Sourced from: http://ivory.idyll.org/blog/2019-nih-hgrc-proposal.html

For the past month, I’ve been consumed in writing and submitting a grant for the NHGRI Human Genome Reference Center funding opportunity. This is a planned $12.5m / 5 year effort to coordinate the new Human Genome Reference Program (also see the Frequently Asked Questions).

We submitted this grant proposal a week ago Tuesday! I joined with three collaborators on this grant proposal: Curii, Genome in a Bottle, and the Church Lab. We also partnered with the Personal Genome Project and the Open Humans platform.

Since we’re all open-science-y people, we agreed to make the grant public after submission. I was thinking about how best to present it in a blog post, but then I remembered that grants are supposed to stand on their own with respect to the RFA. So …here it is, with only a little bit of organization to make it more approachable!

The HGRC call asked for what was in effect one R01 and two R21 grants, along with another R01-sized grant on top. The first R01 was Component 1, a 12 page section discussing how the center would maintain, improve, and provide the Human Genome reference. The first R21 was a 6 page Component 2, describing the community outreach plans of the center, to do training and gather feedback. The second R21 was the 6 page Component 3, describing the logistical coordination of the rest of the Human Genome Reference Program (running meetings, providing materials, etc.) And the last R01 was an overarching summary of the three components, 12 pages in length.

The end PDF submission was over 300 pages in length. Good fun…

One last comment before I provide the links: just like reading someone else’s submitted dissertation, your sole responsibility in reading someone else’s ALREADY SUBMITTED GRANT is to make nice noises, like “Hey, that’s great congrats on submitting it!” and “There are some great ideas in there!” You don’t say “ooh, look, a typo on p3! (How unprofessional! Sucks that you can’t fix it now!)” or “Gosh I would have written that completely differently.” Basically, you should just be nice – we’re going to go through a NIH review panel experience, and I’m sure they’ll be properly critical 🙂

The Actual Grant

Research Strategy – OVERALL – a high level overview of the thing.

Research Strategy – Component 1: Maintain, Improve, Provide the Human Reference Genome – check out our cool validation strategy with Genome-in-a-Bottle-like data sets!

Research Strategy – Component 2: Do Community Outreach and Needs – here we proposed not just doing outreach but also building a community of practice!

Research Strategy – Component 3: Provide Logistical Coordination for Human Genome Reference Program – here we added a standardization effort!

Enjoy!

–titus

Sourced from: https://retrorenovation.com/2019/04/09/lavender-bathroom-history/

The article Lavender sinks, baths and tubs in toilets from 1927-1949 appeared initially on Retro Renovation.

Pam here. Since Jan. 1, I’ve been tenaciously focused on performing a lot of technical tidy up of this site. This has included moving through stories in draft form. And ack! Did I publish this one? It wasn’t a draft — it had been finished and waiting for me! Kate finished it over […]

Sourced from: http://feedproxy.google.com/~r/RamblingRenovators/~3/UMP60mXrFPY/french-bistro-bathroom-orc.html

It turns out all I needed was the right inspiration.

I’ve talked about Cluny here on the blog before. It’s one of my favourite bistros in the city, and is overflowing with decor inspiration. I took the above photo in their bathroom three years ago and I’ve had it filed away in my brain for reference ever since. I love how the simple subway tile is elevated when paired with wood trim and panelling. Taking that idea, of mixing materials, led me to this new and improved design plan for our bathroom renovation:

As you can see, I’ve taken that French bistro inspiration and run with it! 😉

There’s a moment that happens in design or architecture that you call ‘unlocking the plan’. It’s difficult to explain but you know it when you reach it… when you push the design far enough, try out options, until you reach “perfection” and all the elements fall in place and feel right. I’ve only reached that moment only occasionally but when I do, the plan turns out infinitely better.

