Marine researchers used to have to ploddingly enter survey data into cumbersome spreadsheets. But, thanks to StoX – a free, open source program – those days are now gone.
Developed by researchers at the Institute for Marine Research (IMR), StoX was recently documented in an international peer-reviewed journal.
In nutshell, StoX enables marine researchers to feed survey data, such as data from echo sounders and trawl samples, into the program, which then generates an estimate of fish populations. The program also helps researchers to structure and analyse their data, and to calculate the uncertainty associated with their estimates.
After the first version was utilised in an IMR survey in 2014, StoX was quickly embraced by the International Council for the Exploration of the Seas (ICES). The software is now being used in surveys in the North Sea, Norwegian Sea and Barents Sea, and has become the standard tool for estimating populations in the North East Atlantic. It will soon be implemented in Antarctica – at which point it will have been used or tested on every continent.
The software was presented to the international research community in the highly respected journal Methods in Ecology and Evolution. In the article, the developers explain the most important concepts behind StoX:
It documents what the researchers have done, so that their estimates can be checked.
It is flexible, which means it can be adapted to different methods and areas.
The code is open source, and can be downloaded free of charge from the internet.
Cecilie Kvamme is among the IMR researchers who have gained practical experience in using StoX in conjunction with research surveys in the North Sea. According to Kvamme, using the new software is a whole new ballgame compared to entering data from research missions into big, unwieldy Excel spreadsheets. This is especially true in terms of communication between scientists.
“Five different countries participate in our surveys, and after they’re over we all meet up to combine our data,” she says.
Once everyone started using StoX, it made it easy to enter all of our raw data and jointly assess what should be included in the population estimate.
StoX documents each choice researchers makes along the way, so it is possible to review them and make changes at a later date. This was not exactly an easy task when the data was in a spreadsheet.
“Then you almost needed to get inside the heads of the people who had entered the data,” she says.
“We have created a workflow process that holds users’ hands step by step, and saves all of the steps for future reference. The ‘recipe’ is saved as a file in StoX, where it can easily be retrieved by other people,” explains researcher Espen Johnsen, who has led the project in recent years.
StoX is a key element of the IMR’s large-scale project on data infrastructure for field data, Sea2Data. The objective of the project is to quality assure and document the flow of data from the time it is collected at sea until the final survey estimates are produced.
Making it easy for researchers to make and test survey estimates was one of the key aims behind the development of StoX.
Senior Engineer Atle Totland has followed the development of StoX from its modest beginnings 10 years ago. He believes that StoX has greatly increased transparency when it comes to how marine scientists come up with their estimates.
“If I’m responsible for a survey and calculate a survey estimate, the software allows people to see what steps I have taken to reach that estimate. There are no secrets. If I have made any sub-optimal choices, absolutely anyone can go in and identify them,” he says.
The entire development process has taken place at the IMR, but support and suggestions from outsiders have been vital to the completion of the project. Input from international participants in the ICES has been particularly important. The ICES has now adapted its data collection methods to StoX, and has established a joint database where all countries report their data using a common template.
Atle Totland and Espen Johnsen co-authored the article with five other colleagues.
“We have been through a peer review process which demonstrates that our work is of high quality, and the journal thought that it was worth allocating space to our project and was willing to put its reputation behind it. We are very proud of that,” says Johnsen.
The article is Open Access, so it can be read by anyone. The authors hope that this will encourage even more scientists to start using StoX and contribute to its further development.
Espen Johnsen, Atle Totland, Åsmund Skålevik, Arne Johannes Holmin, Gjert Endre Dingsør, Edvin Fuglebakk, Nils Olav Handegard (2019): “StoX: An open source software for marine survey analyses.” Methods in Ecology and Evolution, 9/10, pp. 1377-1628. DOI: 10.1111/2041-210X.13250