Basement Remodeling

When looking to increase your home’s living space the answer may lie right under your feet. Basement remodels come with their own unique set of challenges, they all can be overcome with good planning. Here are ten tips and techniques to help you transform your basement into a functional living space.

The Basement is a different environment that involves structure elements, moisture that can lead to mold as well as has high possibilities for leaks or flooding. This calls for material and a system that was specially created to cover all these factors and will last years after your investment.

Homeowners looking for basement finishing ideas can easily begin to feel overwhelmed. With all the information out there, it’s difficult to know what’s best. In the past, there was only one solution for finishing basement walls and ceilings: drywall. Finished basement floors were carpeted.

The result? The cool, damp basement environment caused the drywall and carpet to grow mold and mildew, and eventually to rot. When this happened, it needed to be ripped up, and homeowners still only had one choice for replacement. Thank goodness there is now a better alternative!

Remodeling your basement typically costs $65,442 and returns 72.8 % of the original cost, according to “Remodeling” magazine’s annual “Cost vs. Value Report.” In the northern Midwest states, where basements are common, a basement remodeling project returns about 13 % less than the average return on investment. In the West, where they are less common, remodeling returns about 93 % of the original cost.

Basement remodels return so much of your investment because the basic structure– walls and floors– already are in place. This lowers construction costs per square foot, saving 10 % to 15 % over the cost of building an addition with comparable features and amenities. Basement remodeling also avoids the complications of property line setbacks and other zoning restrictions that sometimes complicate adding onto your house.

Moisture is the Biggest Hassle

Moisture is a big concern in basement remodeling. Any chronic leaks, condensation, or flooding must be fixed before you convert the space into a living area. Remedial measures cost anywhere from a few hundred dollars to thousands, effectively reducing your return on investment. If you cut those corners, you’ll pay big time in musty smells, creeping mold, and soggy carpet.

Are you looking to create the game room, family room, home theater, office, music room, exercise room, extra bedroom or playroom you’ve always wanted? Our certified basement remodeling experts are able to install the innovative Basement Finishing System in only about two weeks, allowing you to begin to use your basement renovation in less time than you might have ever anticipated. What’s more, this unique basement remodel is particularly well suited for basement environments and includes features such as insulated basement walls and integrated acoustic insulation that can help make your basement feel like a warm and inviting natural extension of your home. Don’t turn to a basement contractor who doesn’t understand the unique challenges that face remodeling a damp, dark basement.

In the northern Midwest states, where basements are common, a basement remodeling project returns about 13 % less than the average return on investment. Basement remodels return so much of your investment because the basic structure– walls and floors– already are in place. Our certified basement remodeling experts are able to install the innovative Basement Finishing System in only about two weeks, allowing you to begin to use your basement renovation in less time than you might have ever anticipated. What’s more, this unique basement remodel is particularly well suited for basement environments and includes features such as insulated basement walls and integrated acoustic insulation that can help make your basement feel like a warm and inviting natural extension of your home. Don’t turn to a basement contractor who doesn’t understand the unique challenges that face remodeling a damp, dark basement.

is this the world’s ugliest kitchen?

Sourced from: http://renovateanddecorate.blogspot.com/2009/02/is-this-worlds-ugliest-kitchen.html


The missing door: poor bugga nearly made it. Was hanging on by one tiny nail. But Steve kept forgetting its state and it fell on his foot one time too many and spent its last few days beside the fridge.

It might well have been. But unfortunately it can’t claim this distinguished title because it NO LONGER EXISTS!!!! It’s sitting all partly smashed up on my front sandpit (what pathetic grass we had has been fried in the heat). And it’s never looked better. Even Z is glad to be rid of the “kitchen mess” as he calls it. Gee, do you wonder why I never posted pics of this room? I’m completely embarassed to show this, but seeing that it’s all in the past, let’s have a laugh, shall we? Yes, I’ve put up with this for five years. My medal better be in the mail…

A few incredibly exciting facts:

* I painted the doors white when we moved in because I couldn’t imagine living with green doors for any amount of time. I did such a crap job, I was wishing for the green to come back.

