Open Source Python Scientific/Engineering Software

The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.

DCMLinux is a complete PACS system, free of charge. Its core is an Ubuntu 14.04 system fully updated and it contains the DCM4CHEE as its PACS server. In the near future it will contain many other addons such as Weasis, Oviyam, Care2x, etc. Just download the iso, burn it to a CD and boot it up. No need to configure any files of dcm4chee, DCMLinux installer asks for everything it needs to configure a running PACS in minutes. Project Wiki : http://wiki.dcmlinux.org Project Forums: http://forums.dcmlinux.org

This software allows you perform six degree of freedom simulations of High Power Rocket (HPR) and model rocket flights. Parachute descent is also simulated. 3D flight trajectories are produced as well as detailed tabular flight data. Running in Monte Carlo mode allows generates multiple possible flight paths and splash down plots, indicating the probability of landing in an area. Peer-reviewed publication in the Journal of Open Research Software (JORS) http://doi.org/10.5334/jors.137 "Cambridge Rocketry Simulator – A Stochastic Six-Degrees-of-Freedom Rocket Flight Simulator"

openBmap collects data and provides open maps and statistics of all communicating objects: cellular antennas, wifi hotspots. All softwares from back-end to client are open-source under AGPL v3 license.

A minimalist approach to share text documents and data annotations. Allows a large number of different annotations to be represented. Project files contain: - simple code to hold/read/write data and perform sample processing. - BioC-formatted corpora - BioC tools that work with BioC corpora BioC goals - simplicity - interoperability - broad use - reuse There should be little investment required to learn to use a format or a software module to process that format. We are interested in reuse, and we focus on common NLP tasks that are broadly useful for textmining.

Microarray Gene Expression Database Group and OMG Gene Expression Standard (MAGE)

DTMF detector library and/or application that reads in the specified audio file and returns/outputs whether DTMF detected and/or list of detected digits. May have GUI and command line interfaces.

The Helsinki Finite-State Transducer toolkit is intended for processing natural language morphologies. The toolkit is demonstrated by wide-coverage implementations of a number of languages of varying morphological complexity.

BioMa is a specimen based Biodiversity database Manager. It is designed to store, organize, and manipulate biodiversity-related scientific data, either for the purposes of museums, scientific collections, or research projects.

Generic directory service (for the EPICS tool set). Directory entries are channels with properties and tags. Applications can query a web service to retrieve channels based on wildcard matching on properties and tags, and manipulate the directory data. Code has been moved to GitHub at https://github.com/ChannelFinder

The co-simulation adapation platform serves as programming framework and middleware to enable coupling of distributed, heterogeneous numerical models. The framework facilitates the adaptation and integration of new sub-models into a common simulation platform.

The Comparative Toxicogenomics Database (under development) will be a publicly-available, web-based database of genes and proteins of human toxicological significance. It is being developed using an Oracle 9i database, Tomcat, and Python.

A complete set of code to build your own robot for cospace dance using: raspberry pi, arduino, xbee and blender,

DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV

Dimenso is a library of numeric types for .Net and Java, that obey dimensional analysis and permit calculations with physical quantities. Due to the lack of C++ - like templates with numeric arguments, code generation is employed using Python.

Easy Equations is a utility using which one can write the mathematical equations. The focus of this utility is to provide user friendly access to write mathematical equations which is helpful for students, lecturers, mathematicians and Research persons who prefer using mathematical equations in a document, PowerPoint or web sites. Works on Windows as well as Linux platforms. Software Requirements: JDK 7 or higher. Linux Platform with kernel version 2.7 or higher.(for Linux users).python necessary only in linux environment to use COPY functionality.python is pre installed in recent linux distributions.

Egotistics is a social network analysis program that allows users to simultaneously explore multiple personal networks (called 'ego networks').

experimaestro is an experiment manager, and is composed of (1) a job scheduler that handles dependencies and locking (2) a modular experiment description framework, that allows easy description of the various parts of an experiments.

Tools for comparative sequence analysis. Includes FamilyRelations (GUI) and a C++ toolkit/Python wrapper for doing fixed-width-window analyses.

GEPETTO (GEne PrioriTization ExTended TOol) is an original open-source framework, distributed under the LGPL license, for gene selection and prioritization on a desktop computer that ensures confidentiality of personal data. It takes advantage of the data integration capabilities in the SM2PH-Central Framework(KD4v,MSV3d,BIRD,..), combined with in-house developed gene prioritization methods. It currently incorporates six prioritization modules, based on gene sequence, protein-protein interactions, gene expression, disease-causing probabilities, genomic context). GEPETTO is written in Java/Python and supported by an advanced modular architecture, which means that it can easily be modified and extended by the user, in order to include alternative scoring methods and new data sources. We intend to extend the system from gene-level to variant-level prioritization, by exploiting the variant data in the MSV3D database. Contact: bmhoan@gmail.com or walter.vincent.fr@gmail.com

ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.1 or later. HOME @ http://rsb.info.nih.gov/ij/

iROS is a meta-operating system for technology-rich "interactive rooms". The core components (Event Heap, DataHeap, iCrafter) provide communication, data storage, and service management for an iRoom.

JBoost is a simple, robust system for classification. JBoost contains implementations of several boosting algorithms in an alternating decision tree framework. In addition, JBoost provides extensible software for adding more learning algorithms.

JReferences is a tool to store and retrieve bibliographic references from a file or MySQL database. It reads BibTeXML, DocBook XML and RIS type references, and can output these and BibTex. A bibtex like alternative is also provided for DocBook XML docu

Java based multi-agent platform built on an organizational model (agent, group, role). MadKit provides general agent facilities (lifecycle management, message passing, distribution, ...), and allows high heterogeneity in agents.