Spinal muscular atrophy (SMA) from Mus musculus
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martina
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Message 2887 - Posted: 19 Sep 2022, 14:16:06 UTC

Hello, we are a group of researchers from the Laboratory of translational architectomics, working on spinal muscular atrophy (SMA), a neurodegenerative disease.

We are working on a project which aims at identifying correlation between genes and features depending on the disease condition. To do so, we need to perform mouse gene network expansion with ribosome profiling data (RiboSeq) from control and SMA samples of multiple tissues.

Falconet
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Message 2888 - Posted: 19 Sep 2022, 14:59:39 UTC - in response to Message 2887.

Can you provide a list of genes related to this work?
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Profile valterc
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Message 2891 - Posted: 20 Sep 2022, 14:45:08 UTC

I just put a small number of the new workunits into the queue, their names contain the string _Mm_.
They should be quite fast, around twenty minutes on my benchmark computer, probably half of this on a modern cpu.
If you happen to catch one please give us some feedback.

martina
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Message 2895 - Posted: 21 Sep 2022, 8:40:34 UTC - in response to Message 2888.

Hi, we are expanding a set of genes identified through ribosome profiling in multiple mice tissues. We are particularly interested in a subset of genes coding for transcripts relevant in Spinal Muscular Atrophy.

You can find it in this work in supplementary table 2a (filtering for the SMN-specific genes): https://www.nature.com/articles/s41556-020-00577-7#Sec37

Falconet
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Message 2896 - Posted: 21 Sep 2022, 8:49:35 UTC
Last modified: 21 Sep 2022, 8:50:43 UTC

Thank you both. I haven't seen any of these yet.
619 genes based on that table.
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Shmya-2
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Message 2904 - Posted: 25 Sep 2022, 5:35:29 UTC - in response to Message 2891.
Last modified: 25 Sep 2022, 5:37:57 UTC

I just put a small number of the new workunits into the queue, their names contain the string _Mm_.
They should be quite fast, around twenty minutes on my benchmark computer, probably half of this on a modern cpu.
If you happen to catch one please give us some feedback.


One task finished without any errors

https://gene.disi.unitn.it/test/result.php?resultid=80633052
[/img]

Profile [VENETO] boboviz
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Message 2908 - Posted: 27 Sep 2022, 14:13:16 UTC - in response to Message 2891.

I just put a small number of the new workunits into the queue, their names contain the string _Mm_.


No one of these wus on my pcs... :-(

Speedy
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Message 2920 - Posted: 2 Oct 2022, 1:48:13 UTC

Looking forward to contributing to this project

Profile valterc
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Message 3071 - Posted: 2 Feb 2023, 17:23:57 UTC

Some "mouse" related workunits will be available in the next days

Speedy
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Message 3072 - Posted: 2 Feb 2023, 20:38:09 UTC - in response to Message 3071.

Nice looking forward to it

Speedy
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Message 3077 - Posted: 6 Feb 2023, 2:31:50 UTC

I managed to pick up 2 tasks and then ran for 31 and 32 minutes respectively on a Ryzen 9 5900 X running Windows 11 pro 2200 version. These were _2 &_3 tasks looks like I was used as a checker both my tasks validated

Speedy
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Message 3141 - Posted: 18 Apr 2023, 23:00:56 UTC

Once these "mouse" related tasks start, do we have any idea of the project time?

Profile valterc
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Message 3145 - Posted: 21 Apr 2023, 9:38:57 UTC - in response to Message 3141.

We don't have plans, right now, for the future of the "mouse" experiment. In the next week we will probably start an experiment on Vitis vinifera. In the meanwhile people are working on the human single-cell data based on Tabula Sapiens.

Falconet
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Message 3349 - Posted: 12 Feb 2024, 17:44:10 UTC

Got some work related to this research.
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entity
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Message 3352 - Posted: 13 Feb 2024, 14:28:06 UTC - in response to Message 3349.

Picked up about 59 so far. 4 validated, 14 pending validation, the rest in progress. Running about 31 minutes on a 1st gen EPYC processor.

kotenok2000
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Message 3354 - Posted: 13 Feb 2024, 20:04:44 UTC

They finish in about 2400 seconds.

I compiled app with
# AVX2+FMA, 64-bit
ARCH += -march=native -mtune=native -msse4.2 -mpopcnt -maes -mpclmul -mavx -mfma -mavx2 -m64 -flto


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