Search Results for "input-output model"

Protenix is an open-source, trainable PyTorch reimplementation of AlphaFold 3, developed by ByteDance with the goal of democratizing high-accuracy protein structure prediction for computational biology and drug-discovery research. Protenix provides a complete pipeline for turning protein sequences (with optional MSA / sequence alignment) or structural inputs (e.g. PDB/CIF) into full 3D atomic-level structure predictions. It supports both “full” models and lightweight variants such as...

Biomolecular Emulator (BioEmu for short) is a model that samples from the approximated equilibrium distribution of structures for a protein monomer, given its amino acid sequence. By default, unphysical structures (steric clashes or chain discontinuities) will be filtered out, so you will typically get fewer samples in the output than requested. The difference can be very large if your protein has large disordered regions, which are very likely to produce clashes.

MCPower-GUI is a desktop application that provides a graphical interface for the MCPower Monte Carlo power analysis library. It guides users through the full workflow across three tabs: Model setup (formula input with live parsing, CSV data upload with auto-detected variable types, effect size sliders, and correlation editing), Analysis configuration (find power for a given sample size or find the minimum sample size for a target power, with multiple testing correction and scenario analysis), and Results (interactive charts, exportable tables, and auto-generated Python replication scripts). ...

Pretty Damn Quick (PDQ) analytically solves queueing network models of computer and manufacturing systems, data networks, etc., written in conventional programming languages. Generic or customized reports of predicted performance measures are output.

The Development System for Auditory Modelling (DSAM) is a computational library designed specifically for producing simulations of the auditory system. It brings together many established auditory models within a flexible programming platform.

Olex2 is visualisation software for small-molecule crystallography developed at Durham University/EPSRC. It provides comprehensive tools for crystallographic model manipulation for the end user and an extensible development framework for programmers. The project has been supported by Olexsys Ltd since 2010.

The intend is to solve the forward-reaction prediction problem, where the reactants are known and the interest is in generating the reaction products using Deep learning. This Graphical User Interface takes simplified molecular-input line-entry system (SMILES) as an input and generates the product SMILE & molecule. Beam search is used in Version 2, to generate top 5 predictions. Maximum input length for the model is 15 (excluding spaces).

SnowyOwl is a gene prediction pipeline that uses RNA-Seq data to train and provide hints for the generation of Hidden Markov Model (HMM)-based gene predictions, and to evaluate the resulting models. The pipeline has been validated and streamlined by comparing its predictions to manually curated gene models in three fungal genomes, and its results show substantial increases in sensitivity and selectivity over previous gene predictions. Sensitivity is gained by repeatedly running the HMM gene predictor Augustus with varied input parameters, and selectivity by choosing the models with best homology to known proteins and best agreement to the RNA-Seq data. ...

Stochastic simulation model of poliovirus Sabin-to-Mahoney genetic state transition (C++ code). Models genotypes, virus populations, and quasispecies cloud. Simulates replication error and copy-choice recombination. Various parameters guiding the model are user-specified. Python code post-processes simulation output to produce report files.

streamline the DSM process in ArcGIS/Numpy/GDAL/Python using Sampling, Statistical elaboration, Prediction to allow the application of extended statistical models generated by the CUBIST (TM) or JMP (TM) software to a set of auxiliary input parameters, thereby bypassing the need to i) manually calculate the equations using Raster calculator; ii) use a grid-to-point conversion process prior to applying the prediction model in the statistical software itself and then a point-to-grid conversion process.

syphon is an extension for mod_openopc, to monitor telnet devices (serial devices) that sit on Serial -to- Ethernet bridges (such as barcode scanners) and export parsed data to an OPC compliant device (such as a PLC).

pyHKL is the interface to DENZO/SCALEPACK packages for X-ray crystallography data processing. It runs jobs remotely and aims at minimizing user input, by including automatic error model correction, rejection accumulation and mosaicity refinement.

Pymerase is a tool intended to generate a python object model, relational database, and an object-relational model connecting the two. However it has been extended to also output webpages and can be easily extended to output whatever else you might like.