* The previous owner’s son thought himself a handyman. He wasn’t. He installed the taps himself did such a bang-up job they didn’t work properly. They were replaced numerous times and ground back and had lots of work but no makeover could save the cold one which exploded one day. I’m so used to using warm/hot water for everything I rarely turn the cold water tap on in the bathroom. He also cut a hole too big for the tap nozzle and didn’t bother doing anything about it. My non-handyman husband figured expanding filler would do the trick temporarily. It sealed the hole, but, well, look at it! Ugh.

* The tiles are on big sheets of some asbestos-ridden material and weren’t the same depth as the rest of the wall, so there was a weird uneven gap no one ever bothered fixing. I don’t remember how the piece of wood make its way there but there it is!


Hmm, what’s sadder? The contact-covered sheets? The mssing door? The paper towel stuffing the hole where the cold water tap used to be? The lovely aged yellow stains or the fish plug that for some INSANE reason I never replaced??????


One of the delightful tile prints I could admire while cooking. They clearly shopped at the Ugly Tile Shop – same place they got the sunflower tiles that were in my old bathroom!


And another one – I guess they just couldn’t decide between the two beauties and chose both…

On a happier note, I did wonder if I was utilising the space enough with the new design. Would I fit everything in? Considering I was ruthless and thew out half the contents of the kitchen cupboards as well, I have a feeling I’ll be just fine. Aside from another bag out of sight, this is all I have! I sense a shopping spree coming on!


I started building the cupboards so I had something to store it in. Four packages down, 48 to go…

So I was feeling the pressure with all your “can’t wait to see the new kitchen” comments. But I guess, looking at this, anything is going to be a huge improvement isn’t it?

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What I wore: Family Pictures

Sourced from: http://originateandrenovate.blogspot.com/2012/09/what-i-wore-family-pictures.html

Life is delicate, No? We work so hard and worry so much about making it the way we want. Yet, We have such little control over it. In a single instant our entire world can change. A child gets sick or a spouse is taken before we can prepare. People save their entire lives just to lose everything they’ve worked for.  Women that would make incredible Mothers struggle to become them.  The worst part is that not one of us is invincible and it’s only a matter of time before we are faced with our own trials. 
 My way of coping with these thoughts is through memories.   Making them, I mean. And taking way more pictures than my family appreciates.  I never want to regret not having documented each and every stage of life. Not because I want to live in the past, but because when things get rough, we need something to remind us what makes it all worth it.
And so you see why I love having family pictures taken. Especially by someone as talented as Jennifer Fauset.  She was a gem to work with, and the photos are exactly what I was looking for. Seriously, I could spend hours on her blog looking at all her beautiful work.

What We Wore:
Me:
Top and Scarf: J. Crew
Skirt: Target
Belt: Downeast Outfitters
Shoes: Steve Madden
Jewelry: Express
Steve:
Undershirt: Target
Button down: J. Crew
Sweater: Gap
Pants: Express
Shoes: Aldo
Alfie:
Shirt: Crew Cuts
Cardigan, Jeans and Shoes: Gap Kids
Juju:
Shirt and Necklace: Crew Cuts
Cardigan: Baby Gap
Jeans: Joe Jeans
Boots: Target
Hairbow: Made by me 

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can you just imagine this coming towards you…

Sourced from: http://renovateanddecorate.blogspot.com/2009/02/can-you-just-imagine-this-coming.html


How frightening.

I’d feel way too guilty whinging about living without a kitchen and blogging about the reno when so many people have lost their lives, homes and livelihood in the disastrous fires so I’m going to give it a miss today. On Friday afternoon there was a fire somewhere in our area – it would have been miles away, but the smoke and smell was quite intense and I found it hard to breathe at times. I thought to myself “here we go…” and sent out a silent sympathetic thought to the firies who we’re in for a big weekend and made bets with my husband how long it’d be before the freeway was closed and the trains stopped running. Pretty much every year the central coast gets blocked off for a while due to fires. This is an incredible pain in the rear for anyone who needs to travel to Sydney or is stuck in Sydney trying to get home. It can be hours – at times days – before you’re given the all clear. After this horiffic weekend in Victoria, we of course, have no right to complain. In fact, I’m sure every one of us up here would have happily been inconvenienced for a while if it meant Victoria had no fires, no deaths, no devastating tragedy. I cannot imagine the emotions being felt down there…

My husband suggested if the latest federal Stimulus Package is passed, they should immediately halve the amounts they’d planned to hand out and give the other half to the fire victims and to rebuilding the demolished communities. He also said part of it should go to upgrading our firefighting equipment, procedures and training. Because as temperatures rise year to year, our country is only going to burn faster, further and with more fury.

