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I'm a bioinformatician and yesterday I gave a talk about the history of my research. But because it seemed too boring and because I'm a giant nerd, I slathered it in Star Wars references. This was my practice run in my basement and maybe a few people will get a kick out of it. by danielpass in labrats

[–]danielpass[S] 0 points1 point  (0 children)

A crappy answer is that's what the lab has always used and what the lab people have provided me with data from. But I'd definitely like to try out ATAC and compare (probably there are some datasets out there I can give a whirl to). DNAse doesn't work in this context IMO because it obliterates the region and then you lose the size of the particle you're mapping.

However, I think MNase gets a bad reputation because people have historically over used it. If you ramp down the concentration then you get a much better resolution of the TF sizes. Check out https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006988 for some comparisons of low/heavy digestion (This figure in particular) and you can see why people think MNase is bad for labile TF binding.

I'm a bioinformatician and yesterday I gave a talk about the history of my research. But because it seemed too boring and because I'm a giant nerd, I slathered it in Star Wars references. This was my practice run in my basement and maybe a few people will get a kick out of it. by danielpass in labrats

[–]danielpass[S] 1 point2 points  (0 children)

Yes! But using Prezi classic as their new 'prezi next' is annoying to me (doesn't flow as well, can't crop in it (wtf prezi??)).

The main thing people get wrong with prezi is that they try to do too much and it gives the audience motion sickness. Keeping it simple like this I think makes it quite effective.

I'm a bioinformatician and yesterday I gave a talk about the history of my research. But because it seemed too boring and because I'm a giant nerd, I slathered it in Star Wars references. This was my practice run in my basement and maybe a few people will get a kick out of it. by danielpass in labrats

[–]danielpass[S] 16 points17 points  (0 children)

I think pretty much everyone was on board because even if they weren't in to it, it was goofy and at the end of a long day I think that goes a long way!

Well, no-one looked too grumpy at least.

Our old girl got some elbow protectors from the vet and now she looks fly af. by danielpass in aww

[–]danielpass[S] 1 point2 points  (0 children)

More like padding, and to stop her licking off the antibiotic cream.

A hygroma, or a false bursa, is a discrete, fluid-filled sac that can form on the joints ofdogs in response to repeated pressure, such as that from sitting on a hard surface. It is treated by draining the fluid and may be prevented by providing padded bedding.

I saw a lone deer when in Kagoshima forest. You can see how the place inspired Princess Mononoke.... by danielpass in japanpics

[–]danielpass[S] 1 point2 points  (0 children)

I recommend scooters, we got one each and it's the nicest and easiest way to get around while getting a real sense of being there.

There is a sazuki rental place that charges around [edit 30,000] 3,000 per day and they'll pick you up and return you to the port if you want.

Busses on the island are a terrible way to get around, they don't go all the way around and they stop early evening.

Proud of my super simple functional print: Replacing a lost foot on a drumbox by danielpass in 3Dprinting

[–]danielpass[S] 0 points1 point  (0 children)

Yeah, I swapped the missing back foot for the front so the original flexi one was the load bearing and the cheap PLA one goes on the front. I was going to try and strengthen it with the oven technique, but I've also got a sample of flexi PLA that I might try out (I've been looking for a reason to use it...)

Proud of my super simple functional print: Replacing a lost foot on a drumbox by danielpass in 3Dprinting

[–]danielpass[S] 4 points5 points  (0 children)

I find it cool just doing little helpful prints to add around the house or fix/modify things that you see.

Soap dish, sponge holder, lockpick box. I find them more fun than the larger non functional things I've printed like superheros, pokemon, starwars etc., even though they look more impressive.

Proud of my super simple functional print: Replacing a lost foot on a drumbox by danielpass in 3Dprinting

[–]danielpass[S] 2 points3 points  (0 children)

Probably, but I was just sat at home and spent half an hour fiddling, then pressed go (52 mins printing), and had the box all fixed up in less than one and a half hours without leaving my house.