To remind you, here’s the room we’re working with:

To test my concept, I did a rendering. I printed out the photo above in black and white on my printer, and then using tracing paper, I created a rough sketch on top of what the new bathroom would look like. Here’s a little video of the sketch in action:

What are the elements of French bistro style?

Typically, it involves:
– subway tile
– black and white
– globe lights
– rattan bistro chairs
– brass hardware
– antiqued mirror
– marble
– open shelving
– chalkboards or vintage art
– linen
– warm woods

You can see how I’ve incorporated many of these in my bathroom design. French bistro style is popular for kitchens – why not use it to inspire a bathroom as well? The marble floor tile and vanity from The Home Depot Canada and the champagne gold Trinsic features from Delta Faucet Canada are the design heavyweights in this scheme but I can truly say I love every element shown in the plan.

All of that sounds well and good, but how much progress have we really made around here? This is what the vanity wall is looking like…

And here’s the tub area:

We’ve taken out most of the wall tile and have had the electrician in to install new boxes for the lights and to disconnect the jacuzzi tub. Once we finish removing the shower wall tiles, we’ll take out the tub and then the floor tiles. And then we can start building everything back up! New cement board and new drywall will go in first followed by the new tub and so.much.tiling!!

***

Want to see how everyone else is doing? Head to the ORC blog to see progress on 300 other renovation projects!

Sourced from: http://ivory.idyll.org/blog/2019-developing-metagenome-classifiers.html

So I was talking to someone about how we think about benchmarking and
developing sourmash, and then it
got long and kind of interesting, so I decided to write it up as a
blog post.

(I asked Luiz Irber for comments, and he had the best reaction ever:
“many feels, no time to write them, mostly agree, publish”)

When benchmarking, often people end up comparing their tool to tools developed to tackle different problems. To no big surprise, the first tool ends up winning out.

Here are questions that we asked ourselves, or decisions we made implicitly, when developing sourmash. Many of these have direct or indirect implications for benchmarking.

Are we developing a library, a command line application, or a Web site? It’s hard to do more than one at a time well. We’ve decided to focus on command line with sourmash, as a light wrapping around a Python library (which was a light wrapping around a C++ library, and will soon be a light wrapping around a Rust library). I think after 3 years we’ve reached a level of maturity where we could also support a Web site (but we don’t really have the focus in the lab to do a good job of it, and would prefer to support someone else if they want to do it).

How sensitive to coverage do we want to be? Phillip Brooks showed that sourmash is really specific and very sensitive, until you have fewer than (approximately) 10,000 reads from your genome of interest. Once your data set has fewer than 10,000 reads from a genome in it, we can’t really detect that genome. (This is of course a tradeoff in terms of speed, underlying approach, database size, etc., and we’re happy with that tradeoff.)

Do we envision our tool being used in isolation, or as one part of an exploratory pipeline? We are firmly in the camp of using sourmash to do hypothesis generation, following which more compute intensive approaches are probably appropriate. For example, sourmash can tell you which known species are in your metagenome, but we haven’t focused too much on assessing how much of those species’ genomes are there – after all, that’s (fairly) easy to do once you narrow down the list of possible genomes. And again, there are tradeoffs with many of the other design considerations below. But if we wanted to have a single software package that did everything we would design it differently (and it would be a lot harder, since you’d probably want to use multiple methods).

Do we envision our tool being used by programmers? We really like having scriptable tools in our lab. That means the tool has decent command line behavior, has a high level Python API, and consumes and emits standard formats. This may not be what everyone wants to focus on though!

Do we care about speed? Premature optimization can make your codebase ugly and complex. We’ve chosen (for now) to instead go with a fairly simple code base, which we then test the bejeezus out of. It supports optimization (Luiz Irber has done some amazing things with a profiler 🙂 but we are against trading simple code for speed, because this is a research platform.

What are our desired memory, disk, and time performance metrics? Do we care about one over the other? In general, we have chosen to prioritize low memory over performance, and performance over low disk space. But this isn’t clear cut, and depends a lot on what methods we find interesting and implementable.