And for those insert-angry-adjective-here animals lighting these fires, I only hope they’re found and punished accordingly. I might not be the world’s biggest advocate of capital punishment, but in this case, I think being burnt at the stake highly appropriate…

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News from the NIH Data Commons Pilot Phase Consortium

Sourced from: http://ivory.idyll.org/blog/2019-nih-data-commons-update.html

You may recall that about a year and a half ago, I got involved in the NIH Data Commons.

Between then and now, we built a project execution plan, ran Phase 1 for six months, and then in October took a planned work moratorium for the purpose of doing future planning.

Then, in February, we received word that the the NIH Data Commons Pilot Phase Consortium (DCPPC) would not continue in its current form. Here’s what we received:

The NIH Office of Data Science Strategy has been asked to lead the next phase of trans-NIH data ecosystem development as described in the NIH Strategic Plan for Data Science. The deliverables from the DCPPC will inform next steps, but we will not pursue a second phase of the DCPPC. New initiatives may emerge from the ODSS and/or from the ICs in response to the Strategic Plan, but they will communicate their plans as they are established.

My award finished at the end of March, and I thought it would be a good time to update y’all (especially since I’ve been receiving questions!)

What did the NIH Data Commons Pilot Phase Consortium achieve?

I think we achieved quite a lot in our fairly short stint! (And there’s a fair amount of public material that was made available as part of it, although it’s not well advertised.)

I’m going to focus on things my team helped with, because that’s what I know best. There were lots of technical prototypes as well, but those were produced by other teams and are not mine to discuss. (See the list of deliverables and their reviews for more info. Happy to connect you to the authors if you’re interested – drop me a line at ctbrown@ucdavis.edu.)

First off, here is the top link to the public site that we created for the end of the first Pilot Phase. There are links and documents in there that I continue to find useful, and expect to find useful for many years to come.

I’m particularly happy with how the Use Case Library effort was proceeding. I think we set a good path for collaboratively developing use cases for Phase 2, and even without a Phase 2 I will be making use of this approach and this material for other projects.

The Centillion search engine that my team built was pretty cool!! See the October writeup of it, here and also the public GitHub page, here.

The “On Commonsing” document we wrote up after a workshop on “Data Commonses” is something that I will be coming back to regularly!

People interested in pragmatic standards development might be interested in Why Multiple Stacks are Necessary.

I continue to think the FAIRshake portal is unreasonably cool… check out the projects.

Personally, I learned a lot about interoperability and creating and growing community from this experience, and I think the same is true of most of the other participants. Completely apart from the technical and infrastructure efforts, the coordination and community aspects of this Pilot Phase seem likely to have long-term positive impacts on how many of us deal with these kinds of projects in the future.

So what’s next?

I’m not sure!

I think it’s fair to say that the problems the NIH Data Commons effort was tackling are not going away (you can see more about these problems in my talk slides from my 2018 talk at the Dutch Techcentre for Life Sciences). And the NIH and broader biomedical research community will certainly be working on many things in this area. And I may not be involved but I’m sure to have opinions. So, stay tuned!

