System76 Transmission Log

3, 2, 1, 0.

Welcome aboard the System

76 transmission Log.

Our broadcast is about to begin.

This is the latest on System 76
computers, manufacturing, and pop OS.

Now for your in-orbit crew.

Hello, hello, everyone.

Welcome back to the System
76 transmission Log.

I'm Alex, our resident, Normy.

And I'm Emma, wondering why we're doing
the intro when it was supposed

to be the banter section, but whatever.

I mean, intro always comes first, right?

No.
I feel like we always do banter first.

Well, in the end, the intro comes first.

All right.

Just as a as a movie magic
secret, we're actually doing this last.

We're not.
We're doing this first.

Oh my God.
Just trying to confuse me.

I did want to point out
I'm wearing pink today.

I came prepared for our hosting here.

What's the rest of that shirt?

The rest of the shirt is…

It's Slither's Snakeman.

It's a snake disguised as a human.

Is that a cartoon?

No, it's just a shirt I found
on the internet from a cartoonist.

But I was curious about if
we could get into some Emma lore here.

When was the first moment you were like,
Oh, pink, that's my jam now?

Well, when I really embraced it,
I was probably 15 or 16.

I mean, I loved it when
I was a kid, of course.

I was really into Barbie, and I just
think pink was the best world to live in.

But yeah, when I was 18 with my first
apartment, everything was pink.

There was a pink pillow floor area.

There was a bright red couch
and a pink table, and everything

on the walls was pink.
The dishes were pink.

Ever since then, I was just
collecting pink stuff.

And slowly, pink clothes
have been making a comeback.

It was really hard to find a pink shirt
or a pink dress for a really long time,

but now I can pretty much
find that stuff anywhere.

Do you have a favorite shade of pink?

I like a berry type of pink.

It's not quite hot pink.
It's not dark.

It's in the middle.

So the inside of a strawberry.

No.

That's pretty light pink, I think.

The color of my shoes is a very good pink.

Okay, that's like a hot pink, I would say.

Well, I like it a little more
subtle, but can't choose them all.

True.

All right.

I have another topic to
discuss really quick.

What's that?
The balloon game.

Oh, yeah.

I wasn't there for it,
but I hear it's pretty popping.

I just realized that you
weren't there for it.

How are you going to talk about it?
Well, I mean, I know.

First of all, what is the balloon game?

Oh, I'm glad you asked.

So everyone at the company
in the factory at the beginning

of the day gets a balloon with helium.

And at the end of the day, whoever is left
with a balloon gets a prize.

But throughout the day, people
can hide their balloon, pop people's

balloons or steal people's balloons.

We had some really competitive people,
had some tricky people hiding them.

I thought Young Chin did a great job
hiding his behind the curtains

in the window because you could totally
see it outside, but you couldn't see it

on the inside, and nobody found it.

He was one of the people left standing.

Then Josh, I went and had a conversation
with him while he was in the shipping

container, asking him if he had seen any
stray balloons It turns out his balloon

was in the top corner of the shipping
container while I was talking to him.

And I ended the contest and I was like,
Congratulations, everybody.

Then he comes in at the last second.

He's like, I still have mine.

Then I asked him to expose
his spot, and it was right there.

And I couldn't believe it.

So I am not very good at the game, but I
thought those two spots were very clever.

Then we had Grace,
who got all the balloons.

She was taking people's balloons
and popping them left and right.

She came in my office at the end
of the day and pulled out her balloon

from under her sleeve.

She was very proud.

She got the most.

Youngchin and Josh were probably
the most clever about it and sneaky,

but all around, it was very fun.

How did she fit an unpopped
balloon up her sleeve?

Very carefully.

She was pretty baggy clothes,
but her balloon had been losing air

throughout the day, too.

So it was a little smaller
than the other balloons.

But yeah, I think she
called it George or something.

She named it.

Well, we're glad George survived.

What would you say was the best technique
that was used for popping these balloons?

I didn't witness any popping.

I only heard it.

But every time you heard a pop, you heard
a giggle, too, which was really funny.

No matter where you were in the factory,
you could hear somebody

laughing about it.

So the balloons weren't
just filled with helium.

They were filled with laughing gas.

They were filled with laughing gas, yes.

Or possessed by goats.

Ghosts, not goats.

I'm pretty sure I- Possessed by goats.

I said it again.
What?

We're leaving that in.

Yeah, that was really fun.
I think we got to do it again, though.

But I have some different ideas.

The person with the most at the end
should probably win an extra prize.

