Scientific/Engineering Software


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Scientific/Engineering Software

  • Monitor Your Most Critical Cloud & SaaS Applications Monitor Your Most Critical Cloud & SaaS Applications Icon
    Monitor Your Most Critical Cloud & SaaS Applications Icon

    Get insights into the performance of applications and services such as AWS, Salesforce, Office 365 and WebEx.

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  • Open PECTool

    Open PECTool - manipulate peroidic error data for Celestron mounts.

    This is clone of the Celestron PECTool used to upload, download and manipulate PEC data. It is intended to work with Celestron Nexstar mounts like NexStar GPS, NexStar GPS-SA, NexStar iSeries, NexStar SE Series, NexStar GT, Advanced-VX, Advanced-GT and CGE mounts. Communication to the hand control is 9600 bits/sec, no parity and one stop bit via the RS-232 port on the base of the hand control. To build it libnexstar version 0.11 or newer is needed, which can be found here: Mac OSX binary is available here:

  • VnDP

    A Vietnamese dependency parsing toolkit

    VnDP is a Vietnamese dependency parsing toolkit which integrates a pre-trained parsing model and a pre-trained POS tagging model. The parsing model was trained on our VnDT Vietnamese dependency Treebank which was automatically converted from the Vietnamese constituent Treebank. See more details in VnDP's website at

  • oxDNA Icon


    A code primarily aimed at DNA and RNA coarse-grained simulations

    oxDNA is a simulation code that was initially conceived as an implementation of the coarse-grained DNA model introduced by T. E. Ouldridge, J. P. K. Doye and A. A. Louis ( It has been since reworked and it is now an extensible simulation+analysis framework. It natively supports DNA, RNA, Lennard-Jones and patchy particle simulations on both CPUs and NVIDIA GPUs.

  • FreeMedForms

    Free Software Medical Suite

    FreeMedForms is free and open source medical suite, available for all current platforms (Linux, Mac OS X, Windows and FreeBSD). It is powerful and fully configurable. It can be adapted to many needs: various medical specialties, para-medical specialties and even veterinary profession.

    Downloads: 153 This Week Last Update: See Project
  • PySptools Icon


    Hyperspectral algorithms for Python

    A lightweight hyperspectral imaging library that provides developers with spectral algorithms for the Python programming language. New for v0.14.x: a scikit-learn bridge (alpha and partial). The functions and classes are organized by topics: * abundance maps: FCLS, NNLS, UCLS * classification: AbundanceClassification, NormXCorr, KMeans SAM, SID, SVC * detection: ACE, CEM, GLRT, MatchedFilter, OSP * distance: chebychev, NormXCorr, SAM, SID * endmembers extraction: ATGP, FIPPI, NFINDR, PPI * material count: HfcVd, HySime * noise: Savitzky Golay, MNF, whiten * sigproc: bilateral * sklearn: HyperEstimatorCrossVal, HyperSVC and others * spectro: convex hull quotient, features extraction (tetracorder style), USGS06 lib interface * util: load_ENVI_file, load_ENVI_spec_lib, corr, cov and others The library do an extensive use of the numpy numeric library and can achieve good speed. The library is mature enough and is very usable even if the development is at a beta step.

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  • MODLEM Icon


    rule-based, WEKA compatible, Machine Learning algorithm

    This project is a WEKA (Waikato Environment for Knowledge Analysis) compatible implementation of MODLEM - a Machine Learning algorithm which induces minimum set of rules. These rules can be adopted as a classifier (in terms of ML). It is a sequential covering algorithm, which was invented to cope with numeric data without discretization. Actually the nominal and numeric attributes are treated in the same way: attribute's space is being searched to find the best rule condition during rule induction. In result numeric attribute's conditions are more precise and closely describe the class. This algorithm contains some aspects of Rough Set Theory: the class definition can be described accordingly to its lower or upper approximation. For more information, see: Stefanowski, Jerzy. The rough set based rule induction technique for classification problems. In: Proc. 6th European Congress on Intelligent Techniques and Soft Computing, vol. 1. Aachen, 1998. s. 109-113.

  • RaTrav

    mean first passage times and node occupancies calculations

    RaTrav tool was designed to support computational biology studies where mean first-passage times (MFPTs) between initial and single or multiple final states in network-like systems are used. The tool approves arbitrary networks (graphs) where a dynamics of the Markovian type takes place. Two methods are made available for which their efficiency is strongly dependent on the topology of the defined network: the combinatorial Hill technique and the Monte Carlo simulation method. References: M. Torchala, P. Chelminiak, M. Kurzynski and P. A. Bates, 'RaTrav: a tool for calculating mean first-passage times on biochemical networks', BMC Syst. Biol. 7, 130 (2013). M. Torchala, P. Chelminiak and P. A. Bates, 'Mean first-passage time calculations: comparison of the deterministic Hill's algorithm with Monte Carlo simulations', Eur. Phys. J. B 85, 116 (2012).

