paper.md and bib.md updates

Author: colmduff

joss_paper/paper/paper.bib

@@ -32,10 +32,10 @@ @article{Black:2025
   	Year = 2025
 }
 @article{Martinez-Acre:2025,
-  	doi = {},
-  	Author = {{Martinez-Acre}, A.},
-  	Journal = {Under review},
-  	Title = {{Critical evaluation of prospective biorefinery configurations to deliver a circular, climate neutral economy}},
+  	doi = {10.1016/j.seta.2025.104563},
+  	Author = {{Martinez-Acre}, A. and {Kargupta}, W. and {Girón Domínguez}, C. and {Odey}, E.A. and {McMahon}, H. and {Diaz Huerta}, J. and {Zimmermann}, J. and {Bishop}, G. and {Gaffey}, J. and {Styles}, D.},
+  	Journal = {Sustainable Energy Technologies and Assessments},
+  	Title = {{An integrated technoeconomic and environmental assessment of biomethane production via anaerobic digestion of food waste in Ireland: Updated insights under market volatility}},
   	Year = 2025
 }
 @article{Bishop:2024,

joss_paper/paper/paper.md

@@ -31,13 +31,13 @@ bibliography: paper.bib
 ---
 # Summary
 
-`OptiGob` is a Python-based tool designed to explore configurations of Ireland’s agriculture, forestry, and other land use (AFOLU) sectors. The main purpose is to assist users in the assessment of environmental and economic impact pathways, based on different land use transition pathways under varying assumptions about agricultural, afforestation, emissions abatement, and carbon dioxide removal (CDR) strategies. `OptiGob` combines data outputs from the GOBLIN Lite for agriculture and land use, from FERS-CBM for forestry, and from the LCAD2.0 for anaerobic digestion, to generate scenarios that respect biophysical constraints. `OptiGob` provides a flexible, customisable, tool for researchers, policymakers, and educators to explore environmental and economic trade-offs associated with land use transition pathways.
+`OptiGob` is a Python-based tool designed to explore configurations of Ireland’s agriculture, forestry, and other land use (AFOLU) sectors. The main purpose is to assist users in the assessment of environmental and economic impact pathways, based on different land use transition pathways under varying assumptions about agriculture, afforestation, emissions abatement, and carbon dioxide removal (CDR) strategies. `OptiGob` combines data outputs from the GOBLIN Lite for agriculture and land use, from FERS-CBM for forestry, and from the LCAD2.0 for anaerobic digestion, to generate scenarios that respect biophysical constraints. `OptiGob` provides a flexible, customisable tool for researchers, policymakers, and educators to explore environmental and economic trade-offs associated with land use transition pathways.
 
 # Statement of need
 
 Ireland's agricultural landscape is dominated by grassland, supporting extensive dairy and suckler beef production. Investment in Ireland's bio-economy requires substantial changes to the AFOLU sector. `OptiGob` allows users to manipulate critical AFOLU levers that determine transition pathways to explore their impacts. `OptiGob` utilises data from GOBLIN Lite [@Duffy:2024; @DuffyB:2022], FERS-CBM [@Black:2025; @Kurz:2008], and LCAD2.0 [@Martinez-Acre:2025] to calculate outputs from agriculture, forestry, and anaerobic digestion. This allows users to explore land use and livestock trade-offs, leveraging the outputs from the upstream models without the overhead of running upstream modelling chains. To the authors' knowledge, `OptiGob` represents the first attempt to do so in the Irish context. 
 
-`OptiGob` estimates the net greenhouse gas (GHG) emissions from land use change and estimates available emissions and land budget for grass-based livestock (Dairy and Suckler cow) production. `Pyomo` [@bynum2021pyomo; @hart2011pyomo] is used to optimise livestock populations, while respecting area commitment (afforestation, anaerobic digestion, BECCS (Bioenergy with Carbon Capture and Storage), protein crops) and emission (CO~2~e in the case of net-zero, or CH~4~ alongside net-zero CO~2~e for N~2~O and CO~2~ under a split gas target) constraints.
+`OptiGob` estimates the net greenhouse gas (GHG) emissions from land use change and available emissions and land budget for grass-based livestock (Dairy and Suckler cow) production. `Pyomo` [@bynum2021pyomo; @hart2011pyomo] is used to optimise livestock populations, while respecting area commitment (afforestation, anaerobic digestion, BECCS (Bioenergy with Carbon Capture and Storage), protein crops) and emission (CO~2~e in the case of net-zero, or CH~4~ alongside net-zero CO~2~e for N~2~O and CO~2~ under a split gas target) constraints.
 
 The GOBLIN framework has been applied in recent studies of net-zero pathways for AFOLU [@Henn:2025; @Bishop:2024; @DuffyB:2022]. `OptiGob` builds upon this framework, providing a single-interface tool for exploring synergies and trade-offs across sectors.
 
@@ -59,7 +59,7 @@ Agricultural productivity is selectable at three tiers. More ambitious scenarios
 
 An illustrative example is provided for a 2050 climate neutrality target year, using a 2020 baseline and a split-gas approach. The CH~4~ emissions are reduced by 30% relative to the baseline, while CO~2~ and N~2~O are balanced under GWP~100~.
 
-Parameter selection reflects the 'frontier' (strong productivity increase) abatement path. The 10:1 dairy-to-beef ratio reflects a dairy-dominated pathway. A higher afforestation rate (16 kha per year), with a composition of 70:30 conifer to broadleaf split. BECCS and bio-energy (anaerobic digestion and willow) are also included. Wetland restoration is assumed to be 90% of exploited peatland, and 50% of organic soils under grass rewetted. Pig and poultry output has also been increased by 20%.
+Parameter selection reflects the 'frontier' (strong productivity increase) abatement path. The 10:1 dairy-to-beef ratio reflects a dairy-dominated pathway. A higher afforestation rate (16 kha per year), with a composition of 70:30 conifer to broadleaf split is applied. BECCS and bio-energy (anaerobic digestion and willow) are also included. Wetland restoration is assumed to be 90% of exploited peatland, and 50% of organic soils under grass rewetted. Pig and poultry output has also been increased by 20%.
 
 Figure 2 shows the emissions and removals by category for the baseline and transition scenario.