May 2, 2025 • 53 mins
In this episode, Peter O'Toole welcomes Sofie Van Gassen, a Postdoctoral Researcher from VIB-UGent. Sofie explains how a computer scientist can end up working in flow cytometry and sets out her vision for the future of data science in flow. She also sets out her twin passions for developing algorithms and pipelines for data analysis—and gardening.
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Intro/outro (00:00):
Welcome to Flowstars, candid conversations
between doctor Peter O'Toole andthe big hitters of flow
cytometry, brought to you byBeckman Coulter at Bite Size
Bio.
Peter O'toole (00:10):
Welcome to Flowstars. And today, I'm joined
by Sophie Van Gassen from VIB.She shares her motivations for
getting involved with FlowCytometry. And someone, one of
the fastest rising stars in FlowCytometry, shares her vision for
the future of data science andthe quality she thinks a good
principal investigator shouldhave. All this coming up in
(00:33):
Flowstars.
Hi. Welcome to this specialedition of Flowstars. I'm Peter
O'Toole from the University ofYork, and today, I'm joined by
Sofie Van Gasson from the VIB inGhent. Sophie, how are you?
Sofie Van Gassen (00:47):
Hi. I'm doing well. Thank you so much for
having me today.
Peter O'toole (00:51):
That's okay. I don't think we've ever met in
person. And yet I know aboutyour work, and it's work that I
don't think I could everreplicate or duplicate. So,
actually, do wanna just veryquickly start for for the
listener or the viewer? What isit? Where is your area of
expertise?
Sofie Van Gassen (01:10):
So I I have a background in computer science,
actually. So not not inimmunology, not in not in
anything biology related. And soI've been working in
bioinformatics. Actually, thetopic of my PhD was machine
learning for flow cytometry. Sothen when I was, like,
considering doing a PhD, I gotintroduced to this to this
technology. And since then, I'vebeen working on flow cytometry
(01:34):
data, and I've been enjoying ita lot. So algorithm development,
developing pipelines forexisting datasets, things like
that. Yeah.
Peter O'toole (01:44):
Did you not say just before we started recording
that you're not good atremembering numbers?
Sofie Van Gassen (01:49):
Yeah. Yeah. Yeah. So that's why the computer
remembers them all for me.
Peter O'toole (01:52):
Right? Okay. Fair enough. Like I say, for someone
who plays with lots of numbers,that's kind of an interesting
problem to have with it. Sookay. So you did a PhD, and you
would give you no. You must yourPhD must have started with flow
cytometry, surely.
Sofie Van Gassen (02:11):
Yeah. Yeah. So the the topic of it was really
flow cytometry. So, basically,my my professor, just noticed
that people were doing all thismanual analysis of this data.
People he was collaborating withand was thinking, like, there
seems to be room in here for forexploring some some algorithms,
(02:31):
seeing whether we can help thesepeople with automating some of
these task, things like that.And so he proposed this topic,
and then we were immediatelycollaborating with with the
people actually measuring thedata. I think that's been a huge
benefit for me that it was notjust, like, in a computer
science group, a theoreticalexercise, like, oh, let's look
(02:51):
at these data points and try tofind some clusters in there, but
that we were actively talking tothe people who were generating
the data and which questions andproblems they were facing. And
so that's that's been the wholefocus of my PhD and actually of
my work still. I I think I'm oneof those few people who kind of
keep doing what they're doingafter their PhD. Like, I'm I'm
(03:12):
now already a number of years aa postdoc, but I'm still doing
kind of the same things as I didduring my PhD. And, of course,
now a bit more guidance than theat the start of my PhD, of
course, when it was mainly theprogramming. But, yeah, topic
wise, it's it's still veryclosely related.
Peter O'toole (03:33):
It's it's an interesting area to have chosen
as a PhD student to to know theimportance, relevance, to be
inspired to do flow cytometry.It's computer science. The world
is your oyster. But why I I'vegot a lot why did you think flow
cytometry was for you?
Sofie Van Gassen (03:52):
Actually, I was very hesitant to do a PhD,
and my professor had to kind ofconvince me because I wanted to
do something applied. I wantedto do something that was used,
and I was a bit afraid if you doa PhD in computer science,
you're just, like, reasoningabout algorithms, and there's
lots of value in that, but itwould not be for me if it was
just a theoretical exercise. Butthen he convinced me, like,
(04:15):
these these people that I'mcollaborating with who are
facing these specific issues.And if you work on this, you
could actively be involved inthat and help them. And so
that's that's applied aspect ofit, even though it's still done
applied and fundamentalresearch, of course, but the
applied aspect of the thealgorithm side of things is what
really convinced me. Heconvinced me, like, if you work
(04:37):
in this, people will use yourtools. And, actually, that's
that's turned out to be the caseby now, so that that's really
cool. And that's also reallywhere I get my my motivation and
my things to do this. Yeah.Absolutely.
Peter O'toole (04:50):
So I can see just by your smile, your eyes, your
enthusiasm that you you'reloving the work, the
environment. And, you know,quite often so I I've employed
lots of data scientists overtime, and I quite often hear,
oh, yes. But you'll never get agood data scientist because they
can earn lots more money workingfor Google or the banks or
(05:12):
someone else. I always disagree.But go on. Why have you chosen
this instead of going earninglots of money for in other
areas?
Sofie Van Gassen (05:22):
I think the combination of the fact that
it's it's just reallyinteresting and really cool to
do, like, that once you're inthere, you you want to keep
working on it. I think the thefact that you know that you're
working in this fundamentalresearch, but also health
related, that it can have animpact on society. And, of
(05:42):
course, like, it will not be myalgorithm in itself, which
immediately impacts the wholesociety, but, like, you're one
small radar in this wholeframework, but you're aiming
towards that. So the the factthat it's life science related,
even though I don't have, like,background in that, I didn't
study any biology, immunology,but the fact that you know that
you can contribute to that fieldalso gives me a lot of
(06:05):
motivation. That's in the thethe the the ultimate dream is,
of course, that you helppatients, right, that you make
people's life better and andgive them better opportunities
for their health. And I'm veryfar away from that. I'm I'm I'm
not a medical doctor. I'm notsomeone with a biological
knowledge, but I know I cancontribute to that. And that's
(06:28):
that also would motivate me waymere more than, for example,
optimizing advertisements orsomething like that, which
indeed you could also do fromthe computer science point of
view.
Peter O'toole (06:40):
I'll I'll pick it up even more because actually,
see, so many of the medicaldiagnosis are through flow
cytometry itself that actuallyyour analysis, the the new
analyses that you're enabling onflow cytometry could have a
profound impact. And so you say,yes, you're not a doctor in a
clinic in a clinic a clinicaldoctor sense, but they are
(07:04):
utterly dependent. All they dois take a sample and then tell
the patient what you've enabledthem to say. So I would say
that, absolutely, you're aclinical doctor. You're the
Sofie Van Gassen (07:13):
scientist. Reasoning in between somewhere
as well. Right? No. No. But thatthat's exactly what I mean.
Right? You know that that yourwork has an impact and that it
can be used by these people whohave the tools to then further
interpret these things and andbring them to the patients, and
that's that's really cool.
Peter O'toole (07:30):
Actually, another question, and it strikes me. So
throughout your PhD, now yourpostdoc at VIB, how many
different groups are you gettingdata from?
Sofie Van Gassen (07:39):
Oh, that's a that's an interesting question.
I don't know if I've countcounted that. So at the
beginning, we were mainlycollaborating with this the
like, this one group that thatmy professor was already
collaborating with. But thisquick very quickly actually
extended through collaborations,through meeting people who had
questions. And I think itdepends a bit also on on how you
(08:02):
define it. So I think there'sthere's a number of groups that
we're actively collaboratingwith. I would say that's, oh,
yeah, a reasonable number,three, four, five, six,
something like that. But thenyou also have many people
reaching out with, like, a asimilar question. Right? So I
have, like, oh, I'm trying touse your tool, but we're
(08:23):
encountering this or that. Canyou give some advice? And that's
actually, of course it it takesa smaller amount. Like, it's not
a long term commitment, but thatway we we get asked about lots
of data from lots of differentgroups. And then once in a
value, we're working also onsome public data that also comes
with its challenges. I'm a verystrong advocate for making data
(08:47):
public. I think this will reallyhelp the field. But just finding
public data online where youdon't know much about it and
don't have insights about themetadata about what was going on
while measuring things can alsobe an extra challenge. So I
appreciate it a lot if thepeople with the biological
question are also involved inthe project rather than just
(09:07):
working on data that is outthere.
Peter O'toole (09:10):
I think what's quite quite interesting is
you're doing a postdoc, but it'sit's not so dissimilar to a core
facility in that your the numberof people you're helping and
advising. And, you know, at thetop end of a core facility,
you're helping designexperiments. You're helping
analyze the data, helping toreally make their science fit
around the technology. And hereyou are the other side of this
(09:31):
downstream because then they getall this analysis. And and
actually, from my side, I'mutterly useless when it comes to
the coding side. And there youare to pick that up, which is a
high end problems.
Sofie Van Gassen (09:45):
Actually, that's that's an interesting
question because that's kind ofwhere I see my future going. I'm
nothing nothing's on paper yet,but you can't keep doing
postdocs forever. Mhmm. And I'mI don't have the ambition to go
for a professor position at thispoint. Never say never, but I
don't really expect thathappening. So I think, right
(10:08):
now, I'm mainly then givingguidance in the algorithm
development and so on. I noticedthat we also get lots of
questions of users who wantguidance in how to use these
tools. And I'm actually talkingto our flow core facility
whether there could be optionsthere to give more support also
from the core facility and thenhave a a future position there,
(10:30):
hopefully, if everything worksout. So I think it's the
Peter O'toole (10:34):
feedback through there, Kurt, that's running the
core facility VIB. Exactly. I II've I've got two lines of
thought now. I don't know whichway to take this in first.
Firstly, I'd say, actually, notgoing down the academic route.
So something we've done at Yorkis set up a data science hub.
And, really, I I would arguethat they're applied academics.
(10:56):
And I think this is reallyimportant because when it comes
to helping with the the datascience side, there's always
talk about bringing new datascience lecturers in to new
group leaders in data science.But, naturally, they have their
own niche area of data sciencethat they want to develop, and
that's not necessarily broadlyapplicable to the wide user base
(11:17):
that would be using the flow ofcore at the VIB, for example.
Whereas, actually, if you'remore applied in the academic
world, you certainly, you candevelop new algorithms, new
solutions, but you have a wholewhole shop of different shelves
to pick problems off and towork. And the problem is you you
can't pick a mix. You have youyou kind of have to be you you
(11:39):
are you have to deal with what'sput in front of you. But I I've
gotta say, I think it's a vitalrole that's no less important
than the primary academic. Andcertainly at York, we try to
make that appear to peer that,you know, it's not academic in
that you are writing your owngrants necessarily, but you're
co eyeing on grants. You're partof the grant team. You're part
(11:59):
of the project team. They'revery much an applied academic
career in a technical setting.No.
Sofie Van Gassen (12:06):
That's that's a really cool concept. I I would
kind of argue that's well, notargue maybe, but the thing that
if you're a good PI, you alsolook for these collaboration
opportunities, and you look forpossibilities to to work
together and to actually seewhere your fields can contribute
to the questions that thatpeople are having as a as a data
(12:30):
analyst researcher. I thinkthat's also what I see happening
in our group. So it's it's thecase for the flow cytometry
research we're doing, but we'realso working on some other
technologies, like, not mepersonally, but other people in
our group with strength,cryptomics, cell cell
communication, all these things,spatial things now also more and
(12:51):
more. And I think that's alsopart of the the strength and the
success of our group is thatwe're really looking of where
are biologists asking questions,where are the boundaries of
what's currently possible withthe the the techniques that are
out there now, and where wherecan we still contribute. And I
think that's really what's yeah.As you would hope for that these
other PIs would also aim to dorather than just staying focused
(13:14):
on, like, I'm doing this onething. Of course, you're do you
have expertise in a specifictopic, but then how can you
apply that in the the settingwhere you are?
Peter O'toole (13:25):
I I think that I I obviously, your professor was
very much minded in thatdirection. I'm not sure. I I
would say he's more the,exception than the rule, but but
certainly not. I I we worked atYork with someone called Julie
Wilson who's exceptionally goodat working with all sorts of
people and was super useful forall of that. You know, she's
(13:46):
just retired, which is gutting.But but it's very hard finding
someone else who's equallyminded to help in these areas.