They have to throw a dart
at a wall of balloons that

each contain a prize in them.

I like that.

Yes.
I like that a lot.

Okay, well, now we know which games
to implement in the future, but maybe

we should get into the news.

Yeah, let's get into the
System 76 lore from the past month.

Okay.

Well, it's the opposite of last month
because we had a ton of news.

Went from lots of releases to gearing up
for some releases down the line.

Yeah.

So this month, we have the tiniest bit
of news, and it's about the smallest bit

of hardware, the little mirror cat.

It's the little baby with big biceps.

It's our compact mini little desktop
in the NUC form factor fits right

on your desk or mounted on
the back of your monitor.

And it is rocking
some Intel Core Ultra CPUs with up to 4.

8 gigahertz processors.

And and a whopping up to 96 gigabytes

of RAM and up to 16 terabytes storage.

So much in such a little
package, still rocking Intel.

But also we added
I can't read your lips there.

I thought you would just know.

I thought you were going
to be like, open firmware.

Oh, yeah.

Look, I'm one of the first stages
in the product release.

Once the product is ready to go,
I absorb all the information about it.

I output it into something for
the website, and then my mind is cleared

of it because I'm on to the next thing.

What you're saying is you forgot that
Meer cat has open from rent.

It's not I forgot so much as I've
stopped thinking about the Meer cat

for the past three weeks.

Okay.

It's been a while for being able
to spout off the highlights, which

is what we're here for on this podcast.

So yes, Meer cat now has openFirmware.

It's our core boot-based
System76 openFirmware.

Part of it is speeding up boot
times, minimizes the Firmware,

so it's more secure, less
vulnerability, all that good stuff.

Yep.

Do you think if you tied a balloon
around a meer cat, it would float?

That's a great question.
We should try that.

Well, I'm pretty sure
one balloon won't do the trick,

but we should see how many balloons
it will take to float a mirror cat?

My guess is three.

Helium is pretty strong in a balloon.
Okay.

They floated a house with it.

Yeah, but he used like
a thousand balloons.

He had a lot of balloons.

It was a big house, though.

You do like a townhouse.

It's half the balloons.
Yeah.

Meer cat, since it's just a little mirror
cat, probably three or four, yeah.

With no mirror potential.

Well, I'm going to test it and we'll
come back to you next month

on the podcast and tell you how it went.
Okay.

Yeah, we got to test it for science.

Yeah, I need to know.

All right.

Well, that's our hardware news.

We have some community news, right?
We do.

We are going to be at a couple
of conferences in March

and also April and May.

To start off in March, we'll be at
SCALE in Pasadena, California,

which is March sixth through 10th.

We'll be hanging out at our booth
along with our friends at Ampere,

who will be next to us.

We'll have two Thelio ASTRO demos
at the Ampere booth showing us

all the cores, all the power,
all the Blender renders you can think of.

And a driving simulator as well, I think.

Yeah, Tier 4's driving simulation
that they had at CES will be doing

the same simulation at our booth
at scale at the Ampere booth.

Then also on the other side of the booth,
we'll have a cosmic section where you can

design your own universe and then
see your cosmic theme in action.

Then also we'll be giving away
two launch keyboards and a lot of swag.

You can get your hands on some hardware
and talk to some of your fellow nerds.

Yeah, Garret, who's on our QA team, he
worked on a really cool universe designer

using the cosmic theming system, so
we're really excited to share that off.

Then also in March, we're going
to be at the PNY my booth at GTC

in San Jose, March 17 through the 21st.

Pny will be showcasing the Thaleomega
and just showing off what

a high-end workstation optimized for
multi-GPU compute and heavy graphics

and peripherals would be performing.

Yeah, subject to change potentially.

But what we've been told is
there will be a demo showing off

some new stuff, and it'll be using
a production workflow, a combination

of Blender, Unreal Engine, and OBS.

So all tools available on Linux,
but just showing off the power

of our hardware is combined.
Cool.

That one's going to be a cool demo.
Yeah.

And then let's see, April,
we have Linux Fest Northwest,

which is my favorite one of the year.

That one's in Bellingham,
Washington, the end of April.

And we'll be doing a talk on how far
Cosmic has come and also have a booth.

And then we'll be hosting
the Saturday barbecue.

I could use some barbecue right about now.

It's actually not really barbecue.

It's just like whatever food
is a good idea that day.

But maybe be just hot dogs like last year.

If you bring some barbecue
sauce, it's barbecue.

Okay, that's fair.

