Posts by Aurum

1) Message boards : News : Target 21: corona_TMPRSS2_v1 (Message 1783)
Posted 6 Jan 2023 by Aurum
Post:
TMPRSS2 is a type II transmembrane protease with broad expression in epithelial cells of the respiratory and gastrointestinal human tracts. It is a cofactor in SARS-CoV-2 entry, and primes viral proteins. Namely, TMPRSS2 cleaves the viral Spro to expose the fusion peptide for cell entry. We are therefore examining TMPRSS2 as a promising strategy to block viral infection in a host-directed therapeutic and/or prophylactic manner.
My attempt to translate this Technical Voodoo speak into lay language:

TMPRSS2 is a protein that is naturally found living in the cell wall of your guts and lungs. It is an enzyme that cuts the viral protein S2 at a certain serine amino acid sequence in the S2 active site. First the SARS-CoV-2 virus binds the ACE2 receptor that naturally lives in the cell membrane of many human cells. Then TMPRSS2 bumps into the bound ACE2 molecule and cuts the viral S2 allowing the virus membrane to merge with the cell membrane and dump the virus contents inside the cell where the human cellular machinery makes many many copies of the virus and spews them out into your blood and fluids to spread. If we can find a small molecule that can bind to TMPRSS2 in such a way that it prevents cutting S2 then the virus will be stuck on the outside of the cell and is not copied. This would greatly slow down Covid progression. It is not likely to stop the disease entirely since it still allows for endosomal entry as shown in the Nature Figure 3 below.

https://en.wikipedia.org/wiki/Transmembrane_protein#/media/File:Group_1_and_2_transmembrane_protein.png
https://www.nature.com/articles/s41580-021-00418-x/figures/3
2) Message boards : News : SiDock@home September Sailing (Message 1147)
Posted 13 Sep 2021 by Aurum
Post:
I have a BOINCstats account. I just do not use BAM and that's where they say the link is.
3) Message boards : News : SiDock@home September Sailing (Message 1145)
Posted 13 Sep 2021 by Aurum
Post:
I tried to enroll my Team In Science We Trust. But since I do not use BAM there's no link for me to join the challenge. Is there another way we can get entered???
4) Message boards : Number crunching : Deadline is too short (Message 904)
Posted 10 May 2021 by Aurum
Post:
This 2 day deadline causes all SD WUs to Run High Priority. This is very annoying since it interferes with any other BOINC project one wants to run. Sometimes it even prevents a GPU from having a CPU. Requires a lot of babysitting to constantly suspend some of the SD WUs so BOINC will behave a little better.
5) Message boards : Number crunching : Resource Zero (Message 887)
Posted 4 May 2021 by Aurum
Post:
It's settled down today. I think it was the feast or famine turmoil at WCG for the last few days messing with my scheduler.
6) Message boards : Number crunching : What is CurieMarieDock on BOINC + zipped input ??? (Message 884)
Posted 4 May 2021 by Aurum
Post:
I saw it in my client_state.xml file. But I think I was seeing a remnant that hadn't updated yet. Now it's this:
<app>
    <name>cmdock-boinc</name>
    <user_friendly_name>CurieMarieDock on BOINC</user_friendly_name>
    <non_cpu_intensive>0</non_cpu_intensive>
</app>
<app>
    <name>cmdock-boinc-zip</name>
    <user_friendly_name>CurieMarieDock on BOINC + zipped input</user_friendly_name>
    <non_cpu_intensive>0</non_cpu_intensive>
</app>
7) Message boards : Number crunching : Resource Zero (Message 883)
Posted 4 May 2021 by Aurum
Post:
Could you specify where exactly did you set Resource=0?
Preferences for this project SiDock@home preferences
Edit Preferences
Resource share 0
Update Preferences

