Dear all first, I recommend you to install the version 4.4.0.2 of ISIS-fish and not the last one, which is still under testing. Second, do you understand French because the manual is still in French .... :-\ ? Le 14/07/2017 10:13, Silvia Angelini a écrit :

Dear Dr. Mahévas,

here we are Silvia Angelini and Lorenzo D'Andrea, we are two researchers working with Dr. Tommaso Russo of the University of Tor Vergata in Rome. Tommaso probably contacted you before to inform that we are using ISIS-Fish in the framework of the MANTIS project. MANTIS aims at investigating how a network of marine managed areas (MMAs) can contribute to improve sustainable fisheries in the Mediterranean. In particular, we would like to explore the effect of spatial closures and other management measures for the most important species of the trawl fishery in the our two case studies, that are one in the Adriatic Sea and the other one in the Strait of Sicily (SoS).

We start setting the ISIS-Fish model for the stock of Mullus barbatus living in the SoS, but to proceed with the work we need to ask some clarifications, summarised in the list that you can find hereunder. Can we gently ask some help for clarifing our doubts? I try to answer your questions but I recommend you to read carefully the two papers of reference of the model (attached to this email). It should help you to understand the processes described and the way they can be set in the interfaces. More information are available and updated on the website of ISIS-Fish but unfortunately most tutorials are in French... You can also explore (as a source of ideas) some databases of fisheries modeled with ISIS-fish and available on the website http://www.isis-fish.org/download.html (Base de donnees Golfe de Gascogne Prospective ou Base Channel Faltfish Fishery).

1) About the population structure, we tried to include the growth both manually or using the growth equation but in both cases the resulting ages and lengths do not match our expectations;

Is it age or length structured? I recommend to start with an age-structured model. if you specify a length-structured model and you want the age of the length group, you need to specify the inverse growth curve. Can you send us your database (exported from the interface Region, http://www.isis-fish.org/v4/user/usermanual/inputs.html#menu-region) and a table with what you expect ?

2) In the Species-Zones section, why all the areas are present in both boxes, spawning and recruitment areas? You first define the population zones (the definition of zones is given in Mahevas et al 2004). Then you precise the recruitment zone (where recruitment takes place) and the spawning zone (where reproduction (concentration of spawners) takes place). And finaly the matrix below allows you to specify the connectivity between spawning zones and recruitment zones. 3) About the life history traits, can you explain how to include the maturity ogive and the reproduction rate? you need to set an equation in the user-interface

example of maturity ogive : double lg=group.getLength(); double Maturite=(1/(1+Math.exp(-0.2*(lg-42.85)))); return Maturite; example of reproduction rate if (group == null) return 0.0; else return 0.4; more examples in http://www.isis-fish.org/v4/user/usermanual/inputs.html#onglet-saisie-des-eq...

4) About the recruitment section: Do we have to include the reproduction equation? no a stock-recruitment equation is enough Fisrt define the spawning season and the number of months between spawning and recruitement. If recruitment spreads over several month you can also define the distribution of recruitment Then, Reproduction equation should be : return 0; Recruitment equation should be implemented in the interface below the reproduction equation, box - "recruitment equation". Two examples are available here : http://www.isis-fish.org/v4/user/scripts.html

5) About the accessibility: How can we get these values? What do they represent? The accessibility of each age group in each area? this parameter is defined in Mahevas et al 2014. It is more availability than accessibility. It represent the proportion of abundance available to fishing (whatever the metier). It is used to compute fishing mortality, multiplying catchability and the standardized fishing effort. You can set it to 1 if you do not have any knowledge about it. Otherwhise it can be estimated during the calibration step of the model.

6) About the price, is this one interpreted as €/kg? It depends on the unity of your weight/age or weight/length relationship. If this one is in kg then price should be in kg. If it is in g than it should be in g. 7) About the stocks section: do we have to fill the Fbar min and max group as in the stock assessment? What is the 'abundance reference month'? And which is the difference of selecting or not selecting 'F computed on landings'? yes abundance reference month is the month at which the assessment working group is supposed to estimate the annual abundance and the annual fishing mortality (generally january)

8) Gears section: what is the standardisation effort? in Mahevas et al 2004 and Pelletier et al 2009

9) About the 'Set of vessels' section: what does 'Fixed costs' mean? There is a list of costs in the 'metier parameters’ section again in Pelletier et al 2009

We are sorry for the long list of questions, but there are different points in which we are stuck. Thank you so much for your help.

Best regards

Silvia and Lorenzo

I hope these few elements will help you.... The "good" way of doing when you have some troubles with ISIS-Fish is to ask your question on the ISIS-Fish mailing list. To subscribe the users mailing list, you should fill a template (http://list.isis-fish.org/cgi-bin/mailman/listinfo/isis-fish-users). Finaly, if you have some funds for traveling, you can also plan a stay in Nantes to interact face-to-face with Isis-fish users and developpers.... Best Stephanie -- ...................................................................... Stephanie MAHEVAS (Stephanie.Mahevas@ifremer.fr) IFREMER/EMH (Ecologie et Modèles pour l'Halieutique) Tel: (33) 2 40 37 41 81 Fax: (33) 2 40 37 40 75 o \ o / _ o __| \ / |__ o _ \ o / o /|\ | /\ ___\o \o | o/ o/__ /\ | /|\ / \ / \ | \ /) | ( \ /o\ / ) | (\ / | / \ / \ ......................................................................