Advancing Marine Biogeochemical and Ecosystem Reanalyses and Forecasts as Tools for Monitoring and Managing Ecosystem Health

Ocean ecosystems are subject to a multitude of stressors, including changes in ocean physics and biogeochemistry, and direct anthropogenic influences. Implementation of protective and adaptive measures for ocean ecosystems requires a combination of ocean observations with analysis and prediction tools. These can guide assessments of the current state of ocean ecosystems, elucidate ongoing trends and shifts, and anticipate impacts of climate change and management policies. Analysis and prediction tools are defined here as ocean circulation models that are coupled to biogeochemical or ecological models. The range of potential applications for these systems is broad, ranging from reanalyses for the assessment of past and current states, and short-term and seasonal forecasts, to scenario simulations including climate change projections. The objectives of this article are to illustrate current capabilities with regard to the three types of applications, and to discuss the challenges and opportunities. Representative examples of global and regional systems are described with particular emphasis on those in operational or pre-operational use. With regard to the benefits and challenges, similar considerations apply to biogeochemical and ecological prediction systems as do to physical systems. However, at present there are at least two major differences: (1) biogeochemical observation streams are much sparser than physical streams presenting a significant hinderance, and (2) biogeochemical and ecological models are largely unconstrained because of insufficient observations. Expansion of biogeochemical and ecological observation systems will allow for significant advances in the development and application of analysis and prediction tools for ocean biogeochemistry and ecosystems, with multiple societal benefits

FreeSolv: a database of experimental and calculated hydration free energies, with input files

This work provides a curated database of experimental and calculated hydration free energies for small neutral molecules in water, along with molecular structures, input files, references, and annotations. We call this the Free Solvation Database, or FreeSolv. Experimental values were taken from prior literature and will continue to be curated, with updated experimental references and data added as they become available. Calculated values are based on alchemical free energy calculations using molecular dynamics simulations. These used the GAFF small molecule force field in TIP3P water with AM1-BCC charges. Values were calculated with the GROMACS simulation package, with full details given in references cited within the database itself. This database builds in part on a previous, 504-molecule database containing similar information. However, additional curation of both experimental data and calculated values has been done here, and the total number of molecules is now up to 643. Additional information is now included in the database, such as SMILES strings, PubChem compound IDs, accurate reference DOIs, and others. One version of the database is provided in the Supporting Information of this article, but as ongoing updates are envisioned, the database is now versioned and hosted online. In addition to providing the database, this work describes its construction process. The database is available free-of-charge via http://www.escholarship.org/uc/item/6sd403pz