–titus

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i Heart Radio

Sourced from: http://originateandrenovate.blogspot.com/2012/09/i-heart-radio.html

Feeling quite happy about being home with these two munchkins after a spontaneous trip to Vegas with Steve to see the i heart radio music festival.  Grandpa stayed over and we made the 6 hour journey on the hope of scoring tickets from someone down there, which was rather crazy considering this concert sold out in under 10 minutes. We did find someone to buy tickets from, but sadly he never showed. Thankfully, having a super chatty husband pays off and some of the clear channel peeps we met down there hooked us up with FREE TICKETS!!  The lineup was insane. No doubt, Taylor Swift, Usher, Rhianna, Aerosmith, Pink, Green Day, Pitbull, Miranda Lambert, Deadmau5, Bon Jovi, Enrique Iglesias, Swedish House Mafia, Lincoln Park, Jason Aldean, Brad Paisley, Lil Wayne, Mary J. Blige (with a special appearance by Prince) and Calvin Harris. The best part was the little to no downtime between acts. However, I did feel old when we didn’t even use our after party credentials because we were too tired. 

1. Had time for a quick haircut by the fabulous Shep before we left.
2. The set up at the concert, the huge screens were pretty deluxe. 
3. The gardens at the Bellagio. That pumpkin is real and yes I’m wearing pants 😉
4.  i Heart Radio LED bracelets that lit up to the music.
5. Scoring free tickets.
6. My most favorite celebrity ever, Gwen Stefani.
7. Pink. Ugh, love her. 
8. After party credentials 
9. Us
As glamorous as it all was, I must admit, I was missing Alfie and Juju something fierce by the end of the 2nd night.
 So while my real life looks more like this ^  and can feel a tad bonkers at times. It’s nice to be reminded that no celebrity, or credential or lifestyle is quite as rewarding as a family.  Glad to be home. 

DIY Concrete Outdoor Coffee Table

Sourced from: https://www.loveandrenovations.com/diy-concrete-coffee-table/

What happens when you fall in love with the perfect outdoor coffee table, only to discover it’s sold out? You make your own! Here are the details on my DIY concrete outdoor cofee table.

back porch with DIY outdoor sofa, a DIY coffee table, and two lounge chairs

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

I don’t mean to sound like a broken record, but I cannot believe how far our backyard has come in the last few months, y’all. I was honestly pretty nervous when you decided that I should tackle our back porch this summer because it felt like such a daunting task, but I am so (so!) glad we did. This space has become one of my very favorite places to be, and I can’t wait to wrap the last few projects up and call this space finished!

If you haven’t been following along with this summer makeover, here’s everything you may have missed:

Today I’m sharing the (gorgeous) DIY outdoor coffee table we built, and then there’s just one more big project to share before the official reveal (NEXT WEEK, Y’ALL!).

This coffee table has been on my mind since the very beginning of this entire renovation. It started when I was shopping for furniture for the porch and I found the Palmera Faux Concrete Coffee Table from World Market (no longer available, but see the other stuff in the line here). It was everything I wanted for this space, and y’all agreed when I put it to a vote over on Instagram.

Of course, it wasn’t until after this coffee table won the vote by a landslide that I discovered that it was out of stock. And, once I contacted World Market I was told they weren’t sure when (or if) it would be brought back.

Perfect.

close up of DIY feather finish outdoor coffee table
concrete coffee table with text overlay - "diy outdoor concrete coffee table"

Thankfully, the design is pretty simple and I felt confident that Corey and I could re-create the same basic look – and probably for a lot less money! This project was incredibly cheap, since we were able to use some scraps from our outdoor sofa for the legs. Even if you need to purchase the wood, the materials for this entire build should set you back no more than $100 or so – and you know I love saving money!

Ready to learn how to make your own?! Let’s do it!

DIY Concrete outdoor cofee table

tools + Materials Needed:

STep One: Build the Legs

For the legs, we used pretty much the exact same process that we used on our outdoor sofa. We loved the invisible joints created by Rockler’s Beadlock Pro and it was the perfect tool to use again for this project. However, you could also use pocket holes or even just extra long screws (like these) if you don’t mind the visible hardware.

Each leg is made up of two 14″ pieces with one 13″ piece in the middle. We put them together using the loose tenon joints but, again, if you aren’t comfortable with those joints or don’t have the jig, I’d recommend just using extra long lag screws and wood glue.

Just like with the couch, I recommend sanding the wood for the legs (starting with 80-grit and working up to 320-grit) before assembling them!

man assembling legs for an outdoor coffee table

Step TWo: Assemble the top Frame

Once the legs are built and dried, you’re ready to assemble the top of the table. We wanted a concrete look without the weight of an actual concrete slab, so we built a wood top and covered it with Henry Feather Finish. I’ve seen people use this stuff on countertops dozens of times over the years, and I’ve always wanted to try it so this was the perfect opportunity!