What’s our desired database resolution? Do we want ALL the genomes? Or just some genomes? We made the decision with sourmash to go for ALL the genomes. This causes problems when you think about the next few questions…

What’s our desired taxonomic resolution? We implicitly settled on strain-level resolution as our goal for sourmash gather, largely because of the algorithm we chose. (It works quite well for that!) But, unsurprisingly, sourmash gather performs quite poorly when looking at organisms from novel genera and families. It’s actually quite hard to do both well.

Who updates the database? And is it easy and straightforward to build new databases, or not? We worked hard on a friendly and flexible database building toolchain, because we expect new genomes to come out on a (very) regular basis (and we wanted to include them in our databases, based on our desired resolution).

Do we want to support private databases, or not? We really like the idea of people using our tool in the privacy of their own lab to search their own collections of genomes. This means that we need to forego certain requirements (e.g. an NCBI taxid).

Do we want a big centralized database, or not? One of our big concerns about models for database distribution & update that require one massive database, that can only realistically be updated by one group, is that they tend to go stale over time (as the group loses interest, etc.) Maintenance is not the strong suit of academic researchers :). So Luiz Irber has been working on IPFS and Dat-based models for database decentralization. This will (soon) permit incremental database updates without massive database download, among other things.

What’s our publication model? Do we want others to use our software for cool things? Or are we trying to publish our own innovative methods that we try and get into high impact-factor journals? Are we building a platform for others to build their own tools? Are we playing around with different methods and ideas and so on? We’re not particularly interested in high-impact factor journals for sourmash, and we have a surprising number of people just using it do their own thing, so we’ve opted for providing citation handles via JOSS and F1000Research.

How do we decide what functionality belongs in sourmash? Did we have explicit use cases that we decided up front? Or do we discover them as we go? I’m much more comfortable doing iterations, finding users, and waiting for inspiration to strike, than I am in planning out sourmash years in advance. But then again, I’m an academic researcher and this fits our needs; we’re not trying to serve a particular community.

What’s our contribution model? Are you interested in supporting collaboration and community development? Or are you interested in limiting external contributions to potential use cases? We are OK interested in both, but it adds a certain level of chaos and coordination challenges to the situation.

–titus

Sourced from: https://www.homebuilding.co.uk/self-build-the-complete-guide/

Opting to self Assemble is a Excellent way to create a home that’s exactly tailored to Suit your needs and Tastes and can often enable you to get more bang for your Dollar

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Sourced from: https://www.loveandrenovations.com/bathroom-tiling-tips/

It’s week 3 of the Jeffrey Court Renovation challenge, and we’re chugging right along! Today we’re looking at the progress we’ve made so far and I’m sharing some bathroom tiling tips.

Well, I’m officially exhausted.

Doing a major bathroom renovation in six weeks is no joke, and this week I am feeling it.

But, oh boy, do we ever have some progress!

If you’re new here, let me catch you up. We’re participating in the Jeffrey Court Renovation challenge, which is a competition-style challenge where 15 different bloggers are all renovating rooms in their home in just 6 weeks. One person will win $5,000 at the end, and we’re seriously hoping it’s us – you can VOTE FOR US beginning today by clicking right here! We’re renovating our kids’ bathroom, and I’m so, so excited to get it done.

• In WEEK ONE, we shared the before photos of the bathroom, along with our design plan.
• In WEEK TWO, we started demo and shared some details of how to demo a bathroom.

This week was all about the tile. As a reminder, we’re using Jeffrey Court’s 6X18 Carrera Ink Jet Tile for the shower and the 7X7 Castelletto for the floor. You can see this week’s renovation log below, or you can click here to watch the video on YouTube!

This post contains affiliate links. Click here to read my full disclosure policy.

I’ve already done a full tutorial on how to tile, so I’m going to skip that here. Instead, I’m going to share a few tips and tricks specific to tiling in the bathroom, and just show you some pretty pictures of how things are looking so far.

