Open Source Scientific/Engineering Software - Page 94
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Scientific/Engineering Software
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123FASTQ
An intuitive and efficient tool for preprocessing Illumina FASTQ reads
123FASTQ performs all the pre-processes of Illumina next-generation sequencing reads (FASTQ files) easier than ever. Download the quick user manual for the latest version: https://dl.adbioinformatics.net/NGSNeeds/myTools/123Fastq_v1.3_Manual.pdf Authors: Milad Eidi, Samaneh Abdolalizadeh, Mohammad Hossein Nassirpour Supervisors: Javad Zahiri, PhD University of California San Diego Masoud Garshasbi, PhD Tarbiat Modares University, Tehran, Iran If you use 123FASTQ, please cite this preprint: 123FASTQ: an intuitive and efficient tool for preprocessing Illumina FASTQ reads https://www.biorxiv.org/content/10.1101/2024.03.08.584032v1 ########################################################## Take care of the details and ensure you use the latest version. We hope this helps... -
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AOFlagger
RFI detector and quality analysis for astronomical radio observations
The AOFlagger is a tool that can find and remove radio-frequency interference (RFI) in radio astronomical observations. The code has been highly optimized for speed and accuracy. It is used by default for the LOFAR radio telescope and thus is in productional stage. The software can run in a fully automated way, but a graphical interface is provided to analyse results and tweak the strategy. The preferred input file format is the Casa Measurement Set (MS) format. I believe that the AOFlagger is the best available flagger, both in terms of accuracy and speed. It has been succesfully used on several interferometric telescopes, including LOFAR, WSRT, VLA, GMRT, ATCA and MWA, and the single-dish telescopes Parkes and Arecibo 305m. Besides the flagger, the software consists of tools to efficiently visualize data in different ways, such as plotting time-frequency diagrams and power spectra. It provides the programs rficonsole, rfigui, aoqplot, aoquality and more. -
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ARIA RDK
Windows binaries for the ARIA RDK environment
ARIA RDK software is the environment for algorithms prototyping on ARIA UWB Sensors. -
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AUTOMGEN runtime is an open source royalty free runtime for open PLCs. By using this runtime, any target systems can become compatible with the AUTOMGEN automation workshop: IEC1131 languages (ladder, SFC, etc.), 2D and 3D scada, WEB SCADA, etc.
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Advanced Numerical Instruments 3D
Advanced numerical instruments: adaptive meshing, FE methods, solvers
Ani3D provides portable libraries for each step in the numerical solution of systems of PDEs with variable tensorial coefficients: (1) unstructured adaptive mesh generation, (2) metric-based mesh adaptation, (3) finite element discretization and interpolation, (4) algebraic solvers. -
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Amplicon is a Python script for designing PCR primer sets. Amplicon is written in Python 2.3 and Tkinter 8.4. The current script was created for Windows and an executable is available. Future versions of the script should be able to run on Linux and Mac
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APLEpy stands for Algebraic Programming Language Extension for Python. It is an open source alternative to commercial products such as AMPL and GAMS. It offers the same high level of abstraction while keeping the advantages of using Python environment.
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This is a project for Andre to share CellML related tools he works on that other people might find useful.
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AntibiogramJ
AntibiogramJ is a Java program for the reading of antibiogram-images
AntibiogramJ is a Java program for the identification, measurement and categorisation of inhibition zones in antibiogram images captured with any device that incorporates a camera (including digital cameras and mobile phones). Citing AntibiogramJ: A. Alonso, C. DomÃnguez, J. Heras, E. Mata, V. Pascual, C. Torres, and M. Zarazaga. AntibiogramJ: a Tool for Analysing Images from Disk Diffusion Tests. Computer Methods and Programs in Biomedicine 143:159-169. 2017. DOI: http://dx.doi.org/10.1016/j.cmpb.2017.03.010 You can see more information about AntibiogramJ in https://sourceforge.net/p/antibiogramj/wiki/Home/ Several videos explaining the use of AntibiogramJ are available in https://sourceforge.net/p/antibiogramj/wiki/Videos/ AntibiogramJ includes now the EUCAST v.9.0. Please address any question or comment to joheras at gmail.com -
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The goal of this project is to develop a flexible and easy to use dive logbook for Palm OS based PDA. The advantages of the old paper logbook should be combined with the power of a computer.
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Arduino CNC Controller
APP for control a manual mill and obtain a CNC Mill
APP for Android 3.1 or greater to implement a CNC Controller that send orders using USB port to Arduino Mega 2560 R3 board to control 3 stepper motor to have a real CNC mill /// APP para Android 3.1 o superior para implementar un Controlador de CNC que envia ordenes usando el puerto USB a la placa Arduino Mega 2560 R3 para controlar 3 motores paso a paso para tener una fresadora de CNC real. -
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Arena is a computer simulation in which programs compete for CPU time and access to main memory. Processes such as the dynamics of punctuated equilibrium, host-parasite co-evolution and density dependent natural selection are amenable to investigation.