To build the top, we started by making a 29″X44″ rectangle frame using 2X4s. We ended up deciding it was too thick, and we cut down the excess, so I’d actually recommend just starting with 2X2s to make your life easier! We used wood glue and screws to assemble this part of the table.

man assembling a table top

Once the outside is built, you’ll add your supports for the legs. We just cut two 2×4’s to fit inside the rectangle, then placed them 5″ in from either side – they’re attached with wood glue and screws, just like the rest of the top!

Then, we set everything up really quickly to see how we liked it – and, of course, this is when we noticed that the top was much too thick! Corey just ran it through the table saw to cut it down, but I’d recommend starting with 2X2’s for the outside pieces – that’s about what we cut it down to.

frame for diy outdoor coffee table

To attach the legs to the top, simply apply wood glue to the tops of the legs and then drill the top into the legs from the top of the supports.

Step three: attach plywood to top

Next, we wrapped the entire frame with some 1/4″ plywood. You should have five pieces, cut to the specific measurements listed above (though, I recommend that you double-check the measurements on your specific table before cutting, just in case you made any small mistake along the way that would cause it to be a slightly different size!).

Attach the large piece of plywood to the top using wood glue and nails (we use this power nailer), and then attach the side pieces on the sides of the frame with the same method. After you’ve attached all of the plywood, you should use some wood filler to fill in any gaps, cracks, or nail holes!

It should look something like this when you’re all done!

base of DIY outdoor concrete cofeee table

Step Three: finish the legs

Now the bones of the table are finished and it’s time to make it look pretty! I chose to stain the legs using Varathane’s Dark Walnut stain, but you could also paint them if you prefer. My original plan was to actually paint them black, but I didn’t have any exterior paint on hand so I decided to use something I did have instead.

Once you’ve stained the legs, be sure to apply spar urethane to protect them from the elements outside. It typically requires several coats with sanding in-between, so don’t rush this step!

Step Four: Apply Feather Finish to top

Now you’re ready for the fun (and slightly terrifying) part: applying the feather finish to the top!

The most common brand of feather finish I’ve seen used for this kind of project is Ardex Feather Finish, but I didn’t wait to wait for it to be shipped so I just grabbed the Henry brand Feather Finish in store. I think they’re pretty comparable, so either should be fine.

To apply your feather finish to the table top, start by mixing it up (mine had a ratio of 2 parts water to 1 part powder) in small batches. I just mixed mine in one of these little pails (with a liner) and I found that it was just the right size. If I tried to get too much going at once, it started to harden towards the end of the batch – and this stuff is much easier to work with when it’s on the looser side! Think of the texture you’re shooting for as a loose cake frosting – it should be super easy to spread but thick enough that it won’t just slide off the edges of the table when you apply it vertically.

I applied three layers of feather finish (though, I probably could have gotten away with just two). The first two layers really just need to provide coverage – don’t stress too much about making them smooth! I used both an angled trowel and a wide putty knife to apply the concrete and I found that the best strategy was to get the concrete on the table and mostly spread out with the trowel, then switch to the putty knife to really spread it out and smooth it as much as possible.

After each layer dries, grab some 80-grit sandpaper and your orbital sander and go to town – you’re looking to just smooth out the rough edges and the ridges in the table. You aren’t shooting for perfection with these first two layers!

hand applying concrete feather finish to a table top
concrete table top with two layers applied

On the final layer, I worked much slower when applying the concrete and I really tried to focus on minimizing any lines in the finish. This is the layer everyone will see, and it’s the one you’ll be sanding to perfection, so really take your time with it!

Once it has dried fully, you’re ready for the final sanding process. I started with 80-grit sandpaper, then slowly stair-stepped my way all the way up to 320 (meaning, I sanded the entire thing with 80-grit, then 100-grit, then 120-grit, etc.). It takes a long time to get it fully sanded, but the buttery smooth texture is worth it.

finished concrete table top

Step Five: Seal the table top

After I finished the table top, it was time to seal it. Thankfully, since this is just a coffee table and not concrete counters (which is where I see this product used most often), I didn’t need to worry about a food-safe sealer! I used this wet look sealer and it was a breeze to apply!

