your weatherman without the man
A lightweight, customizable OS X menubar app to display weather and forecast conditions. Select from four weather sources to bring you weather at your fingertips. The Classic version is like a classic car - restored to its former glory, polished, and enhanced. Runs on all Mac computers with Intel processors! Visit the original project for some legacy background as well as Ed's rewrite in the Swift language. <https://sourceforge.net/projects/heat-meteo/>
Fortran library to compute positions of celestial bodies
libTheSky is a Fortran library to compute positions of celestial bodies (Moon, planets, stars) and events (conjunctions, eclipses). It forms the core of the software that produces the Dutch popular-astronomy website http://hemel.waarnemen.com
Quantum Information Toolkit is a comprehensive, easy-to-use interactive numerical toolkit for quantum information and computing, available for both MATLAB and Python.
specific protein interaction networks from transcript expression
Although protein-protein interaction networks are an ubiquitous component of modern systems biology, comparatively few efforts have been made to tailor their topology to the actual cellular condition under study. Since a simple reduction of the networks to the subset of expressed genes only scratches the surface of higher organisms’ regulatory capabilities, we propose the advanced method PPIXpress that allows to exploit expression data at the transcript-level and is thus able to also reveal alterations in protein connectivity caused by alternative splicing. The original publication can be found on https://bioinformatics.oxfordjournals.org/content/32/4/571 .
Drive your obsolete Tek oscilloscope remotely with python
Control a Tek TDS-820 remotely via a GPIB interface using linux-gpib, python, matplotlib and tkinter. The programming manual is used to generate an XML schema which is then used to assist in building extra functionality into the tkinter user interface.
A MATLAB program for 2D particle tracking or 3D DHM based tracking.
We present a versatile and fast MATLAB program (UmUTracker) that automatically detects and tracks particles by analyzing long video sequences acquired by either light microscopy or digital holography microscopy (DHM). Our program finds the 2D particle center position using an isosceles triangle transform and the axial position by a fast implementation of Rayleigh-Sommerfeld numerical reconstruction algorithm using a one dimensional radial intensity profile. *Updates v1.1: 2017/11/21- Bug fix & Blob detection functions. Please visit our homepage for more information: http://www.physics.umu.se/english/research/biological-physics/the-biophysics-and-biophotonics-group/ *Please cite our work using the following information: Zhang, H., T. Stangner, K. Wiklund, A. Rodriguez, and M. Andersson. 2017. UmUTracker: A versatile MATLAB program for automated particle tracking of 2D light microscopy or 3D digital holography data. Comput. Phys. Commun. 219: 390–399.
Python GUI program to work with Geiger counters like GMC-300/320/500
GeigerLog is a Python based GUI program to work with GQ Electronic's GMC-300 / 320 and now also GMC-500 Geiger counters. Available as "scripts" to run where a proper Python environment exists, or as "bundle", which brings its own Python environment (but currently runs on Linux only). GeigerLog allows reading of Geiger counter data, logging to file, printing to screen and plotting as graph, showing Count Rate vs. Time, both in various, selectable units. The history stored on the Geiger counter's internal memory can be extracted, analyzed and graphed in the same way. The graph is live auto-updated and allows various customization. Time ranges for analysis can be set manually or per left/right mouse click. GeigerLog can control some functions of a connected counter (limited to GMC-3xx counters!). Advanced analysis of the data now permits count rate histograms with Poisson fit for quality control of data, and FFT analysis for any periodic signal hidden within the data.
RTS game for learning Algorithm Design
Tools to analyse output from the stellar-evolution code ev/STARS/TWIN
The evTools package provides tools to manipulate and display output from the binary stellar-evolution code ev (also known as STARS and TWIN).
Analyse output from MCMC codes like SPINspiral and lalinference_mcmc
analyseMCMC post-processes, analyses and plots output from the LIGO/Virgo gravitational-wave inspiral parameter-estimation codes SPINspiral and lalinference_mcmc.
Chess for the Blind for the JAWS or NVDA Screen Readers
Winboard 4.5 32-bit is a free Windows accessible Chess program that works automatically with the JAWS or the free NVDA screen reader. It is for the blind, low sighted or those who can not use a mouse. It provides vocal announcements of position changes and other selectable board conditions. Blind players also use a separate "tactile chess board". Winboard 4.5 has full keyboard access to move pieces and run menu items. Partial sighted players use high contrast mode and adjust board, piece, most font sizes and colors. Available languages are English, German, Spanish, Italian, Dutch and Russian. Games may be viewed, modified or saved in standard PGN format. Two Chess engines supply play and grand master strength move analysis. Connect to the Free Internet Chess Server (FICS) and play humans. Modify verbosity in screen reader configurations and in the Winboard "Sound" dialog under the "General" menu. Find all documentation in the "doc" folder under the Winboard directory of your C drive.
A MATLAB Automatic Differentiation Tool
ADiGator is a source transformation via operator overloading tool for the automatic differentiation of mathematical functions written in MATLAB. Given a user written file, together with information on the inputs of said file, ADiGator uses forward mode automatic differentiation to generate a new file which contains the calculations required to compute the numeric derivatives of the original user function. Furthermore, these calculations are written entirely in the native MATLAB language, and thus the process may be repeated to obtain nth order derivative files. The package is particularly appealing for applications where the same derivative must be found at multiple different points, i.e. non-linear root finding/optimization, stiff ode integration, etc.
Библиотека УГО компонентов для Kicad
Eng: The library of Conventional Graphic Symbols (CGS) for Kicad is based on russian international standards also known as GOSTs. Рус: Библиотека компонентов для Kicad, созданных в полном соответствии с требованиями УГО по международным нормативам ГОСТ.