Yeah.
Sofie Van Gassen (13:54):
And, of course, people have different
mindsets about these things.That's that's true.
Peter O'toole (13:59):
So so now we just need to make sure the VIB create
that post and give you a.
Sofie Van Gassen (14:04):
Fingers crossed. It's it's looking good
so far. But yeah.
Peter O'toole (14:07):
So the other question was, would you move out
of flow data as well, just likethe group has? Would you move
into the imaging side? Soworking with, oh gosh, evelyn
now, I think, isn't it, that'sleading the call?
Sofie Van Gassen (14:19):
Yeah. Yeah. Yeah. Exactly.
Peter O'toole (14:21):
VIB or would it go with Evelyn and the
transcriptomics data? Would yoube looking at, you know,
evolving or diversifying to notjust flow cytometry but into the
other technologies that areclosely associated?
Sofie Van Gassen (14:37):
So, of course, it's again the never say never.
But in first instance and that'sactually a bit what happened
after my PhD as well. I I see alot of my peers after they've
done their PhD, either, like, golook for another challenge or
they're saying, like, okay. Thiswas now enough of this. Let's
let's do something else. I feltlike, okay. During my PhD, I've
built up all this expertise, andit feels really nice to be able
(15:00):
to use that and and to build onthat. So I feel like that at
this point, for sure, I canstill contribute useful things
to the cytometry field, andthat's that also where maybe
it's also part of just being abit in your comfort zone
sometimes. But that having thatexpertise also makes it easiest
to to contribute there. We aremaybe exploring, like, very
(15:25):
slightly out of that boundary inthe sense, like, now you have
these s eight sorter, which alsomakes the images. So, okay, then
you suddenly need a differentset of techniques to to analyze
these images as well. We'relooking a bit at the the spatial
proteomics maxima and so on. So,like, there's also some
extension there, but my my mainfocus is still really cytometry.
(15:45):
I think I'm yeah. I like I said,I was introduced to cytometry at
the start of my PhD. I kind offell in love with it. So I think
for now, I'll I'll stick withcytometry as my main topic. I
don't see me, like, suddenlycompletely switching to
transcriptomics out of nowhere.And I think there are still
quite a bit of challenges leftin the cytometry field that's
(16:08):
that there keeps being excitingpuzzles there as well.
Peter O'toole (16:11):
So I'm gonna take you back in time now to I I
won't say which year. I know.Don't go years. But can you
remember what the first job isthat you ever wanted to be when
you were really young? I knowyou were six, seven, eight,
nine, 10. What was the first jobthat you thought, oh, I'd like
to be that?
Sofie Van Gassen (16:28):
When I was very, very little, I think I
wanted to be a zookeeper orsomething like that. Right. I I
liked seeing all these animals.And so I don't think that was a
very realistic dream. I don'tthink we even had any pets at
home except maybe a few fish. SoI had absolutely zero experience
with interacting with animals,but that seems very, very
(16:51):
magical at the time. Then Ithink when I was around yeah.
What will it be? 11, 12 yearsold? I I also had a a short
period where I wanted to become,like, an Egyptologist or
something like that. Yep. Andthen I I think looking back on
that, that was more the thepuzzle aspect of it, the the
unreadable hieroglyphs andwanting to, like, solve these
(17:14):
puzzles. And even thoughcomputer science is something
very different, I think it'sit's the puzzle solving aspect
there that that intrigued meabout these unknown things from
history.
Peter O'toole (17:26):
So what got you into computing computer science?
Sofie Van Gassen (17:30):
Yeah. That's actually the the the love for
puzzles, for logic, for, yeah,reasoning about things, all the
these kind of things. It's thethings I had fun with, like
solving math problems. Thesekind of things were quite fun,
and that kind of got me there.And then while I was studying
(17:52):
computer science, I noticed alsothat I really had the interest
in machine learning, artificialintelligence, the data analysis
aspects of it that was moreintriguing to me than just,
like, the computer architectureor or these kind of of topics
that we have we're havingcourses on.
Peter O'toole (18:12):
And where did you where was your degree, your
first degree?
Sofie Van Gassen (18:16):
Also in Ghent, so I I really stuck to
Peter O'toole (18:19):
Oh, you're Ghent. Ghent. Ghent.
Sofie Van Gassen (18:21):
Yes. Yes. Exactly. Like I was saying, it's
a kind of exception that I'mstill so close to where I've
been all this time. I've beenvery lucky that I've had that
opportunity.
Peter O'toole (18:31):
That must have been Ugand and then on to VIB.
Sofie Van Gassen (18:34):
Well so no. I'm I'm still I have the double
affiliation. Right? So I'm stillin Ugand. Yeah. Yeah. Yeah. So
It's long time at UCan. That'sbasically been my main
institute. I've I've done a astay abroad of two months, and
then I had another stay abroadof a few weeks. But, like, my
(18:54):
actual main institute's alwaysbeen UCan so far.
Peter O'toole (18:58):
My undergraduate was also Essex, PhD Essex, first
postdoc Essex. So I was so so sonot so dissimilar. So so there's
nothing
Sofie Van Gassen (19:08):
It doesn't happen that often, I have the
impression. I think it's it's Iknow I'm aware I've been very
lucky to have that opportunityin academia where there's a lot
of stress often on, movingabroad and all these things.
Peter O'toole (19:20):
I think it's also lucky if you find yourself in
the best research one of thebest research groups. And so
actually moving is instead ofmoving up because you're losing.
You you you if you're in areally good established research
group that is highly regarded,actually, the opportunities
there are really good. And ifthey're really good supervisors
and they let let your careerflourish, then I think they're
really good.
Sofie Van Gassen (19:41):
Yeah. Yeah. That's that's for sure.
Peter O'toole (19:43):
You're a VIB. You know, it it is a stunning
resource. So and and New Guenth,and it's a lovely city.
Sofie Van Gassen (19:51):
Absolutely. And I think it's also that's the
more personal, but I like beingrelatively close to to family
and friends. So moving abroadfor a longer time, it's, yeah,
been more challenging for me, Ithink.
Peter O'toole (20:07):
So thinking about traveling, have you been you
must have been to Saito. Yes.Yes. I think How many Saito's
have you been to?
Sofie Van Gassen (20:16):
Sorry?
Peter O'toole (20:16):
How many Saito's have you been to?
Sofie Van Gassen (20:18):
How many so my my first Cyto was Fort
Lauderdale. I just looked it up.That was apparently in 02/2014.
That was actually the first yearof my PhD, and then we were
very, very lucky because wethere was one of these flow cap
challenges, and I think it wasactually the last one that's
(20:40):
been. But there were there was,like, a a global call. We have
this specific dataset andthere's specific question about
it. Please submit your yourresults for this, and then then
we we can all learn from eachother by doing that. And it was
a really great experience. So weknew that the the results were
were going to be discussed atthat conference, which at that
(21:03):
point was, like, still, for uspersonally, very unknown. Mhmm.
But then we were welcomed so sowarmly. It was really an amazing
experience for me. I've been tosome like, if you go to a
bioinformatics conference,basically, everyone's working on
transcriptomics, and you're justthere explaining what cytometry
(21:24):
is. Or if you go more to animmunology kind of thing where
people know what cytometry is,but then they have no clue what
these algorithms are. So you'rereally explaining that. Well, at
Cyto, we're the other people whoare making algorithms for
cytometry. So that wasabsolutely a great experience.
(21:44):
And I think I've been every yearsince then, except, of course,
the the years of the pandemic.And then the first year after,
then my son was still too small.So then I then I also stayed at
home. That was Philadelphia.That's the one I missed. But,
otherwise, I've been every year,and I think that's absolutely
the highlight of the year. Yeah.I really enjoy Cyto a lot.
Peter O'toole (22:05):
Is there still a data analyst meeting within each
site. I don't go to that site,so I don't know. But is it if I
look at the imaging side,there's always every now and
then, we have a then we have ahackathon, and everyone just
comes together and talks shopand solves the problem or looks
at a few different things. Do wehave that flow cytometry?
Sofie Van Gassen (22:27):
So I don't think there's anything like a a
hackathon upfront or anythinglike that, but it's very nice to
see how the program is changing.Where before, there was then
maybe one or two sessions aboutdata data analysis software and
so on. And then over the years,that's increasing and
increasing, and now you can,like, completely fill your Cyto
(22:50):
program just with data analysisrelated sessions. And that's
that's nice to see also how howthe impact on the on the
community is changing with allthe high parameter data being
generated right now. People havemore and more of a need for all
these tools. So even even if younow go to a a more, whatever,
(23:13):
other topic focused session,there will be probably be some
discussion about the thealgorithms used to tackle these
issues, which you would not havehad a few ten years ago. Yeah.
Peter O'toole (23:26):
I'm too late for this year, obviously, because
Denver's well well in well-beingput into place. But I know in
the imaging and the flow worldin The UK, we have a flow
cytometry facilities meeting. Soall the flow staff we got the
European virtual flow meetingwhere all the flow core staff
meet. I don't know if youattended that this
Sofie Van Gassen (23:44):
My my colleague participated. Sarah
was there.
Peter O'toole (23:47):
And then, like, microscopy similar. But,
actually, wouldn't it be greatto have a flow data science
similar type of meeting whereeveryone just talks and talks
about funding, how jobrecognition, career paths? Oh,
actually, in The UK, we havesomething called the technology
specialist network, and theythey they look after those
(24:08):
technology specialists, whichincludes data scientists, to
make sure the career paths arenow being properly developed
because, you know, look, you'retoo young to know this, but
twenty years ago, these jobsdidn't really exist. And now
they're they're very much at theforefront because they're
pivotal now to underpin thescience. They're they're
absolutely vital. But thenthat's not necessarily the
(24:28):
careers are being properlyestablished. That's why I think
we spoke about a bit earlier.You're an obvious person who
needs to make sure of that. Buteven if you succeed, you then
need to share that to make sureothers can succeed within their
institutes.
Sofie Van Gassen (24:41):
Yeah. Sure. I think it it's something that's
slowly becoming relevant. Ithink if you like, ten years
ago, there were not enoughpeople around doing
computational cytometry toreally or on that, and then it
it's nice to be embedded in thelarger conference. It's still
nice to be embedded in the largeconference. But I think there's
more and more room for thatwhere more and more people are
(25:02):
actually working on this topicand and making great changes
there. Yeah.
Peter O'toole (25:08):
You can make a great pre congress meeting,
though. So so if you think aboutit till that day zero with the
pre congress on Saturday,Sunday, that would be an ideal
session to bring everyonetogether to talk shop.
Sofie Van Gassen (25:19):
Something something to think about. Yes. I
I think what we're it's it'sdifferent, of course, in in AIM,
but we're also last year, we,for the first time, organized
this computational Cytometrysummer school where we had a
week that was the because Cytoswas in Europe, we we kind of had
that the week before. I alsolearned never organize something
(25:42):
you're heavily involved with,like, the full week before
Cytos. That's just too much forall the things you also want to
be preparing for Saito, so thatwas a lot at the same time. But
it was a lot of fun, and we'rewe're doing it again this year,
not the week before Saitobecause Saito is in US anyway,
so that's that wouldn't makesense. And, yeah, that's that's
(26:04):
also fun to see how how manypeople are interested in
learning these things and andhow many people are are picking
up all these tools and willingto their programming in R to be
able to get things running. Ithink that's that's really cool
to see. So that's also a veryfun environment to be in. Yeah.
Peter O'toole (26:23):
I I have a another question. So, actually,
from my side, I had a PhDstudent called Lorva Wiggins
with Will Brackenbury and JulieWilson, who I mentioned earlier,
who three different threedifferent type of I'm the
imaging cytometry person. I hadsomeone with a biological
question. That's Will. I hadJulie who had the data science.
Yeah. And Laura was a masterycomputer science. Never done any
(26:47):
biology just like yourself aswell. Yeah. But one of the first
things we did was get her in thelab and generate her own data as
well. So, actually, have youbeen in the lab? Have you
generated your own flightcytometry data?
Sofie Van Gassen (27:00):
Have you generated your own data? It's
maybe a bit too much of astretch, but I did follow along.
Like, a day in the lab,following along with someone,
being allowed to do some of thenoncrucial steps that can't
really go wrong even if you'renot fully sure of what you're
doing kind of thing. And I thinkthat's been very informative. I
(27:20):
really appreciate it a lot. I'vehad that opportunity a few times
by now. And every time you getmore insights about how the data
is generated, which does have animpact on your downstream
analysis.
