Posts by robertmiles

21) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 87797)
Posted 3 Dec 2017 by Profile robertmiles
Post:
New member here.

Boinc is not transferring data for Rosetts@home to my laptop. Communication has been continually deferred all night long.

Other Boinc projects are working fine.

Any ideas?

You might mention some details that could affect transfers. For example, what version of BOINC are you running? What operating system are you using (for example, Windows 10)? 32-bit or 64-bit? What CPU does your computer use?

How much memory does your computer have? Rosetta@Home requires more than most other BOINC projects.

Have Rosetta@Home tasks been failing on your computer lately? If enough have, expect rather few tasks for the next few days.

Note that if you're running Windows 10 and have installed the recent Fall Update, expect some things not to work until you turn your computer off for at least one minute, then turn it on and let it reboot. The usual restart without power off is NOT adequate just after installing this update.

What share of time on your computer did you assign Rosetta@Home? If 0, then expect Rosetta@Home tasks only when BOINC has tried and failed to get tasks from all other BOINC projects it is participating in.
22) Message boards : Rosetta@home Science : A zinc transporter and type 2 diabetes (Message 87669)
Posted 12 Nov 2017 by Profile robertmiles
Post:
Zinc supplementation may lower diabetes progression risk
https://www.healio.com/endocrinology/diabetes/news/in-the-journals/%7B3c3f00ad-1cba-44d9-8702-ea4f2f03755b%7D/zinc-supplementation-may-lower-diabetes-progression-risk?utm_source=selligent&utm_medium=email&utm_campaign=endocrinology%20news&m_bt=12084761059
type 2
23) Message boards : Number crunching : Minirosetta 3.73-3.78 (Message 87517)
Posted 14 Oct 2017 by Profile robertmiles
Post:
I've just had four 3,78 compute errors.

http://boinc.bakerlab.org/result.php?resultid=947115613

http://boinc.bakerlab.org/result.php?resultid=947116461

http://boinc.bakerlab.org/result.php?resultid=947115957

http://boinc.bakerlab.org/result.php?resultid=947119040

All look likely to be due to a missing input file with a name ending in .9mers .
24) Message boards : Rosetta@home Science : A zinc transporter and type 2 diabetes (Message 87321)
Posted 18 Sep 2017 by Profile robertmiles
Post:
Another reason why you might want to add zinc to the metal ions you can model attached to proteins:

Research advances efforts to screen children for type 1 diabetes
https://www.upi.com/Health_News/2017/09/13/Research-advances-efforts-to-screen-children-for-Type-1-diabetes/2551505310742/
25) Message boards : Cafe Rosetta : Some links to Alzheimer's news (Message 87228)
Posted 6 Sep 2017 by Profile robertmiles
Post:
High fat diets could benefit Alzheimer's patients, a new brain study suggests
http://www.diabetes.co.uk/news/2017/sep/high-fat-diets-could-benefit-alzheimer's-patients,-a-new-brain-study-suggests-99996398.html?utm_source=Communicator&utm_medium=Email&utm_content=Untitled25&utm_campaign=Hospital+meals%3a+the+good%2c+the+bad%2c+and+the+absolutely+terrible&utm_dispatch%20ID=5866771&utm_email%20name=DCUK+NL+-+05%2f09%2f17
26) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 87220)
Posted 6 Sep 2017 by Profile robertmiles
Post:
Uploads currently aren't working, The delay before the next try is over 4 hours, so this may have started several hours ago. Is someone working on this problem?

