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Programming for distributed memory machines has always been a tedious task, but necessary because compilers have not been sufficiently able to optimize for such machines themselves. Molly is an extension to the LLVM compiler toolchain that…
Multiplexed imaging data are revolutionizing our understanding of the composition and organization of tissues and tumors. A critical aspect of such tissue profiling is quantifying the spatial relationship relationships among cells at…
Throughout our history, we, humans, have sought to better control and understand our environment. To this end, we have extended our natural senses with a host of sensors-tools that enable us to detect both the very large, such as the…
As it is getting increasingly difficult to achieve gains in the density and power efficiency of microelectronic computing devices because of lithographic techniques reaching fundamental physical limits, new approaches are required to…
Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is…
We present a fully modular and scalable software pipeline for processing electron microscope (EM) images of brain slices into 3D visualization of individual neurons and demonstrate an end-to-end segmentation of a large EM volume using a…
Biological living materials, such as animal bones and plant stems, are able to self-heal, regenerate, adapt and make decisions under environmental pressures. Despite recent successful efforts to imbue synthetic materials with some of these…
Real time computer control is an essential feature of scanning probe microscopes, which have become essential tools for the characterization and investigation of nanometer scale samples. Most commercial (and some open-source) scanning probe…
Cells are the fundamental unit of biological organization, and identifying them in imaging data - cell segmentation - is a critical task for various cellular imaging experiments. While deep learning methods have led to substantial progress…
For decades, researchers have been applying computer simulation to address problems in biology. However, many of these "grand challenges" in computational biology, such as simulating how proteins fold, remained unsolved due to their great…
Many fabric handling and 2D deformable material tasks in homes and industry require singulating layers of material such as opening a bag or arranging garments for sewing. In contrast to methods requiring specialized sensing or end…
PaPy, which stands for parallel pipelines in Python, is a highly flexible framework that enables the construction of robust, scalable workflows for either generating or processing voluminous datasets. A workflow is created from user-written…
Systems composed of soft matter (e.g., liquids, polymers, foams, gels, colloids, and most biological materials) are ubiquitous in science and engineering, but molecular simulations of such systems pose particular computational challenges,…
We propose Slim Graph: the first programming model and framework for practical lossy graph compression that facilitates high-performance approximate graph processing, storage, and analytics. Slim Graph enables the developer to express…
Programmable biomolecule-mediated computing is a new computing paradigm as compared to contemporary electronic computing. It employs nucleic acids and analogous biomolecular structures as information-storing and -processing substrates to…
A low cost remote imaging platform for biological applications was developed. The "Picroscope" is a device that allows the user to perform longitudinal imaging studies on multi-well cell culture plates. Here we present the network…
Computational experiments have become essential for scientific discovery, allowing researchers to test hypotheses, analyze complex datasets, and validate findings. However, as computational experiments grow in scale and complexity, ensuring…
We present PolyHoop, a lightweight standalone C++ implementation of a mechanical model to simulate the dynamics of soft particles and cellular tissues in two dimensions. With only few geometrical and physical parameters, PolyHoop is capable…
ScopeSim is a flexible multipurpose instrument data simulation framework built in Python. It enables both raw and reduced observation data to be simulated for a wide range of telescopes and instruments quickly and efficiently on a personal…
Adaptive response to a varying environment is a common feature of biological organisms. Reproducing such features in electronic systems and circuits is of great importance for a variety of applications. Here, we consider memory models…