I applied three thin coats using a regular old paintbrush. It’s very thin, so be careful not to allow it to pool at all as it’s drying. Each coat needs to dry for about an hour before applying the next one, and I found that it stayed really smooth and I didn’t need to sand in-between coats at all.

hand with a paintbrush applying concrete sealer

Once it’s fully dry, you’re good to go!

I am so, so happy with how this little faux concrete table turned out and I honestly can’t wait to tackle another project using feather finish concrete! It was so much fun, and the finished look is truly, absolutely beautiful.

back porch with DIY concrete coffee table
close up of DIY concrete coffee table
back porch with DIY concrete coffee table

With this project complete, we’ve only got one big project left back here before we’re ready to accessorize and call this back porch complete!

Be on the lookout for the final project later this week, and the full reveal is coming next week!

What do you think I should use the feather finish on next? An indoor dining table? Nightstands? I kind of want to cover everything with it!

The post DIY Concrete Outdoor Coffee Table appeared first on Love & Renovations.

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Comparing two genome binnings quickly with sourmash

Sourced from: http://ivory.idyll.org/blog/2019-comparing-binnings.html

tl;dr? Compare and cluster two collections of 1000+ metagenome-assembled genomes in a few minutes with sourmash!


A week ago, someone e-mailed me with an interesting question: how can we compare two collections of genome bins with sourmash?

Why would you want to do this? Well, there’s lots of reasons! The main
one that caught my attention is comparing genomes extracted from
metagenomes via two different binning procedures – that’s where I
started almost two years ago,
with two sets of bins extracted from the Tara ocean data. You
might also want to merge bins that were similar to produce a
(hopefully) more complete bin, or you could intersect bins that were
similar to produce a consensus bin that might be higher quality, or
you could identify bins that were in one collection and not in the
other, to round out your collection.

I’m assuming this is done by lots of workflows – I note, for example,
that the metaWRAP workflow
includes a ‘bin refinement’ step that must do something like this.

I (ahem) haven’t really read up on what others do, because I was mostly
interested in hacking something together myself. So here goes :).

How do you compare two collections of bins??

There are a few different strategies. My previous attempts were —

In both cases, my conclusions ended with “wow, there are some real differences
here” but I never dug deeply into what was going on in detail.

This time, though, I had a bit more experience under my belt and I
realized that a fairly simple thing to do would be to cluster all of
the bins together while tracking the origin of each bin, and then
deconvolving the clusters so that you could dig into each cluster at
arbitrary detail.

The basic strategy

  1. Load in two lists of sourmash signatures.

  2. Compare them all.

  3. Perform some kind of clustering on the all-by-all comparison.

  4. Output clusters.

Conveniently, I had already implemented the key bits in a Jupyter
notebook about a year ago
(here),
so it was ready to go! I turned it into a command-line script called
cocluster.py
and tested it out; on data where I knew the answer, it performed fine, grouping
identical bins together and grouping or splitting strain variants depending
on the cut point for the dendrogram.

You do have to run it on collections of already-computed signatures;
an example command line for cocluster.py is:

cocluster.py --first podar-ref/?.fa.sig --second podar-ref/*.fa.sig -k 31

This version outputs a dendrogram showing the clustering, as well as a
spreadsheet containing the cluster assignments.

Speeding it up

The problem is, it’s kind of slow for big data sets where you have to do millions of comparisons!

Since comparing N signatures against N signatures is inherently an N**2
problem, any work we can put into filtering out signatures at the front
end of the analysis will be paid back in serious coin.

So, I added two optimizations.

First, you can now pass in a --threshold argument that specifies, in
basepairs, roughly how many bp need to be shared by a signature from
the first list with any of the signatures in the second list. If this
threshold isn’t met, the signature from the first list is dropped. Then
do the same for each signature in the second list with respect to the first
list.