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Arnav Digital Signal Processing
A real-time Discrete Signal Processing software and API for MS Windows
A real-time Discrete Signal Processing software and API for Microsoft Windows OS which can connect to SDR devices like RTL-SDR and USRP. The API can be called from C/C++ programs as well from any .NET 4.5 client applications. -
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AstronomicalAlgorithms is a FREE portable ANSI C implementation of some of the algorithms published in Astronomical Algorithms by Jean Meeus (2nd edition, December 1998, Willmann-Bell ISBN 0943396638)
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Auto Draw is an set of vba and arx applications, for land development in AutoCad. It will include and a set of tools like hatches,linetypes and blocks.
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Automatic cell lineage reconstruction
Automatic segmentation and tracking for 3D time-lapse microscopy
From Amat et al., Nature Methods, 2014*: "The comprehensive reconstruction of cell lineages in complex multicellular organisms is a central goal of developmental biology. We present an open-source computational framework for segmentation and tracking of cell nuclei with high accuracy and speed. We demonstrate its (1) generality, by reconstructing cell lineages in four-dimensional, terabyte-sized image data of fruit-fly, zebrafish and mouse embryos, acquired with three different types of fluorescence microscopes, (2) scalability, by analyzing advanced stages of development with up to 20,000 cells per time point, at 26,000 cells min-1 on a single computer workstation, and (3) ease of use, by adjusting only two parameters across all data sets and providing visualization and editing tools for efficient data curation. Our approach achieves on average 97.0% linkage accuracy across all species and imaging modalities." *Please cite this paper if you use this code for your research -
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AzConvert is an open source program to convert different scripts of Azerbaijani language (Latin, Arabic and Cyrillic) to each other. It's written in Qt.
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BACnetRail
BACnetRail - BACnet IP network monitoring tool
BACnetRail is a free BACnet network discovery tool, with a few useful monitoring function. The software connects to the BACnet network with an IP/UDP connection. For more information check the readme file. -
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BAIT
Software to help analyse Strand-Seq data
Software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data. -
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BANNER is a named entity recognition system intended primarily for biomedical text. It uses conditional random fields as the primary recognition engine and includes a wide survey of the best techniques described in recent literature.
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BEDS - Bed Evaluation & Design System
A system for designing and evaluating patient flow in hospitals.
BEDS evaluates patient flow in hospitals. Specifically, BEDS evaluates the occupancy of beds and the probability of receiving a bed on arrival to the hospital. BEDS is built on the assumption that patients arrive with a stationary intensity, and that the distribution governing their length-of-stay is also stationary. Thus, BEDS works only when modeling inpatient wards. BEDS further assumes a setup consisting of a number of patient types and wards. The wards contain a fixed capacity. Patient types are defined by their arrival intensity (how many arrive per day on average), and their average length-of-stay. Patients have a single preference for hospitalization in a specific ward. If the preferred ward is fully occupied on arrival, the patient is relocated to an alternative ward with a known probability. Several scientific studies have shown that this simple setup is an adequate approximation for describing the occupancy in inpatient wards. -
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The 'BandSystem' spectral analysis system is a rule-based system for the classification of mineral spectra. It consists of a preprocessor, a feature extractor, and a rule-based system to identify minerals from infra-red reflectance spectra.
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Barcelona Trees
A Guide of the Trees of Barcelona City
This program is a data visualization and navigation tool using a database created from datasets provided by the Barcelona city council, over a map of the city of Barcelona. The motivation of this program is to help answering questions such as: * What trees are nearby? (from manual location or GPS) * What trees are on a given street? * Where can I find specimens of a certain genus/species? * For each specimen, obtain more information about its species from existing data on Wikipedia and public images. -
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Bellman
Conway's Life pattern searcher
Bellman, named after the character in Lewis Carroll's The Hunting of the Snark, is a program for searching for catalytic interactions in Conway's Game of Life and potentially other similar cellular automata. Results are derived directly from the automaton's evolution rule, not generated from a list of candidate catalysts as with previous searchers. -
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BioUtils Perl Library
A collection of Perl modules for handling fasta/q sequences and files.
WARNING: BioUtils has been migrated to Github (Nov 2017). For the most up-to-date versions and info please visit: https://github.com/islandhopper81/BioUtils BioUtils are a collection of Perl modules for DNA sequence analysis in bioinformatics. BioUtils is a significantly faster and more memory efficient alternative to BioPerl. However, it's functionality is currently limited to the features listed below.