Open Source Scientific/Engineering Software - Page 68
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Scientific/Engineering Software
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A high-performance and ease-of-use implementation of the Modbus protocol written in Java by Infinite Automation Systems Inc.. Supports ASCII, RTU, TCP, and UDP transports as slave or master, automatic request partitioning and response data type parsing. For commercial licenses see www.InfiniteAutomation.com Get the most recent code here: https://github.com/infiniteautomation/modbus4j For support: http://infiniteautomation.com/forum/category/11/modbus4j-general-discussion
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sim85 - the 8085 simulator. Project to implement a full development enviornment for the intel 8085 processor.
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Simple 8085 assembler and disassembler for educational use. The 8085asm generates the map file and intel hex file. It support the directives EQU, ORG, DB, DS and END.
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This project is a general AVR bootloader, for different type of AVR device, all you need to do is modify macro definition, and you don not need to modify the main program.
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Here you can find the following Tools and libs for the famous ASURO robot. ASUROLIB: C library for the ASURO. ASURINO+ASUROBOOT: An Arduino library and Arduino/STK500v1 compatible Bootloader for the ASURO.
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Autmated Peptide Screening
Screening peptides for MHC and/or MHC-T cell receptor affinity
Modified version of AutoGrow, autogrow.ucsd.edu/ , with a mutation script added in the class files, and a global change of the defined mutation point from Hydrogen atoms to Calphas, to allow placement of Amino Acids. Deposited are 3 versions, used for my PhD Thesis. These allow for mutation of short 2-15 amino acid peptides, and associated screening of these using AutoDock or AutoDock Vina, allowing for 8 CPU systems to screen 10K peptides a day or 1-2K with flexible residues added in. A detailed method for determining the peptide ligand for any sequenced and modeled T cell receptor will be published and link added at some point. These scripts are written quickly in a couple weeks to meet a task and could be re-written more eloquently. I may or may not work on this project again, the goal would be to introduce amino acids into any protein in openCL to allow automated design on GPU's.Limits-The standard PDB codes used slightly modified, proline not at angles, peptide shld be linear, -
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The UIMA Annotator (called BRUTUS - Business Rules from Unstructured Text and Unstructured Sources) is a component for the UIMA Framework that allows for capturing business knowledge formalized in Structured English syntax (based on OMG's SBVR) with MOF
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Ballistic Calculator
Open Source Ballistic Calculator in C#
!!! This project is currently CLOSED. There is a new version of API available under LGPL license at https://github.com/gehtsoft-usa/BallisticCalculator1 There is a new version of application in progress (ported to net framework 5.0) https://github.com/nikolaygekht/ballistic.calculator.app Ballisitic Calculator based on JBM's implementation 3-degree of freedom model, ported to C#, improved to support metric system and extended by some math from Litz's "Applied Ballistic" book. Calculator displays ballistic tables, graphs, comparison graph and reticle images. The application is free to use under GNU license -
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Bandicoot
fast C++ library for GPU linear algebra & scientific computing
* Fast GPU linear algebra library (matrix maths) for the C++ language, aiming towards a good balance between speed and ease of use * Provides high-level syntax and functionality deliberately similar to Matlab * Provides an API that is aiming to be compatible with Armadillo for easy transition between CPU and GPU linear algebra code * Useful for algorithm development directly in C++, or quick conversion of research code into production environments * Distributed under the permissive Apache 2.0 license, useful for both open-source and proprietary (closed-source) software * Can be used for machine learning, pattern recognition, computer vision, signal processing, bioinformatics, statistics, finance, etc * Downloads: http://coot.sourceforge.io/download.html * Documentation: http://coot.sourceforge.io/docs.html * Bug reports: http://coot.sourceforge.io/faq.html * Git repo: https://gitlab.com/conradsnicta/bandicoot-code -
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BioUtils - Proteomics
Lightweight framework for handling biological and bioinformatical data
The BioUtils - Proteomics package is a lightweight Java framework for handling commonly used data produced and needed in the field of Mass spectrometry in general and especially in the field of Proteomics. It's stable, intuitive to use and good integrated with Java 6 SDK and later. -
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CERCA
CERCA – Citation Extraction & Reference Checking Assistant
CERCA is an open-source research tool that supports the verification of bibliographic references in scientific manuscripts. It extracts references from PDF files and checks their existence and consistency against authoritative metadata sources, producing explainable diagnostics, audit logs, and reproducible reports. It is intended for: - Researchers performing final manuscript checks - Reviewers assessing reference consistency - Editors supporting editorial quality control - Meta-research and reproducibility workflows CERCA is an experimental tool. It does not replace manual verification. CERCA is a Java desktop application built with JavaFX. To run it, you need a JRE that includes JavaFX, such as Azul Zulu JRE. Developed by: Lidiany Cerqueira, PhD Computer Science Researcher -
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CNC Splitter
This program splits a FANUC ALL-PROG.TXT backup file.