Uploads still aren't working, but reporting tasks that have finished uploading is working. I haven't tried downloads today.
27) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 87214)
Posted 5 Sep 2017 by Profile robertmiles
Post:
Uploads currently aren't working, The delay before the next try is over 4 hours, so this may have started several hours ago. Is someone working on this problem?
28) Message boards : Cafe Rosetta : Some links to Alzheimer's news (Message 87165)
Posted 30 Aug 2017 by Profile robertmiles
Post:
Big brains and high IQ linked to small gene change
http://www.bionews.org.uk/page_140562.asp

Eye Scan Could Detect Alzheimer’s Before Symptoms Occur
https://www.rdmag.com/article/2017/08/eye-scan-could-detect-alzheimers-symptoms-occur

Alzheimer's gene plays role in childhood IQ
http://www.medicalnewstoday.com/articles/318809.php
29) Message boards : Cafe Rosetta : Some links to Alzheimer's news (Message 87033)
Posted 11 Aug 2017 by Profile robertmiles
Post:
Genetics and dementia - Alzheimer Scotland information sheet IS35 - genetics.pdf
http://www.alzscot.org/assets/0000/0170/genetics.pdf

BDNF Gene Mutation May Speed Up Memory Loss in Alzheimer's
http://www.physiciansbriefing.com/Article.asp?AID=722341

Cancer Drug That Might Slow Parkinson's, Alzheimer's Headed For Bigger Tests
http://www.npr.org/sections/health-shots/2017/03/15/520170960/cancer-drug-that-might-slow-parkinson-s-alzheimer-s-headed-for-bigger-tests

Cellular ‘garbage disposal’ units fingered in Alzheimer’s development
http://www.fiercebiotech.com/research/cellular-garbage-disposal-units-fingered-alzheimer-s-development

Designer antibodies block Alzheimer’s plaque from forming
http://www.fiercebiotech.com/research/designer-antibodies-block-alzheimer-s-plaques-from-forming

I've seen signs that amyloids are the brain's way of binding harmful some harmful chemicals for which the
brain has no natural way of sending them out of the brain. At least one medical trial found a way to
dissolve amyloids in the brain but found that this did not help Alzheimer's. Could this mean that the
harmful chemicals, not the amyloids, are the cause of Alzheimer's? If so. expect all methods that
dissolve the amyloids without removing the harmful chemicals to be more likely to make Alzheimer's worse
than to help it.
30) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 86770)
Posted 30 Jun 2017 by Profile robertmiles
Post:
Tom Miller's system is encountering errors like this within the first two minutes of execution:
ERROR: unrecognized residue CYB
ERROR:: Exit from: ..\..\..\src\core\io\pose_from_sfr\PoseFromSFRBuilder.cc line: 1030
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

</stderr_txt>

The task names all start with tj_6_28_e_NCAA...

Other systems encounter the same error as the tasks are reassigned.

Looks like Rosetta@home needs to set up a way to mark such classes of workunits as set up incorrectly and therefore not to be counted when deciding how many tasks a user can download.
31) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 81576)
Posted 11 Jun 2017 by Profile robertmiles
Post:
Another issue with these overrunning tasks: checkpointing isn\'t working properly. I\'ve got a couple of b21* tasks that have been running for over 12 hours and are stuck on step 7205 having done 52 and 12 tasks respectively. Yet the last checkpoint for each is 18 minutes.

A lot of compute errors lately for workunits with names beginning with b21_ or b22_. For most of them finished by a wingmate, the wingmate gave a compute error also.

Could you check if this series of workunits has built-in errors?

Running under 64-bit Windows 10.

Not overrunning; they hit a compute error when about a quarter done.

Problem not seen for workunits with names beginning with anything else.
32) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 81486)
Posted 18 Apr 2017 by Profile robertmiles
Post:
Could you modify your Server Status web page to show which of the server programs handle uploads and downloads?


I just added some text:

Web servers: boinc, srv1, srv2, srv3, srv4, srv5 (upload and download servers)


boinc is load balanced among the srv web servers. The srv servers handle uploads and downloads.

Looks good so far, but could you also add the status of all those servers to help us tell when to expect upload and download problems?
33) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 81448)
Posted 15 Apr 2017 by Profile robertmiles
Post:
Could you modify your Server Status web page to show which of the server programs handle uploads and downloads?
34) Message boards : Cafe Rosetta : BMAA, Alzheimer\'s, Parkinson\'s, and ALS (Message 81207)
Posted 21 Feb 2017 by Profile robertmiles
Post:
I just found that Brichos is a family of molecules, not just one.

