Re: StarGenetics issues

From: Ramon Ramirez-Linan <no email>
Date: Thu, 15 Jul 2021 15:52:55 -0400

Hi Jacob,

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.

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 (https://aws.amazon.com/hpc/parallelcluster/).
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

If anyone is interested in seeing a demo let me know, I am using open
source technology

Ramon



On Thu, Jul 15, 2021 at 3:30 PM Jacob Barhak <jacob.barhak_at_gmail.com> wrote:

> Greetings,
>
> 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?
>
> I am curious to what are the newer tools that can create a cluster of
> nodes with a shared NFS directory,
>
> 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:
>
> -
>
> Jacob Barhak, The Reference Model is a Multi-Scale Ensemble Model of
> COVID-19. Self Published Interactive Manuscript. Publication Date:
> 27-May-2021
> http://doi.org/10.34235/b7eaa32b-1a6b-444f-9848-76f83f5a733c
> -
>
> Jacob Barhak: The Reference Model for COVID-19 - The First Multi-Scale
> Ensemble Disease Model, MIDAS Webinar - 28 May 2021,
> https://jacob-barhak.github.io/COVID19_Ensemble_MIDAS_Webinar.html
> Video: https://youtu.be/-z8N40TdKDk?t=1860
>
>
> -
>
> Jacob Barhak. How Dask Helped Model Diseases and Specifically
> COVID-19. Blog at Coiled. June 23, 2021 *https://coiled.io/how-dask-helped-model-diseases-and-specifically-covid-19/
> <https://coiled.io/how-dask-helped-model-diseases-and-specifically-covid-19/>*
>
>
> 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.
>
> Jacob
>
>
>
> On Wed, Jul 14, 2021 at 10:27 AM Arman Eshaghi <arman.eshaghi_at_gmail.com>
> wrote:
>
>> StarCluster was a decade ahead of its time in 2010. But is it still
>> relevant with AWS batch?
>>
>> Arman
>>
>> On Wed, Jul 14, 2021 at 4:00 PM Ramon Ramirez-Linan <rlinan_at_navteca.com>
>> wrote:
>>
>>> That is a great use Ed.
>>> We use Pcluster at everage Spot Instances too, from earth science to
>>> space science
>>>
>>> Ramon
>>>
>>> On Wed, Jul 14, 2021 at 10:15 AM Ed Gray <gray_ed_at_hotmail.com> wrote:
>>>
>>>> We used StarCluster to leverage spot instance pricing for
>>>> bioinformatics. Many compute years over a weekend to chug through 40000
>>>> genes over 10 species.
>>>>
>>>>
>>>> -------- Original message --------
>>>> From: Ramon Ramirez-Linan <rlinan_at_navteca.com>
>>>> Date: 7/14/21 8:01 AM (GMT-06:00)
>>>> To: Ed Gray <gray_ed_at_hotmail.com>
>>>> Cc: Ryan G <ngsbioinformatics_at_gmail.com>, "Marcey, David" <
>>>> marcey_at_callutheran.edu>, starcluster_at_mit.edu
>>>> Subject: Re: [StarCluster] StarGenetics issues
>>>>
>>>> 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.
>>>>
>>>> Ramon
>>>>
>>>> On Tue, Jul 13, 2021 at 6:47 PM Ed Gray <gray_ed_at_hotmail.com> wrote:
>>>>
>>>>> oh man, finally a StarCluster group email and its unrelated.
>>>>>
>>>>> wow.
>>>>>
>>>>> oh how the mighty have fallen.
>>>>>
>>>>>
>>>>> -------- Original message --------
>>>>> From: Ryan G <ngsbioinformatics_at_gmail.com>
>>>>> Date: 7/13/21 5:40 PM (GMT-06:00)
>>>>> To: "Marcey, David" <marcey_at_callutheran.edu>
>>>>> Cc: starcluster_at_mit.edu
>>>>> Subject: Re: [StarCluster] StarGenetics issues
>>>>>
>>>>> To my knowledge, that tool is not related to starcluster.
>>>>>
>>>>> Please excuse any typos -- Sent from my iPad
>>>>>
>>>>> On Jul 13, 2021, at 3:24 PM, Marcey, David <marcey_at_callutheran.edu>