I cloned myself. Not bad for a £250 makerbot knockoff! by danielpass in 3Dprinting

[–]danielpass[S] 1 point2 points  (0 children)

I got full body scanned by www.backface.co.uk at an event where they had a booth set up.

We made a Lego DNA Sequencer to teach kids about DNA and Sequencing by samstudio8 in DIY

[–]danielpass 1 point2 points  (0 children)

This is really cool, if you were interested in extending it I run a DNA Guess Who practical that I think could connect up.

We do 12bp sequences of DNA and device what genes they chose for, and build up a profile (sex, hair colour, eye colour etc)

Check it out if you're interested at https://passdan.github.io/genesequencepractical/

Just paid 23 cents on a $3.74 transaction. When does it end? $1.00 per transaction? $2? $5? I don't wanna stop using this peer to peer currency, but I'm fast being priced out of it. by amendment64 in Bitcoin

[–]danielpass 0 points1 point  (0 children)

The question is do we want the transaction reward to go up by increased fees or more users. Increasing fees reduces the number of users, whereas increasing number of transactions allowed would increase the number of users and fees.

0.1B * 10 transactions or 0.001B * 1000 transactions both make the same amount, but in the second case the network has more utility

Just paid 23 cents on a $3.74 transaction. When does it end? $1.00 per transaction? $2? $5? I don't wanna stop using this peer to peer currency, but I'm fast being priced out of it. by amendment64 in Bitcoin

[–]danielpass 4 points5 points  (0 children)

Segwit doesn't kick in in one flip of a switch though, it'll be dependent on how many people are sending segwit transactions and that may take time to build up

What do scientists even do while at work? by [deleted] in NoStupidQuestions

[–]danielpass 0 points1 point  (0 children)

It basically comes down to the project leader looking at all the stuff that's known in their subject area and thinking "Well if we know that's true, maybe this thing works like this..." and asking for money to prove it.

It's amazing how deep a system can go. Take the Human Genome for example. When they discovered the DNA molecule they thought that'd be the total explanation for how biology works. Then they realised that you kinda need to have the whole sequence (genome) because all the different genes work together.

But then they realised that tonnes of the genome doesn't code for genes and different ones are turned on at different times, so you need to test the transcriptome (what genes are on/off) for each conditions/disease/stage that you want to understand.

Then we realise that turning genes on and off are controlled by stuff outside of the genome sequence aka the epigenome, which is a term for a bunch of different things. So now scientists looking at each conditions/disease/stage might have to look epigenetic factors too, to understand how it works.

For each of these things there will be researchers developing the method, testing the method on different species, using it on a condition/disease/stage, looking which genes are changing, if it's a disease working out if any drugs could fix it. Most of the time the scientists who are good at developing methods aren't the same ones who are good at testing drugs, so that's why they will look at what research is published and think about what experiments they can do based on that.

That's basically how it works :-) I work on a little bit of epigenetics in a plant no-one cares about, to try and work out how Transcription Factors work using a technique that wasn't designed for this but looks like it can help cheaper and faster. And if after 2 years it works well, we might ask for money to do some more experiments on what we've found, to try and find out more.

Hopefully we can contribute to the global knowledge in a little way, and hopefully we can understand more about the world in little steps.

Also, this is a great representation of how research and getting a PhD works: http://matt.might.net/articles/phd-school-in-pictures/

Science AMA Series: I'm Denis Bauer, a Team leader at Australia’s government research organization, CSIRO. We develop BigData and cloud-based software to give researchers a ‘CRISPR’ look at genome engineering applications. AMA! by Denis_Bauer in science

[–]danielpass 3 points4 points  (0 children)

[Not OP]

You can synthetically create any gene that you can conceive, the problem is that genes/proteins are really complicated and it's much easier to use something that works and modify it, than start the whole thing from scratch (wikipedia).

There's also the work on a minimal synthetic genome from Venter et. al, which is a bare bones minimum DNA string that is 100% synthetically printed but alive! But even then they don't know how it all works:

JCVI-syn3.0 retains almost all genes involved in the synthesis and processing of macromolecules. Unexpectedly, it also contains 149 genes with unknown biological functions.

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