  • Nest-o-Patch Icon


    Software for analysis of patch-clamp recordings and other wave data

    This program was designed mainly for preconditioning and analysis of electrophysiological data, including patch-clamp and 2-electrode voltage clamp recordings. The program includes tools both for basic analysis of whole-cell recordings or analysis of single channel properties. Program can display and analyse long traces incuding many sweeps, series and even groups simultaneously. Current amplitudes or time intervals are easily measured. Single channel conductance, kinetics, NPo, as well as number of channels in a patch and their open probability may be estimated with the analysis of dwelling time at each conductance level. The program directly reads files, created by Pulse and PatchMaster software (HEKA Elektronik Dr. Schulze GmbH) as well as ASCII files. However, the program may be useful in various applications when editing and measurements in a 2-dimentional (for example time-current) wave are required.

  • MiModD Icon


    Mutation Identification in Model Organism Genomes using Desktop PCs

    MiModD is a software package for genomic variant identification from next-generation sequencing (NGS) data with optimized usage of system resources and a user-friendly interface. For most model organism genomes it lets the user carry out a complete analysis from unaligned genomic NGS read data to an annotated list of variants on a regular Desktop PC within a few hours. Its user-interface is beginner-friendly and designed to encourage geneticists to analyze NGS data themselves without the help of a trained bioinformatician.

  • CHP: C# HTN-Planner Icon

    CHP: C# HTN-Planner

    A simple HTN-planner written in C#

    C# HTN-Planner (CHP), a simple HTN-Planner written in C#. A domain-independent automated planning system based on ordered task decomposition, similar to SHOP2. It includes a Microsoft Visual Studio project (CHP) and a Unity3D project (CUHP), both with some examples. It is inspired by Dana Nau's Pyhop implementation and the book Automated Planning: Theory and Practice by Malik Ghallab et al.

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  • UniModeling

    UniModeling is a big data analytics tool for the unified modeling and reasoning in outdoor and indoor spaces. UniModeling supports constructing unified graph models of outdoor and indoor spaces and RFID deployments in these spaces. It enables probabilistic incorporation of RFID data that facilitates the tracking of moving objects and enables the search for them to be optimized. Furthermore, UniModeling is empowered with three reasoning applications that pertain to the positioning of RFID readers in outdoor and indoor spaces and the points of potential traffic (over)load in these spaces. The project source is hosted at: Post your questions to UniModeling mailing list at:

  • GPS to Radio-controlled Clock Icon

    GPS to Radio-controlled Clock

    GPS to Radio-controlled Clock

    The purpose of this simple DIY project is to build an electronic circuit that received the GPS time signal, convert it to the radio-controlled clock format, and transmit that signal to the clock. Once built, there is no need for setup and maintenance, all you need is put this unit close to the window to receive GPS signal, and it will transmit the time signal to your radio-controlled clock.

  • Frevo Icon


    Frevo is probably the simplest tool for evolutionary design

    FREVO is an open-source framework developed in Java to help engineers and scientists in evolutionary design or optimization tasks. The major feature of FREVO is the componentwise decomposition and separation of the key building blocks for each optimization tasks. We identify these as the problem definition, solution representation and the optimization method. This structure enables the components to be designed separately allowing the user to easily swap and evaluate different configurations and methods or to connect an external simulation tool.

  • wxChaos Icon


    An open source fractal generator extensible with scripts.

    wxChaos aims to be relatively simple and yet providing the user with many predefined fractals and algorithms to create beautiful results in less time. It also allows the user to create new fractals with user formulas and user scripts.

  • ViralFusionSeq [VFS] Icon

    ViralFusionSeq [VFS]

    Accurately discover viral integration events and fusion transcripts

    VFS was fullly tested under Ubuntu/Debian system. ** Announcement 1**: VFS is superior to Virus-Clip. As of 2016, VFS is the only viral integration tool available at NIH HPC system. ViralFusionSeq (VFS) is a versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base resolution. VFS combines soft-clipping information, read-pair analysis, and targeted de novo assembly to discover and annotate viral-human fusion events. A simple yet effective empirical statistical model is used to evaluate the quality of fusion breakpoints. Minimal user defined parameters are required. Source code with user manual and installation guide of VFS is available at sourceforge's "Files" section. Citation:

  • piv_clustering Icon


    structural clustering of atomic trajectories based on PIV

    This program allows to perform a structural cluster analysis of atomic trajectories obtained, e.g., from molecular dynamics simulations. At variance with other approaches, it is possible to analyse also processes in solution, e.g., chemical reactions in liquid water, since the distance metric is based on a Permutation Invariant Vector (PIV) that is symmetric under exchange of identical atoms or molecules, including on the same footing both solute and solvent degrees of freedom. The approach is general and the definition of PIV only requires to specify the range of interatomic distances that is relevant for the process under study. Alternatively, also the SPRINT topological coordinates can be employed, that are particularly suited for nanostructures. The output is a partitioning of the trajectory into a few structural clusters (i.e., sets of frames), allowing for simpler analysis and visualization. Please read and cite Gallet & Pietrucci, J. Chem. Phys. 139, 074101 (2013)

  • EpicsSharp

    A client, server and gateway implementation for the EPICS protocol

    A .NET implementation of a client, server and gateway for the EPICS protocol. Let you fully integrate your .NET software with other EPICS clients, or servers.