>>>>> wrote:
>>>>>
>>>>> 
>>>>>
>>>>> I’m using the Star Genetics Instructor page to create new SG problems (
>>>>> http://star-genetics-instructor.surge.sh/).
>>>>>
>>>>>
>>>>>
>>>>> The encrypt and save does not work for me if I use genes on different
>>>>> chromosomes. Firefox or Chrome browser.
>>>>>
>>>>>
>>>>>
>>>>> I can encrypt and save if multiple genes are on different chromosomes.
>>>>>
>>>>>
>>>>>
>>>>> However, I am getting anomalous results in simple dihybrid crosses
>>>>> with unlinked genes.
>>>>>
>>>>>
>>>>>
>>>>> Any advice would be most appreciated!
>>>>>
>>>>>
>>>>>
>>>>> David Marcey
>>>>>
>>>>>
>>>>>
>>>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>>>>
>>>>> David J. Marcey
>>>>>
>>>>> Fletcher Jones Professor of Developmental Biology
>>>>>
>>>>> The Center for Active Learning
>>>>>
>>>>> California Lutheran University
>>>>>
>>>>> 60 West Olsen Road., MC#3700
>>>>>
>>>>> Thousand Oaks, CA 91360
>>>>>
>>>>> marcey_at_callutheran.edu
>>>>>
>>>>>
>>>>>
>>>>> *he/him/his*
>>>>>
>>>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>>>> _______________________________________________
>>>>> StarCluster mailing list
>>>>> StarCluster_at_mit.edu
>>>>> http://mailman.mit.edu/mailman/listinfo/starcluster
>>>>>
>>>>> _______________________________________________
>>>>> StarCluster mailing list
>>>>> StarCluster_at_mit.edu
>>>>> http://mailman.mit.edu/mailman/listinfo/starcluster
>>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> Ramon Ramirez-Linan |
>>>> * Navteca | C: 301.789.9139 | * _at_ramonlinan
>>>> <https://twitter.com/RamonLinan>
>>>> Emerging Technology, Innovation Solutions
>>>> (NAICS Codes - 518210, 541511, 541512, 541519, 541990)
>>>> *Co-founder*
>>>>
>>>> www.navteca.com | _at_Navteca <https://twitter.com/Navteca>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> www.navteca.com | _at_Navteca <https://twitter.com/Navteca>
>>>>
>>>
>>>
>>> --
>>>
>>> Ramon Ramirez-Linan |
>>> *Navteca | C: 301.789.9139 | * _at_ramonlinan
>>> <https://twitter.com/RamonLinan>
>>> Emerging Technology, Innovation Solutions
>>> (NAICS Codes - 518210, 541511, 541512, 541519, 541990)
>>> *Co-founder*
>>>
>>> www.navteca.com | _at_Navteca <https://twitter.com/Navteca>
>>>
>>>
>>>
>>>
>>>
>>>
>>> www.navteca.com | _at_Navteca <https://twitter.com/Navteca>
>>> _______________________________________________
>>> StarCluster mailing list
>>> StarCluster_at_mit.edu
>>> http://mailman.mit.edu/mailman/listinfo/starcluster
>>>
>>
>>
>> --
>> *---------------------------------------------*
>> *This is a private email account. Do not send messages to it that contain
>> patient identifiable data or if your organisation has concerns regarding
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>> _______________________________________________
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>> http://mailman.mit.edu/mailman/listinfo/starcluster
>>
>

-- 
Ramon Ramirez-Linan |
*Navteca | C: 301.789.9139 | * _at_ramonlinan <https://twitter.com/RamonLinan>
Emerging Technology, Innovation Solutions
(NAICS Codes - 518210, 541511, 541512, 541519, 541990)
*Co-founder*
 www.navteca.com   |  _at_Navteca  <https://twitter.com/Navteca>
-- 
 www.navteca.com <https://www.navteca.com/>   |  _at_Navteca  
<https://twitter.com/Navteca>

Received on Thu Jul 15 2021 - 15:53:18 EDT