In Resource Zero mode the project only sends a WU when there's a shortage.
8) Message boards : Number crunching : What is CurieMarieDock on BOINC + zipped input ??? (Message 873)
Posted 3 May 2021 by Aurum
Post:
I see you're running more of these. Not sure if you intended or not but they're running as:
<name>rxdock-boinc</name>
while being entitled:
CurieMarieDock on BOINC + zipped input
9) Message boards : Number crunching : Resource Zero (Message 872)
Posted 3 May 2021 by Aurum
Post:
Today SiDock stopped honoring the Resource = 0 setting and sent too many WUs.
10) Message boards : News : Half a year, the BOINC Workshop and a move to the new server (Message 863)
Posted 2 May 2021 by Aurum
Post:
Be interesting to see what happens to OpenPandemics when folks want to continue running OPNG but are stuck getting OPN simultaneously.
This may be easy to do. Here's the setup that's working for me:
Set SD to Resource Zero.
My BOINC work queue is set to 0.50/0.01 days.
Set WCG OpenPandemics - COVID-19 Project Limit to 64.
Suspend enough OPN WUs so that SD WUs DL and add up to more than half a day.
Unsuspend OPN WUs.
OPNG WUs continue to be DLed but no more OPN WUs.
If you want only OPNG wus it easy.
in your wcg device profile (home, woek, school) select only OpenPandemics.
Then below "processor Usage" set " Allow research to run on my CPU?" to "NO"
in " Graphics Card Usage" enable your GPU by setting "YES" near your GPU type
Save the profile
Didn't think of that since I'm in the habit leaving HST Unlimited. Also, when SD runs out of WUs OPN will backfill.
Be aware that OPenPandemics is currently under GPU stress test, so there are lot of wus. After that thwy will return to low numbr wus
Not any more. Only 2 days left of stress test and now they're having storage/backend problems.
11) Message boards : News : Half a year, the BOINC Workshop and a move to the new server (Message 859)
Posted 2 May 2021 by Aurum
Post:
Be interesting to see what happens to OpenPandemics when folks want to continue running OPNG but are stuck getting OPN simultaneously.
This may be easy to do. Here's the setup that's working for me:
Set SD to Resource Zero.
My BOINC work queue is set to 0.50/0.01 days.
Set WCG OpenPandemics - COVID-19 Project Limit to 64.
Suspend enough OPN WUs so that SD WUs DL and add up to more than half a day.
Unsuspend OPN WUs.
OPNG WUs continue to be DLed but no more OPN WUs.
12) Message boards : Number crunching : What is CurieMarieDock on BOINC + zipped input ??? (Message 850)
Posted 2 May 2021 by Aurum
Post:
There's a new entry in Edit Preferences: CurieMarieDock on BOINC + zipped input.
I see on Server Status there are none available. I searched for "zipped" but find nothing.
What is it and when should one enable it ???
13) Message boards : Number crunching : No checkpoints? (Message 849)
Posted 2 May 2021 by Aurum
Post:
Does SiDock use adaptive replication (Q2R2 changes to Q1R1) or does it always stay as Q2R2 ???
14) Message boards : News : Half a year, the BOINC Workshop and a move to the new server (Message 848)
Posted 2 May 2021 by Aurum
Post:
People will be able to download "valid" wus from May 2nd. Therefore hype would have been there anyway. However such long wus will surely help to spread the load. They need only build plenty wu buffer before sunday
I was being facetious but you know there will be a huge phalanx of synthetic computers with synthetic CPUs sucking down as many WUs as they can starting as soon as they can. Then in 3 days real hardware moves to the fore.

Be interesting to see what happens to OpenPandemics when folks want to continue running OPNG but are stuck getting OPN simultaneously. I predict WCG will see a lot of aborted OPN WUs.
15) Message boards : News : Half a year, the BOINC Workshop and a move to the new server (Message 839)
Posted 29 Apr 2021 by Aurum
Post:
The BOINC Pentathlon team selected SiDock@home as this year's Marathon project. The Marathon discipline is announced on 30 April and runs for two weeks from 05 through 18 May.
SiDock@home team
By leaking the secret you can look forward to massive bunkering like you can't imagine. You're really going to need that new server.
16) Message boards : Cafe : Whitelist SiDock for Gridcoin - What say ye? (Message 738)
Posted 24 Mar 2021 by Aurum
Post:
Gridcoin. Good idea ;-). Do you have experience how to set this.
Crtomir

Project admins need to post a statement at github expressing their enthusiasm for whitelisting:
https://github.com/gridcoin-community/Gridcoin-Tasks/issues/244

From https://gridcoin.us/wiki/whitelist-process.html
2. The project admin is contacted to see if they would be interested in going on the whitelist. They must agree somewhere public (at least before a poll) so people can verify.
17) Message boards : Cafe : Whitelist SiDock for Gridcoin - What say ye? (Message 737)
Posted 24 Mar 2021 by Aurum
Post:
Dear fellow members of the Boinc community,
I'm pleased to announce that the core group of the SiDock@Home project approved GridCoin idea, but we need some time to prepare our servers and also to set up
checkpoints (important task in our priority list). We estimate that we will be ready to launch GridCoin in two months. What are next steps.
Crtomir
1. There's no requirement in the Gridcoin rules for checkpointing, but, we BOINCers sure would appreciate it.
2. Don't give them any excuses to delay, start GRC now.
3. Whitelisting for GRC will open the door for these aggregators to come here:
Charity Engine 1 & 2 (over a million CPU threads: https://www.charityengine.com/marketplace#continue)
Team Gridcoin (about 1,000 members)
grcpool.com, grcpool.com-2 and grcpool.com-3 (13,804 members)
Don't delay, do it today.
18) Message boards : News : Fifth Target is SARS-CoV-2 EProtein (Message 736)
Posted 24 Mar 2021 by Aurum
Post:
With the longer runtimes for the 5th target, lack of checkpointing is becoming more of a problem. I've had to remove these from machines that aren't always running 24 hours a day. I'll gladly put them back if checkpointing is implemented though...
Thanks, Chris

I accidently tripped a circuit breaker and a rack of computers turned off. Lost several hundred CPU hours as they restarted from the beginning. We really need checkpointing for these big WUs. TIA
19) Message boards : News : Fifth Target is SARS-CoV-2 EProtein (Message 682)
Posted 20 Mar 2021 by Aurum
Post:
Sweet!!! I'm loaded up and they're running. Starting off estimating 1:16 minutes. :-)
20) Message boards : Cafe : Whitelist SiDock for Gridcoin - What say ye? (Message 681)
Posted 20 Mar 2021 by Aurum
Post:
I created the Gridcoin wallet poll and the Github discussion thread:
https://github.com/gridcoin-community/Gridcoin-Tasks/issues/244

The poll is now active. If you don't see it then click Reload Polls.


Next 20

©2024 SiDock@home Team