Peter O'toole (27:32):
Mhmm.
Sofie Van Gassen (27:33):
So I think that's absolutely crucial to
understand what you're actuallydoing. Right? It's not just
numbers. They're coming fromsomewhere. And I think on the
one hand, to be aware, forexample, which kind of quality
control makes sense, which kindof quality control is needed,
you get informed a lot byactually following along the
(27:53):
experiments measurements. But onthe other hand, one additional
advantage of it is just to beable to talk to the researchers
generating the data tounderstanding their point of
view and also to be a bit moreunderstanding sometimes. Maybe,
like, we we can complain of, oh,why is it not perfectly
(28:14):
standardized? Why is noteverything typed exactly the
same? And that till the pointswhere you're following in the
long in the lab and you'reunderstanding, like, oh, wait.
This is not so straightforwardthan it is for me afterwards
when I'm seeing the data. So Iwill keep encouraging everyone
to try to standardize things andso on, but it also helps a lot
with understanding that whatwhat happens in the lab is
(28:36):
sometimes unpredictable, allthese things. And and seeing
that firsthand really makes adifference in in how you can
treat that afterwards. Yeah.Absolutely.
Peter O'toole (28:45):
You kind of answered my next question
because it's exactly why we gotLaura to get her own data so she
can understand the provenance,the the limitations. Because I
can imagine and you saidsometimes it means you won't ask
the users to do things thataren't really possible. And you
get you understand why the datais frustrating because not
everything in the data is as youwant it to be just because
(29:06):
biology doesn't allow it. Ithink you're absolutely right.
So those days experience of whatwe've given you that that
insight to understand thatbiology is pretty
nonreproducible to a largeextent.
Samples are very limiting. Youcan't get lots and lots.
Sometimes it's very, veryprecious, and you get
statistically challenging.
Sofie Van Gassen (29:27):
Yeah. Yeah. Yeah. Exactly. And I think I
think being aware of that andand the best way to become aware
of it is seeing it firsthandreally helps a lot in in how you
tackle these things. I fully has
Peter O'toole (29:41):
been the hardest time in your career to date? You
you must be one of the youngestpeople I've ever done a podcast
with, but there's alwayschallenging times, especially
early in the career. So whenwould you say the most
challenging time has been?
Sofie Van Gassen (29:54):
That's a good question. I think maybe one of
the challenging time for me is,like, the switch from PhD to
postdoc maybe or, like, the theshort period after that. Because
maybe also because I stayed inthe same research group. Right?
I kind of kept doing the samething, but I was more and more
(30:16):
guiding people. But that feltlike not really doing my work
because it was not like I stillhave, like, some own research
projects, and then more and morealso following along with other
people and thinking along withthem, which I enjoyed a lot,
which is also why I'm stilldoing it, but which had
sometimes a thing like, oh, butwhat did I actually do this
(30:37):
week? My my whole week flewpast, and I did not do anything,
and then created a certain levelof stress. And getting to
reframe that in my head of,okay. But actually guiding these
people is the main function I'mdoing now, and it's okay that I
don't get to programming in Revery day of the week. So so
that that's that's period whereI was, like, slowly growing from
(31:02):
one function to the other Mhmm.Came with some moments of stress
for sure.
Peter O'toole (31:07):
Okay.
Sofie Van Gassen (31:08):
I
Peter O'toole (31:08):
And I've got to ask so so those I know most
people are listening to this,but if so I I I I can see
Sofie's background. Is that aplate of peas as your
background?
Sofie Van Gassen (31:21):
I I I don't know. I'm in this meeting room
here. I think it's some kind ofmoss. I mean, I I It
Peter O'toole (31:28):
looks like a plate of mushy peas, and it's
just a bit of wall art in thebackground.
Sofie Van Gassen (31:32):
It's it's a bit of wall art that should
represent moss, I think. I can Ican put like, there's another
one over there?
Peter O'toole (31:42):
I've never seen that when I've been there.
Sofie Van Gassen (31:44):
It's just how our meeting rooms here in the
institute are decorated.
Peter O'toole (31:50):
It's a complete digression. So you say you have
a a daughter or a son?
Sofie Van Gassen (31:54):
A son. A son. He's about three years old now.
Yeah.
Peter O'toole (31:59):
And how have you found managing the work life
balance?
Sofie Van Gassen (32:05):
I think it's actually relatively okay in the
sense that I was already in thehabit of not working too many
hours from home. So I I stayquite strictly to my working
hours for my job. Of course,there's always some exceptions
if there's a specific deadlineor whatever, but, like, I think
compared to some colleagues andI think at some moments, I this
(32:27):
also costs you stress. Like,should I be doing more hours?
This or that. But then in theend, you notice, like, no. This
is actually what is expected ofme, and that that is fine. So in
that sense, it's it's been quitequite doable. However, since
this September, he started goingto yeah. What do you call it in
(32:48):
English? Kindergarten then,guess, but, like, a
Peter O'toole (32:50):
Yeah.
Sofie Van Gassen (32:51):
School. And then I don't know how this is
abroad, but in Belgium soWednesdays, they only go half a
day, and then they could go to akind of daycare solution in the
afternoon, but I decided to gowork for fifths. So I'm home on
Wednesdays to to take care ofhim. And so that switch from
working full time to four fifthshas been a bit challenging
(33:13):
because, actually, like, okay.You you I have quite a bit of
control of what I'm doing withwith my day, so I just need to
learn to estimate better thatyou can't do everything you were
doing in five fifths and fourfifths. And so that that also
comes with these challengessometimes, like, where did this
week go? It's already passedbecause you're you're missing a
whole day every week. Right?But, otherwise, next to that, I
(33:37):
think it's it's been quite okay.Yeah. And I I also have the
feeling that that we're in avery, how how to say it,
accepting environment. Like,people are understanding if you
need to leave early a day or youneed to suddenly miss a day
because the kid is sick and youneed to be at home or things
like that. Like, people areflexible about these things, and
(33:58):
they're understanding aboutthese things. So that's that's,
again, being a good place to beat here in the institute for
sure.
Peter O'toole (34:07):
So I asked about the most challenging times. You
talked about more challengesthere. What about the if you
could go back and relive any oneyear, which year would you go
and relive?
Sofie Van Gassen (34:17):
Oh, a specific year to relive.
Peter O'toole (34:19):
Well, it doesn't have to be the year itself.
Sofie Van Gassen (34:21):
Doesn't have to be No. No. But, like The
Peter O'toole (34:23):
first year of the AC, the first year is your
postdoc, the year you've justhad, the year you went to Saito,
what what was the most fun yearthat you think, wow, that was a
blast.
Sofie Van Gassen (34:33):
That's a difficult question. I think
every year's come every yearcomes with some some ups and
some downs, and I'm I'm for surealso looking forward to the
future. So I'm I'm not one ofthese persons of, like, the the
the best is in the past orsomething like like, the the
best is yet to come, hopefully.But I think, like, the probably
(34:58):
the start of my PhD would be thethe moment I would refer to
where you're just starting toexplore all these things. You
have quite a bit of freedom inin all the things you're doing.
You don't have too manycommitments yet that you you
need to uphold. So, yeah, if Ihave to pick something, I would
say that, but it's certainly notthat I'm that I'm here like, oh,
(35:19):
I wish I could go back there.No. I'm I'm very happy to just
keep moving forward.
Peter O'toole (35:25):
So my next I'm gonna ask some quick fire
questions.
Sofie Van Gassen (35:28):
Okay.
Peter O'toole (35:29):
Okay? So are you an early bird or an ITALM?
Sofie Van Gassen (35:35):
Slowly becoming more and more early
bird. Would have been differenta few years ago.
Peter O'toole (35:42):
PC or Mac?
Sofie Van Gassen (35:44):
Oh, PC.
Peter O'toole (35:45):
Yeah. Oh, okay. McDonald's or Burger King?
Sofie Van Gassen (35:51):
I've never been to Burger King. McDonald's
sometimes, but also not veryoften. So I'm okay with neither.
Like, don't need that either.
Peter O'toole (36:01):
You have a three year old that will that will go
up in numbers. Sure. What isyour favorite takeaway then?
What's your favorite fast food,your favorite takeaway?
Sofie Van Gassen (36:15):
When I was young, would have said Chinese,
but now I'm eating vegetarian.And at least here in Belgium,
you don't have that many manyoptions there. So now I probably
just go for fries.
Peter O'toole (36:28):
Good. Oh, I'd choose Belgium, I suppose.
Sofie Van Gassen (36:30):
Yeah. It's all traditions to a pulse. Right?
Peter O'toole (36:33):
One of the two. Tea or coffee?
Sofie Van Gassen (36:36):
Tea, for sure.
Peter O'toole (36:38):
Chocolate or cheese?
Sofie Van Gassen (36:43):
Would miss both a lot if they would not be
there. Let's say cheese wins.
Peter O'toole (36:49):
Okay. Beer or wine?
Sofie Van Gassen (36:53):
Neither. I don't drink any alcohol.
Peter O'toole (36:55):
No. And you're in the land of trapeze beers. Oh,
of any country. It's the onecountry you'd have to have beer.
Make
Sofie Van Gassen (37:04):
some for it with the chocolate.
Peter O'toole (37:06):
With what is your favorite food?
Sofie Van Gassen (37:10):
Favorite food? It's also a difficult question.
I think it it's I like variety,like, not having to eat the same
thing every day. I don't have avery strongly spoken favorite
there.
Peter O'toole (37:23):
Is there any food you really dislike other than
obviously meat? But is there anyfood that you the taste just
imagine you went to Saito andyou went for the evening meal,
and that was on the menu to go,oh, no. How am I gonna eat that?
Sofie Van Gassen (37:41):
I'm trying to come up with something. No. I I
think the main disappointmentwas be like, oh, there's no
vegetarian option or things likethat. But yeah.
Peter O'toole (37:53):
Do you like to eat in or eat out?
Sofie Van Gassen (37:58):
I enjoy eating out. Yeah. We don't do it that
often, but, yeah, then the timesit happens, it's nice.
Peter O'toole (38:04):
Would you rather cook or clean?
Sofie Van Gassen (38:12):
Preferably neither, but if I have to, I
choose, I guess cleaning. I'mnot I'm not not the best cook.
Peter O'toole (38:19):
So is you a part of the cook at the house?
Sofie Van Gassen (38:21):
Yeah. Yeah. Yeah.
Peter O'toole (38:22):
Yeah? And what's their signature dish?
Sofie Van Gassen (38:26):
Oh, I don't know. I think
Peter O'toole (38:29):
What's the what's the favorite dish that he they
cook for you?
Sofie Van Gassen (38:36):
Also a good question. I think there's it's
it's also just the variety.We're also, like he it's also
not that his big ambition is isis cooking or his big passion is
cooking, so we're kind of justmaking do with easy dishes that
are ready quickly. And that'swhy we then enjoy eating out
once in a while, right, whenneither of us have to cook.
Peter O'toole (38:57):
Because my next question so that was going to be
which what what is it cookedthat you least like?
Sofie Van Gassen (39:05):
Yeah. I also don't have a very specific
answer to that. I think it'sit's I'm sorry. I'm very bad
with the names of I'm justtrying get
Peter O'toole (39:12):
you into trouble because you'll probably watch
this back. And you'll go, whyyou never told me you didn't
like that? And then you forgetit again. Oh, there was your I
think you guys never have itagain.
Sofie Van Gassen (39:22):
Sorry?
Peter O'toole (39:23):
There was your opportunity to say something,
and you never have to eat thatagain.
Sofie Van Gassen (39:27):
Oh, yeah. No. I don't think there's anything
like that. That's that's stillon the menu list right now.
Peter O'toole (39:34):
TV or book?
Sofie Van Gassen (39:36):
Books, for sure. Yeah.
Peter O'toole (39:38):
What are you reading at the moment?
Sofie Van Gassen (39:43):
I think the last thing I read was a very
silly rom com genre book, butthen before that, some nice
science fiction. So a balance ofthose, let's say, in general.
And once in a while, a nonfiction book, but that's that's
only once in a while, mainlyfiction. Yeah.
Peter O'toole (40:05):
Okay. And what's your favorite film? Favorite
movie?
Sofie Van Gassen (40:10):
Oh, that's also a very difficult question.
