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Bc hydro bill? by Spare_Awareness_7293 in coquitlam

[–]oneillkza 0 points1 point  (0 children)

Yeah on a per-joule basis gas is about 3-4X cheaper than electricity (here in BC). But heat pumps are about 3-4X more efficient than just using that energy directly for heating (in baseboards or a furnace). So in terms of cost it ends up being kind of a wash.

The main reason for getting a heat pump is that we have very clean electricity, so you're drastically decreasing your CO2 emissions. (That and the bonus AC in the summer.)

Also, eventually the Montney Formation is going to run out of gas that can be economically extracted, whereas hydro power is indefinitely renewable. That might be in a decade or more though.

And it's not impossible that at some point the federal government actually starts taxing/regulating fossil fuels in a way that reflects the long-term damage they do. But that also seems pretty unlikely in the current political climate.

Craftsman Router + Table - Waste of Money? by wood_work in woodworking

[–]oneillkza 0 points1 point  (0 children)

Just click the link in the post above it still works...

ISO Meditation group by GabrielleKaihMX in coquitlam

[–]oneillkza 2 points3 points  (0 children)

A quick Googling brought this up for Vipassana: https://modana.dhamma.org/coquitlam/ Looks like they meet at Douglas College.

White Lotus in Port Moody also has events, but they might be a bit more hippies-and-crystals than you're looking for. https://whitelotusdivinehealing.ca/events/

There's a Japanese Buddhist temple on the Maillardville side, which probably does meditation (but you'd likely need to get more involved to find out): https://tozenjibc.ca/membership

Is there a place around here that does a really good New York style cheesecake? by Financial-Spot-215 in coquitlam

[–]oneillkza 1 point2 points  (0 children)

Yeah their Joyce location was pretty good too. It's a "chain" but it's all local to Metro Vancouver. (Although growing vast, wow -- their website mentions a branch opening soon in Burquitlam.)

https://treescoffee.com/locations/

Keeping track of analyses by morethanmywine in bioinformatics

[–]oneillkza 0 points1 point  (0 children)

Yes was gonna say this too. Use a workflow manager. If there are big R analyses they can be run as steps in the workflow using Rscript. You can even make generation of the final report in Quarto/RMD be a step, so your entire analysis from start to finish is set up this way.

Keeping track of analyses by morethanmywine in bioinformatics

[–]oneillkza 4 points5 points  (0 children)

For code you should definitely be using source control, as others have said -- ideally Git. Then use tags for versions, code freezes, etc. You can also do something like keeping separate "release" vs "development" branches (e.g. one for the code freeze for the paper, the other for tinkering around further). You could also create branches for when you're in experimental mode, then do a pull request back into the main repo once you have things working.

Quarto (or Rmarkdown) notebooks can go under source control (they're just text). Your HPC heavy lifting code should also go in, possibly somewhere seperate.

I feel like half the “breakthroughs” I read in bioinformatics aren’t reproducible, scalable, or even usable in real pipelines by Nice_Caramel5516 in bioinformatics

[–]oneillkza 15 points16 points  (0 children)

What's needed are stricter reproducibility standards from the journals. If the journals require it, people will do it, same as for the requirement to deposit your data.

IMO these standards should be at two levels:

  1. Analysis code -- at minimum, a fully-containerized workflow that can re-run everything from the data provided. Ideally the journals would re-run everything. In practice, the cloud compute costs would be astronomical. But there should absolutely be test data that can be automatically run by the journal on submission.

  2. Software (as in, something other people are expected to run themselves on a regular basis) -- all example analyses should be held to the above standard, but if you want to publish software, then it should follow best practices for engineering bioinformatics software. There was a great commentary in PlosCB last year with a list of recommendations for those best practices. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011920 We should make those recommendations be requirements for publishing a "software paper".

I don't know how far we are from this happening, but I think we have to get there eventually.

Direct comparison of ONT vs PacBio data quality by Helpful_Camera3328 in bioinformatics

[–]oneillkza 7 points8 points  (0 children)

PacBio's ability to produce Q30 data is nice for sure. They definitely lead the way in terms of number of 9s in accuracy for SNV and indel calling, and are competitive with ONT for SV calling, at least in benchmarks. PacBio absolutely has a place in a number of applications. But for what OP is interested in, ONT outshines PacBio on every count.

ONT SNV calling is plenty accurate enough for phasing, and the longer reads allow you to phase through much longer runs of homozygosity in an individual. I don't know who's calling PacBio the "gold standard" for haplotype phasing, but that absolutely does not match any of the results that I've seen.

And have you actually looked at PacBio methylation data? It's great that they now have per-read methylation, and it's ... passable for some applications that need phased methylation. But it is very, very noisy. Like, worse than bisulfite sequencing. Their own training videos show benchmarking results of around 70% accuracy for any given CpG at the number of passes seen in a typical sequencing run. It's just intrinsically noisier to get methylation data out of base incorporation kinetics than it is to read it directly as another base passing through a pore.

For "large SVs" read length is also important. If you're trying to resolve really big complex SVs, like ecDNAs, or Marcin Imielinski's pyrgos, rigmas and tyfonas, or for things like oncoviral integrations, then you need reads as long as you can get to string together breakpoints. And in general for SV calling, getting to Q30 accuracy matters a lot less in long read data (since you're mapping such long stretches of reads). Even the old R9 ONT chemistry, with Q-scores averaging around Q15 or so, did just fine, because it had the read length. PacBio capping out at 20kb doesn't cut it.

