Computer science offers a large set of tools for prototyping, writing, running, testing, validating, sharing and reproducing results; however, computational science lags behind. In the best case, authors may provide their source code as a compressed archive and they may feel confident their research is reproducible. But this is not exactly true. James Buckheit and David Donoho proposed more than two decades ago that an article about computational results is advertising, not scholarship. The actual scholarship is the full software environment, code, and data that produced the result. This implies new workflows, in particular in peer-reviews. Existing journals have been slow to adapt: source codes are rarely requested and are hardly ever actually executed to check that they produce the results advertised in the article. ReScience is a peer-reviewed journal that targets computational research and encourages the explicit replication of already published research, promoting new and open-source implementations in order to ensure that the original research can be replicated from its description. To achieve this goal, the whole publishing chain is radically different from other traditional scientific journals. ReScience resides on GitHub where each new implementation of a computational study is made available together with comments, explanations, and software tests.

The transmembrane ionic currents that underlie changes in a cell's membrane potential give rise to electric fields in the extracellular space. In the context of brain activity, these electric fields form the basis for extracellularly recorded signals, such as multiunit activity, local field potentials and electroencephalograms. Understanding the underlying neuronal dynamics and localizing current sources using these signals is often challenging, and therefore effective computational modeling approaches are critical. Typically, the electric fields from neural activity are modeled in a post-hoc form, i.e., a traditional neuronal model is used to first generate the membrane currents, which in turn are then used to calculate the electric fields. When the conductivity of the extracellular space is high, the electric fields are weak, and therefore treating membrane currents and electric fields separately is justified. However, in brain regions of lower conductivity, extracellular fields can feed back and significantly influence the underlying transmembrane currents and dynamics of nearby neurons—this is often referred to as ephaptic coupling. The closed-loop nature of ephaptic coupling cannot be modeled using the post-hoc approaches implemented by existing software tools; instead, electric fields and neuronal dynamics must be solved simultaneously. To this end, we have developed a generalized modeling toolbox for studying ephaptic coupling in compartmental neuron models: E L FENN (E L ectric Field Effects in Neural Networks). In open loop conditions, we validate the separate components of E L FENN for modeling membrane dynamics and associated field potentials against standard approaches (NEURON and LFPy). Unlike standard approaches however, E L FENN enables the closed-loop condition to be modeled as well, in that the field potentials can feed back and influence membrane dynamics. As an example closed-loop case, we use E L FENN to study phase-locking of action potentials generated by a population of axons running parallel in a bundle. Being able to efficiently explore ephaptic coupling from a computational perspective using tools, such as E L FENN will allow us to better understand the physical basis of electric fields in the brain, as well as the conditions in which these fields may influence neuronal dynamics in general.

Identifying and understanding the current sources that give rise to bioelectric fields is a fundamental problem in the biological sciences. It is very difficult, for example, to attribute the time-varying features of an electroencephalogram recorded from the head surface to the neural activity of specific brain areas; model systems can provide important insight into such problems. Some species of fish actively generate an oscillating (c. 1000 Hz) quasi-dipole electric field to communicate and sense their environment in the dark. A specialized electric organ comprises neuron-like cells whose collective signal underlies this electric field. As a step towards understanding the detailed biophysics of signal generation in these fish, we use an anatomically-detailed finite-element modelling approach to reverse-engineer the electric organ signal over one oscillation cycle. We find that the spatiotemporal profile of current along the electric organ constitutes a travelling wave that is well-described by two spatial Fourier components varying in time. The conduction velocity of this wave is faster than action potential conduction in any known neuronal axon (>200 m/s), suggesting that the spatiotemporal features of high-frequency electric organ discharges are not constrained by the conduction velocities of spinal neuron pathways.

Sensory systems encode environmental information that is necessary for adaptive behavioural choices, and thus greatly influence the evolution of animal behaviour and the underlying neural circuits. Here, we evaluate how the quality of sensory information impacts the jamming avoidance response (JAR) in weakly electric fish. To sense their environment, these fish generate an oscillating electric field: the electric organ discharge (EOD). Nearby fish with similar EOD frequencies perform the JAR to increase the difference between their EOD frequencies, i.e. their difference frequency (DF). The fish determines the sign of the DF: when it has a lower frequency (DF > 0), EOD frequency is decreased and vice versa We study the sensory basis of the JAR in two species: have a high frequency ( 1000 Hz), spatio-temporally heterogeneous electric field, whereas sp. have a low frequency ( 300 Hz), spatially uniform field. We show that the increased complexity of the field decreases the reliability of sensory cues used to determine the DF. Interestingly, responds to all JAR stimuli by increasing EOD frequency, having lost the neural pathway that produces JAR-related decreases in EOD frequency. Our results suggest that electric field complexity may have influenced the evolution of the JAR by degrading the related sensory information.

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