After demo was complete and everything was cleaned (including replacing some insulation and plastic moisture barrier), we re-installed backer board. We’ve learned through renovating a couple of bathrooms that a lot of homes just have drywall behind the shower tile. This isn’t ideal! This one actually had two layers of drywall under the tile, which you can tell if you look back at the before photos and note how far the tile sticks out from the wall. It was strange, and the look always bothered me! We installed cement backer-board, which is meant for areas that are exposed to a lot of water, and it should be much longer-lasting.

You can see here that we also had a bit of regular drywall to replace in the room. We put up the drywall but haven’t done any taping or patching yet. The walls will need a bit of work before I paint, including taping the drywall, removing some wallpaper that we discovered under the trim, and adding some texture on the new drywall to match the old walls. I’m a bit nervous about making it all look good, but that’s a problem for future Amanda.

Current Amanda is just glad the tiling is done!

Once all of the concrete backer board was taped and sealed, it was (finally!) time to tile! Here are a few quick tips and thoughts about tiling in a bathroom that will hopefully help you out:

Tips for tiling in a bathroom

• As a reminder, we’re using this tile in the shower and this tile on the flooring.
• It’s much less messy to apply the mortar to the tile and not the wall. It took me a long time to learn this, and it’s especially effective with large-scale tile like the ones we used in the shower. When you’re applying mortar on the wall, it can often drip down and create a mess on the tiles below it and in the bathtub (or floor). Instead, just apply some mortar to the tile then put it on the wall.
• If you need to cut a hole for the bathtub or shower faucet, you can just attach one of these simple hole saw bits to your regular drill. It’s incredible easy (I was honestly surprised), and the bit costs less than $20!

• Be sure to lay out a row of tile in both the shower and on the floor to dry fit it before you install anything. It would be terrible to just start installing and then realize that the last tile in one of your rows will only need to be 1″ thick! Just lay them on the floor to get a general idea of what the sizing will be, and as long as one side isn’t absurdly short, you’ll be fine.
• If you need to stop for longer than an hour or so, take the time to clean up your work area. Use a bucket of water and a wet washcloth to scrub any of the drippy mortar from the bathtub and the tiles you’ve already installed. It’s a huge pain to scrape it off once it’s fully dried, but it’s easy before it sets. I had to do this a few different times, since I was mostly working after the kids were in bed or during nap times.



• Use a level as you work to be sure each row you lay is level, and you can also use it along the ends to be sure the row going up the wall is level too. We’ll be installing some trim pieces to finish out the bathtub surround, so it was important that the main tile was laid in a perfectly straight line.
• If you have a small bathroom, consider a large-scale tile! As soon as I started tiling, I notice how much bigger the bathroom felt with the large tiles in the shower. It feels so luxurious, and I love how it looks.

I cannot emphasize enough how excited I am about how this bathroom is coming together. This tile is beyond gorgeous, and I’m pretty thrilled with our choices.

On the agenda this week is grouting (which will make aaaaall the difference!), installing the tub and shower faucets, and hopefully getting the toilet installed so we can have more than one functioning bathroom again!



Be sure to go check out the progress from the other designers, and this is the first week you can VOTE for your favorite (which is us, right?). I can’t tell you how much I’d appreciate if you’d click over and vote for us!

The post Bathroom Tiling Tips Bathroom Renovation Week 3 appeared first on Love & Renovations.

Sourced from: http://originateandrenovate.blogspot.com/2013/03/how-to-gather-fabric-using-bakers-twine.html

Sourced from: http://www.ccr-mag.com/dollar-general-details-store-openings-improvements/

Money General will open 975 new places and redesign 1,000 existing shops this season, together with self-checkouts and improvements to segments including beauty and health, the company said. The 15,300-store merchant will also enlarge its new food and home products offerings, also it’therefore developing a digital plan designed because of its core base of lower-income customers. Read the CNN story here