Benchmark instances for multiobjective combinatorial optimization
Benchmark instances for multiobjective combinatorial optimization
A biochemical property prediction system
Computationally predicts the pharmacokinetic properties of drug candidates using Quantitative Structure Property Relationships (QSPR) modelling. Assembles a set of tools and databases for predicting the physical properties of small molecules. The program models a given property's dependence on a collection of molecular and structural descriptors using a training set of molecules. Neural networks and support vector regression are available, as well as linear models. The models generated by this analysis can then be used to predict the properties of compounds during the development of new and novel drugs. The program and its databases are all open-source.
Eukaryotic Genome Assembler
!!! NEW !!! 1/2017 - We now have a version optimized for running Human assemblies on AWS: https://sourceforge.net/projects/meraculous20/files/Meraculous-v220.127.116.11-smp_patch1-2-gcac7312.tar.gz/download ----------------------------------------- Meraculous-2D is a whole genome assembler for NGS reads (Illumina) that is capable of assembling large, diploid genomes with modest computational requirements. Features include: - Fast and memory-efficient k-mer counts - Efficient deBruijn graph traversal - Two modes of handling of diploid allelic variation - Improved scaffolding that produces more complete assemblies without compromising scaffolding accuracy. The assembly is driven by a robust pipeline which performs data fragmentation and load balancing, as well as submission and monitoring of multiple task arrays on a Grid Engine-type cluster or a standalone multi-core server. Manuscripts in submission: https://arxiv.org/abs/1703.09852 https://arxiv.org/abs/1608.01031
Android, UIQ 3.0, Series 60 Edition 5 open-source software
Android, Symbian UIQ 3.0 and Symbian Series 60 Edition 5 open-source software, tools, libraries and themes. Most notable the FX-602P / FX-603P Simulator and the HP-45 Emulator are hosted here.
Hybrid Lineage Transcriptome Explorer
HyLiTE (Hybrid Lineage Transcriptome Explorer) analyzes high-throughput transcriptome data from allopolyploid species. Allopolyploidy describes the formation of a new hybrid organism from the union of two or more different parents. Allopolyploid species carry multiple copies of each gene (homeologs), which often exhibit unusual expression patterns. Homeolog expression levels can technically be determined from next generation sequencing data (RNA-seq), but in practice, assigning reads to one homeolog over another is extremely challenging, particularly on a whole-genome scale. HyLiTE automates this process, and allows gene expression patterns to be explored even in very complex allopolyploid species.
Open pharmacovigilance data extraction, mining and analysis tool
OpenVigil provides a webinterface to analyse pharmacovigilance data, i.e., spontanous or systematic collections of treatments (drugs) and observed adverse events ("drug side effects"). FDA Adverse Event Reporting System (AERS) and other pharmacovigilance data (e.g., Canadian or German) are supported. The OpenVigil web-based analysis tools offer several analysis modes like extraction, filtering, mining of data and analyses via measurements of disproportionality like proportional reporting ratio or reporting odds ratios) and export to spreadsheets programs like Microsoft Excel or statistics programs like R. OpenVigil 1 operates on raw data, OpenVigil 2 on cleaned data (using drugbank.ca and drugs@FDA), OpenVigilFDA uses the official FDA online API. OpenVigil 2 supports query for ATC codes or certain chemical moieties. Other tools of the OpenVigil project include a calculator for measurements of disproportionality for a 2x2 contingency table and a drugname mapper using RxNorm.
Command-line tools for astronomy and astrophysics
Command-line tools for astronomy and astrophysics, written in Fortran.
Simple tool for numerical calculation
TU Calc is a modular tool that aims to gather numerical methods for solution of mathematical problems. Interacting with the user through a GUI that is analogous to the windows desktop.
A tool for CNC toolpath generation. Model data in, G-Codes out. The system is kept as generic as possible. Machines with up to 9 axis can be defined. Machine simulator included.
Python binding to the libindi library
This project offers a python binding to the libindi library. It uses the Simplified Wrapper and Interface Generator (SWIG). You may generate a PyIndi module which mainly defines an IndiClient class. This class could be used to build python scripts able to interact with indi servers using sendNew* methods and implementing new* methods of the BaseMediator class. PyQt applications may also be built on top of IndiClient, thus allowing rapid development of GUI Indi clients. Besides Python there are also bindings for node.js, Tcl (incomplete) and PHP (not useful). As application examples you will find a Python Websocket server with which you may build a web application interacting with Indi servers, and a simple PyQt application similar to the Kstars Indi Control Panel (was built as an exercise). Finally there is an equatorial mount 3D simulator written with Freecad and Python, planned to be connected with the PyIndi module.
Toolboxes for parameter continuation and bifurcation analysis.
Development platform and toolboxes for constrained parameter continuation, e.g., bifurcation analysis of dynamical systems. This material is based upon work partially supported by the National Science Foundation under Grant No. 1016467 and the Danish research council (FTP) under the project number 0602-00753B. Any opinions, findings, and conclusions or recommendations expressed on this site are those of the authors and do not necessarily reflect the views of the National Science Foundation or other funding sources. In the most recent release, documentation and tutorials are available for the following toolboxes: * ep : continuation and bifurcations of equilibrium points * coll : continuation of constrained collections of trajectory segments, including multi-segment boundary-value problems * po : continuation and bifurcations of periodic orbits in smooth and hybrid systems * recipes : collection of examples from the book Recipes for Continuation