(soft music)
- Hi, and welcome to the Illumina customer solutions lab,
I'm Brian.
- And I'm Jill.
We're here today to give you an introduction to
BaseSpace Clarity LIMS, or just LIMS for short.
BaseSpace Clarity LIMS helps genomic labs that perform
sequencing, array, or any other genomics applications
to keep track of their wet-lab work flows,
as well as their samples.
- That's right, Jill.
Here in the customer solutions lab, I use all the
Illumina solutions before they make their way to customers.
And I can attest to how important it is to be able to know
where your samples are at any time in the work flow,
what's been done to them and by whom,
and where they're headed next.
Starting with a biological sample and prepping it
for sequencing or a microarray involves many steps
and often involves quite a few people,
it can be very complex.
Yet, believe it or not, there's a number of labs
that perform complex genomic studies struggling with only
whiteboards or spreadsheet applications to track their
workflows and experiments.
- We think that if more labs understood what a LIMS
is capable of, and the problems it solves,
then more labs would be using them.
So today, we wanted to describe in more detail
what a LIMS does and specifically talk about
BaseSpace Clarity LIMS.
Shall we get started?
- Sounds great.
What I'm most excited to hear about is what I
have to deal with on a daily basis as a lab manager,
and that is, what's happening to my samples.
Where are they headed in the workflow
and where are they headed next?
Can you tell me how this works in BaseSpace Clarity LIMS?
- Sure, let's get this whiteboard out of the way,
we won't be needing it anymore.
BaseSpace Clarity LIMS has a lot of functionality
but at it's core, it helps labs track samples
from the time they enter their lab until the sequencing
or microarray experiment is complete.
So, one example is this dashboard.
Depending on who you are in the lab,
we have different views tailored to your needs.
For you, from the lab management perspective,
you might want to focus on the high level view
of our overview dashboard.
This dashboard summarizes all of the samples that are
currently active in your system, as well as giving you
a graphical display of where those samples are
throughout the workflow.
So, as you can see here, I've got 315 samples in the
PCR-Free library prep.
That gives me an idea that in a day or so,
those samples are gonna be ready for my HiSeq instrument
for sequencing.
However, if you're a project manager, this high level of
detail might not be what you're interested in.
You want to drill down into that next level of granularity
using our projects dashboard.
You can still see the overall status of the lab
but it gives you the ability to click in to any
particular project to see the status.
For example, this whole genome sequencing project
has 377 samples in progress and I can even click in
to that next level of detail for exactly where
those samples are throughout my PCR-Free workflow.
And you can even pull a complete history of a sample
in case of an audit.
Using the search functionality, I can see every step
a sample has ever completed and if I want to,
I can dig in to see the exact timestamp of who did that work
and when it was done.
If you want to get really granular, there's a complete
audit trail.
I should also mention the e-signature and the reagent
tracking features.
Both of these support your work in a regulated environment.
Now we all know that labs require a lot of expertise
to accomplish their goals.
We've got people like you, Brian, as lab managers
but there are also technicians, scientists, informatics,
as well as lab directors.
That's the beauty of BaseSpace Clarity LIMS,
it helps each user track the information that they're
most interest in.
If I'm a lab technician, for example, I can go to the
lab view and precisely see each sample that needs to be
worked on today.
And only seeing the information that you're interested in
and that's applicable to your job helps you focus,
as well as creates more efficiency in the lab.
So, as a lab technician, if I see there are samples here at
Fragment DNA that I need to work on, I can simply go to the
ice bucket and check those samples out.
Ice bucket is a great metaphor for the way things work
in the lab.
I'm basically taking possession of these so no one else
is working on them at the same time I am.
- This is great, Jill, but how do you actually get
the samples into BaseSpace Clarity LIMS?
You know, sometimes I get a sample or two at a time
and then other times it might be a full plate.
I suspect that other customers might have the same problem.
- Depending on what type of lab you have Brian,
we have lots of options.
If you're the type of lab that gets one or two samples
at a time, you're likely gonna use our sample management
screen.
However, if you're receiving full plates or hundreds
or thousands of samples, you'll want to use our batch
upload, or programmatic options to get samples
into the system.
And here's where the really important work begins, Brian.
Once the samples are uploaded, you can assign a workflow
and let that workflow drive what happens to your samples.
It prevents you from getting steps out of order
and also puts your lab managers mind at ease that
your standard operating procedures are being followed.
- Maybe you can tell me a little bit about the different
workflows that BaseSpace Clarity LIMS can support.