Maybe my answer can be more thatit's really been quite a long
time since I watched any movies.Like, the the question from,
like, television or books was avery easy question. I really
don't watch a lot of television.But
Peter O'toole (40:27):
you must come on. It was Mont before Edinburgh. It
was Montreal. Surely, youwatched movies on the plane.
Sofie Van Gassen (40:37):
Not that I remember right now, but probably
something, but nothing thatthat's stuck enough to to
remember right now. And theprobability, like, actually, on
a on a plane that I just sleepthe whole time is also quite
probable.
Peter O'toole (40:53):
Well, you could sleep on long haul flights.
Sofie Van Gassen (40:55):
I I think I don't know which one it was. It
was coming back from The States,but, like, it was not Montreal.
It was already longer ago. Butwe're I just, like I was not
fully awake yet anymore, Ithink, when we still had to lift
off, and then we landed, and wewere there. I kind of missed
Peter O'toole (41:12):
all of flights. We're on the East Coast meetings
then. So
Sofie Van Gassen (41:16):
it's Probably. Probably. Yes.
Peter O'toole (41:17):
Wilson Hall. Okay. Star Wars or Star Trek?
Sofie Van Gassen (41:25):
I think I've seen more Star Wars than Star
Trek, but I'm not strongly bigfan of either. And and and I
think probably from thereasoning point of view, I would
prefer Star Trek over Star Wars.
Peter O'toole (41:40):
Okay. Music. What's what's your favorite
music style?
Sofie Van Gassen (41:46):
Oh, actually, I'm listening more and more to
classical music lately, which asa I didn't really do as a as a
teenager or something, but,like, lately, that's bringing
back some calm and some nicememories from Sunday mornings as
a kid and so on. While then youthink, like, oh, why can't we
listen to my more fun musicrather than the boring, grow up
(42:07):
music? But I'm really gettingback to that more and more now.
Yeah.
Peter O'toole (42:12):
Favorite color?
Sofie Van Gassen (42:14):
Let's say green.
Peter O'toole (42:17):
Vixi green or GFP green?
Sofie Van Gassen (42:20):
What?
Peter O'toole (42:21):
Vixi green or GFP?
Sofie Van Gassen (42:24):
No. That's, like therefore, I'm too far away
from the instrument to to havean ounce of medicine.
Peter O'toole (42:33):
Okay. So moving moving on. Who would you say has
been your biggest inspiration inyour career so far?
Sofie Van Gassen (42:39):
That's also a difficult question. Right? I
think just in general, all thecomputational cytometrists, so
all the people at CyTO that arereally showing what change
algorithms can make, I'mthinking of Brian Brinkman,
Nima, all the all these peoplethat this many of them have been
(43:01):
a big inspiration for sure of ofbelieving that this is a field,
like that it's okay to focus onthis one field of cytometry and
trying to see what difference wecan make there. And then I think
otherwise, and it's maybe a bitmore vague, but all the the
people who show me that the workcan have an impact to all the
the people I'm collaboratingwith. And then I'm actually also
(43:25):
thinking in particular of Gerd,so our our the the head of our
core who's always there and justsaying, yes. We need these kind
of things. That's for sure alsobeen a big inspiration.
Peter O'toole (43:38):
And and but Dirt's a big name in the flow
world as well. So I I guess andyou've been there a fair while.
So and he's developed his namevery strongly since he's been
with the VIB.
Sofie Van Gassen (43:49):
So I I think it like, my first title was also
his first Saito as far as I'maware.
Peter O'toole (43:55):
So I can imagine anyone new going to VIB now
might find it quite intimidatingjust because he's such a big
name, whereas, actually, he'she's he's lovely. He's really
cool.
Sofie Van Gassen (44:05):
That's what I would say as well. Yeah. Yeah.
No no need to be intimidated. Ithink we're we're all very happy
for new people to learn aboutall these things, to start
exploring these things, to havefun with it, to do amazing
discoveries with cytometry.
Absolutely.
Peter O'toole (44:20):
To ask inspirations, does is there any
what's your biggest motivation?What motivates you? Who
motivates you? What motivatesyou?
Sofie Van Gassen (44:28):
Think my motivation, if I, like, look
back on things, is mainly havingother people being happy with
things. So so seeing peoplebeing able to use the tools that
I developed, like seeingFlowsome popping up on on work
of people I've never heard of,that that's amazing knowing that
you contributed something. Andthen also just in the
(44:50):
collaborations, I think if Ihave to do work on my own just
for myself, I'm a whole lot lessmotivated than if it's a group
effort or I know that someoneelse is involved who also cares
about the project. That's thatmakes a big difference for me.
Peter O'toole (45:04):
If this was an interview to work in the core
facility, you'd be doing verywell with that answer. It's very
much about
Sofie Van Gassen (45:11):
That's also why I was thinking. Like, this
seems seems like a good goodoption if that could become
possible. Right? That's that'sthe kind of thing I'm getting
excited about.
Peter O'toole (45:20):
Do you have any pet hates? What what annoys you?
What little things annoy you?Not necessarily in work in life
in general. What are your pethates?
What things annoy you?
Sofie Van Gassen (45:31):
That's a good question. I think when when
people are too too strict or or,like, don't have enough empathy
for someone else where they're,like, getting very, like, oh,
why doesn't this person do yeah.But you need to hear their part
of the story as well. Right? Andthere's probably a good reason
(45:52):
and things like that or or wherethere's, like yeah. I don't
know. People being very like,oh, but this is the way it
should be done, and this is canbe the only way. And then yeah.
But in some situations, there isa good reason for an exception
or these kind of things. So sobeing too strict in that sense,
I think, would be the main thingthat comes to mind.
Peter O'toole (46:15):
I I quite like that because that's almost
having an intolerance tointolerance.
Sofie Van Gassen (46:20):
Yeah. But that's that's I think that's
that's that's fair. I thinkthat's a good thing. That's the
one thing to be intolerant aboutis too much intolerance. I think
that's a good
Peter O'toole (46:30):
Yeah. No. I I a few inches. Actually, I I fully
agree. Yeah. I I findintolerant.
Sofie Van Gassen (46:35):
Reassuring to hear.
Peter O'toole (46:37):
Yeah. So outside of work, what hobbies do you do?
Sofie Van Gassen (46:41):
Yeah. So we already mentioned books. I like
reading quite a bit. Since Isince we, like, have our own
house, I also quite likegardening. My my parents had a
very nice garden with lots offlowers and so on, and I was
never really actively involvedin that as a kid. I was mainly,
(47:02):
like, somewhere inside reading abook. But then once once I moved
on my own, it was like, yeah, ifif I don't do anything in the
garden, there will not happenanything in the garden. And then
then I really started enjoyingthat as well. So that was also
very nice to, like, morereconnect with my mom in in that
sense. Yeah. And think thatwould be the main two things
(47:26):
right now. Yeah. And, of course,enjoying time with family with
my cats. Yeah.
Peter O'toole (47:33):
You said you don't have pets, so your
garden's gonna be easier tomaintain.
Sofie Van Gassen (47:37):
No. So I have a cat. I have a cat. Yeah. Yeah.
We still got it, like, fiveyears ago.
Peter O'toole (47:44):
Okay. So what sort of garden is it? Is it sort
of plants? Is it shrubs? Is ittrees? Is it is it are you
growing
Sofie Van Gassen (47:53):
in the community? Where we're currently
living, it's a quite smallgarden, but it's fully plants
with with plants. So there'sthere's no lawn. It's it's all,
yeah, mainly smaller plants, afew edible things, but also not
that like, I do that for the funof it, that it's fun to make
some like, to grow somethingthat you can eat, but not for,
(48:16):
like, our daily function oranything. That's more as a as a
hobby project than as an actualgoal of not having to go to the
supermarket kind of thing. Butso, yeah, lots of flowers,
things like that. We will movein yeah. Still still quite a
(48:37):
while to go. But then we'll havea bigger garden, so then we'll
be able to combine some lawnwith hopefully still lots of
plants as well. So
Peter O'toole (48:45):
excellent. That's
Sofie Van Gassen (48:46):
And then maybe even some room for trees. We'll
see. Yeah. So some smaller treesshould for sure be possible then
as well.
Peter O'toole (48:53):
So I like your future. You're already thinking
about house, what that's gonnabe like. The garden is obviously
a big prerequisite. If I was toask you, if you're coming up to
time, if I was to ask you, whatwhat would you see as the
biggest challenge in the worldof data science and flow
cytometry? Where would whatwould you like to see be solved?
What would you like to beeasier? Any of those.
Sofie Van Gassen (49:15):
In in in cytometry. Right? And I I think,
actually, maybe this is a verynice moment to give a shout out
to the SoulCAP initiative, wherewe're trying to standardize the
annotation of cytometry data,and I really very strongly
believe in that. So right now,everyone has their own gating
strategy. And when one person istalking about the certain cell
(49:39):
type, they might mean somethingelse than someone else talking
with a population with the samename. And then especially with
all the clustering and so on,it's also like, okay. You have a
cluster result, but which cellsare these now? It's that's still
a whole other question. So Ithink that's one of the big next
questions to be solved. And ifanyone would be interested to
working on this with the SoulCAPinitiative, we were really
(50:03):
making a a huge effort at this,and we would be very happy for
anyone to be involved in that.So then for sure reach out about
it. That would be great.
Peter O'toole (50:12):
Are you on any of the ISAC committees?
Sofie Van Gassen (50:17):
I'm on the data committee. It has not been
very active lately. I hope thatthat will pick up again at some
point. I was also on a taskforce at some point about site
to you when all the webinarswere going to be labeled and so
on, so I I helped a bit with thethe data science related ones
there. Yeah. But so main mainlythe data committee. And then now
(50:41):
there's also this task forcebeing started about more about
the data analysis education, somore fitting in the the flow
contents committee there. I'malso excited about that,
bringing more awareness aboutthe algorithms to all the people
using them who are now maybejust clicking a button without
really knowing what they'redoing. So so bringing that
(51:03):
message across is also exciting.
Peter O'toole (51:06):
There's quite a lot of potential there.
Sofie Van Gassen (51:08):
Yeah. Exactly. So
Peter O'toole (51:09):
that's what we're doing those things at the
moment.
Sofie Van Gassen (51:12):
That's what we're we're trying to make
happen. Exactly.
Peter O'toole (51:15):
Take it. Grab it. And and go
Sofie Van Gassen (51:17):
for it. Yeah. Exactly. That's that's that's
why the the subcommittee or taskforce or whatever it's called.
It's, it's it's being beingstarted right now. Yeah.
Peter O'toole (51:27):
And do you know what task forces, I think, could
be better than committees?Because task forces are far are
liberated. They don't have thebureaucracy of a committee. They
can just get on and do an actionand actually deliver things much
better.
Sofie Van Gassen (51:41):
I think there's there's value in both.
Right? So you
Peter O'toole (51:43):
you Yeah. Yeah. No.
Sofie Van Gassen (51:44):
I think you need to you need to have both.
But it's true. Like, I thinkwith the the task forces are
more actionable. Right? You youyou have a concrete plan, and
you go for it, and then and thenit gets done while the
committees are a bit more on onlong term vision and these
things. So it's, yeah, it's twodifferent things that both have
a lot of value, I think, for thecommunity.
Peter O'toole (52:04):
So, Sofie, I think I've come to to the time
point for the podcast. Thank youso much for joining me today.
Everyone who's listened,watched, thank you for your do
go back and look at the otherFlowstars. Sophie mentioned Ryan
Brinkman. Go go listen to hispodcast. He was, absolutely
brilliant. You've heard aboutIsaac and Saito, and, we've got
(52:26):
Virginia Litwin, as one of theco guests of this season that
you're listening to now. But youcan go back and listen to
previous presidents such asJessica Houston, Johnny Moore,
Paul Smith, Paul Robinson, oh,Wallace, the lot of them. But,
Sophie, today, god, it'sexciting having you in the
world, isn't it, Flow Cytometry?I think we're so fortunate to
(52:49):
have yourself and others likeyou really come to the fore and
putting your expertise in ourworld for data science and being
passionate about it. And Ireally hope you get that job in
the call because I think you'dbe brilliant at it. Sofie.
Sofie Van Gassen (53:04):
Yeah. Thank you so
Peter O'toole (53:04):
very much.
Sofie Van Gassen (53:05):
Thanks so much for having me, especially in
this long list of names. Itfeels like a bit intimidating to
be among all those great names,but it it was a very nice
opportunity. Thanks so much.
