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June townhall

Summer time with no Summer break

Oops… Zoom didn’t record the Townhall of June. We could say, ‘be there or be square!’ but of course we know we all have busy agendas and many of you like to watch the quarterly update of ARISE, the Townhall, at your leisure, especially with such a nice summer.

And there is a lot to tell! So let’s give you a brief overview here on what is happening:

From Sample to DNA sequence identification

The Netherlands harbors ca 45k species, yet for almost 20k we are still missing the DNA to recognize them through barcoding technology. To allow a future where monitoring based on DNA is the new normal we need to also get barcodes for that other 50%. Our targetlist is ready to be used by any species organization, expert or hobbyist willing to help out. We will provide any material you need, including a very cool sampling tool (ADA) on your phone, and the sampling team is ready to take on whatever comes in. The aim is to go from 5k species per year to 100k species per year (2030) and mid-2023 we’re already at 5k, so moving up that needle. Amongst these are some new fungal species for the Netherlands, now published.

fungal hyphae
Cladophialophora laricicola, a new species of fungus discovered in the Netherlands

Cheaper than ever

The optimization of the DNA lab processes, including Nanopore technology, has enabled lowering the cost price for a sample to 2 Euros! A major achievement by the sequencing team to make species recognition through barcoding accessible for anyone. We also hosted a great number of students who helped us with some great R&D on for instance getting DNA from museum specimens, validating barcoding for bulk specimens, e.g. malaise traps, and improving bioinformatic workflows.

From sensor image to digital identification

Eight different sensor types, and over 100 sensors altogether, are in the field and being tested to optimize digital monitoring strategies. The monitoring demonstration team is making big steps towards an automated monitoring network. The sensor dashboard built by the team gives insights into all those sensors in one place!, and is already being used by some landowners and key stakeholders. More sensors also means developing various new AI models for recognition, e.g. geese counting or human detection, which is, for instance, done through student assignments of Hogeschool van Amsterdam or Fontys Hogeschool. The digital species identification team is working on a flow to enable making such new models easily available in the ARISE AI repository. Soon anyone can start using them and even better, soon such new models can be automatically evaluated by a Grand challenges tool - work in progress. Through the ARISE AI platform the first batches of images can already be analyzed - click & analyze!

The really techie stuff underneath

Now no cool stuff can happen without a proper foundation. In the case of ARISE it means bringing together various data types, from smart nestbox to DNA sequence of a museum specimen and also from various digital locations. There is no other infrastructure that has ever attempted bringing together such a wide variety and enabling communication between such data to answer biodiversity questions. The biocloud team has been building such foundational components and after many data and infrastructure challenges our ARISE Lakehouse, orchestrating all that data, is almost ready for its first full dataflows. That means image, sound, sequence and many more data types can soon be streamed through the biocloud and connect various in- and outputs.

Sugar, spice and everything nice

It’s definitely been a whirlwind this past quarter, next to all the hard labor happening within the team. The minister of science, Robbert Dijkgraaf, and head of NWO, Marcel Levi, came to visit ARISE. The intelligent nestboxes developed by University of Twente which connect to ARISE made it to the national news, TV, Article. With a team of twelve we visited Canada (see other blog), we have officially launched the national species challenge, aka Targetlist (see other blog), and Capgemini is currently hosting a global data science challenge which will deliver the top 5 AI models for sound recognition for insects, e.g. crickets and cicadas.

Now you may think we deserve a Summer break… and of course we will enjoy the outdoors when we can. Yet at the same time there is so much more to build! To give you a glimpse of the future…our goal is to deliver the end to end pipeline to our first Diopsis sensor users this Summer. A big milestone which will open the gate to welcome more sensors, more data and more users for digital species recognition. On the sampling side we have some great events coming up to involve citizens and experts in our quest to obtain reference species (see other blog and invite). And of course that data should become available to the world, so the data pipelines and digital environment around DNA sequence data, our core sequencing cloud, will get its first prototypes up and running in the upcoming months. Alltogether something you really don’t want to miss.


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