- Sure.
BaseSpace Clarity LIMS was designed by scientists
specifically for the genomics applications.
It has preconfigured options for all your common
genomics workflows, like Next-Gen sequencing or microarray.
Let's take a look at an example workflow.
This workflow is the TruSeq PCR-Free for
the HiSeq instrument.
You probably noticed that these workflows have all been
preconfigured to the manufacturers protocol.
We did all the work of finding out exactly what these
protocols entailed and prepopulated them into the system
for a lot of the common applications.
As you can imagine, this saves time when getting
into production, as well as allows you to standardize
your own workflows.
- Now, the workflow that you showed me here is really
interesting, however, one of my challenges is that I work
with many workflows.
Can BaseSpace Clarity LIMS support those?
- Sure.
We have a lot of preconfigured options around protocols
and workflows that come standard in the system.
But even so, we know that there are cases where those
workflows will need to be modified.
And we took great pains to make sure this process
was as easy as possible.
You can build workflows through our configuration screen,
easily string them together, and then optionally lock them
down to enforce your own labs standard operating
procedures.
What this does is enable labs, not only to have access
to their production workflows, but helps them adapt to
new technologies that might be needed in the future.
Ultimately, this helps labs protect their investment
in LIMS and in their lab as well.
- Now, I've noticed another challenge with LIMS is
getting folks to adopt it.
You know, maybe it's a little bit clunky and doesn't
act the way that their lab does.
- Sure, we hear this a lot from people in the industry.
And the way that we've addressed this is by making
BaseSpace Clarity LIMS as intuitive as possible.
We built it to think the way a scientist does.
It's also highly configurable and both of these qualities
ensure that BaseSpace Clarity LIMS reflects the way you work
in your laboratory.
Which, in turn, makes it easier for people to adopt it
and use it.
- Now, you've shown me how to configure
BaseSpace Clairty LIMS, is it easy to customize?
- Now, the difference between configuration and
customization is an important one to point out.
Configuration, we mean the user can use the web interface
without have to modify any underlying code.
By customization, on the other hand, we mean that users
with programming or bioinformatics backgrounds can extend
the system by modifying.
If you have access to development resources or informatics
staff, it's straight forward to customize the LIMS
using our application programming interface, or API.
The API is a set of rules, protocols, and tools
that allow for customizing and extending
BaseSpace Clarity LIMS.
It's language agnostic and gives developers
and informaticians a diverse range of options
with which to customize.
Some of the most common examples we see in the field of
customizations are around automating sample entry
to reduce that need for mundane task and eliminate
or reduce the amount of errors you might have.
Integrating with external systems like freezer management
or phenotypic systems that hold phenotypic data.
This big one is automating of day to day library
prep task, mostly through the integration with liquid
handling or robotic applications.
Finally, pipelining and initiating secondary analysis
to allow a smooth flow between samples and LIMS,
sequencing, and downstream analysis.
I should also point out that we have several
toolkits available in BaseSpace Clarity LIMS.
I would say they fall somewhere between configuration
and customization.
It's not point and click on the screen
but it's doesn't require coding expertise either.
These toolkits allow you to enable your workflow
with business logic and most of the time,
a skilled Microsoft excel user can utilize these toolkits.
- Thanks for the tour.
As a lab manager, I can definitely see why it's imperative
to use a LIMS if you are conducting genomic studies.
And how a LIMS becomes even more important if you're
doing next generation sequencing, have a number of complex
workflows, work in a regulated environment,
or experiencing an increase in sample volume.
BaseSpace Clarity LIMS will help me track all of my samples
as they move from accessioning to sequencing and into
analysis, and easily check on their status.
- And hopefully, we've shown you how in addition to knowing
where all of your samples are, which helps you save time
and direct your work, that BaseSpace Clarity LIMS is a
system built by scientists for genomics.
This means it easily integrates with common laboratory
instruments, has preconfigured options for getting into
production quickly, makes the system easier to use
and adopt.
That easy configuration also means set up of new workflows
so you can adapt to the new methodology using genomics,
speaks your language and is capable of easily being
configured by any member of your lab.
And above and beyond all of the configuration that anybody
can do, I hope I've shown you a bit about the API
and how qualified users can use it to extend the system
even further.
Integrate to other laboratory systems,
automate repetitive task,
or even initiate downstream analysis.
(soft music)
Not to mention, you can get rid of that whiteboard
and all of your spreadsheets.
- We encourage you to learn more about how our
technology is changing the world of genomics.
(dramatic chimes)