Peter O'toole (53:17):
It's a pleasure. It would have been great to have
them at this stage of theircareer. So this is why this is
so important. Sophie, thank you.
Sofie Van Gassen (53:25):
Thanks so much.
Welcome to Flowstars, candid conversations
between doctor Peter O'Toole andthe big hitters of flow
cytometry, brought to you byBeckman Coulter at Bite Size
Bio.
Peter O'toole (00:10):
Welcome to Flowstars. And today, I'm joined
by Sophie Van Gassen from VIB.She shares her motivations for
getting involved with FlowCytometry. And someone, one of
the fastest rising stars in FlowCytometry, shares her vision for
the future of data science andthe quality she thinks a good
principal investigator shouldhave. All this coming up in
(00:33):
Flowstars.
Hi. Welcome to this specialedition of Flowstars. I'm Peter
O'Toole from the University ofYork, and today, I'm joined by
Sofie Van Gasson from the VIB inGhent. Sophie, how are you?
Sofie Van Gassen (00:47):
Hi. I'm doing well. Thank you so much for
having me today.
Peter O'toole (00:51):
That's okay. I don't think we've ever met in
person. And yet I know aboutyour work, and it's work that I
don't think I could everreplicate or duplicate. So,
actually, do wanna just veryquickly start for for the
listener or the viewer? What isit? Where is your area of
expertise?
Sofie Van Gassen (01:10):
So I I have a background in computer science,
actually. So not not inimmunology, not in not in
anything biology related. And soI've been working in
bioinformatics. Actually, thetopic of my PhD was machine
learning for flow cytometry. Sothen when I was, like,
considering doing a PhD, I gotintroduced to this to this
technology. And since then, I'vebeen working on flow cytometry
(01:34):
data, and I've been enjoying ita lot. So algorithm development,
developing pipelines forexisting datasets, things like
that. Yeah.
Peter O'toole (01:44):
Did you not say just before we started recording
that you're not good atremembering numbers?
Sofie Van Gassen (01:49):
Yeah. Yeah. Yeah. So that's why the computer
remembers them all for me.
Peter O'toole (01:52):
Right? Okay. Fair enough. Like I say, for someone
who plays with lots of numbers,that's kind of an interesting
problem to have with it. Sookay. So you did a PhD, and you
would give you no. You must yourPhD must have started with flow
cytometry, surely.
Sofie Van Gassen (02:11):
Yeah. Yeah. So the the topic of it was really
flow cytometry. So, basically,my my professor, just noticed
that people were doing all thismanual analysis of this data.
People he was collaborating withand was thinking, like, there
seems to be room in here for forexploring some some algorithms,
(02:31):
seeing whether we can help thesepeople with automating some of
these task, things like that.And so he proposed this topic,
and then we were immediatelycollaborating with with the
people actually measuring thedata. I think that's been a huge
benefit for me that it was notjust, like, in a computer
science group, a theoreticalexercise, like, oh, let's look
(02:51):
at these data points and try tofind some clusters in there, but
that we were actively talking tothe people who were generating
the data and which questions andproblems they were facing. And
so that's that's been the wholefocus of my PhD and actually of
my work still. I I think I'm oneof those few people who kind of
keep doing what they're doingafter their PhD. Like, I'm I'm
(03:12):
now already a number of years aa postdoc, but I'm still doing
kind of the same things as I didduring my PhD. And, of course,
now a bit more guidance than theat the start of my PhD, of
course, when it was mainly theprogramming. But, yeah, topic
wise, it's it's still veryclosely related.
Peter O'toole (03:33):
It's it's an interesting area to have chosen
as a PhD student to to know theimportance, relevance, to be
inspired to do flow cytometry.It's computer science. The world
is your oyster. But why I I'vegot a lot why did you think flow
cytometry was for you?
Sofie Van Gassen (03:52):
Actually, I was very hesitant to do a PhD,
and my professor had to kind ofconvince me because I wanted to
do something applied. I wantedto do something that was used,
and I was a bit afraid if you doa PhD in computer science,
you're just, like, reasoningabout algorithms, and there's
lots of value in that, but itwould not be for me if it was
just a theoretical exercise. Butthen he convinced me, like,
(04:15):
these these people that I'mcollaborating with who are
facing these specific issues.And if you work on this, you
could actively be involved inthat and help them. And so
that's that's applied aspect ofit, even though it's still done
applied and fundamentalresearch, of course, but the
applied aspect of the thealgorithm side of things is what
really convinced me. Heconvinced me, like, if you work
(04:37):
in this, people will use yourtools. And, actually, that's
that's turned out to be the caseby now, so that that's really
cool. And that's also reallywhere I get my my motivation and
my things to do this. Yeah.Absolutely.
Peter O'toole (04:50):
So I can see just by your smile, your eyes, your
enthusiasm that you you'reloving the work, the
environment. And, you know,quite often so I I've employed
lots of data scientists overtime, and I quite often hear,
oh, yes. But you'll never get agood data scientist because they
can earn lots more money workingfor Google or the banks or
(05:12):
someone else. I always disagree.But go on. Why have you chosen
this instead of going earninglots of money for in other
areas?
Sofie Van Gassen (05:22):
I think the combination of the fact that
it's it's just reallyinteresting and really cool to
do, like, that once you're inthere, you you want to keep
working on it. I think the thefact that you know that you're
working in this fundamentalresearch, but also health
related, that it can have animpact on society. And, of
(05:42):
course, like, it will not be myalgorithm in itself, which
immediately impacts the wholesociety, but, like, you're one
small radar in this wholeframework, but you're aiming
towards that. So the the factthat it's life science related,
even though I don't have, like,background in that, I didn't
study any biology, immunology,but the fact that you know that
you can contribute to that fieldalso gives me a lot of
(06:05):
motivation. That's in the thethe the the ultimate dream is,
of course, that you helppatients, right, that you make
people's life better and andgive them better opportunities
for their health. And I'm veryfar away from that. I'm I'm I'm
not a medical doctor. I'm notsomeone with a biological
knowledge, but I know I cancontribute to that. And that's
(06:28):
that also would motivate me waymere more than, for example,
optimizing advertisements orsomething like that, which
indeed you could also do fromthe computer science point of
view.
Peter O'toole (06:40):
I'll I'll pick it up even more because actually,
see, so many of the medicaldiagnosis are through flow
cytometry itself that actuallyyour analysis, the the new
analyses that you're enabling onflow cytometry could have a
profound impact. And so you say,yes, you're not a doctor in a
clinic in a clinic a clinicaldoctor sense, but they are
(07:04):
utterly dependent. All they dois take a sample and then tell
the patient what you've enabledthem to say. So I would say
that, absolutely, you're aclinical doctor. You're the
Sofie Van Gassen (07:13):
scientist. Reasoning in between somewhere
as well. Right? No. No. But thatthat's exactly what I mean.
Right? You know that that yourwork has an impact and that it
can be used by these people whohave the tools to then further
interpret these things and andbring them to the patients, and
that's that's really cool.
Peter O'toole (07:30):
Actually, another question, and it strikes me. So
throughout your PhD, now yourpostdoc at VIB, how many
different groups are you gettingdata from?
Sofie Van Gassen (07:39):
Oh, that's a that's an interesting question.
I don't know if I've countcounted that. So at the
beginning, we were mainlycollaborating with this the
like, this one group that thatmy professor was already
collaborating with. But thisquick very quickly actually
extended through collaborations,through meeting people who had
questions. And I think itdepends a bit also on on how you
(08:02):
define it. So I think there'sthere's a number of groups that
we're actively collaboratingwith. I would say that's, oh,
yeah, a reasonable number,three, four, five, six,
something like that. But thenyou also have many people
reaching out with, like, a asimilar question. Right? So I
have, like, oh, I'm trying touse your tool, but we're
(08:23):
encountering this or that. Canyou give some advice? And that's
actually, of course it it takesa smaller amount. Like, it's not
a long term commitment, but thatway we we get asked about lots
of data from lots of differentgroups. And then once in a
value, we're working also onsome public data that also comes
with its challenges. I'm a verystrong advocate for making data
(08:47):
public. I think this will reallyhelp the field. But just finding
public data online where youdon't know much about it and
don't have insights about themetadata about what was going on
while measuring things can alsobe an extra challenge. So I
appreciate it a lot if thepeople with the biological
question are also involved inthe project rather than just
(09:07):
working on data that is outthere.
Peter O'toole (09:10):
I think what's quite quite interesting is
you're doing a postdoc, but it'sit's not so dissimilar to a core
facility in that your the numberof people you're helping and
advising. And, you know, at thetop end of a core facility,
you're helping designexperiments. You're helping
analyze the data, helping toreally make their science fit
around the technology. And hereyou are the other side of this
(09:31):
downstream because then they getall this analysis. And and
actually, from my side, I'mutterly useless when it comes to
the coding side. And there youare to pick that up, which is a
high end problems.
Sofie Van Gassen (09:45):
Actually, that's that's an interesting
question because that's kind ofwhere I see my future going. I'm
nothing nothing's on paper yet,but you can't keep doing
postdocs forever. Mhmm. And I'mI don't have the ambition to go
for a professor position at thispoint. Never say never, but I
don't really expect thathappening. So I think, right
(10:08):
now, I'm mainly then givingguidance in the algorithm
development and so on. I noticedthat we also get lots of
questions of users who wantguidance in how to use these
tools. And I'm actually talkingto our flow core facility
whether there could be optionsthere to give more support also
from the core facility and thenhave a a future position there,
(10:30):
hopefully, if everything worksout. So I think it's the
Peter O'toole (10:34):
feedback through there, Kurt, that's running the
core facility VIB. Exactly. I II've I've got two lines of
thought now. I don't know whichway to take this in first.
Firstly, I'd say, actually, notgoing down the academic route.
So something we've done at Yorkis set up a data science hub.
And, really, I I would arguethat they're applied academics.
(10:56):
And I think this is reallyimportant because when it comes
to helping with the the datascience side, there's always
talk about bringing new datascience lecturers in to new
group leaders in data science.But, naturally, they have their
own niche area of data sciencethat they want to develop, and
that's not necessarily broadlyapplicable to the wide user base
(11:17):
that would be using the flow ofcore at the VIB, for example.
Whereas, actually, if you'remore applied in the academic
world, you certainly, you candevelop new algorithms, new
solutions, but you have a wholewhole shop of different shelves
to pick problems off and towork. And the problem is you you
can't pick a mix. You have youyou kind of have to be you you
(11:39):
are you have to deal with what'sput in front of you. But I I've
gotta say, I think it's a vitalrole that's no less important
than the primary academic. Andcertainly at York, we try to
make that appear to peer that,you know, it's not academic in
that you are writing your owngrants necessarily, but you're
co eyeing on grants. You're partof the grant team. You're part
(11:59):
of the project team. They'revery much an applied academic
career in a technical setting.No.
Sofie Van Gassen (12:06):
That's that's a really cool concept. I I would
kind of argue that's well, notargue maybe, but the thing that
if you're a good PI, you alsolook for these collaboration
opportunities, and you look forpossibilities to to work
together and to actually seewhere your fields can contribute
to the questions that thatpeople are having as a as a data
(12:30):
analyst researcher. I thinkthat's also what I see happening
in our group. So it's it's thecase for the flow cytometry
research we're doing, but we'realso working on some other
technologies, like, not mepersonally, but other people in
our group with strength,cryptomics, cell cell
communication, all these things,spatial things now also more and
(12:51):
more. And I think that's alsopart of the the strength and the
success of our group is thatwe're really looking of where
are biologists asking questions,where are the boundaries of
what's currently possible withthe the the techniques that are
out there now, and where wherecan we still contribute. And I
think that's really what's yeah.As you would hope for that these
other PIs would also aim to dorather than just staying focused
(13:14):
on, like, I'm doing this onething. Of course, you're do you
have expertise in a specifictopic, but then how can you
apply that in the the settingwhere you are?
Peter O'toole (13:25):
I I think that I I obviously, your professor was
very much minded in thatdirection. I'm not sure. I I
would say he's more the,exception than the rule, but but
certainly not. I I we worked atYork with someone called Julie
Wilson who's exceptionally goodat working with all sorts of
people and was super useful forall of that. You know, she's
(13:46):
just retired, which is gutting.But but it's very hard finding
someone else who's equallyminded to help in these areas.
Yeah.
Sofie Van Gassen (13:54):
And, of course, people have different
mindsets about these things.That's that's true.
