[StarCluster] StarGenetics issues
Jacob Barhak
jacob.barhak at gmail.com
Thu Jul 15 15:29:59 EDT 2021
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*
>>>>
>>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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>>>
>>>
>>> --
>>>
>>> Ramon Ramirez-Linan |
>>> * Navteca | C: 301.789.9139 | * @ramonlinan
>>> <https://twitter.com/RamonLinan>
>>> Emerging Technology, Innovation Solutions
>>> (NAICS Codes - 518210, 541511, 541512, 541519, 541990)
>>> *Co-founder*
>>>
>>> www.navteca.com | @Navteca <https://twitter.com/Navteca>
>>>
>>>
>>>
>>>
>>>
>>>
>>> www.navteca.com | @Navteca <https://twitter.com/Navteca>
>>>
>>
>>
>> --
>>
>> Ramon Ramirez-Linan |
>> *Navteca | C: 301.789.9139 | * @ramonlinan
>> <https://twitter.com/RamonLinan>
>> Emerging Technology, Innovation Solutions
>> (NAICS Codes - 518210, 541511, 541512, 541519, 541990)
>> *Co-founder*
>>
>> www.navteca.com | @Navteca <https://twitter.com/Navteca>
>>
>>
>>
>>
>>
>>
>> www.navteca.com | @Navteca <https://twitter.com/Navteca>
>> _______________________________________________
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>> StarCluster at mit.edu
>> http://mailman.mit.edu/mailman/listinfo/starcluster
>>
>
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