Some articles that may name the most important type:

(title will not copy and paste)
BCJ article

Molecular inhibitor breaks cycle that leads to Alzheimer’s
Molecular inhibitor breaks cycle that leads to Alzheimer’s

High-resolution structure of a BRICHOS domain and its implications for anti-amyloid chaperone activity on lung surfactant protein C.
High-resolution structure of a BRICHOS domain

BRICHOS Domains Efficiently Delay Fibrillation of Amyloid β-Peptide*
BRICHOS Domains Efficiently Delay Fibrillation of Amyloid β-Peptide

Molecule could protect against Alzheimer\'s disease
Molecule could protect against Alzheimer\'s disease

Brichos protein may prevent brain damage in Alzheimer’s
Brichos protein may prevent brain damage in Alzheimer’s
35) Message boards : Cafe Rosetta : BMAA, Alzheimer\'s, Parkinson\'s, and ALS (Message 81206)
Posted 21 Feb 2017 by Profile robertmiles
Post:
Alzheimer\'s researchers find molecule that delays onset of disease
Guardian.article

Could the Rosetta@Home researchers interested in Alzheimer\'s check whether the 3D structure of the Brichos molecule is ready to use, and if not, add it to the list of molecules for structure investigation?
36) Message boards : Cafe Rosetta : BMAA, Alzheimer\'s, Parkinson\'s, and ALS (Message 80996)
Posted 11 Jan 2017 by Profile robertmiles
Post:
Most of the site is accessible only from within Sweden. However, I was able to access enough to use Google Translate to get this summary:

Paul Alan Cox, professor and director of the Institute for ethnomedicine in Wyoming, USA, shows one of the winners of the Earth\'s climate is getting warmer, namely the cyanobacteria. They like the heat, increasing in number and produce a neurotoxin called BMAA. This toxin is now suspected in turn cause including ALS and Alzheimer\'s disease in humans. Preferring Gets Title: Climate change, biodiversity and human health. Moderator: Henrik Ekman. Organizers: King Carl XVI Gustaf\'s 50th årsfond for Science, Technology and Environment, Royal. Agriculture and Forestry Academy, Royal Academy. Sciences, Engineering Sciences and the Confederation of Swedish Enterprise. From the arrangement Faith in the Future held in the Bernadotte Library at the Royal Palace March 22, 2012.


Some articles that seem relevant (some appear to be research papers, some written for the public):

Algae bloom toxin linked to Alzheimer\'s, other diseases
http://www.cbsnews.com/news/algae-bloom-toxin-linked-to-alzheimers-and-other-neurodegenerative-diseases/

Secrets to Alzheimer\'s, ALS and Parkinson\'s Disease: Dr. Paul Alan Cox at TEDxJacksonHole
https://www.youtube.com/watch?v=7jWi6WQQ9wo
You can skip the ad before the video.

New research offers hope for Alzheimer’s patients
http://www.jhnewsandguide.com/news/health/new-research-offers-hope-for-alzheimer-s-patients/article_ab9326a2-ddaf-53bf-84cd-9fe814f3fb19.html

The Emerging Science of BMAA: Do Cyanobacteria Contribute to Neurodegenerative Disease?
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3295368/

Dietary exposure to an environmental toxin triggers neurofibrillary tangles and amyloid deposits in the brain
http://rspb.royalsocietypublishing.org/content/283/1823/20152397

Research points to pond scum connection for ALS, Alzheimer’s diseases
http://www.mypalmbeachpost.com/lifestyles/health/research-points-pond-scum-connection-for-als-alzheimer-diseases/O23lvN1VdNFoxOBPGt86hI/