Peter O'toole (13:59):
So so now we just need to make sure the VIB create
that post and give you a.
Sofie Van Gassen (14:04):
Fingers crossed. It's it's looking good
so far. But yeah.
Peter O'toole (14:07):
So the other question was, would you move out
of flow data as well, just likethe group has? Would you move
into the imaging side? Soworking with, oh gosh, evelyn
now, I think, isn't it, that'sleading the call?
Sofie Van Gassen (14:19):
Yeah. Yeah. Yeah. Exactly.
Peter O'toole (14:21):
VIB or would it go with Evelyn and the
transcriptomics data? Would yoube looking at, you know,
evolving or diversifying to notjust flow cytometry but into the
other technologies that areclosely associated?
Sofie Van Gassen (14:37):
So, of course, it's again the never say never.
But in first instance and that'sactually a bit what happened
after my PhD as well. I I see alot of my peers after they've
done their PhD, either, like, golook for another challenge or
they're saying, like, okay. Thiswas now enough of this. Let's
let's do something else. I feltlike, okay. During my PhD, I've
built up all this expertise, andit feels really nice to be able
(15:00):
to use that and and to build onthat. So I feel like that at
this point, for sure, I canstill contribute useful things
to the cytometry field, andthat's that also where maybe
it's also part of just being abit in your comfort zone
sometimes. But that having thatexpertise also makes it easiest
to to contribute there. We aremaybe exploring, like, very
(15:25):
slightly out of that boundary inthe sense, like, now you have
these s eight sorter, which alsomakes the images. So, okay, then
you suddenly need a differentset of techniques to to analyze
these images as well. We'relooking a bit at the the spatial
proteomics maxima and so on. So,like, there's also some
extension there, but my my mainfocus is still really cytometry.
(15:45):
I think I'm yeah. I like I said,I was introduced to cytometry at
the start of my PhD. I kind offell in love with it. So I think
for now, I'll I'll stick withcytometry as my main topic. I
don't see me, like, suddenlycompletely switching to
transcriptomics out of nowhere.And I think there are still
quite a bit of challenges leftin the cytometry field that's
(16:08):
that there keeps being excitingpuzzles there as well.
Peter O'toole (16:11):
So I'm gonna take you back in time now to I I
won't say which year. I know.Don't go years. But can you
remember what the first job isthat you ever wanted to be when
you were really young? I knowyou were six, seven, eight,
nine, 10. What was the first jobthat you thought, oh, I'd like
to be that?
Sofie Van Gassen (16:28):
When I was very, very little, I think I
wanted to be a zookeeper orsomething like that. Right. I I
liked seeing all these animals.And so I don't think that was a
very realistic dream. I don'tthink we even had any pets at
home except maybe a few fish. SoI had absolutely zero experience
with interacting with animals,but that seems very, very
(16:51):
magical at the time. Then Ithink when I was around yeah.
What will it be? 11, 12 yearsold? I I also had a a short
period where I wanted to become,like, an Egyptologist or
something like that. Yep. Andthen I I think looking back on
that, that was more the thepuzzle aspect of it, the the
unreadable hieroglyphs andwanting to, like, solve these
(17:14):
puzzles. And even thoughcomputer science is something
very different, I think it'sit's the puzzle solving aspect
there that that intrigued meabout these unknown things from
history.
Peter O'toole (17:26):
So what got you into computing computer science?
Sofie Van Gassen (17:30):
Yeah. That's actually the the the love for
puzzles, for logic, for, yeah,reasoning about things, all the
these kind of things. It's thethings I had fun with, like
solving math problems. Thesekind of things were quite fun,
and that kind of got me there.And then while I was studying
(17:52):
computer science, I noticed alsothat I really had the interest
in machine learning, artificialintelligence, the data analysis
aspects of it that was moreintriguing to me than just,
like, the computer architectureor or these kind of of topics
that we have we're havingcourses on.
Peter O'toole (18:12):
And where did you where was your degree, your
first degree?
Sofie Van Gassen (18:16):
Also in Ghent, so I I really stuck to
Peter O'toole (18:19):
Oh, you're Ghent. Ghent. Ghent.
Sofie Van Gassen (18:21):
Yes. Yes. Exactly. Like I was saying, it's
a kind of exception that I'mstill so close to where I've
been all this time. I've beenvery lucky that I've had that
opportunity.
Peter O'toole (18:31):
That must have been Ugand and then on to VIB.
Sofie Van Gassen (18:34):
Well so no. I'm I'm still I have the double
affiliation. Right? So I'm stillin Ugand. Yeah. Yeah. Yeah. So
It's long time at UCan. That'sbasically been my main
institute. I've I've done a astay abroad of two months, and
then I had another stay abroadof a few weeks. But, like, my
(18:54):
actual main institute's alwaysbeen UCan so far.
Peter O'toole (18:58):
My undergraduate was also Essex, PhD Essex, first
postdoc Essex. So I was so so sonot so dissimilar. So so there's
nothing
Sofie Van Gassen (19:08):
It doesn't happen that often, I have the
impression. I think it's it's Iknow I'm aware I've been very
lucky to have that opportunityin academia where there's a lot
of stress often on, movingabroad and all these things.
Peter O'toole (19:20):
I think it's also lucky if you find yourself in
the best research one of thebest research groups. And so
actually moving is instead ofmoving up because you're losing.
You you you if you're in areally good established research
group that is highly regarded,actually, the opportunities
there are really good. And ifthey're really good supervisors
and they let let your careerflourish, then I think they're
really good.
Sofie Van Gassen (19:41):
Yeah. Yeah. That's that's for sure.
Peter O'toole (19:43):
You're a VIB. You know, it it is a stunning
resource. So and and New Guenth,and it's a lovely city.
Sofie Van Gassen (19:51):
Absolutely. And I think it's also that's the
more personal, but I like beingrelatively close to to family
and friends. So moving abroadfor a longer time, it's, yeah,
been more challenging for me, Ithink.
Peter O'toole (20:07):
So thinking about traveling, have you been you
must have been to Saito. Yes.Yes. I think How many Saito's
have you been to?
Sofie Van Gassen (20:16):
Sorry?
Peter O'toole (20:16):
How many Saito's have you been to?
Sofie Van Gassen (20:18):
How many so my my first Cyto was Fort
Lauderdale. I just looked it up.That was apparently in 02/2014.
That was actually the first yearof my PhD, and then we were
very, very lucky because wethere was one of these flow cap
challenges, and I think it wasactually the last one that's
(20:40):
been. But there were there was,like, a a global call. We have
this specific dataset andthere's specific question about
it. Please submit your yourresults for this, and then then
we we can all learn from eachother by doing that. And it was
a really great experience. So weknew that the the results were
were going to be discussed atthat conference, which at that
(21:03):
point was, like, still, for uspersonally, very unknown. Mhmm.
But then we were welcomed so sowarmly. It was really an amazing
experience for me. I've been tosome like, if you go to a
bioinformatics conference,basically, everyone's working on
transcriptomics, and you're justthere explaining what cytometry
(21:24):
is. Or if you go more to animmunology kind of thing where
people know what cytometry is,but then they have no clue what
these algorithms are. So you'rereally explaining that. Well, at
Cyto, we're the other people whoare making algorithms for
cytometry. So that wasabsolutely a great experience.
(21:44):
And I think I've been every yearsince then, except, of course,
the the years of the pandemic.And then the first year after,
then my son was still too small.So then I then I also stayed at
home. That was Philadelphia.That's the one I missed. But,
otherwise, I've been every year,and I think that's absolutely
the highlight of the year. Yeah.I really enjoy Cyto a lot.
Peter O'toole (22:05):
Is there still a data analyst meeting within each
site. I don't go to that site,so I don't know. But is it if I
look at the imaging side,there's always every now and
then, we have a then we have ahackathon, and everyone just
comes together and talks shopand solves the problem or looks
at a few different things. Do wehave that flow cytometry?
Sofie Van Gassen (22:27):
So I don't think there's anything like a a
hackathon upfront or anythinglike that, but it's very nice to
see how the program is changing.Where before, there was then
maybe one or two sessions aboutdata data analysis software and
so on. And then over the years,that's increasing and
increasing, and now you can,like, completely fill your Cyto
(22:50):
program just with data analysisrelated sessions. And that's
that's nice to see also how howthe impact on the on the
community is changing with allthe high parameter data being
generated right now. People havemore and more of a need for all
these tools. So even even if younow go to a a more, whatever,
(23:13):
other topic focused session,there will be probably be some
discussion about the thealgorithms used to tackle these
issues, which you would not havehad a few ten years ago. Yeah.
Peter O'toole (23:26):
I'm too late for this year, obviously, because
Denver's well well in well-beingput into place. But I know in
the imaging and the flow worldin The UK, we have a flow
cytometry facilities meeting. Soall the flow staff we got the
European virtual flow meetingwhere all the flow core staff
meet. I don't know if youattended that this
Sofie Van Gassen (23:44):
My my colleague participated. Sarah
was there.
Peter O'toole (23:47):
And then, like, microscopy similar. But,
actually, wouldn't it be greatto have a flow data science
similar type of meeting whereeveryone just talks and talks
about funding, how jobrecognition, career paths? Oh,
actually, in The UK, we havesomething called the technology
specialist network, and theythey they look after those
(24:08):
technology specialists, whichincludes data scientists, to
make sure the career paths arenow being properly developed
because, you know, look, you'retoo young to know this, but
twenty years ago, these jobsdidn't really exist. And now
they're they're very much at theforefront because they're
pivotal now to underpin thescience. They're they're
absolutely vital. But thenthat's not necessarily the
(24:28):
careers are being properlyestablished. That's why I think
we spoke about a bit earlier.You're an obvious person who
needs to make sure of that. Buteven if you succeed, you then
need to share that to make sureothers can succeed within their
institutes.
Sofie Van Gassen (24:41):
Yeah. Sure. I think it it's something that's
slowly becoming relevant. Ithink if you like, ten years
ago, there were not enoughpeople around doing
computational cytometry toreally or on that, and then it
it's nice to be embedded in thelarger conference. It's still
nice to be embedded in the largeconference. But I think there's
more and more room for thatwhere more and more people are
(25:02):
actually working on this topicand and making great changes
there. Yeah.
Peter O'toole (25:08):
You can make a great pre congress meeting,
though. So so if you think aboutit till that day zero with the
pre congress on Saturday,Sunday, that would be an ideal
session to bring everyonetogether to talk shop.
Sofie Van Gassen (25:19):
Something something to think about. Yes. I
I think what we're it's it'sdifferent, of course, in in AIM,
but we're also last year, we,for the first time, organized
this computational Cytometrysummer school where we had a
week that was the because Cytoswas in Europe, we we kind of had
that the week before. I alsolearned never organize something
(25:42):
you're heavily involved with,like, the full week before
Cytos. That's just too much forall the things you also want to
be preparing for Saito, so thatwas a lot at the same time. But
it was a lot of fun, and we'rewe're doing it again this year,
not the week before Saitobecause Saito is in US anyway,
so that's that wouldn't makesense. And, yeah, that's that's
(26:04):
also fun to see how how manypeople are interested in
learning these things and andhow many people are are picking
up all these tools and willingto their programming in R to be
able to get things running. Ithink that's that's really cool
to see. So that's also a veryfun environment to be in. Yeah.
Peter O'toole (26:23):
I I have a another question. So, actually,
from my side, I had a PhDstudent called Lorva Wiggins
with Will Brackenbury and JulieWilson, who I mentioned earlier,
who three different threedifferent type of I'm the
imaging cytometry person. I hadsomeone with a biological
question. That's Will. I hadJulie who had the data science.
Yeah. And Laura was a masterycomputer science. Never done any
(26:47):
biology just like yourself aswell. Yeah. But one of the first
things we did was get her in thelab and generate her own data as
well. So, actually, have youbeen in the lab? Have you
generated your own flightcytometry data?
Sofie Van Gassen (27:00):
Have you generated your own data? It's
maybe a bit too much of astretch, but I did follow along.
Like, a day in the lab,following along with someone,
being allowed to do some of thenoncrucial steps that can't
really go wrong even if you'renot fully sure of what you're
doing kind of thing. And I thinkthat's been very informative. I
(27:20):
really appreciate it a lot. I'vehad that opportunity a few times
by now. And every time you getmore insights about how the data
is generated, which does have animpact on your downstream
analysis.
Peter O'toole (27:32):
Mhmm.
