The document discusses how to create an integrated lab by using an electronic lab notebook (ELN) as a central system that integrates with other lab tools and data sources. It notes that a professor spent too much time copying data between spreadsheets and would benefit from a fully integrated system. Such a system using an ELN as the central source of truth can automatically pull in raw data from instruments and push it to analysis tools, saving time and improving traceability. Inventory can also be tracked to automate reagent reordering. The document recommends starting with an ELN and further integrating additional sources over time.

2. Recently I have spent 1 day with an assistant
professor, who just started his own lab …

3. ... I shadowed him for a day and he showed me
how he runs his lab, coordinates team meetings,
and tracks progress …

4. He is a very organized person and had put in place a very
sophisticated system of spreadsheets for everything (from tracking
experiments to ordering reagents).
However, for this system to work, he had to spend: 4 hours each
day!

5. At the end of the day, he confessed: "I spend way too much time
copy-pasting data in different spreadsheets. If only all this data
could work together.".

6. ... so here is my advice on
How To Create an Integrated Lab:

8. As the science output increases due to the progress of technology,
you will need fully integrated systems that can automate the data flow.
Relying on a number of spreadsheets, notebooks and other systems to
track progress and inventory is error-prone and very tedious to maintain.

10. In order to achieve interoperability of data, we have to have a "common
denominator", a software tool that is the single source of truth.
Scientists' work varies heavily between fields, methods, equipment
availability, and budget to name just a few. Therefore, every
scientist needs a different set of tools to perform their research.

11. The only approach that we see viable for the future is to have a "central
nervous system", which has an API (application programming
interface) and integrates with other, specific tools (from data acquisition
to analysis and publishing).
Electronic lab notebooks (ELN) seem to be a natural fit for this.

13. Many of cloud providers (Google, Dropbox, Microsoft) also offer
their tools for data and document editing, so it is essential that
they are integrated with an ELN.
The output of scientific data is exponentially increasing and digital
storage space has become a bottleneck.

14. There are already many platforms out there that collect data
from different sources and send them to the cloud. It is then
relatively easy to pull all this data into an ELN.
Being able to pull raw data automatically from scientific instruments not
only saves time but also makes everything much more traceable.

15. It takes too long before the data becomes the final graph or image.
Being able to push raw data directly to analytic tools would also save a
lot of time as well as track the analysis automatically.
The number of data analysis tools is growing even faster than the number
of lab instruments and many scientists use over 50 tools for their work.

16. Having inventory associated with experiments you do, can enable the
system to make predictions about the amounts required, as well as
automate the ordering of reagents once they are below a threshold.
One of the most challenging and time-consuming things in a lab: to keep track
of inventory. It is usually done through a master Excel file, with lists never
completely up to date that may leave you without a reagent mid-experiment.

17. This way we can also track which modifications we made to the
materials and methods of other researchers and position our
research within the realm of broader science.
All of the above should be integrated with relevant existing knowledge in the
scientific literature. It would enable us to see what inspired us to do an
experiment and why we made some assumptions.

18. Starting with an ELN and going from paper to digital is a good 1st step.
We are nowhere near the complete solution to scientific data interoperability.
However, a lot of ELN vendors are coming up with clever integrations, falling
into their natural place as the single source of truth.

19. „Once you are comfortable with a digital system in
your lab, integrations are just one step away."

20. With SciNote we have already integrated Gilson IoT platform, Protocols.io
and Microsoft online + we have a few of them lined up already.
SciNote is open source and free to use, so I recommend you
give it a try at: SciNote.net

21. Read Full Article
Written by: Klemen Zupancic, PhD – CEO
Experienced business development professional with a PhD in Biomedicine – Genomics
and a demonstrated history of working in the Computer Software industry.