Open Source Python Scientific/Engineering Software - Page 31

A C++ library for the computation of bifurcation diagrams: it provides tools for the integration of systems of ODEs that depend on parameters. A Python interface is included.

Modern Open Source LIMS (Laboratory Information Management System) · Professionally supported by experts The Bika code was migrated to https://github.com/bikalims Getting Started: https://github.com/bikalims/bika.lims/blob/main/README.md Modern Bika releases are built on the Senaite LIMS core, the LIMS that originated as a Bika fork. It is therefore as new and modern as Senaite, frequently upgraded and has many very useful add-ons. Bika expands on Senaite's lean design by adding modules for bulk sample importing, two tier Sample Point Locations, instrument result importers extra COA templates etc. while remaining within ISO 17025 guidelines Other differentiation is per lab discipline, e.g. branches for environmental management, health care, geochemistry snd cannabis. User Manual: www.bikalims.org/new-manual Videos: www.bikalims.org/resources/bika-lims-videos Screenshots: www.bikalims.org/resources/screenshots Supported by Bika Lab Systems, www.bikalabs.com

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. BioEmu outputs structures in backbone frame representation. To reconstruct the side-chains, several tools are available. As an example, we interface with HPacker to conduct side-chain reconstruction and also provide basic tooling for running a short molecular dynamics (MD) equilibration.

BioMa is a specimen based Biodiversity database Manager. It is designed to store, organize, and manipulate biodiversity-related scientific data, either for the purposes of museums, scientific collections, or research projects.

This software screens a given peak list against web based NMR databases (nmrshiftdb, HMDB...) and return possible molecules. It also take a given molecule to return expected peaks list.

Biologic Institute's Stylus simulation software suite. (See the SVN repository for source code.)

Biological Annotation Tool is a general-purpose high speed environment for manipulating biological sequence annotations in multiple input and output formats. A plugin-style API permits much extensibility.

A collection of corpus and access routines for developing biological literature analysis systems.

Biskit is a python library for structural bioinformatics research. It simplifies the analysis of macromolecular structures, protein complexes, and molecular dynamics trajectories and offers a platform for the rapid integration of external programs. PLEASE NOTE: The Biskit source code as well as any later releases are now hosted on https://github.com/graik/biskit The sourceforge repo is only kept here for reference.

This is a Python script for Blender which uses short (quaternion-based, floretion-based) algorithms to draw curves in space. The user can create new shapes and curves by setting a variety of parameters.

Combines Blender's graphical interface and rendering capabilities with MBDyn's multi-body dynamics, aerodynamics, and aeroelastics simulation and analysis, for rapid modeling and realistic rendering of physics based multi-body simulations.

Blitzer is a simple tool for driving the SX-Blitz microcontroller programmer from Parallax. There is now a version for PalmOS devices.

Blivion is a software tool for analysing biolayer interferometry measurements of the binding of large vesicles such as influenza virus onto a two-dimensional ligand-coated substrate.

"Blue Planet" is a research project simulating the behaviour and darwinian evolution of unicellular lifeforms, each controlled by its own genetic program. Moreover, "Blue Planet Inhabitants" are suited for swarm intelligence and swarm research.

Compares botnet detection methods by computing the error metrics by reading the labels on a NetFlow file. The original NetFlow should have a new column for the ground-truth label, and a new column with the prediction label for each botnet detection method. This program computes all the error metrics (TPR, TNR, FPR, FNR, Precision, Accuracy, ErrorRate, FMeasure1, FMeasure2, FMeasure0.5) and output the comparison results. It also ouputs a png plot. The program can compare in a flow-by-flow basis, or it can apply our new botnet detection error metrics, that is time-based, detects IP addresses instead of flows and it is weighted to favor sooner detections. See the paper for more details.

BoulderALE is an RNA alignment editor, which allows for the annotation of basepairs, annotation and collapsing of features (horizontal) and sequences (vertical), along with 2D display of sequences and base composition given a secondary structure.

Volumetric file viewer for the human brain. Easy, powerful and flexible fMRI/MRI brain research and clinical neuro-surgery tool. Using state of the art open VTK 3D library, the proven Qt GUI toolkit, coded in Python.

Brainlab is a Python toolkit to aid in the design, simulation, and analysis of spiking neural networks with the NeoCortical Simulator (NCS).

This project aims to organize a brainstorm or a bibliographic revision in a network (graph). With this organization the users are able to visualize the main points of the brainstorm (the hubs in the network). Moreover, they can access the information through the rede, interactively, clicking on the edges or nodes! All information is associated with a reference list (imported from a bibtex file). This project uses Python, Web2py, MariaDB and VIS.js (D3.js).

BrennerMD is a public domain Fortran molecular dynamics program by Donald Brenner and other people. This project is to maintain the original source code and to build a Python interface on top of it.

This project is UI to guide the user through the steps of home brewing. Each beer has a recipe of ingredients, but it also has a “recipe” for the process to make the beer. This app allows you to load a recipe (BeerXML), guide you through the brewing steps and record any details so that you can improve next time. By default, this app relies on user inputs and feedback from the real-world. There are easy hooks to a link up a real system, so that if you wanted to automate some of the input and feedback it could be possible (ex. read temperature from sensor. Turn heat source on/off). This project uses the free Maker Edition of the Ignition platform. https://inductiveautomation.com/ignition/maker-edition Sierra Nevada and Stone Brewery use the (paid) Ignition platform. https://inductiveautomation.com/resources/casestudy/ignition-system-meets-all-user-requests https://inductiveautomation.com/resources/casestudy/brewery-improves-efficiency-in-multiple-areas-with-ignition

The Bristol Cloud Service simulation runner is a cloud computing Software as a Service designed to enable users to quickly launch simulation code on Amazon AWS' Elastic Compute Cloud (EC2). BRiCS is written in Python using the Django framework and interacts with EC2 using the boto API. BriCS enables multiple simulation runs to be launched in parallel from a web browser. Model configuration (parameters) files are uploaded via the browser and results files are downloadable on completion. BriCS enables researchers with software simulation models to access the rapid scale out opportunities of the cloud. Why wait days or weeks for a series of trials to complete when you can run them in parallel in the time it takes to complete one?

LaTex to braille translator for Maths, intended to be able to support multiple braille codes.

Video monitoring tool for insect analysis