Open Source Scientific/Engineering Software - Page 97

This package is developed to perform stationary 13C metabolic flux analysis for estimation of intracellular flux distribution.

Traditional methods for isolation of microsatellites (SSRs) are often expensive and time consuming. Nowadays is easier and cheaper to obtain genomic data from next generation sequencing. Then, at least two software need to be applied in order to obtain SSR primers of SSR flanking sequences for PCR assays. Here we propose new software that allows the user to work with several sequences for PCR primer design in one step.

Function Plotter is a simple-to-use application that provides you with a quick and easy solution for plotting 2D mathematical functions. No advanced mathematics or programming knowledge is required, and the program can draw functions in milliseconds. It's based on Qt 5.5.0, OpenGL 2.0, and muparser 2.2.5. A complete list of all supported functions and operators is available on the muparser library website: www.beltoforion.de/article.php?a=muparser

FunkyPlot is an interactive plotting tool for mathematical functions, designed for pupils and students.

GComb is an open-source quick and easy Java tool intended to ease the lives of all 3D printing hobbyists by providing a look inside a “sliced” GCode file and a better view of what is going to be printed, before it is printed. It works by parsing GCode files and producing an image for each layer of the printed object, any of which can then be viewed. GComb was originally written on Mac OS X using Eclipse with Java version 1.7.0_25, and was made for a Makerbot™ The Replicator Dual printing Skeinforge 50-generated GCode files. The jar file in the package was compiled for use by Java versions 1.5 and greator but, its compatibility on different operating systems and utility for different printers and slicers than those it was written for is not assured. However, we coders did our best to make sure that our implementation would not depend on comments in GCode or slicer-specific details, so it should work given files generated by Slic3r and others as well as Skeinforge.

GDSread is a simple command line utility written in Free Pascal. GDSread can read and convert a Calma GDS stream file and output an ASCII formatted list file and a new GDS file with updated timestamp. If specified - it can modify the output GDS database by scaling it and/or replace cell names. Check out readme.rtf.

GENESIS (GEneral NEural SImulation System) is a software platform for the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, large networks, and systems-level processes.

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

GLogic is a logic gate simulator for linux and an adaptation of the gLogic package....

GMES is a free finite-difference time-domain (FDTD) simulation Python package developed at GIST to model photonic devices. Its features include simulation in 1D, 2D, and 3D Cartesian coordinates, distributed memory parallelism on any system supporting the MPI standard, portable to any Unix-like system, variuos dispersive ε(ω) models, CPML absorbing boundaries and/or Bloch-periodic boundary conditions, and arbitrary material and source distributions. GMES officially stands for GIST Maxwell’s Equations Solver.

displays the current phase of the Moon as an applet for the gnome panel. Clicking on the applet displays sundry data pertaining to the moon including various clock functions. The user can select between a real image as well as a cartoon image of the

GamesCrafters is an undergraduate research group at the University of California, Berkeley. GAMESMAN is our software for building text & X11 apps for finite, 2-person abstract perfect-information games (e.g., TicTacToe & chess). We've authored 40+ games

GapFiller is a seed-and-extend local assembler to fill the gap within paired reads. It can be used for both DNA and RNA and it has been tested on Illumina data. GapFiller can be used whenever a sequence is to be assembled starting from reads lying on its ends, provided a loose estimate of sequence length.

A small Python utility used to manage multiple concurrent installations of Genesis 2000.

Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools. Commonly used biological software and example script files for different assembly pipelines have also been provided, where the example script files can be updated to suit one’s experimental needs. Genobuntu attempts to reduce the amount of time and energy needed to build software workstations and it can also act as a good teaching source for a class room setting. Therefore, Genobuntu offers a well-tailored environment for both novices and experts working in the field of genome assembly.

GenomeView is a genome browser and annotation editor that displays reference sequence, annotation, multiple alignments, short read alignments and graphs. Most major data formats are supported. Local and internet files can be loaded. This project has moved to GitHub: https://github.com/GenomeView/genomeview

A compact gesture recognition program (currently for Windows), used with mouse or pen (on graphic tablets). Longer term aim is to create a gesture recognition library that can be easily used in other programs.Please read the forum for more information

GnuPinch is a pinch analysis and supertargeting tool. GnuPinch can calculate heat exchanger networks (HEN) with minimum energy requeriments and minimum cost. It also can calculate other parameters of the pinch analysis of a chemical process.

GoFigure2 is an open-source, cross-platform application for visualizing, processing and analyzing of multidimensional microscopy data. Users can visualize, segment and track cells through time, detect cell-division and ultimately generate lineages.

GPS Trip computer, used to calculate distance (3 counters), quikly clear any of them, back counting

Provides a GUI interface to grammatical structure and relations (as parsed by the Stanford Parser) of any text. Contains grammatical relation editor to modify, import, export grammatical relation definitions (tregex patterns and features).

GuruxDLMS is moved to GitHub. http://github.com/Gurux

HBS Analyzer is a methylation calling tool for hairpin-bisulfite sequencing data. HBS Analyzer can accept raw hairpin-bisulfite sequencing data in FASTA or FASTQ format, align the paired end reads to the reference genome and call methylation. Given the double stranded nature of the data that is used, HBS analyzer can identify errors caused by PCR and sequencing along with identifying hemi-methylated sites. This error information is also considered while making the methylation call and hence methylation sites introduced by SNPs are also identified along with the known methylation sites in the genome.

A base for programs. Includes algorythms for Q-learning and SOM's etc. too. Examples: Hamron: Simulates evolution, uses the 2D-renderer. DriveUnit: created for school, for a robotic arm, uses the 3D-renderer. Hlearn: http://www.sagenb.org/home/pub/8