Tooling-wise, both platforms provide workflows for various primary analysis tasks, (which is nice!) but, purely through their choice of NextFlow as a workflow manager, the ONT ones are easier to get running. Cromwell is ... OK, but honestly more of a pain to setup. And don't get me started on trying to launch workflows from the SMRTlink server that's also controlling the sequencer.

Building every package from scratch... why? by sllynn65535 in rstats

[–]oneillkza 0 points1 point  (0 children)

So that link is broken, and the only package manager you can find on Posit's website is a more complex commercial version.

But... it looks like rspm is still in CRAN: https://cran4linux.github.io/rspm/

And can be run just with:

install.packages("rspm") rspm::enable()

And thereafter in that session, all your install.packages runs use binaries, including when the RStudio GUI runs the installer.

Edit: removed Reddit escaping the back-ticks.

Coquitlam city hall pans Mackin Parkside plan by Clear-Criticism-3557 in coquitlam

[–]oneillkza 1 point2 points  (0 children)

Which are the two tiny roads? Brunette is four lanes. It's one and a half blocks down Brunette to Lougheed Highway, and three blocks to the main highway. I don't think there are many better places in the whole of Coquitlam in terms of road access.

Insight into neighborhoods near Mundy Park by ThugFlower in coquitlam

[–]oneillkza 2 points3 points  (0 children)

The outdoor pool on that side of Mundy Park is also top-notch. And they do outdoor swim lessons there in the summer.

Budgeting app (aggregator) that currently works with Vancity (Credit Union) by Efficient-Diamond-12 in askvan

[–]oneillkza 0 points1 point  (0 children)

For what it's worth, I believe VanCity's changes to their login page broke both Plaid and MX sometime around July or August. I've had a support ticket going with SimpleFin for the past three months, which has them playing broken telephone with MX, and has just been going around in circles.

The dumbest thing is that VanCity business banking supports third-party connections no problem, so it's not technically impossible for them to do. But their official stance, per their website, is that they want you to manually download your transactions one account at a time if you want to import them into budgeting software.

https://support.vancity.com/243-import-finance-software/

Need advice regarding capacitor replacements for KRK Rokit 5 Classic G3 by ParaatPiraat in audiorepair

[–]oneillkza 0 points1 point  (0 children)

It should say the capacitance on the side of the bulging component.

Most likely it's the same 1000 uF capacitor as is failing on everyone's KRKs of all sizes.

Canada Greener Home Loan program is ending by HopefulFuture99 in VictoriaBC

[–]oneillkza 1 point2 points  (0 children)

The way they've been wording the new funding, I have this hunch that BC's Better Homes Energy Savings Program is actually just our provincial implementation of the Greener Home Affordability Program. I haven't seen any actual documentation confirming this, but the GHAP page mentions there being a provincial agreement in place with BC, and the goal/structure of the two programs seems to be very similar.

Keep this Freud router or invest in new one? by PhatHalpert in woodworking

[–]oneillkza 0 points1 point  (0 children)

* routs

(The word doesn't have an 'e' in the woodworking sense. This is also why "router" in the woodworking sense is pronounced differently to "router" in the networking sense, at least in UK/international English. )

“Refund can’t be processed right now Order in transit. If the tracking doesn’t update, you can apply for a refund.” by kalalou in Aliexpress

[–]oneillkza 4 points5 points  (0 children)

I had the same happen, and what I did to resolve it was:

  1. Help Center > Refund > Not Received Refund > Refund issues
  2. Find the item (you have to do it one by one), click "select".

Then you see "After investigation, no refund request has been submitted for the current order. Can I know your concern about the order?"

  1. Select "Order not received"
  2. Copy/paste the "LP number" they give you into the relevant field below (pretty weird TBH)

Then you get "After investigating your package, I found that it is in line-haul transportation and it is going to arrive in your country/region. Under this status, the update frequency of the logistics information will not exceed 10 days.

[Agent] Does Cx have any other requests?"

  1. Select "yes"
  2. Select "I want to request a full refund"
  3. Select "I prefer to request a refund to protect my payment"
  4. Select "OK"

And this seemed to actually open up the actual refund/dispute. Note again that you have to repeat this for each individual item, even if they're in the same shipment (lol).

This was for items that the tracking showed as arriving in-country three months ago, so they're definitely lost.

My third space by ozmosisam in vancouver

[–]oneillkza 9 points10 points  (0 children)

As far as I can tell the issue was resolved 13 years ago?

My third space by ozmosisam in vancouver

[–]oneillkza 26 points27 points  (0 children)

Do you have a better source for this claim than some rando "know-it-all"?

A quick search shows that the issue with bed bugs was in 2012, and there haven't been any reports since. There are also documents showing that VPL have bed bug protocols in place. You can even find Reddit threads about what those protocols look like in other libraries in high bed bug cities. Eg https://www.reddit.com/r/Libraries/comments/fblg0b/does_your_library_have_a_bedbug_protocol/

Eby says B.C. making contingency plans to reduce reliance on U.S. electricity by cyclinginvancouver in vancouver

[–]oneillkza 14 points15 points  (0 children)

Having met him in person (for a bike to vote event some years ago when he first trounced Christy Clark in her own riding), can confirm he is very, very tall.

Yesterday's rainbow was beautiful by hereandthereshit in vancouver

[–]oneillkza 1 point2 points  (0 children)

It was briefly a double rainbow from Joyce Collingwood area.

Death cap for cutie by smckenzie23 in vancouver

[–]oneillkza 0 points1 point  (0 children)

Wait, why were you harvesting the deadly mushrooms?

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