Join us with your barbecue sauce,
B-Y-O-B-S.

Bring your own BS.

To the Linux Fest Northwest Barbecue.

Hope to see you guys there.

All right, what's happening
in the cosmic universe?

Cosmic universe.
Let's see.

There is potential for delaying
a week to get some more features

into the Alpha 6 release.

So I could say some stuff
that's potentially wrong.

An easier way to go about this
is just head to the blog

for actual up to date news blog.
System76.

Com.

But what I know and I've heard inklings of
is we now have desktop icons.

You right click the desktop,
you go to desktop view settings,

and that'll bring up some toggles
for showing desktop icons, showing

the trash icons, adjusting the size
and spacing, things of that nature.

There's also some more polish updates
to the way workspaces functions.

Multimonitor setups, you can now
drag and drop windows into the other

workspace overview on another display.

You can also drag and drop
minimized windows.

When you drag a window out of a stack
to another workspace, it'll now only move

that window like you'd expect I think
previously it would move the whole stack.

There's more updates along
those lines just to make workspaces

feel polished and intuitive.

There's file menu features
built out for the cosmic media player

and potential for the initial setup

applet, OS update settings, and

a desktop zoom feature for accessibility.

Those things may or may
not have been released.

Check the blog for accurate information,
but if not released in Alpha 6,

probably by Alpha 7.

So all that said,
exciting things for Cosmic.

I very much enjoy using it.

I think I'm still on
2204 LTS, I've learned.

But even being there, I mean,
it's been working great for my workflow.

I don't really get into the
nitty-gritty and more surface level,

but it's been going well.

I have seen that the compositor on 2204

LTS will no longer be getting updates, so

make sure you're upgraded to 2404.

I think the ISOs are 2404,
so you should be all right.

Thank you for that piece of advice.
Yeah.

All right.

Well, we have a very
interesting interview today.

Yeah, we have R.
J.

Noling here to talk about
his work in genomic research.

It's been really bugging me all week
to get this interview out there.

Here we go.

My name is R.
J.

Noling.

I'm an Associate Professor
of Computer Science

at the Milwaukee School of Engineering.

I'm also the program director
for our master's in machine learning.

My research is focused
on what I call genomic data science.

I work with biologists
to process the raw sequencing data

into a usable form and then
analyze it using data science techniques.

In many cases, the data
we're collecting during an experiment,

there's a particular research question
in mind, and often I'm helping them

determine what evidence the data might
provide to help answer that question.

Earlier, you mentioned you
looked at my website, you saw insects.

Yeah, I primarily work
with insect genomes.

A lot of my collaborators
work on mosquitoes such as Anopheles

gambiae, that vector malaria,
as well as Edo gypti, which is

a mosquito vector is Dengue fever.

So these are medically important
organisms to public health.

So it's mostly for public health
that you're doing all of this,

or are there other reasons?

So I'm doing it mostly
from a pure biology aspect.

I want to better understand
the biological systems.

We hope that by studying these insects,
we'll also learn things that

are transferable to other organisms.

But it so happens that
the biologist I work with

may have more specific questions.

For example, one of my collaborators
is trying to better understand why

some of the Anopheles mosquitoes,
their immune system can fight off

the malaria parasite and some can't.

Even Even if they're from the same
family, literally the same mom

and dad, there's differences.

She's trying to understand
a genetic basis of that.

On my end, most of the work
I'm doing isn't necessarily

specific to the mosquito.

The data I have is specific
to the mosquito, but the techniques

I'm using are general.

In the case of malaria, that could lead to
breeding mosquitoes to eventually...

Yeah.

If there's a gene associated to eliminate
the vulnerability to malaria.

Yeah, you're actually right.

There's been some experiments, what
they call gene drive, to try to basically

produce sterile males and such.

Other groups have been developing
techniques to like, okay, can we release

some genetically modified mosquitoes
into a population, and hopefully, they

will basically take over that population.

And now, most the population will no
longer do a certain thing or something.

So in this particular case, yeah, if
we We can find what makes it so that some

of the mosquitoes, their immune system,
can't destroy the malaria parasite.

We can then use gene drive techniques
to basically ensure that the mosquitoes

can fight off the malaria parasite
so that they don't transmit it to humans.

That's very interesting.
Yeah.

How did you get into this?

Actually, I was exposed to bioinformatics
through a summer internship

arranged by a family member.

When I was in high school, I interned
at the University of Connecticut Health

Center, making a simple website
with some data from a paper,

and I really fell in love with it.