  • Lagrange Rally 3D Icon

    Lagrange Rally 3D

    3D vehicle simulator based on Lagrangian dynamics to simulate dynamics

    3D vehicle simulator in which vechicle's configuration as a whole (articulated body) , is represented by a 'vector' of generalised coordinates. so concepts like usual position and orientation of main body and wheels is all defined by the generalised coordinates.Using Lagrangian dynamics, theese coordinates are evolving in time in a realistic manner according to F=ma but as if there were also all constraint forces concretasing the presence of joints: hinge, prismatic, rigid connection, etc. all derivatives are done with finite differences, so it's all simple. in 3 videos I explain all the mechanics and its simulation up to this simple but pow method.Pure Lagrangian mechanics until now has not been used much or at all,in simulation videogames,but i decided to try it because it was promising, very simple compared to the fnal results, and there was not much docu on its use in simulation games: this lack was completed now. will com also a non-GL version vid:

  • Weka4OC GUI for Overlapping clustering Icon

    Weka4OC GUI for Overlapping clustering

    Weka4OC: Weka for Overlapping Clustering is a GUI extending WEKA

    This is a GUI application for learning non disjoint groups based on Weka machine learning framework. It offers a variety of learning methods, based on k-means, able to produce overlapping clusters. The application also contains an evaluation framework that calculates several external validation measures. The application offers a visualization tool to discover overlapping groups.

  • LAVA for AFM Icon

    LAVA for AFM

    Lloyd's Algorithm-based Volumetric Analysis for AFM Images

    This MATLAB-based program enables analysis of AFM images. In particular, it allows the user to measure the volume of all distinguishable features in an image and to isolate and sort those particles. As the name implies, LAVA uses Lloyd's Algorithm, also known as k-means sorting, to identify a small set of volumes representative of the actual distribution of particle in the image. Although developed for determining feature volume, LAVA is also completely compatible with other types of image analysis, such as fluorescence intensity. Work is in progress to provide three-channel functionality, allowing comparison of relative intensity of red, green, and blue channels in multi-color images.

  • AhoTTS - TTS for Basque and Spanish

    Text-to-Speech for Basque and Spanish

    Text-to-Speech conversor for Basque and Spanish. It includes linguistic processing and built voices for the languages aforementioned. Its acoustic engine is based on hts_engine and it uses a high quality vocoder called AhoCoder. Developed by Aholab Signal Processing Laboratory:

  • CADET Icon


    Chromatography Analysis and Design Toolkit

    We have moved to GitHub: The Chromatography Analysis and Design Toolkit (CADET) is developed at the Institute of Bio- and Geosciences 1 (IBG-1) under supervision of Dr. Eric von Lieres. The core of the CADET software is a fast and accurate solver for the General Rate Model (GRM) of packed bed liquid chromatography. The CADET solver covers a wide range of GRM variants, combining different transport and binding models with state-of-the-art mathematical algorithms and scientific computing techniques. The CADET framework also comprises a MATLAB interface and standard routines for parameter estimation, process optimization and experimental design. CADET is freely distributed as a contribution to the scientific community. If you find it useful for your own work, we would appreciate acknowledgements of the CADET software and citations of our papers:

  • Lambda Droid

    Lambda Calculus Interpreter for Android

    A lambda calculus interpreter for android.

  • Charmol Icon


    Program for molecular graphics

    Charmol is a command-line based program for making high-quality pictures of molecular structures for Linux and MacOS. It produces POV-Ray rendered images or files in VRML format for viewing in 3D. Charmol is capable of making pictures containing: - from small- to large-size molecules - more molecules together (different settings possible) - orbitals using molden and fchk files (GTO functions up to 'h' angular momentum supported) - surfaces using gaussian cube files (also color-mapped surfaces according to potential) - schematic representation of vibrations using arrows - user-defined arrows representing vectorial properties - measuring gauges - combinations of these features (more orbitals together, orbitals and arrows together etc.) Charmol allows for fine tuning of the final molecular design.

  • mesoFON

    mesoFON is an individual-based mangrove forest model, a KiWi extension

    mesoFON is an individual-based mangrove forest model. It is a Java implementation of the KiWi model done with RePast Simphony. It contains several new features: (1) You can add up to 10 species via the GUI. However, in principle, the number of species to be included programmatically is unlimited. (2) You can use a variety of growth functions via typing them in as a string on the GUI. (3) The model is transparent, sinc it comes with the Eclipse workbench of RePast.

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