Open Source Python Scientific/Engineering Software - Page 43

GemSIM is a software package for generating realistic simulated next-generation sequencing reads with quality score values. Both Illumina and Roche/454 reads (single or paired end) can be simulated using appropriate empirical error models.

Libraries for interacting with Tinytag Data Loggers from Gemini. Please note that this project is no longer maintained.

Here we introduce a Genomic Epidemiology Ontology (GenEpiO) that covers vocabulary necessary to identify, document and research food-borne pathogens and associated outbreaks. We envision various subdomains including genomic laboratory testing, specimen and isolate metadata, and epidemiological case investigations. The project files are currently hosted at https://github.com/GenEpiO/genepio/ . Here we provide the genepio-consortium@lists.sourceforge.net listserve. Terms for these subdomains have partially been implemented in the main file, **genepio.owl**, which imports terms from over 25 OboFoundry.org ontologies. Also we have added a number of terms that so far haven't been covered via OboFoundry. Recognizing that GenEpiO encompasses many domains, we are advocating a consortium approach for enhancing its content via interested parties that need particular domain terminology.

Gene-Environment iNteraction Simulator 2 (GENS2) simulates interactions among two genetic and one environmental factor and also allows for epistatic interactions. GENS2 is based on data with realistic patterns of linkage disequilibrium, and imposes no limitations either on the number of individuals to be simulated or on number of non-predisposing genetic/environmental factors to be considered. The GENS2 tool is able to simulate gene-environment and gene-gene interactions. To make the Simulator more intuitive, the input parameters are expressed as standard epidemiological quantities. GENS2 is written in Python language and takes advantage of operators and modules provided by the simuPOP simulation environment. It can be used through a graphical or a command-line interface.

A collection of tools for use in gene naming, including standardization, selection, and comparison.

This Project moved to https://sourceforge.net/projects/synbiowave/ because the name GeneWave is a registered trademark... Please do not use this project anymore.

We aim to develop a transformative computational method for automatic discovery of a set of dynamical rules that best captures both state transition and topological transformation in the data of spatio-temporal evolution of a complex network.

Because GAjoe of ATSAS cannot deal with WAXS range, and no parameters can be modified. I made a code by myself to use GA for finding best EOM for SAXS/WAXS. The project need ATSAS crysol and a folder with multiple pdb files to use.

Genetic data converter, for hapmap.org and hapmixmap data formats. Reads data in tabular format and writes in hapmixmap format. It's possible to add extensions to output different data formats.

A small simulator for Mendelian genetics, genetic drift, natural selection and random mutations, built on matplotlib and wxpython. A graph will be generated that traces the distribution of genotypes at successive generations.

BiSA is a bioinformatics database resource that allows investigators to run a number of overlapping genomic region analyses using their own datasets, or against the pre-loaded Knowledge Base. Analysis results can be restricted to a chromosome; the minimum base pair overlap in two sets or maximum distance between regions can be set; as can the maximum allowed distance between region centres. BiSA is capable of reporting overlapping regions that share common base pairs; regions that are nearby; regions that are not overlapping; average region sizes. BiSA can also annotate binding regions of interest with nearby genes. The results of overlap analysis can be imported into the Knowledge Base, allowing them to go into downstream analysis and independent annotation. A Venn diagram tool is also integrated into the software to allow users to visualize overlap results.

The Geocanvas project aims to provide a very small and simple set of APIs to assist the developer in creating geographically referenced canvas applications within the GTK/Gnome environment.

Directory of geoinformational data and metadata, like georeferenced list of streets in your city, or list of known nomenclature map tiles, and tools to process this data.

Graphical tool for managing database of geocaches and waypoints, importing GPX files and exporting geocaches to many formats including GPX, POI, HTML and others.

GeoSolver is a Python library for solving geometric constraint problems. A graphical testing and demostration application, the Geometric Constraint Workbench is included with the software.

Geomatrix, collection of C/C++ libraries to be used for symbolic description of n-dimensional geometric models. Operates internally with a representation that constructs complex objects based on primitives, allowing loss-less modifcation of models.

This project examines techniques to model three-dimensional rigid body motion using the geometric algebra of Dual Quaternions and how such models compare to more traditional models when used in underconstrained filtering applications.

Geometry Amateur, mechanical geometry prover

Geotag Merge is designed to combine track data from a GPS unit with EXIF data in a series of photographs. A handheld GPS can be simply carried while taking photos, and the photos can later be automatically gettagged (by matching timestamps).

GerbTool is a set of tools for modifying gerber and excellon drill files. GerbTool can be used to tile multiple gerber files as a single job, and can be run interactively or in batch mode.

Glimmer is an open source (GPL) three-dimensional thermomechanical ice sheet model, designed to be interfaced to a range of global climate models.

GluCat is a generic library of C++ templates that implement universal Clifford algebras over the field of real numbers. The PyClical extension module for Python gives users an easy Python scripting interface for calculations in Clifford algebras. The name PyClical is an homage to Pertti Lounesto's CLICAL.

GmshMorph is a tool to be used with GMSH, the meshing program by Christophe Geuzaine and Jean-François Remacle, for oceanographic and land-based fluid dynamics modelling. The program shapes meshes produced by GMSH to fit specified contour data.

Data processing algorithms based on the gnostical theory of uncertain data possess high robustness with respect to both outlying data and changes of their statistical characteristics.

This project has been moved to Github, Look there instead