Could environmental toxins trigger amyloid plaques in the brain? An interview with Dr Paul Alan Cox
http://www.news-medical.net/news/20160314/Could-environmental-toxins-trigger-amyloid-plaques-in-the-brain-An-interview-with-Dr-Paul-Alan-Cox.aspx

Environmental toxin linked to dementia, study shows
https://www.washingtonpost.com/local/social-issues/environmental-toxin-linked-to-dementia-study-shows/2016/01/19/e78b7ac4-bef7-11e5-83d4-42e3bceea902_story.html?utm_term=.907f2b7cabaa

Tangles and Toxins: An interview with Dr Paul Alan Cox
http://www.hurondigitalpathology.com/resource/tangles-toxins-interview-dr-paul-alan-cox/


Mentions vervet monkeys as an animal model for such research.

Does not appear to mention whether l-serine has been tried enough on humans to decide whether it offers humans any help with these conditions.
37) Message boards : Cafe Rosetta : On the way to gene editing without causing cancer (Message 80970)
Posted 2 Jan 2017 by Profile robertmiles
Post:
A simple guide to CRISPR, one of the biggest science stories of 2016

Inserting a new gene at a random point in the old genes is known to give a significant risk of cancer about ten years later. This gives a way to control where it is inserted, and therefore avoid the risk of causing cancer.
38) Message boards : Number crunching : This New Biomarker Can Help Predict Alzheimer's Disease In Patients (Message 80968)
Posted 2 Jan 2017 by Profile robertmiles
Post:
This New Biomarker Can Help Predict Alzheimer's Disease In Patients
39) Message boards : Rosetta@home Science : Rosetta@home Research Updates (Message 80805)
Posted 30 Oct 2016 by Profile robertmiles
Post:
Research Update:

We recently published an article in Nature titled "Accurate de novo design of hyperstable constrained peptides". We would like to thank all Rosetta@Home participants for their help with this work. In the paper, we present computational methods for designing small stapled peptides with exceptional stabilities. These methods and designed peptides provide platform for rational design of new peptide-based therapeutics. Constrained (stapled) peptides combine the stability of conventional small-molecule drugs with the selectivity and potency of antibody therapeutics. Ability to precisely design these peptides in custom shapes and sizes opens up possibilities for "on-demand" design of peptide-based therapeutics.

Other developments describe in the paper:

1) We can now accurately design 18-47 amino acid peptides that incorporate multiple cross-links.
2) We can now design peptides that incorporate unnatural amino acids. Specifically, we designed peptides with a mix of natural L-amino amino acids and D-amino acids (mirror images of L-amino acids). D-amino acids tend to provide better protease resistance and lower immunogenicity; both of which are desired properties in a therapeutic peptide. Unnatural amino acids also let us sample much more diverse shapes and functions.
3) We can now design peptides that are cyclized via a peptide bond between their N- and C-terminus. Cyclic peptides provide increased resistance against exopeptidases as they have no free ends, and thus are ideal candidates for engineering peptide therapeutics.

We are now working to use these computational methods for designing peptides that target therapeutically relevant targets, such as, enzymes that impart antibiotic resistance in pathogenic bacteria.

Structure prediction runs on Rosetta@Home for these designed peptide models played a key role in selection of good designs that were experimentally synthesized and characterized. So, thanks a lot to all of you for your help in making this work possible.


Gaurav, do any of those new peptides include BMAA? That amino acid is normally found only in blue-green algae and in cyanobacteria, but has also been found in the brains of many Alzheimer's victims. Look for papers on recent Nobel prizes if you need more details.
40) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 80783)
Posted 26 Oct 2016 by Profile robertmiles
Post:
[snip]

some of the simulations being run on R@H can complete in just a few days

DAYS? For one work unit? I've never read anywhere if the researchers prefer a long run-time-per-WU over a short run-time-per-WU so I've always (7 years now) had my preferences set to shorter WUs.
Thanks for the input Timo, I appreciate it.

I've read that they wanted longer workunits selected as a way to reduce the load on the server. I haven't seen whether they changed their minds on that, though.


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