Posts by Falconet
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1)
Message boards :
Number crunching :
Unexplained tasks in my account
(Message 108394)
Posted 30 May 2023 by Falconet Post: Maybe you need to click on "show all tasks" button on the tasks tab of your BOINC Manager. You are returning work so they should be there. |
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2)
Message boards :
Rosetta@home Science :
De novo design of modular peptide-binding proteins by superhelical matching
(Message 108284)
Posted 5 Apr 2023 by Falconet Post: No mention of Rosetta@home in the acknowledgement section but it is mentioned under Methods - Generation of DHR scaffolds. https://www.nature.com/articles/s41586-023-05909-9 |
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3)
Message boards :
Rosetta@home Science :
Neoleukin Therapeutics Receives Clinical Hold Letter from U.S. FDA Related to CMC Assay Development for NL-201
(Message 107760)
Posted 15 Nov 2022 by Falconet Post: +1 |
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4)
Message boards :
Rosetta@home Science :
Neoleukin Therapeutics Receives Clinical Hold Letter from U.S. FDA Related to CMC Assay Development for NL-201
(Message 107758)
Posted 15 Nov 2022 by Falconet Post: That's terrible news. I remember this article on the vaccine in which some South Korean health officials questioned the efficacy of the vaccine without the booster. http://www.koreabiomed.com/news/articleView.html?idxno=14354 Regardless, the vaccine works but it arrived too late considering many people have already been vaccinated and we have bivalent vaccines available. |
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5)
Message boards :
Cafe Rosetta :
Moderators Contact Point (Explanations, Assistance etc) Post here!
(Message 107681)
Posted 6 Nov 2022 by Falconet Post: Hello again, There is no work available so it's not an issue on your end. |
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6)
Message boards :
Number crunching :
Problems and Technical Issues with Rosetta@home
(Message 107582)
Posted 25 Oct 2022 by Falconet Post: I don't expect Krembil to like this, since it means little work for the MCM1 subproject they are especially interested in.Then why don't Krembil put some more money into their falling apart server? I think we should start calling them Crumble. Krembil isn't exactly a multi-billion dollar corporation like IBM is. They have a much smaller budget and the WCG team is asking for donations. |
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7)
Message boards :
Number crunching :
Problems and Technical Issues with Rosetta@home
(Message 107197)
Posted 9 Oct 2022 by Falconet Post: I also have a bunch pending validation, like 15 or so, nothing validated for days. The exact same task? Are you sure you're not using the "show only active tasks" feature and thus the tasks are running normally and are replaced in the BOINC view by new ones every time one finishes? Looking at your task list, everything seems fine. |
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8)
Message boards :
News :
COVID-19 vaccine with IPD nanoparticles wins full approval abroad
(Message 106882)
Posted 8 Sep 2022 by Falconet Post: A month-old article about the need for an additional safety review of the vaccine. "According to the minutes, members of the central pharmaceutical review panel said SKYCovione’s safety was within the permissible level. However, due to the small number of cases, panelists said it was difficult to conclude the safety and that the vaccine needed continued monitoring." |
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9)
Message boards :
Number crunching :
Virtual Box Not Installed
(Message 106407)
Posted 20 Jun 2022 by Falconet Post: Rosetta 4.20 work has been very rare for many, many months now. It's not specific to your computer. If you aren't receiving work for Rosetta 4.20, it's because there isn't any available. |
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10)
Message boards :
Number crunching :
Rosetta WUs
(Message 106398)
Posted 16 Jun 2022 by Falconet Post: Rosetta work is extremely rare these days. I think they retired Rosetta Mini years ago. |
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11)
Message boards :
Number crunching :
fedora 32 and 36
(Message 106366)
Posted 9 Jun 2022 by Falconet Post: The Python's aren't multithreaded but they reserve a lot of RAM even if they only use a fraction of it. That's why you can't run 1 Python per thread unless you have enough RAM (several GB, I don't remember the exact number) for each of them. |
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12)
Message boards :
News :
Outage notice
(Message 106189)
Posted 12 May 2022 by Falconet Post: I'm not getting any tasks either. I've change NO settings. Been a few days now. No choice but to switch to a different project. A few months back I tried the python projects and my computer would crash all the time. Reinstalled everything disabled python and all was well until a few days ago. Pretty sure it's not me. It's not you. Non-Python work has been extremely rare since October or something, I guess. |
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13)
Message boards :
Technical News :
Due to user feedback and an attempt to reduce the load on our servers, we increased the default target run time from 3 to 6 hours, increased job deadlines to 14 days, and added the target cpu runtime option of 2 days
(Message 106185)
Posted 11 May 2022 by Falconet Post: It is what it is. I managed to run some Python's with no issues but in-between those, there were some bad ones. Up to the Rosetta@home team to work on improving the software, if that is their wish. Yes, I am looking forward to getting back to WCG. The next update is on the 12th. In the meantime, I've mostly been running Einstein@home. |
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14)
Message boards :
Technical News :
Due to user feedback and an attempt to reduce the load on our servers, we increased the default target run time from 3 to 6 hours, increased job deadlines to 14 days, and added the target cpu runtime option of 2 days
(Message 106182)
