Open Source Python Scientific/Engineering Software - Page 72

We present a modeling framework aimed at capturing both the positional and temporal behavior of transcriptional regulatory proteins. There is growing evidence that transcriptional regulation is the complex behavior that emerges not solely from the individual components, but rather from their collective behavior, including competition and cooperation. Our framework describes individual regulatory components using generic action oriented descriptions of their biochemical interactions with a DNA sequence. All the possible actions are based on the current state of factors bound to the DNA. We developed a rule builder to automatically generate the complete set of biochemical interaction rules for any given DNA sequence. Off-the-shelf stochastic simulation engines can model the behavior of a system of rules and the resulting changes in the configuration of bound factors can be visualized.

StormSiren is an Internet application that allows individuals to receive alert notifications via Email, SMS, Jabber Instant Messaging, playing sound files, external program execution, MythTV visual alerts, and OSD (On Screen Display) visual alerts of wea

StrATo (Strain Analysis Tool) loads GE Vingmed heart strain value reports file and performs a statistical peak analysis and curve uniformity evaluation, cutting off sampled noise, plotting results and offering a printout to attach in medical reports.

StreamAlert is a serverless, real-time data analysis framework that empowers you to ingest, analyze, and alert on data from any environment, using data sources and alerting logic you define. Computer security teams use StreamAlert to scan terabytes of log data every day for incident detection and response. Incoming log data will be classified and processed by the rules engine. Alerts are then sent to one or more outputs. Rules are written in Python; they can utilize any Python libraries or functions. Merge similar alerts and automatically promote new rules if they are not too noisy. Ingested logs and generated alerts can be retroactively searched for compliance and research. Serverless design is cheaper, easier to maintain, and scales to terabytes per day. Deployment is automated, simple, safe and repeatable for any AWS account. Secure by design, least-privilege execution, containerized analysis, and encrypted data storage.

Small Python programs for the structural designer / Pequeños programas para el diseñador de estructuras hechas en Python

CISTS seeks to assist Civil Engineers in the analysis of beams, their loads, and properties.

Tools and programs I have written for various purposes and those used in it.

SunlightDPD provides a home for open source codes related to the dissipative particle dynamics (DPD) simulation method. Currently the file release contains the HNC integral equation code.

SunlightLB is an open-source 3d lattice Boltzmann code which can be used to solve a variety of hydrodynamics problems, including passive scalar transport problems.

idyuts is \"I Dare You to Use This Shell\"; a pre-hibernate approach to replacing an ORM written with jython functors into a pure-Java language command pattern. The \"pipeline codegen artifacts\" are simple IoC templates, and trivial to adapt

SuperG is a code library written in Python intended to quickly enable programmers in a scientific environment to manage data files created by dispersed scientific instrumentation.

This repository is the home of the Superstaq development team's open-source work. Our quantum software platform is optimized across the quantum stack and enables users to write quantum programs in Cirq or Qiskit and target a variety of quantum computers and simulators.

SureFit generates 3D mesh surfaces (in VTK and Caret formats) from 3D structural MRI volumes (in formats such as Analyze, AFNI, raw).

This project simulates a multi-agent system (swarm) behavior both graphically and not. The purpose of this project is to research the properties suggested in "stability analysis of swarms" V.Gazi & K.M.Passino. Using the vpython library for 3D modeling

Symath is a symbolic algebra utility that manipulates expressions as you would by hand. The aim is to provide a utility for students to use to solve complex systems as well as learn how it is done.

SynBioLib -- your toolkit for synthetic biology applications. SynBioLib aims to establish a platform on which the Synthetic Biology community can develop and share code that is common to many tasks and programs.

Synthetic Biology Software Suite (SynBioSS) is composed of a wiki for biochemical kinetic constants, a graphical interface for simulating synthetic biological pathways, and a simulator that runs on either a desktop or supercomputer.

Syzygy is a toolkit for the analysis of targeted (pooled/individual) resequencing datasets.

This project is intended to provide Git access to the code of the original project, TA-Lib, which uses Subversion. It is intended for system integrators wishing to use TA-Lib in their Git-managed project through Git submodules or subtrees. No actual development is being done here; all development happens in the original project.

The Toolkit for Advanced Discriminative Modeling (TADM) is a C++ implementation for estimating the parameters of discriminative models, such as maximum entropy models. It uses the PETSc and TAO toolkits to provide high performance and scalability.

TANGO is an object oriented control system for Linux and Windows. It provides a framework in C++, Java and Python for implementing distributed control objects an accessing them via a well-defined API. This sourceforge project a

A bioinformatics tool for the annotation and tag-counting of next-gen Illumina Solexa datasets. TASE works with CASAVA 1.0 builds, providing annotation, tag counts and visualization in a rapid manner.

TAVIA is a free, open-source desktop application for statistics and scientific graphing. It offers a project-based workspace with editable data tables, linked analyses, and scientific graphs in one interface. TAVIA imports CSV, TSV, TXT, simple XLSX, and GraphPad Prism .pzfx files, and exports tables to CSV, TSV, and XLSX. Available analyses include summary statistics, Student and Welch t-tests, Mann-Whitney tests, ordinary and Welch ANOVA, Kruskal-Wallis tests, multiple-comparison corrections, and linear or quadratic regression. A prototype four-parameter dose-response fit is also included. Results can be linked to XY, line, histogram, mean bar, and box plots with annotations and statistical overlays, then exported as PNG, PDF, or SVG. TAVIA is currently alpha software, so bugs and rough edges are expected. Testing, feedback, and bug reports are welcome. Licensed under GPLv3, Based on Python 3, TAVIA is implicitly available for Windows, macOS, and Linux.

TCellXTalk is a comprehensive database of experimentally detected phosphorylation, ubiquitination and acetylation sites in human T cells. The web-app at www.TCellXTalk.org makes TCellXTalk accessible from Internet, and enables the in silico prediction of potential co-modified peptides to facilitate their experimental detection, using targeted or directed mass spectrometry, for the study of protein post-translational modification cross-talk. More detailed information on TCellXTalk and the people at the CSIC/UAB Proteomics Laboratory behind it can be obtained at https://www.tcellxtalk.org/about/ - Casanovas, A., Gallardo, Ó., Carrascal, M., Abian, J., TCellXTalk facilitates the detection of co-modified peptides for the study of protein post-translational modification cross-talk in T cells. Bioinformatics 2019, 35-8, 1404–1413, DOI 10.1093/bioinformatics/bty805 ( https://doi.org/10.1093/bioinformatics/bty805 )

TEACUP automates many aspects of running TCP performance experiments in a specially-constructed physical testbed. TEACUP enables repeatable testing of different TCP algorithms over a range of emulated network path conditions, bottleneck rate limits and bottleneck queuing disciplines. TEACUP utilises a text-based configuration file to define experiments as combinations of parameters specifying desired network path and end host conditions. When multiple values are provided (e.g. for TCP congestion control algorithm), an experiment is made up of multiple tests. For each experiment and test, TEACUP collects a range of data, such as tcpdump files of traffic seen or TCP stack information (e.g. using Web10G). TEACUP also collects a variety of metadata from the end hosts and bottleneck router, such as the actual OS/kernel version(s) used. TEACUP also provides some simple tools for analysing the results of experiments, such as plotting a flow's experienced RTT over time.