com</a>> </div>
<div>Date: 7/14/21 8:01 AM (GMT-06:00) </div>
<div>To: Ed Gray <<a href="mailto:gray_ed@hotmail.com" target="_blank">gray_ed@hotmail.com</a>> </div>
<div>Cc: Ryan G <<a href="mailto:ngsbioinformatics@gmail.com" target="_blank">ngsbioinformatics@gmail.com</a>>, "Marcey, David" <<a href="mailto:marcey@callutheran.edu" target="_blank">marcey@callutheran.edu</a>>, <a href="mailto:starcluster@mit.edu" target="_blank">starcluster@mit.edu</a>
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<div>Subject: Re: [StarCluster] StarGenetics issues </div>
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<div dir="ltr">I was an active user of StarCluster for HPC on the agency I work for, but since AWS launched Pcluster I dont see the point and have switched to this other tool.
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<div>Ramon</div>
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<div dir="ltr" class="gmail_attr">On Tue, Jul 13, 2021 at 6:47 PM Ed Gray <<a href="mailto:gray_ed@hotmail.com" target="_blank">gray_ed@hotmail.com</a>> wrote:<br>
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<div dir="auto">oh man, finally a StarCluster group email and its unrelated.
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<div dir="auto">wow.</div>
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<div dir="auto">oh how the mighty have fallen.</div>
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<div>-------- Original message --------</div>
<div>From: Ryan G <<a href="mailto:ngsbioinformatics@gmail.com" target="_blank">ngsbioinformatics@gmail.com</a>>
</div>
<div>Date: 7/13/21 5:40 PM (GMT-06:00) </div>
<div>To: "Marcey, David" <<a href="mailto:marcey@callutheran.edu" target="_blank">marcey@callutheran.edu</a>>
</div>
<div>Cc: <a href="mailto:starcluster@mit.edu" target="_blank">starcluster@mit.edu</a>
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<div>Subject: Re: [StarCluster] StarGenetics issues </div>
<div><br>
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<div>To my knowledge, that tool is not related to starcluster. <br>
<br>
<div dir="ltr">Please excuse any typos -- Sent from my iPad</div>
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<blockquote type="cite">On Jul 13, 2021, at 3:24 PM, Marcey, David <<a href="mailto:marcey@callutheran.edu" target="_blank">marcey@callutheran.edu</a>> wrote:<br>
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<p class="MsoNormal"><span style="color:black">I’m using the Star Genetics Instructor page to create new SG problems (<a href="http://star-genetics-instructor.surge.sh/" target="_blank"><span style="color:rgb(5,99,193)">http://star-genetics-instructor.surge.sh/</span></a>).</span></p>
<p class="MsoNormal" style="font-variant-caps:normal;text-align:start;word-spacing:0px">
<span style="color:black"> </span></p>
<p class="MsoNormal" style="font-variant-caps:normal;text-align:start;word-spacing:0px">
<span style="color:black">The encrypt and save does not work for me if I use genes on different chromosomes. Firefox or Chrome browser.</span></p>
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<span style="color:black"> </span></p>
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<span style="color:black">I can encrypt and save if multiple genes are on different chromosomes.</span></p>
<p class="MsoNormal"><span style="color:black"> </span></p>
<p class="MsoNormal"><span style="color:black">However, I am getting anomalous results in simple dihybrid crosses with unlinked genes.</span></p>
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<span style="color:black"> </span></p>
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<span style="color:black">Any advice would be most appreciated!</span></p>
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<p class="MsoNormal"><span style="color:black">David Marcey</span></p>
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<p class="MsoNormal"><span style="font-size:13.5pt;font-family:Arial,sans-serif;color:black">David J. Marcey</span></p>
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<p class="MsoNormal"><span style="font-size:13.5pt;font-family:Arial,sans-serif;color:black">Fletcher Jones Professor of Developmental Biology</span></p>
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<p class="MsoNormal"><span style="font-size:13.5pt;font-family:Arial,sans-serif;color:black">The Center for Active Learning</span></p>
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<p class="MsoNormal"><span style="font-size:13.5pt;font-family:Arial,sans-serif;color:black">California Lutheran University</span></p>
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<p class="MsoNormal"><span style="font-size:13.5pt;font-family:Arial,sans-serif;color:black">60 West Olsen Road., MC#3700</span></p>
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<p class="MsoNormal"><span style="font-size:13.5pt;font-family:Arial,sans-serif;color:black">Thousand Oaks, CA 91360</span></p>
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<p class="MsoNormal"><span style="font-size:13.5pt;font-family:Arial,sans-serif;color:black"><a href="mailto:marcey@callutheran.edu" target="_blank"><span style="color:blue">marcey@callutheran.edu</span></a></span></p>
<p class="MsoNormal"><i><span style="font-size:14pt;font-family:Arial,sans-serif;background:white"> </span></i></p>
<p class="MsoNormal"><i><span style="font-size:14pt;font-family:Arial,sans-serif;color:black;background:white">he/him/his</span></i><span style="font-size:14pt;font-family:Arial,sans-serif;color:black;background:white"> </span><span style="font-size:14pt"></span></p>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div></div></div><div dir="ltr"><div dir="ltr"><font color="#073763"><br></font><div dir="ltr" style="font-size:12.8px"><font color="#073763"><font face="arial, helvetica, sans-serif"><span style="font-size:11pt">Ramon Ramirez-Linan | </span></font></font><b style="font-size:small;color:rgb(11,83,148)"><div dir="ltr" style="display:inline"><b><div dir="ltr" style="display:inline"><span style="font-weight:normal">Navteca | C: 301.789.9139 | </span></div></b></div></b><span style="font-family:Calibri,sans-serif;font-size:11pt;color:rgb(7,55,99)"> </span><a href="https://twitter.com/RamonLinan" style="color:rgb(17,85,204);font-family:Calibri,sans-serif;font-size:11pt" target="_blank">@ramonlinan</a></div><div dir="ltr" style="font-size:12.8px"><span style="color:rgb(11,83,148);font-size:small">Emerging Technology, Innovation Solutions</span><br style="color:rgb(11,83,148);font-size:small"><span style="color:rgb(11,83,148);font-size:small">(NAICS Codes - 518210, 541511, 541512, 541519, 541990)</span></div><div style="font-size:12.8px"><font face="arial, helvetica, sans-serif" color="#073763"><b>Co-founder</b></font></div><div style="font-size:12.8px"><span style="font-size:13px"><br></span></div><div style="font-size:12.8px"><span style="font-size:13px"> </span><a href="https://www.navteca.com/" style="font-size:13px;color:rgb(17,85,204)" target="_blank">www.navteca.com</a><span style="font-size:13px"> | </span><a href="https://twitter.com/Navteca" style="font-size:13px;color:rgb(17,85,204)" target="_blank">@Navteca </a><br></div><div dir="ltr" style="font-size:12.8px"><div><br></div><div><br></div><div><div style="font-size:small"><font face="Arial, Helvetica, sans-serif"><span style="font-size:13px"></span></font></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
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<div><font face="Arial, Helvetica, sans-serif"><span style="font-size:13px"><br></span></font></div><div><font face="Arial, Helvetica, sans-serif"><span style="font-size:13px"><br></span></font></div><div><font face="Arial, Helvetica, sans-serif"><span style="font-size:13px"><br></span></font></div><font face="Arial, Helvetica, sans-serif"><span style="font-size:13px"><div> <a href="https://www.navteca.com/" target="_blank">www.navteca.com</a> | <a href="https://twitter.com/Navteca" target="_blank">@Navteca </a></div></span></font>