An online tool to easily run stock assessment models, using SS3 and SWO as an example

Stock assessment software are complex and advanced technical skills are required to develop the models. Producing output becomes time-intensive and even more complex as thousands of simulations must be run on supercomputers in order to include the multiple sources of uncertainty in assessment results. As few stock assessment participants have the specific technical skills required to reproduce these outputs, our aim has been to develop a Virtual Research Environment (VRE) that enables any user to easily parameterize, execute and edit online various steps of the stock assessment work flow using SS3 (a widely-used statistical catch-at-age model), with standardized data outputs. A collaborative environment such as the VRE uses simple tools to enable the storage and access of the data and source codes necessary to replicate past results or to try new parameterizations of the model. The VRE will provide various collaborative web services, including: (i) a workspace to share documents or data, (ii) webpages or an RStudio server to process data online, and (iii) an automated reporting service to dynamically generate documents to package the results. Here, we illustrate the stock assessment work flow through the VRE, using the last stock assessment of yellowfin, provided by the IOTC, as an example. Currently, we are also able to replicate past stock assessments of swordfish and bigeye tuna, and theoretically, any species model using SS3 can be similarly replicated. Increasing access to this complex model will bring more transparency and collaboration within working groups by providing ∗IRD, UMR MARBEC (IRD/Ifremer/Univ.Montpellier/CNRS), IRD Réunion, 97744 St Denis, La Réunion, France; anneelise.nieblas@ird.fr †IFREMERDOI, rue Jean Bertho, 97822 LE PORT CEDEX, La Réunion, France ‡IRD UMR MARBEC 248, Av. Jean Monnet, 34200 Sète, France §IOTC, Le Chantier Mall, Victoria Mahé, Seychelles ¶IRD, UMR MARBEC (IRD/Ifremer/Univ.Montpellier/CNRS), IOC, Rue de l’Institut, Ebène, Maurice