Sofie Van Gassen (27:33):
So I think that's absolutely crucial to
understand what you're actuallydoing. Right? It's not just
numbers. They're coming fromsomewhere. And I think on the
one hand, to be aware, forexample, which kind of quality
control makes sense, which kindof quality control is needed,
you get informed a lot byactually following along the
(27:53):
experiments measurements. But onthe other hand, one additional
advantage of it is just to beable to talk to the researchers
generating the data tounderstanding their point of
view and also to be a bit moreunderstanding sometimes. Maybe,
like, we we can complain of, oh,why is it not perfectly
(28:14):
standardized? Why is noteverything typed exactly the
same? And that till the pointswhere you're following in the
long in the lab and you'reunderstanding, like, oh, wait.
This is not so straightforwardthan it is for me afterwards
when I'm seeing the data. So Iwill keep encouraging everyone
to try to standardize things andso on, but it also helps a lot
with understanding that whatwhat happens in the lab is
(28:36):
sometimes unpredictable, allthese things. And and seeing
that firsthand really makes adifference in in how you can
treat that afterwards. Yeah.Absolutely.
Peter O'toole (28:45):
You kind of answered my next question
because it's exactly why we gotLaura to get her own data so she
can understand the provenance,the the limitations. Because I
can imagine and you saidsometimes it means you won't ask
the users to do things thataren't really possible. And you
get you understand why the datais frustrating because not
everything in the data is as youwant it to be just because
(29:06):
biology doesn't allow it. Ithink you're absolutely right.
So those days experience of whatwe've given you that that
insight to understand thatbiology is pretty
nonreproducible to a largeextent.
Samples are very limiting. Youcan't get lots and lots.
Sometimes it's very, veryprecious, and you get
statistically challenging.
Sofie Van Gassen (29:27):
Yeah. Yeah. Yeah. Exactly. And I think I
think being aware of that andand the best way to become aware
of it is seeing it firsthandreally helps a lot in in how you
tackle these things. I fully has
Peter O'toole (29:41):
been the hardest time in your career to date? You
you must be one of the youngestpeople I've ever done a podcast
with, but there's alwayschallenging times, especially
early in the career. So whenwould you say the most
challenging time has been?
Sofie Van Gassen (29:54):
That's a good question. I think maybe one of
the challenging time for me is,like, the switch from PhD to
postdoc maybe or, like, the theshort period after that. Because
maybe also because I stayed inthe same research group. Right?
I kind of kept doing the samething, but I was more and more
(30:16):
guiding people. But that feltlike not really doing my work
because it was not like I stillhave, like, some own research
projects, and then more and morealso following along with other
people and thinking along withthem, which I enjoyed a lot,
which is also why I'm stilldoing it, but which had
sometimes a thing like, oh, butwhat did I actually do this
(30:37):
week? My my whole week flewpast, and I did not do anything,
and then created a certain levelof stress. And getting to
reframe that in my head of,okay. But actually guiding these
people is the main function I'mdoing now, and it's okay that I
don't get to programming in Revery day of the week. So so
that that's that's period whereI was, like, slowly growing from
(31:02):
one function to the other Mhmm.Came with some moments of stress
for sure.
Peter O'toole (31:07):
Okay.
Sofie Van Gassen (31:08):
I
Peter O'toole (31:08):
And I've got to ask so so those I know most
people are listening to this,but if so I I I I can see
Sofie's background. Is that aplate of peas as your
background?
Sofie Van Gassen (31:21):
I I I don't know. I'm in this meeting room
here. I think it's some kind ofmoss. I mean, I I It
Peter O'toole (31:28):
looks like a plate of mushy peas, and it's
just a bit of wall art in thebackground.
Sofie Van Gassen (31:32):
It's it's a bit of wall art that should
represent moss, I think. I can Ican put like, there's another
one over there?
Peter O'toole (31:42):
I've never seen that when I've been there.
Sofie Van Gassen (31:44):
It's just how our meeting rooms here in the
institute are decorated.
Peter O'toole (31:50):
It's a complete digression. So you say you have
a a daughter or a son?
Sofie Van Gassen (31:54):
A son. A son. He's about three years old now.
Yeah.
Peter O'toole (31:59):
And how have you found managing the work life
balance?
Sofie Van Gassen (32:05):
I think it's actually relatively okay in the
sense that I was already in thehabit of not working too many
hours from home. So I I stayquite strictly to my working
hours for my job. Of course,there's always some exceptions
if there's a specific deadlineor whatever, but, like, I think
compared to some colleagues andI think at some moments, I this
(32:27):
also costs you stress. Like,should I be doing more hours?
This or that. But then in theend, you notice, like, no. This
is actually what is expected ofme, and that that is fine. So in
that sense, it's it's been quitequite doable. However, since
this September, he started goingto yeah. What do you call it in
(32:48):
English? Kindergarten then,guess, but, like, a
Peter O'toole (32:50):
Yeah.
Sofie Van Gassen (32:51):
School. And then I don't know how this is
abroad, but in Belgium soWednesdays, they only go half a
day, and then they could go to akind of daycare solution in the
afternoon, but I decided to gowork for fifths. So I'm home on
Wednesdays to to take care ofhim. And so that switch from
working full time to four fifthshas been a bit challenging
(33:13):
because, actually, like, okay.You you I have quite a bit of
control of what I'm doing withwith my day, so I just need to
learn to estimate better thatyou can't do everything you were
doing in five fifths and fourfifths. And so that that also
comes with these challengessometimes, like, where did this
week go? It's already passedbecause you're you're missing a
whole day every week. Right?But, otherwise, next to that, I
(33:37):
think it's it's been quite okay.Yeah. And I I also have the
feeling that that we're in avery, how how to say it,
accepting environment. Like,people are understanding if you
need to leave early a day or youneed to suddenly miss a day
because the kid is sick and youneed to be at home or things
like that. Like, people areflexible about these things, and
(33:58):
they're understanding aboutthese things. So that's that's,
again, being a good place to beat here in the institute for
sure.
Peter O'toole (34:07):
So I asked about the most challenging times. You
talked about more challengesthere. What about the if you
could go back and relive any oneyear, which year would you go
and relive?
Sofie Van Gassen (34:17):
Oh, a specific year to relive.
Peter O'toole (34:19):
Well, it doesn't have to be the year itself.
Sofie Van Gassen (34:21):
Doesn't have to be No. No. But, like The
Peter O'toole (34:23):
first year of the AC, the first year is your
postdoc, the year you've justhad, the year you went to Saito,
what what was the most fun yearthat you think, wow, that was a
blast.
Sofie Van Gassen (34:33):
That's a difficult question. I think
every year's come every yearcomes with some some ups and
some downs, and I'm I'm for surealso looking forward to the
future. So I'm I'm not one ofthese persons of, like, the the
the best is in the past orsomething like like, the the
best is yet to come, hopefully.But I think, like, the probably
(34:58):
the start of my PhD would be thethe moment I would refer to
where you're just starting toexplore all these things. You
have quite a bit of freedom inin all the things you're doing.
You don't have too manycommitments yet that you you
need to uphold. So, yeah, if Ihave to pick something, I would
say that, but it's certainly notthat I'm that I'm here like, oh,
(35:19):
I wish I could go back there.No. I'm I'm very happy to just
keep moving forward.
Peter O'toole (35:25):
So my next I'm gonna ask some quick fire
questions.
Sofie Van Gassen (35:28):
Okay.
Peter O'toole (35:29):
Okay? So are you an early bird or an ITALM?
Sofie Van Gassen (35:35):
Slowly becoming more and more early
bird. Would have been differenta few years ago.
Peter O'toole (35:42):
PC or Mac?
Sofie Van Gassen (35:44):
Oh, PC.
Peter O'toole (35:45):
Yeah. Oh, okay. McDonald's or Burger King?
Sofie Van Gassen (35:51):
I've never been to Burger King. McDonald's
sometimes, but also not veryoften. So I'm okay with neither.
Like, don't need that either.
Peter O'toole (36:01):
You have a three year old that will that will go
up in numbers. Sure. What isyour favorite takeaway then?
What's your favorite fast food,your favorite takeaway?
Sofie Van Gassen (36:15):
When I was young, would have said Chinese,
but now I'm eating vegetarian.And at least here in Belgium,
you don't have that many manyoptions there. So now I probably
just go for fries.
Peter O'toole (36:28):
Good. Oh, I'd choose Belgium, I suppose.
Sofie Van Gassen (36:30):
Yeah. It's all traditions to a pulse. Right?
Peter O'toole (36:33):
One of the two. Tea or coffee?
Sofie Van Gassen (36:36):
Tea, for sure.
Peter O'toole (36:38):
Chocolate or cheese?
Sofie Van Gassen (36:43):
Would miss both a lot if they would not be
there. Let's say cheese wins.
Peter O'toole (36:49):
Okay. Beer or wine?
Sofie Van Gassen (36:53):
Neither. I don't drink any alcohol.
Peter O'toole (36:55):
No. And you're in the land of trapeze beers. Oh,
of any country. It's the onecountry you'd have to have beer.
Make
Sofie Van Gassen (37:04):
some for it with the chocolate.
Peter O'toole (37:06):
With what is your favorite food?
Sofie Van Gassen (37:10):
Favorite food? It's also a difficult question.
I think it it's I like variety,like, not having to eat the same
thing every day. I don't have avery strongly spoken favorite
there.
Peter O'toole (37:23):
Is there any food you really dislike other than
obviously meat? But is there anyfood that you the taste just
imagine you went to Saito andyou went for the evening meal,
and that was on the menu to go,oh, no. How am I gonna eat that?
Sofie Van Gassen (37:41):
I'm trying to come up with something. No. I I
think the main disappointmentwas be like, oh, there's no
vegetarian option or things likethat. But yeah.
Peter O'toole (37:53):
Do you like to eat in or eat out?
Sofie Van Gassen (37:58):
I enjoy eating out. Yeah. We don't do it that
often, but, yeah, then the timesit happens, it's nice.
Peter O'toole (38:04):
Would you rather cook or clean?
Sofie Van Gassen (38:12):
Preferably neither, but if I have to, I
choose, I guess cleaning. I'mnot I'm not not the best cook.
Peter O'toole (38:19):
So is you a part of the cook at the house?
Sofie Van Gassen (38:21):
Yeah. Yeah. Yeah.
Peter O'toole (38:22):
Yeah? And what's their signature dish?
Sofie Van Gassen (38:26):
Oh, I don't know. I think
Peter O'toole (38:29):
What's the what's the favorite dish that he they
cook for you?
Sofie Van Gassen (38:36):
Also a good question. I think there's it's
it's also just the variety.We're also, like he it's also
not that his big ambition is isis cooking or his big passion is
cooking, so we're kind of justmaking do with easy dishes that
are ready quickly. And that'swhy we then enjoy eating out
once in a while, right, whenneither of us have to cook.
Peter O'toole (38:57):
Because my next question so that was going to be
which what what is it cookedthat you least like?
Sofie Van Gassen (39:05):
Yeah. I also don't have a very specific
answer to that. I think it'sit's I'm sorry. I'm very bad
with the names of I'm justtrying get
Peter O'toole (39:12):
you into trouble because you'll probably watch
this back. And you'll go, whyyou never told me you didn't
like that? And then you forgetit again. Oh, there was your I
think you guys never have itagain.
Sofie Van Gassen (39:22):
Sorry?
Peter O'toole (39:23):
There was your opportunity to say something,
and you never have to eat thatagain.
Sofie Van Gassen (39:27):
Oh, yeah. No. I don't think there's anything
like that. That's that's stillon the menu list right now.
Peter O'toole (39:34):
TV or book?
Sofie Van Gassen (39:36):
Books, for sure. Yeah.
Peter O'toole (39:38):
What are you reading at the moment?
Sofie Van Gassen (39:43):
I think the last thing I read was a very
silly rom com genre book, butthen before that, some nice
science fiction. So a balance ofthose, let's say, in general.
And once in a while, a nonfiction book, but that's that's
only once in a while, mainlyfiction. Yeah.
Peter O'toole (40:05):
Okay. And what's your favorite film? Favorite
movie?
Sofie Van Gassen (40:10):
Oh, that's also a very difficult question.
Maybe my answer can be more thatit's really been quite a long
time since I watched any movies.Like, the the question from,
like, television or books was avery easy question. I really
don't watch a lot of television.But
Peter O'toole (40:27):
you must come on. It was Mont before Edinburgh. It
was Montreal. Surely, youwatched movies on the plane.