Posted 11 May 2022 by Falconet Post: It is absolutely beyond my computing intelligence to remotely understand what is going on with the processing of PYTHON tasks.It is inconceivable that 50-51 seconds of computing time is needed to achieve 1 second reduction in time remaining. At that rate of processing virtually over 90% or so of downloaded tasks will be declared "no response" because they exceeded the time limit for reporting. Apparently I will disconnect from Rosetta after I await an overnight response from someone that can enlighten me as to what is the problem Surely I am doing something wrong. Billy, I haven't run Python in a long time but please check the properties tab of those tasks. If you notice a very large discrepancy between elapsed time and CPU time (for example, 4 hours of elapsed time but 1 minute of CPU time), abort. No one from the Rosetta@home will reply to you. |
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15)
Message boards :
Rosetta@home Science :
No task to do work
(Message 106176)
Posted 10 May 2022 by Falconet Post: There is no Rosetta 4.2 work available - that's the kind of work that Rosetta had tasks for all these years. Nowadays, there is only sporadic work for 4.20. If you wish, you can install VirtualBox and you will be able to run the Rosetta Python tasks. Be aware that these take up significant amounts of space, RAM (they use very little RAM but reserve a lot of it, so you won't run 1 task per thread) and sometimes, they get stuck doing nothing. If you don't want to run these, simply leave Rosetta be and you might get some of that very rare Rosetta 4.2 work. I see you've ran WCG in the past. WCG might come back up uite soon. You can also add other BOINC projects (Einstein@home, for example, if you like radio astronomy and gravitational wave research). |
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16)
Message boards :
Rosetta@home Science :
IPD COVD-19 Vaccine Awaiting Aproval after Phase 3 Trials
(Message 106166)
Posted 5 May 2022 by Falconet Post: - I don't think we should assume that everything the IPD/Bakerlab does involves Rosetta@home. If we did contribute to those, then why didn't they write "Rosetta@home contributed to this research" like they do on other papers? Or a forum post in which they mention "Rosetta@home helped with forward folding experiments" like they did on the NL-201 post? - If Rosetta@home was involved in the antiviral research described in the paper, then instead of saying "Rosetta@home wasn't directly involved in the research", then they can say that, actually, we were involved in the research described in that paper. But they don't say that, they specifically say that those antivirals were not related to the Rosetta@home design efforts and they don't acknowledge Rosetta@home on the paper, although they acknowledge on the forum post that other antivirals were designed via Rosetta@home but none of those are described on that paper (or any other paper that I'm aware of). - Again, we contributed to the COVID-19 research. We helped weed out the bad designs and found good candidates. They just found better ones using the in-house/Microsoft Azure/etc resources they had during the early days of the pandemic. Nothing wrong with that. But unless they credit Rosetta@home with something, I won't immediately assume that Rosetta@home was involved. In any case, I'm just happy the vaccine works and that the antivirals are progressing into clinical trials. That's what matters the most. |
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17)
Message boards :
Rosetta@home Science :
CASP 15
(Message 106164)
Posted 4 May 2022 by Falconet Post: Does anyone know if we'll be running any of these tasks? Nothing on the Robetta server so far. https://robetta.bakerlab.org/queue.php?id=&username=casp&target=&seq= |
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18)
Message boards :
Rosetta@home Science :
IPD COVD-19 Vaccine Awaiting Aproval after Phase 3 Trials
(Message 106162)
Posted 3 May 2022 by Falconet Post: Ah I see the confusion. When I said "the same vaccine", I meant the same vaccine that was originally developed at the IPD and later licensed to both SK and Icosavax, as I stated in parenthesizes. Regarding the antivirals paper, it does mention Rosetta but not Rosetta@home. Per the admin forum post, Rosetta@home did not directly contribute to that paper but did "participate in the development of relevant scaffolds". I read that as in none of the proteins from the paper were designed via Rosetta@home but rather using the Rosetta software with their in-house/cloud resources. Rosetta@home did help develop the software so indirectly, we did help. For some reason, I linked to the 2nd page of the thread I wished to share - which is this- I'm assuming this is what SK is now developing in the form of a nasal spray antiviral. IIRC, the paper did mention that the lead designs were suitable as a nasal spray. I had not seen that video, thanks for sharing. |
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19)
Message boards :
Rosetta@home Science :
IPD COVD-19 Vaccine Awaiting Aproval after Phase 3 Trials
(Message 106160)
Posted 3 May 2022 by Falconet Post: The IPD article confirms that GBP510 is now known as SKYCovione and that it will be distributed via COVAX. It's also confirmed at the SK Bioscience article that this is GBP510 but that it now has a commercial name. I assume the Nasal Spray is about those protein designs published a while ago and mentioned on this Forum Post: "Although R@h was not directly used for the work described in the publication (link provided below), R@h was used for designing relevant scaffolds. Additionally, there are currently many similar designs that bind SARS-Cov-2 and related targets that were engineered using R@h." The research paper on that post doesn't refer to Rosetta@home. |
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20)
Message boards :
Rosetta@home Science :
IPD COVD-19 Vaccine Awaiting Aproval after Phase 3 Trials
(Message 106138)
Posted 30 Apr 2022 by Falconet Post: The article doesn't mention Rosetta (the software) though a retweet on the IPD Twitter account posted by the account "Cyrus Biotechnology" says: "Congrats @UWproteindesign @KingLabIPD! We hope this will be the first of many Rosetta designed approved therapeutics!" In any case, they designed the proteins so they probably did use Rosetta, just not Rosetta@home. Although, neither of these 2 papers on the pre-clinical results of the vaccine (before it was even licensed to SK Bioscience or Icosavax) even mention the name "Rosetta". https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7604136/ https://www.nature.com/articles/s41586-021-03530-2#Ack1 |
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