I loved that I could apply
my computing skills to understanding

something in the real world.

I like the nature of the work itself.

Like data processing is interesting to me.

I made it I focused in college,
and then I went and got a PhD.

During college, while many
of my colleagues were doing

internships with companies,
I was doing research with professors.

I did spend a couple of years
in industry after my PhD,

so I was at Red Hat for two years.

And then an online advertising company
called Adroll for two years.

I started my faculty position
at the Milwaukee School

of Engineering in fall 2018.

When along that journey
did you discover Linux, was it

at Red Hat or was it before then?

It involved Red Hat, but
it was not while I was at Red Hat.

It's actually middle school.

Someone gave me a box
copy of Red Hat Linux 6.

2.

I want to clarify, I did not
omit the word enterprise.

This was before it became
Red Hat enterprise Linux.

This was old Red Hat.

And so if I remember correctly,
the version I had ran

Nome desktop version one.
Oh, wow.

And so then I started using Slackware
in high school, and I later

switched to Debian.

And so now all my research machines,
I use Debian for all my workstations

and servers, basically.

And then my laptop and desktop,
I use Apple products.

With regards to your workflow, what
software tools are you using, mainly?

So when we get the raw data,
we clean it with something

like trim PEEK, and then we align it
to genomes using something like BWA.

We'll use a software package
called GATK to try to identify where

individual samples differ from a genome.

We might also use, depending on if it's
a different workflow, a tool called MAX

for what's called peak calling.

There's certain experiments that basically
highlight certain parts of the genome.

It's like this part of the genome
has activity of interest.

Then once we get all have produced
that output, then we can switch to

more traditional data science tools
like using pandas in Jupiter notebooks

and scikit learn and things like that.

I see.

For your desktop, I know
you have a Thelioastra.

How has working with Thelioastra
affected your workflow and your project?

It's massively increased my throughput.

The data sets I work
with have a lot of samples.

The biologist will seek the DNA
from a thousand mosquitoes.

Well, it's hard to get much peralysm
for an individual sample, but the samples

can be processed independently.

The ability to have 120 cores instead
of 24 cores means I can process

a lot more samples at once.

It also tends to be very memory-intensive.

So the fact that I can have 512 gig
of ECC RAM is also an important component

of scaling up that pipeline.

And these pipelines
often take weeks to run.

So it can cut it down from a month
to a week or a few days.

Wow.
It's a big improvement.

Yeah.

What led to your decision to go with
System 76 and the Thaleo ASTRA?

Honestly, it was priced So I've
been wanting an Ampere ultra system

for a while because I had a workstation
with an AMD Threadripper processor

and a 24 cores and 120 gigs
around that I got five or six years ago.

And that's been my main research machine.

It was time for an upgrade.

But whenever I would look at other systems
with AMD Threadripper processors,

I just couldn't get more cores
or much more memory within my budget.

The Ampere ultra platform offers a really
nice price point for getting a lot of

cores and a lot of RAM at the same time.

And I need both to do my work.

And System76 was the only company
I could find that really was supporting

a workstation option for Impair.

And I can say also I'm glad
I went with System 76 because support

has been super helpful.
I haven't run into any major problems.

It's just my ignorance.

I didn't realize that because
it's running a server motherboard,

that it takes a really long time
to post before the boot screen shows.

I thought something was wrong with it
when I got it, when it's like, why isn't

this showing anything after five minutes?

And it turns out I just
needed to wait longer.

But the support was super
helpful, and I really appreciate

my interactions with the company.

I I think that has potentially turned me
into a repeat buyer in the future.

That's awesome.

Yeah, support has been
a long time pride point for us, for sure.

Do you have advice for people who
want to get into genomic data science?

Yes.

So unfortunately, most of the people
I know doing this are at universities.

There are some companies in industry like
Illumina, which provides some

of the sequencing technology,
also hires a number of bioinformaticians

and data scientists and software
engineers, but still primarily most of the

people in this field are in universities.

So you pretty much need a PhD.

That said, I have worked with people
in PhDs in a wide range of fields,

from computer science to biology
to statistics, physics, chemistry,

applied math, whatever, that
we all work on these projects together.

And so I think one thing
I had to figure out is that

you have to pick a home field.

So in my particular case, I'm very
comfortable teaching computer science

and data science courses.

So getting a PhD in computer science was
the right fit for me, even if my research

itself is very interdisciplinary.

And so the trick is to find
a faculty member who's working

in bioinformatics who can advise students
in a PhD program that you would

be successful in, basically.