Sofie Van Gassen (40:37):
Not that I remember right now, but probably
something, but nothing thatthat's stuck enough to to
remember right now. And theprobability, like, actually, on
a on a plane that I just sleepthe whole time is also quite
probable.
Peter O'toole (40:53):
Well, you could sleep on long haul flights.
Sofie Van Gassen (40:55):
I I think I don't know which one it was. It
was coming back from The States,but, like, it was not Montreal.
It was already longer ago. Butwe're I just, like I was not
fully awake yet anymore, Ithink, when we still had to lift
off, and then we landed, and wewere there. I kind of missed
Peter O'toole (41:12):
all of flights. We're on the East Coast meetings
then. So
Sofie Van Gassen (41:16):
it's Probably. Probably. Yes.
Peter O'toole (41:17):
Wilson Hall. Okay. Star Wars or Star Trek?
Sofie Van Gassen (41:25):
I think I've seen more Star Wars than Star
Trek, but I'm not strongly bigfan of either. And and and I
think probably from thereasoning point of view, I would
prefer Star Trek over Star Wars.
Peter O'toole (41:40):
Okay. Music. What's what's your favorite
music style?
Sofie Van Gassen (41:46):
Oh, actually, I'm listening more and more to
classical music lately, which asa I didn't really do as a as a
teenager or something, but,like, lately, that's bringing
back some calm and some nicememories from Sunday mornings as
a kid and so on. While then youthink, like, oh, why can't we
listen to my more fun musicrather than the boring, grow up
(42:07):
music? But I'm really gettingback to that more and more now.
Yeah.
Peter O'toole (42:12):
Favorite color?
Sofie Van Gassen (42:14):
Let's say green.
Peter O'toole (42:17):
Vixi green or GFP green?
Sofie Van Gassen (42:20):
What?
Peter O'toole (42:21):
Vixi green or GFP?
Sofie Van Gassen (42:24):
No. That's, like therefore, I'm too far away
from the instrument to to havean ounce of medicine.
Peter O'toole (42:33):
Okay. So moving moving on. Who would you say has
been your biggest inspiration inyour career so far?
Sofie Van Gassen (42:39):
That's also a difficult question. Right? I
think just in general, all thecomputational cytometrists, so
all the people at CyTO that arereally showing what change
algorithms can make, I'mthinking of Brian Brinkman,
Nima, all the all these peoplethat this many of them have been
(43:01):
a big inspiration for sure of ofbelieving that this is a field,
like that it's okay to focus onthis one field of cytometry and
trying to see what difference wecan make there. And then I think
otherwise, and it's maybe a bitmore vague, but all the the
people who show me that the workcan have an impact to all the
the people I'm collaboratingwith. And then I'm actually also
(43:25):
thinking in particular of Gerd,so our our the the head of our
core who's always there and justsaying, yes. We need these kind
of things. That's for sure alsobeen a big inspiration.
Peter O'toole (43:38):
And and but Dirt's a big name in the flow
world as well. So I I guess andyou've been there a fair while.
So and he's developed his namevery strongly since he's been
with the VIB.
Sofie Van Gassen (43:49):
So I I think it like, my first title was also
his first Saito as far as I'maware.
Peter O'toole (43:55):
So I can imagine anyone new going to VIB now
might find it quite intimidatingjust because he's such a big
name, whereas, actually, he'she's he's lovely. He's really
cool.
Sofie Van Gassen (44:05):
That's what I would say as well. Yeah. Yeah.
No no need to be intimidated. Ithink we're we're all very happy
for new people to learn aboutall these things, to start
exploring these things, to havefun with it, to do amazing
discoveries with cytometry.
Absolutely.
Peter O'toole (44:20):
To ask inspirations, does is there any
what's your biggest motivation?What motivates you? Who
motivates you? What motivatesyou?
Sofie Van Gassen (44:28):
Think my motivation, if I, like, look
back on things, is mainly havingother people being happy with
things. So so seeing peoplebeing able to use the tools that
I developed, like seeingFlowsome popping up on on work
of people I've never heard of,that that's amazing knowing that
you contributed something. Andthen also just in the
(44:50):
collaborations, I think if Ihave to do work on my own just
for myself, I'm a whole lot lessmotivated than if it's a group
effort or I know that someoneelse is involved who also cares
about the project. That's thatmakes a big difference for me.
Peter O'toole (45:04):
If this was an interview to work in the core
facility, you'd be doing verywell with that answer. It's very
much about
Sofie Van Gassen (45:11):
That's also why I was thinking. Like, this
seems seems like a good goodoption if that could become
possible. Right? That's that'sthe kind of thing I'm getting
excited about.
Peter O'toole (45:20):
Do you have any pet hates? What what annoys you?
What little things annoy you?Not necessarily in work in life
in general. What are your pethates?
What things annoy you?
Sofie Van Gassen (45:31):
That's a good question. I think when when
people are too too strict or or,like, don't have enough empathy
for someone else where they're,like, getting very, like, oh,
why doesn't this person do yeah.But you need to hear their part
of the story as well. Right? Andthere's probably a good reason
(45:52):
and things like that or or wherethere's, like yeah. I don't
know. People being very like,oh, but this is the way it
should be done, and this is canbe the only way. And then yeah.
But in some situations, there isa good reason for an exception
or these kind of things. So sobeing too strict in that sense,
I think, would be the main thingthat comes to mind.
Peter O'toole (46:15):
I I quite like that because that's almost
having an intolerance tointolerance.
Sofie Van Gassen (46:20):
Yeah. But that's that's I think that's
that's that's fair. I thinkthat's a good thing. That's the
one thing to be intolerant aboutis too much intolerance. I think
that's a good
Peter O'toole (46:30):
Yeah. No. I I a few inches. Actually, I I fully
agree. Yeah. I I findintolerant.
Sofie Van Gassen (46:35):
Reassuring to hear.
Peter O'toole (46:37):
Yeah. So outside of work, what hobbies do you do?
Sofie Van Gassen (46:41):
Yeah. So we already mentioned books. I like
reading quite a bit. Since Isince we, like, have our own
house, I also quite likegardening. My my parents had a
very nice garden with lots offlowers and so on, and I was
never really actively involvedin that as a kid. I was mainly,
(47:02):
like, somewhere inside reading abook. But then once once I moved
on my own, it was like, yeah, ifif I don't do anything in the
garden, there will not happenanything in the garden. And then
then I really started enjoyingthat as well. So that was also
very nice to, like, morereconnect with my mom in in that
sense. Yeah. And think thatwould be the main two things
(47:26):
right now. Yeah. And, of course,enjoying time with family with
my cats. Yeah.
Peter O'toole (47:33):
You said you don't have pets, so your
garden's gonna be easier tomaintain.
Sofie Van Gassen (47:37):
No. So I have a cat. I have a cat. Yeah. Yeah.
We still got it, like, fiveyears ago.
Peter O'toole (47:44):
Okay. So what sort of garden is it? Is it sort
of plants? Is it shrubs? Is ittrees? Is it is it are you
growing
Sofie Van Gassen (47:53):
in the community? Where we're currently
living, it's a quite smallgarden, but it's fully plants
with with plants. So there'sthere's no lawn. It's it's all,
yeah, mainly smaller plants, afew edible things, but also not
that like, I do that for the funof it, that it's fun to make
some like, to grow somethingthat you can eat, but not for,
(48:16):
like, our daily function oranything. That's more as a as a
hobby project than as an actualgoal of not having to go to the
supermarket kind of thing. Butso, yeah, lots of flowers,
things like that. We will movein yeah. Still still quite a
(48:37):
while to go. But then we'll havea bigger garden, so then we'll
be able to combine some lawnwith hopefully still lots of
plants as well. So
Peter O'toole (48:45):
excellent. That's
Sofie Van Gassen (48:46):
And then maybe even some room for trees. We'll
see. Yeah. So some smaller treesshould for sure be possible then
as well.
Peter O'toole (48:53):
So I like your future. You're already thinking
about house, what that's gonnabe like. The garden is obviously
a big prerequisite. If I was toask you, if you're coming up to
time, if I was to ask you, whatwhat would you see as the
biggest challenge in the worldof data science and flow
cytometry? Where would whatwould you like to see be solved?
What would you like to beeasier? Any of those.
Sofie Van Gassen (49:15):
In in in cytometry. Right? And I I think,
actually, maybe this is a verynice moment to give a shout out
to the SoulCAP initiative, wherewe're trying to standardize the
annotation of cytometry data,and I really very strongly
believe in that. So right now,everyone has their own gating
strategy. And when one person istalking about the certain cell
(49:39):
type, they might mean somethingelse than someone else talking
with a population with the samename. And then especially with
all the clustering and so on,it's also like, okay. You have a
cluster result, but which cellsare these now? It's that's still
a whole other question. So Ithink that's one of the big next
questions to be solved. And ifanyone would be interested to
working on this with the SoulCAPinitiative, we were really
(50:03):
making a a huge effort at this,and we would be very happy for
anyone to be involved in that.So then for sure reach out about
it. That would be great.
Peter O'toole (50:12):
Are you on any of the ISAC committees?
Sofie Van Gassen (50:17):
I'm on the data committee. It has not been
very active lately. I hope thatthat will pick up again at some
point. I was also on a taskforce at some point about site
to you when all the webinarswere going to be labeled and so
on, so I I helped a bit with thethe data science related ones
there. Yeah. But so main mainlythe data committee. And then now
(50:41):
there's also this task forcebeing started about more about
the data analysis education, somore fitting in the the flow
contents committee there. I'malso excited about that,
bringing more awareness aboutthe algorithms to all the people
using them who are now maybejust clicking a button without
really knowing what they'redoing. So so bringing that
(51:03):
message across is also exciting.
Peter O'toole (51:06):
There's quite a lot of potential there.
Sofie Van Gassen (51:08):
Yeah. Exactly. So
Peter O'toole (51:09):
that's what we're doing those things at the
moment.
Sofie Van Gassen (51:12):
That's what we're we're trying to make
happen. Exactly.
Peter O'toole (51:15):
Take it. Grab it. And and go
Sofie Van Gassen (51:17):
for it. Yeah. Exactly. That's that's that's
why the the subcommittee or taskforce or whatever it's called.
It's, it's it's being beingstarted right now. Yeah.
Peter O'toole (51:27):
And do you know what task forces, I think, could
be better than committees?Because task forces are far are
liberated. They don't have thebureaucracy of a committee. They
can just get on and do an actionand actually deliver things much
better.
Sofie Van Gassen (51:41):
I think there's there's value in both.
Right? So you
Peter O'toole (51:43):
you Yeah. Yeah. No.
Sofie Van Gassen (51:44):
I think you need to you need to have both.
But it's true. Like, I thinkwith the the task forces are
more actionable. Right? You youyou have a concrete plan, and
you go for it, and then and thenit gets done while the
committees are a bit more on onlong term vision and these
things. So it's, yeah, it's twodifferent things that both have
a lot of value, I think, for thecommunity.
Peter O'toole (52:04):
So, Sofie, I think I've come to to the time
point for the podcast. Thank youso much for joining me today.
Everyone who's listened,watched, thank you for your do
go back and look at the otherFlowstars. Sophie mentioned Ryan
Brinkman. Go go listen to hispodcast. He was, absolutely
brilliant. You've heard aboutIsaac and Saito, and, we've got
(52:26):
Virginia Litwin, as one of theco guests of this season that
you're listening to now. But youcan go back and listen to
previous presidents such asJessica Houston, Johnny Moore,
Paul Smith, Paul Robinson, oh,Wallace, the lot of them. But,
Sophie, today, god, it'sexciting having you in the
world, isn't it, Flow Cytometry?I think we're so fortunate to
(52:49):
have yourself and others likeyou really come to the fore and
putting your expertise in ourworld for data science and being
passionate about it. And Ireally hope you get that job in
the call because I think you'dbe brilliant at it. Sofie.
Sofie Van Gassen (53:04):
Yeah. Thank you so
Peter O'toole (53:04):
very much.
Sofie Van Gassen (53:05):
Thanks so much for having me, especially in
this long list of names. Itfeels like a bit intimidating to
be among all those great names,but it it was a very nice
opportunity. Thanks so much.
Peter O'toole (53:17):
It's a pleasure. It would have been great to have
them at this stage of theircareer. So this is why this is
so important. Sophie, thank you.
Sofie Van Gassen (53:25):
Thanks so much.
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