This program splits a FANUC ALL-PROG.TXT program backup file in to individual files. -
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Calcoo is a scientific calculator (with both RPN and algebraic modes) designed to provide maximum usability.
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Coordinates Converter
Coordinates Converter
Coordinates Converter is a software that gives you the possibility to convert coordinates in 2D or 3D mode on the fly. Geared toward all types of users, it features approachable options. In 2D mode, it's possible to convert Cartesian to Polar (set the X and Y values) or vice versa, (set the r and theta values). In 3D mode, you can convert between Cartesian to Cylindrical-Spherical (set the X, Y and Z values), Spherical to Cartesian-Cylindrical (set the r, theta and pi values), or Cylindrical to Cartesian-Spherical (set the r, theta and h values). My blog: https://vegettadbz.blogspot.com/ -
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CueMol
CueMol - Molecular Visualization Framework
CueMol - Molecular Visualization Framework based on OpenGL, Mozilla XULRunner, and javascript -
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Data2FCS
Data2FCS is a simple tool to convert text data files to FCS3.1 data.
Impressum / Legal Notice Sven Mostböck Murlingengasse 25/5 1120 Wien Austria e-mail: sven_mostboeck@users.sourceforge.net second contact option: use the open discussion on the FCSalyzer sourceforge page: http://sourceforge.net/p/fcsalyzer/discussion/ Information: Flow cytometry software is a perfect way to analyse complex data sets with large sample size. Data can be easily visualized to identify correlations and subpopulations. Subpopulations can be selected and analysed separately. However, such software required data in the FCS data standard. Data2FCS converts data from text files to FCS data files. A special treat is the possibility to transform categorical data into numerical data. The resulting FCS data file can be analysed in regular flow cytometry softwares, such as the open source FCSaylzer. For more info, take a look at the Wiki. Data2FCS needs Java 1.7 or higher to run. -
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The Dataverse Network is a Java EE5 app that enables researchers to share data on-line. It provides data citation standards, facilitates preservation, distribution and replication of data, and includes statistical analysis. More at: http://thedata.org
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Distributed MultiThreaded Checkpointing
Checkpoint/Restart functionality for Linux processes
DMTCP (Distributed MultiThreaded Checkpointing) transparently checkpoints a single-host or distributed computation in user-space -- with no modifications to user code or to the O/S. It works on most Linux applications, including Python, Matlab, R, GUI desktops, MPI, etc. It is robust and widely used (on Sourceforge since 2007). For the newest releases of DMTCP, please go to: https://github.com/dmtcp/dmtcp Among the applications supported by DMTCP are MPI (various implementations), OpenMP, MATLAB, Python, Perl, R, and many programming languages and shell scripting languages. With the use of TightVNC, it can also checkpoint and restart X-Window applications. The OpenGL library for 3D-graphics is supported through a special plugin. It also has strong support for HPC (High Performance Computing) environments, including MPI and SLURM, through the github MANA project: https://github.com/mpickpt/mana -
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DualSPHysics
C++/CUDA/OpenMP based Smoothed Particle Hydrodynamics (SPH) Solver
DualSPHysics is based on the Smoothed Particle Hydrodynamics method and can be downloaded from the official website (www.dual.sphysics.org). The code is developed to study free-surface flow phenomena where Eulerian methods can be difficult to apply, such as waves or impact of dam-breaks on off-shore structures. DualSPHysics is a set of C++, CUDA and Java codes based on the SPHysics FORTRAN project (www.sphysics.org) that are designed to deal with real-life engineering problems and are provided along with pre-compiled binaries and source for Windows/Linux/Unix as well as a number of example test cases. -
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ESTScan is a program that can detect coding regions in DNA/RNA sequences, even if they are of low quality (e.g. EST sequences). ESTScan will also detect and correct sequencing errors that lead to frameshifts.
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EqmodGui
User interface for INDI Eqmod telescope driver
Eqmodgui is a user interface for Linux INDI Eqmod telescope driver. It allow to easily set the main parameters require to use this driver and manage the alignment data. Eqmod is now very simple to use on Linux. This software is part of a full suite for astronomical observation: https://sourceforge.net/projects/skychart/ https://sourceforge.net/projects/ccdciel/ https://sourceforge.net/projects/indistarter/ See also: https://sourceforge.net/projects/indi/ -
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FreeFOAM is no longer maintained. Please consider using one of the official OpenFOAM distributions instead.
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Fuzzy Logic Tools (FLT) is a C++ framework for storage, analysis and design of fully general multiple-input multiple-output (MIMO) Takagi-Sugeno fuzzy control systems, without constraints in the order of either the inputs or the output vectors.
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GFtbox is a Matlab package for simulating biological growth of leaves, petals, and similar organs.
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Firmware mod for the GWInstek GPP-x32x series lab bench supply.
