Related papers: IMPi: An interactive homology modeling pipeline
Protein Structure Prediction (PSP) is an unsolved problem in the field of computational biology. The problem of protein structure prediction is about predicting the native conformation of a protein, while its sequence of amino acids is…
Antimicrobial peptides (AMPs) play important roles in cancer, autoimmune diseases, and aging. A critical aspect of AMP functionality is their targeted interaction with pathogen membranes, which often possess altered lipid compositions.…
Cooperative Distributed Model Predictive Control (DiMPC) architecture employs local MPC controllers to control different subsystems, exchanging information with each other through an iterative procedure to enhance overall control…
We introduce a natural language interface for building stochastic pi calculus models of biological systems. In this language, complex constructs describing biochemical events are built from basic primitives of association, dissociation and…
We introduce Dimple, a fully open-source API for probabilistic modeling. Dimple allows the user to specify probabilistic models in the form of graphical models, Bayesian networks, or factor graphs, and performs inference (by automatically…
A goal of computational studies of protein-protein interfaces (PPIs) is to predict the binding site between two monomers that form a heterodimer. The simplest version of this problem is to rigidly re-dock the bound forms of the monomers,…
Protein-Protein Interactions (PPIs) are fundamental in various biological processes and play a key role in life activities. The growing demand and cost of experimental PPI assays require computational methods for efficient PPI prediction.…
This paper describes a scalable active learning pipeline prototype for large-scale brain mapping that leverages high performance computing power. It enables high-throughput evaluation of algorithm results, which, after human review, are…
This system paper documents the technical foundations for the extension of the Topology ToolKit (TTK) to distributed-memory parallelism with the Message Passing Interface (MPI). While several recent papers introduced topology-based…
Structural biology has made significant progress in determining membrane proteins, leading to a remarkable increase in the number of available structures in dedicated databases. The inherent complexity of membrane protein structures,…
Human-machine interfaces (HMI) facilitate communication between humans and machines, and their importance has increased in modern technology. However, traditional HMIs are often static and do not adapt to individual user preferences or…
The true costs of high performance computing are currently dominated by software. Addressing these costs requires shifting to high productivity languages such as Matlab. MatlabMPI is a Matlab implementation of the Message Passing Interface…
The design and development of effective drug formulations is a critical process in pharmaceutical research, particularly for small molecule active pharmaceutical ingredients. This paper introduces a novel agentic preformulation pathway…
The last 15 years have seen a surge of new multi-chip optical and near-IR imagers. While some of them are accompanied by specific reduction pipelines, user-friendly and generic reduction tools are uncommon. In this paper I introduce THELI,…
Software libraries for Topological Data Analysis (TDA) offer limited support for interactive visualization. Most libraries only allow to visualize topological descriptors (e.g., persistence diagrams), and lose the connection with the…
Sequential recommendation systems alleviate the problem of information overload, and have attracted increasing attention in the literature. Most prior works usually obtain an overall representation based on the user's behavior sequence,…
We present SIPGI, a spectroscopic pipeline to reduce optical/near-infrared data from slit-based spectrographs. SIPGI is a complete spectroscopic data reduction environment which retains the high level of flexibility and accuracy typical of…
The Message Passing Interface (MPI) has been extremely successful as a portable way to program high-performance parallel computers. This success has occurred in spite of the view of many that message passing is difficult and that other…
The implicit 2D3V particle-in-cell (PIC) code developed to study the interaction of ultrashort pulse lasers with matter [G. M. Petrov and J. Davis, Computer Phys. Comm. 179, 868 (2008); Phys. Plasmas 18, 073102 (2011)] has been parallelized…
The protein-protein interactions (PPIs) are crucial for understanding the majority of cellular processes. PPIs play important role in gene transcription regulation, cellular signaling, molecular basis of immune response and more. Moreover,…