And for college students,
you need to start talking to professors

and seeing if you can get opportunities
to do research with them in an undergrad.

That'll tell you if you like the work,
and that's how you build up your resume

to increase your chances
of getting accepted into a PhD program.

That's awesome advice.
Thank you.

Yeah.

Looking forward to the future
with machine learning and genomic data

science, how can you combine those
in the future to make innovations?

Yeah, some of the work that
I find most interesting recently.

One thing to know is our genome
doesn't just have genes.

It has other non-coding elements
that play an important role.

So one example of these
are called enhanceers.

Enhancers help determine
how many copies of the gene are produced.

And we're actually just
learning that a lot of diseases

are caused not by changes in the gene
themselves, but in the enhanceers.

So your body just may not
produce as many copies of the gene.

So one thing, though,
is that the enhanceers are hard

to find computationally.

Generally, people use experimental
techniques, but there's been some

really interesting work lately using
deep learning to identify enhanceers

in an accurate mannerism.

So because it's finally pretty
accurate, we could actually go through

all the publicly available genomes
of the NCBI database provided by the NIH

and find the enhanceers for all of them.

And then that would allow us
to do cross-species comparisons.

Another thing is that enhanceers
are generally not located near

the genes they interact with.

They're pretty far apart.

So there's been some work
to try to computationally determine

which enhanceers act on which genes,
which will help us better understand

what genes they impact and thus
what potential disease is.

The other thing is trying
to understand how genetic variation

within the enhanceers has an impact.

Sometimes the DNA changes
and it does nothing.

Sometimes it increases the number
of copies of a DNA, sometimes it

decreases it, but it's hard to predict.

So all of these things,
if we can build accurate machine learning

models to do this,
we can vastly speed up research and reduce

costs and study organisms that we can't
study right now because it may be

infeasible to do the actual experimental
lab work for whatever reason.

Is that what you're most excited
about for the future your field?

I get really excited when I can understand
the mechanisms of the biology.

In some ways, I'm a biologist
who uses a computer as my instrument.

I'm excited for advancements
that will allow us to better

understand how the biology works.

That's my main motivation.

How can people get in touch
with you if they want to

learn more or connect with you?

They can check out my website, rnowling.
Github.

Io, or they can send me
an email email at nowlind@msoe.

Edu.
Awesome.

Is there anything else you'd
like to add or share with the audience?

Just that I've really enjoyed my
experience with the Thelio Aster so far.

It's been a great machine
and worth every dollar, and it really

does offer a lot for the price.
Highly recommend it.

We're so happy to hear that.
Thank you so much.

We really appreciate you
coming on to share your experience

and your story and your work.

I'm happy to be here.

All right.

Well, that's our...

Well, no, it's not our show
because we have a game.

We have a game.
Yes.

What's our game?
Okay.

In the spirit of the balloon game,
I got here first.

As you know, I always get here first.

I hid a balloon in this studio,
and you have to find it.

But you only have 30 seconds.

Thirty seconds?

Am I able to from where I'm sitting
or do I have to get up?

There are no hints.

I don't know why you're
asking questions about hints.

I'm asking because I have headphones on.

Do I have to take them off
and get up and walk around?

Yes.
Okay.

It's going to take me 10 seconds
to get out of this chair.

Hold on.
I got to start the Timer.

Can you start it once
I'm out of the chair?

Yes.

Okay, ready?

Stop looking.
Okay, go.

Not under the piano.

Looking under the piano.
Not there.

Not behind here.

Is it in your jacket?

No.

Five, four, three, two, one.
I found it.

No, you didn't.

No, I didn't.

All right.

Finally, I stumped you on a game.

I feel like every single podcast you win.

So I really needed a win here.
What's your prize?

Pride.

I'll show you where it's at.

I have to get out of the chair.

You only have 20 seconds to find it.

I even looked there.
I know.

That's why I was so lucky.

All right.

It was between two large foam boards.

Like sound.

Sound suppressant boards.
Sound blockers.

But table-sized.

All right.
Well, I'm not saying that.

I'd say good job, but you
didn't do good that time.

No, but I want a balloon.

All right.

Well, thanks for joining us today, guys.

We'll see you next month.

On the System 76 transmission log.

Over and out.

Three, two, one.

This has been the System

76 transmission log.

For more inspiration, check out the
website and follow us on social media.

On your descent back to Earth,
please keep your hands and feet

inside the transport beam at all times.

Captain, sign off in transmission.