Second, you can now downsample the signatures by specifying a
--scaled parameter. (Read more about this here.) The logic here is that if you’re comparing
genomes, you probably don’t really need to look at a high resolution to
get a rough estimate of what’s going on. This optimization speeds up every
comparison done.

Together, this made it straightforward to apply this stuff to scads of
genomes!

More/better output

Last but not least, I updated the script to output clusters, and provide summary output too!

An example!

Here is an annotated example of the complete workflow – this is done on the reference genome data set from Shakya et al., 2013, which we updated in Awad et al., 2017. This genome collection contains 64 genomes, some of which are strain variants of each other.

Briefly, after computing signatures, cocluster.py
calculates an all-by-all comparison for the two input collections, that results in a matrix like this (not currently output by cocluster.py) —

comparison matrix

The dendrogram is then cut at some given phenetic distance – in this case I chose 1.8, based on
visual inspection of this next dendrogram:

dendrogram annotated with distances

The cocluster.py script then outputs a cluster details CSV file that lists all of the clusters and their members. (The clustered signatures themselves are also provided, along with singletons.)

And, finally, all of this activity is logged and summarized in the results output:

...
total clusters: 60
num 1:1 pairs: 56
num singletons in first: 0
num singletons in second: 0
num multi-sig clusters w/only first: 0
num multi-sig clusters w/only second: 0
num multi-sig clusters mixed: 4

The full set of commands is listed in this Snakefile, and commands to repeat it are in the appendix below.

Playing with real data

Since both the Tully et al. and the Delmont et al. papers have been
published now, I first re-downloaded the published data and calculated
all the signatures for the 3500 or so genomes — see the instructions
and Snakefile in github.com/ctb/2019-tara-binning2/.

Once downloaded, computing the signatures takes about 15 minutes, using
snakemake -j 16.

Then, I ran the cocluster script from https://github.com/ctb/2017-sourmash-cluster like so:

./2017-sourmash-cluster/cocluster.py --threshold=50000 -k 31 
    --first ../data/tara/tara-tully/*.sig 
    --second ../data/tara/tara-delmont/NON_REDUNDANT_MAGs/*.sig 
    --prefix=tara.coclust --cut-point=1.0

This took about 2 minutes to run on my HPC cluster, and produced the
following output with a cut point of 1.0 (which is pretty liberal).

...
total clusters: 2838
num 1:1 pairs: 331
num singletons in first: 1886
num singletons in second: 443
num multi-sig clusters w/only first: 42
num multi-sig clusters w/only second: 4
num multi-sig clusters mixed: 132

When I re-run it with a more stringent cut-point of 0.1, I get:

% ./2017-sourmash-cluster/cocluster.py --threshold=50000 -k 31 
    --first ../data/tara/tara-tully/*.sig 
    --second ../data/tara/tara-delmont/NON_REDUNDANT_MAGs/*.sig 
    --prefix=tara.coclust --cut-point=0.1
...
total clusters: 3520
num 1:1 pairs: 43
num singletons in first: 2557
num singletons in second: 906
num multi-sig clusters w/only first: 6
num multi-sig clusters w/only second: 0
num multi-sig clusters mixed: 8

Basically this means that:

  • when doing stringent clustering, there are 3520 different clusters;
  • 43 of the clusters provide a 1-1 match between bins from the Delmont and Tully studies;
  • 2557 of the Tully signatures don’t cluster with anything else;
  • 906 of the Delmont signatures don’t cluster with anything else;
  • there are 6 clusters that contain more than one Tully signature, and no Delmont signatures
  • there are 0 clusters that contain more than one Delmont signatures, and no Tully signatures;
  • 8 of the clusters have more than two signatures and contain at least
    one Tully and at least one Delmont signature.

I’ll dig into some of these results in a separate blog post!

–titus

Appendix: repeating the podar analysis

This workflow will take about 1 minute to run, once the software is installed.

To repeat the analysis of 64 genomes above (see output), do the following.

