Open Source Python Scientific/Engineering Software - Page 41

dAnalytics is a software made for educational purposes to work with discriminant analysis. It's a very simple calculator over bi-dimensional populations. You input a file with two columns (one for each variable) and tryout different separations of populations (blue and red) and analyze it's efficiency by observing the eigen value result for the attempted separation. It also gives many information about the statistics both of the input and the separated populations. There's a documentation folder in the software which brings a quick start guide for this software.

This program is a web application to collect and organize data of text analysis. It works with sets of texts and the analysis are done on portions of the length of a sentence. One of the preprocessing modules is based on CoGroo (A LibreOffice & OpenOffice.org Portuguese Grammar Checker).

Dockserver-talk is a python module that provides an easy way to build custom clients that communicate with Teledyne Webb Research's dockserver software, used to control "Slocum" underwater gliders. The package comes with two applications built on top of dockserverTalk: BUGS: a program to monitor and display the position of gliders (as well as buoys and ships) with respect to a given GPS location (from an external source). Surfalarm: a program that can send text messages or make direct phone calls, acting upon a glider to surface and connect to a dockserver, being in a mission, or aborted. Serial2rudics: a helper program that lets a glider simulator connected to a serial port appear as a glider connecting and disconnection via rudics/iridium when at ther surface or underwater, respectively.

This Python script reads in a DXF (ascii) file and generates a PCB output compatible with PCB Designer, part of the gEDA suite. It is designed for two purposes: One is to generate a PCB snippet from a mechanical drawing (such as a board outline), the other is to produce element files from CAD drawings. PCB snippets are easily imported into an existing gEDA-PCB project using File -> Load Layout to Buffer. Generated element files are ready to use (except for special cases like no-paste flags and rounded pads).

Application to create 'electronic fluorescent pictographic' representations of gene expression patterns. Created at the Provart lab of the department of Cell & Systems Biology, University of Toronto.

This is a implementation of the 'enhanced Topic-based Vector Space Model' (eTVSM) using the python language. A Java-Version and maybe other java-code contributions are planned.

Genome coverage, the number of sequencing reads mapped to a position in a genome, is an insightful indicator of irregularities within sequencing experiments. While the average genome coverage is frequently used within algorithms in computational genomics, the complete information available in coverage profiles (i.e. histograms over all coverages) is currently not exploited to its full extent. Thus, biases such as fragmented or erroneous reference genomes often remain unaccounted for. Making this information accessible can improve the quality of sequencing experiments and quantitative analyses. fitGCP is a framework for fitting mixtures of probability distributions to genome coverage profiles. Besides commonly used distributions, fitGCP uses distributions tailored to account for common artifacts. The mixture models are iteratively fitted based on the Expectation-Maximization algorithm. Please find the accompanying paper here: http://dx.doi.org/10.1093/bioinformatics/btt147

Fulguro is an optimized 2D library for image processing with Mathematical Morphology and Linear processing

Python based webservice to manage and display information from some fiber-GISes.

A toolbox of open source geospatial essentials

go2Sim measures semantic similarity between genes annotated with Gene Ontology terms. Resnik and Wang methods supported. A new improvement of the methods is currently in development, it will be available as soon as the results have been published.

Goldify is a set of tools that allow automated addition of links into electronic documents. Its main purpose is to allow such addition of links into documents that wish to link to the IUPAC GoldBook (http://goldbook.iupac.org).

Development of quality C++ and Python objects for high energy physics computations.

Healthcare Xchange Protocol for interoperative communications. Data exchange/transfer, platform independent,XML-RPC, HL7, SOAP, EDIFACT, simple,easy, authenticated, secure, transparent, no geo-restrictions, open sourced, peer reviewed, collab development

iTag has been designed for researchers that rely on photographic census techniques of animals that are hard to detect via image recognition algorithms and was originally developed for counting Grey Seals in the German wadden sea during March 2013. It has since then been further expanded and has now reached beta status. iTag allows Users to define up to 9 different categories and name them accordingly. In addition, 4 modifiers are available to further increase the options during a tagging session. Users are able to load a series of Images into a session and add tags on objects on these images within previously defined categories and modifiers. Upon ending the session, result files are produced including (if provided by the EXIF data) the gps information for each Picture, the number of objects in each category and a detailed result file that describes each individual object. In addition, all images that were tagged are saved.

iTree: scalable multithreaded phylogenomic pipeline

A program to help physics students understand Kinematics and Dynamics. Writen in Python.

Latex2slides is a simple graphical program that produces a set of HTML/JPEG slides from a TeX or LaTeX source. Each Postscript page is converted to a JPEG image using ImageMagick's convert. The program then makes one HTML page for each JPEG (or slide), a

A plug-in for Abaqus FEA with empiric data for many types of materials (linear, nonlinear, ortotropic). A simple GUI for creating properties for common materials and sections for bulk and shells.

metaProt is a python pipeline to analyze and extract data from protein sequences found in metagenomic projects. It integrates several existing tools (HMMer, Pepstats, Blast...) to be used against custom databases. Please, read the README.txt file to find more about this.

A collection of software made by Milos Rancic.

mod_openopc is a full featured implementation of the OpenOPC library for Python. It is cross platform compatible (full Python 2.5 and up). We used to recommend running it on a POSIX platform (Unix / Linux), but thanks to modest efforts since 2014, performance in Windows OS environments is excellent.

Navlib is a collection of algorithms created to solve the navigation problem for 2D non-holonomic vehicles. It includes code for computational geometry, system identification, path planning, and control. Written in C++ with python extensions.

NESSY is an open source software to analyse NMR relaxation dispersion data of either CPMG or R1p (R1rho) dispersion experiments. The graphical interface enables simple management of large experimental data sets and simple and automated analysis. NESSY automatically calculates effective transverse relaxation rate (R2eff) and performs model selection between different relaxation dispersion models.

Forked Ubuntu 14.04 minimal install with XOrg and FluxBox desktop environment for web-based pipeline construction and job submission. HOWTO: 1) Set VM network settings to a bridged adapter type. 2) Load VM to client 3) From host: $ ssh -X ubuntu@<foobar> 'firefox && butterfly.server.py --unsecure' --- passwd = 616287xx 5) or ssh into host with X forwarding, and type runme This will launch an X-session of Firefox on the client, which will then be forwarded to the host. The first homepage tab links to our pipeline constructer. The second homepage tab links to a xterm session on the client. Software included (location - name): path - biobambam path - bwa path - bowtie2 path - bowtie path - cufflinks path - bcftools path - tophat path - scalpel path - samtools path - sra-toolkit path - bamtools path - delly path - delly-parallel path - picard-tools path - fastahack path - twoBitToFa ~/prog/java/ - mutect ~/prog/python/ - platypus ~/prog/java/ - gatk