Software Development 


ModECI (Model Exchange and Convergence Initiative) is a project that seeks to accelerate the convergence of progress in the brain, cognitive and computer sciences by facilitating the exchange of computational models, through the development of a standardized model description format, that expresses models in the form of a computational graph in which each node is a computational component and edges specify connections between them that determine the flow of computation. The format is implemented in serialized forms (e.g., JSON, YAML) that allows the exchange of models in machine-readable form among a broad range of existing environments — from biologically detailed ones (e.g., NeuroML, Emergent, and Nengo) and system-level level packages (such as PsyNeuLink) to abstract symbol processing environments used in cognitive science (such as ACT-R) and neural network modeling ones served by the ONNX standard used in the machine learning community (e.g., PyTorch and TensorFlow).



PsyNeuLink is an open-source Python package designed for neuroscientists, psychologists, computational psychiatrists, and others interested in building system-level models for exploring brain function, psychological processes and behavior, as well as the connections between these topics and machine learning. It provides customizable components and an environment for connecting and executing them, allowing users to assemble, simulate, document, and share models of neural mechanisms and psychological processes. PsyNeuLink allows components to be constructed that implement various, possibly disparate functions, at potentially different levels of analysis and/or timescale of operation, and integrate these into a coherent modeling environment that can be used to simulate and study their interaction. 

PsyNeuLink currently includes a suite of core components for implementing models of various forms of processing, learning, and control, as well as examples of how these components can be customized and connected in order to implement published models. PsyNeuLink welcomes contributions to both the library of components, which is meant to be enhanced and extended, as well as the repository of models, which can serve as a concise, executable, and easy to interpret format for sharing and comparing computational models. 



The reliability and validity of experimental results heavily relies on rigorous, reproducible experimental design. SweetPea is an experimental design environment that simplifies and standardizes the format in which experimental factors are expressed and combined, and used to generate balanced samples of valid trial sequences. With SweetPea, researchers specify a broad range of experiments via factors, relationships between factors, and sequential constraints. The generated trials are sampled with equal likelihood from every possible sequence of trials that satisfies the design, thereby avoiding biases introduced by traditional trial sequence generation methods.



BrainIAK (Brain Imaging Analysis Kit) is a Python-based, open source software package, developed in collaboration with Intel Labs, that supports the application of advanced methods from machine learning and multivariate statistics to the analysis of neuroimaging data. It applies advanced machine learning methods and high-performance computing to analyzing neuroimaging data. BrainIAK is tightly integrated with SciKit-Learn, and includes modules for Full Correlation Matrix Analysis (FCMA), Multi-voxel Pattern Analysis (MVPA), a suite of methods for Shared Response Modeling (SRM), Topographic Factor Analysis (TFA), Bayesian-derived methods for Representational Similarity Analysis (RSA), and more. 



PsyScope is the first graphical environment for the design and execution of cognitive behavioral experiments. It functions as graphical user interface (GUI) software program that allows researchers to design and run psychological experiments. PsyScope provides the ability to present stimuli in text, graphic, and acoustic form, and can be used to record manual or voice responses with millisecond accuracy. It incorporates a fully general scripting language, as well as a graphic interface, and is extensible through the use of plug-and-play add-on modules. PsyScope runs on Apple Macintosh computers and was originally designed for use with the Mac OS 9 platform. The design of PsyScope also provided one of the foundations for E-Prime, a PC/Windows-based commercially supported package that was developed in collaboration with Psychology Software Tools (PST) Inc. and is also in widespread use.