# create a new conda environment w/python 3.7
conda create -y -c bioconda -p /tmp/podar-coclust 
    python=3.7.3 sourmash snakemake

# activate conda environment
conda activate /tmp/podar-coclust

# grab the cocluster script and podar workflow
git clone https://github.com/ctb/2017-sourmash-cluster/
cd 2017-sourmash-cluster/podar-coclust

# clean out the existing files & run!
snakemake clean
snakemake -j 4 -p all

This last step will download the necessary files, compute the signatures, and run cocluster.py.

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kitchen reno part 1

Sourced from: http://renovateanddecorate.blogspot.com/2009/02/kitchen-reno-part-1.html


What I’m looking at right now. You should see the other side of the living room!

Am completely knackered, so not going to bore with all the details just yet, but let me update you in numbers and pictures…
Number of days without a kitchen: 8
Number of sandwiches eaten: 42
Number of arms incredibly sore from sanding and painting three times in one day: 2 (they would be mine)
Number of hiccups so far: 6
Most number of trips to the hardware store in one day: 6
Number of cabinets in place: 5
Number of cabinets to still be put into place: 10
Number of taps working: 0
Number of appliances working: 0
Number of holes in the wrong place the electician cut into the wall that was already sanded and painted? 2
Number of flies killed because the doors were open all day every day: 723. Wait. 724
Number of times we’ve fallen onto our butts because the floor is so damn slippery from all the swept up sawdust? Me: 2; Steve: 1; Z: 4
Number of days before my dad can come back and finish putting the kitchen in: 12 🙁
Number of hours before we can get water and power on in the kitchen: oh god please let it be no more than 15!


Day 1: Looking better already!


The mouse’s house (left) and grass growing inside the wall!!


Several floorboards had to be replaced. We nearly had this gaping hole overnight, but luckily the new floor was put in on time.


Day 2: Electrical and plumbing work


Day 5: new walls in and plastered and lights installed


Day 6: dad and his little helper putting together the cabinets. Funnily enough, that plastic hammer worked: teh nails actually went in!


Day 7: Pantry done. The other cabinets on that wall are not flush with the wall yet. Dad needs to come back and put the benchtop on. Am hoping the electrician can connect the oven and cooktop tomorrow. I’m tired of sandwiches and takeaway!


My temporary benchtop!! These are the offcuts from the other side’s bench and the cut out from the sink hole!

And just because I don’t have enough things in my life to keep me busy (!) I signed up to Twitter last week and actually spent longer than two minutes on it tonight working it out. I think I’ve got it. Here is where I’ll be sending all those little quirks, annoyances or snippets of news too minor or time-consuming to blog about. And much excitement is the fact I can SMS the updates and they’ll appear magically on my Twitter profile. How genius. Not sure how long I’ll follow this fad (am really good at losing interest in things – Facebook? I only get on to look at friends photos now!), but for now, you can follow me at twitter.com/belindagraham

Dreaming of our little one.

Sourced from: http://originateandrenovate.blogspot.com/2012/10/dreaming-of-our-little-one.html

Jennifer Fauset of Fauset Photography has put together an auction for her sister who has been trying for years to have a baby. She recently found out that IVF is her best option and to help a little with the enormous financial burden, Sew Obsessed has donated some items to auction away for a fraction of the retail price.   Here are pics of the goods. click over to their Facebook Page to start the bidding (bidding ends Oct. 8). 
Moda’s Lilly and Will Bundle and Cupcake pincushion 

Lot of: Mini Iron, straight pins, fabric circle cutter, fabric markers, measuring tape and Heather Bailey’s smarty girl book bag pattern.
I also donated a couple paper party crowns. Use them for a Bridal or Baby shower, or save it and use  year after year for Birthday dinners. (One size fits Baby  – Adult)   Ahh yes, and what’s more… The shipping is FREE!  

There are tons of vendors involved, so check it out. It’s  Great way to score some good deals and, of course,  help someone fulfill their dream of becoming a Mother.

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Kitchen Extension: Creating the Ultimate Kitchen Diner

Sourced from: https://www.homebuilding.co.uk/how-to-create-a-kitchen-diner/

Including a kitchen expansion or knocking through? If you are looking to create an open-plan, sociable space but can not decide what to do, read our guide
The article Kitchen Extension: Making the Best Kitchen Diner appeared first on Homebuilding & Renovating.

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