Objective Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate, comprehensive models of complex cells. Methods We organized the 2015 Whole-Cell Modeling Summer School to teach WC modeling and evaluate the need for new WC modeling standards and software by recoding a recently published WC model in SBML. Results Our analysis revealed several challenges to representing WC models using the current standards. Conclusion We, therefore, propose several new WC modeling standards, software, and databases. Significance We anticipate that these new standards and software will enable more comprehensive models.

The scientific community observes the ocean for applications in the fields of oceanography and climate research. To recover in situ data, more than 3000 profiling floats are operated in the framework of the Argo program. Each float performs cycles between the sea surface and a depth of 2000 m. Scientific data are gathered while the float is traveling upward from the depths of the oceans and are then transmitted via a satellite communication system at the end of each cycle. During its time at the surface, mainly dedicated to transmissions, the float is vulnerable and subject to drift, which limits its use in many studies. Moreover, transmission times are becoming longer due to a trend toward high-resolution or multisensor profiles. Consequently, the transmission system embedded in the profiling floats had to evolve. Argos-3 is the latest generation of the Argos satellite communication system. It has been designed to allow instruments to transmit more data in a small time budget and as an alternative to Iridium, already implemented on profiling floats in restrictive applications. This study aims to evaluate the implementation of Argos-3 on Arvor profiling floats. Tests were carried out first in the laboratory, before being implemented on the Arvor float and deployed at sea. This study proves that the high-data-rate mode suffered from European electromagnetic noise, which is incompatible with this application. The interactive low-data-rate mode was successfully qualified; it is capable of transmitting an entire dataset in a few minutes, compared to 8–10 h for the previous Argos-2 system.

The oceans are a fundamental source for climate balance, sustainability of resources and life on Earth, therefore society has a strong and pressing interest in maintaining and, where possible, restoring the health of the marine ecosystems. Effective, integrated ocean observation is key to suggesting actions to reduce anthropogenic impact from coastal to deep-sea environments and address the main challenges of the 21st century, which are summarized in the UN Sustainable Development Goals and Blue Growth strategies. The European Multidisciplinary Seafloor and water column Observatory (EMSO), is a European Research Infrastructure Consortium (ERIC), with the aim of providing long-term observations via fixed-point ocean observatories in key environmental locations across European seas from the Arctic to the Black Sea. These may be supported by ship-based observations and autonomous systems such as gliders. In this paper, we present the EMSO Generic Instrument Module (EGIM), a deployment ready multi-sensor instrumentation module, designed to measure physical, biogeochemical, biological and ecosystem variables consistently, in a range of marine environments, over long periods of time. Here, we describe the system, features, configuration, operation and data management. We demonstrate, through a series of coastal and oceanic pilot experiments that the EGIM is a valuable standard ocean observation module, which can significantly improve the capacity of existing ocean observatories and provides the basis for new observatories. The diverse examples of use included the monitoring of fish activity response upon oceanographic variability, hydrothermal vent fluids and particle dispersion, passive acoustic monitoring of marine mammals and time series of environmental variation in the water column. With the EGIM available to all the EMSO Regional Facilities, EMSO will be reaching a milestone in standardization and interoperability, marking a key capability advancement in addressing issues of sustainability in resource and habitat management of the oceans.

The EGIM aims to set up a number of ocean locations where the same set of core variables, including temperature, conductivity, pressure, dissolved O2, turbidity, ocean currents, and passive acoustics, are measured homogeneously: using identical hardware, the same sensor references, the same qualification methods, the same calibration methods, the same data format and access, and the same maintenance procedures. The EGIM provides all the services required to ensure the best measurement quality and long-term reliability in line with the Best Practices Handbook by FIXO3 and ESONET-EMSO Label, these services being sensor power distribution, time stamping, data storage and backup, protection against the environment and against fouling and bi-directional communication services… The EGIM is flexible and matches all EMSO site and discipline specific requirements. Operating modes, power requirements, mechanical design, embedded software enable the EGIM to adapt to the various EMSO node configurations: mooring line, sea bed station, cabled or non-cabled and surface buoy. Its compact and its modularity covers an array of deployment scenarios including being able to accommodate new instruments. This will be a key point to the modularity, inter-operability and capacity of the future evolution of the system. Having the EGIM as the sole reference for all nodes is a crucial step towards standardization, increasing global reliability and reducing costs across EMSO.

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