Search Results for "sql command line" - Page 54

MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools.

guileplayer is a Scheme binding for libplayerc - the Player client library, part of Player/Stage project. It can be used with guile (GNU Scheme interpreter) version 1.6 or later.

A high-performance simulation package for sampling the chemical and reaction-diffusion master equations. Primarily intended for running stochastic simulations of microbial cells.

We here present a novel computer algorithm, called AutoClickChem, capable of performing many click-chemistry reactions in silico. In silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization.

Simulator for transmission electron microscope images and tilt series of biological samples.

xyz2eps.py is an command line utility written in Python programing language which prints the geometry from xyz-file directly to the eps-file format. Originally it was designed to study the problems related to grain boundaries in graphene.

Diva is a command-line tool for dispersal-vicariance analysis, a simple method for inferring the distributional history of organisms (Ronquist, F. 1997. Systematic Biology 46:193-201).

Displays mummer/nucmer mappings and prints PNG to stdout via the "show-coords -lcdTH" output. The output file is <coords-output>.png. Command line options allow for different features when producing the image. Within the code there are comment blocks which give examples of how to further customize it i.e. grouping based on name similarity, color, etc. This program is aimed at providing full customization within the limits of the Bio-Graphics module. Current version supported is Bio-Graphics-2.25

ZORRO is a probabilistic masking program that assigns confidence scores to each column in a multiple seqeunce alignment. These scores can then be used to account for alignment accuracy in phylogenetic inference pipelines.

LutefiskXP is ANSI C compliant software used to perform de novo peptide sequencing from tandem mass spectra.

Software for parsimony-based tree fitting, which can be used for analysis of problems in historical biogeography, coevolution, and in species tree - gene tree fitting.

Alignment of the assembled sequences to a reference genome is a common way to obtain a likely order for the contigs, though most of times the final decision is taken by the user. We present the jContigSort, a tool that sorts the genome contigs.

This project is based on a personal effort for researches on dynamics of coevovling networks. As a physicist, I am trying to build a framework for discrete-time dynamics of general networks, and its software libraries with APIs.

Randaudio lets you use your soundcard as a hardware random number generator.

A fast efficient way of dealing with large amounts of Blast or Repeatmasker data.

Ns is a discrete event simulator targeted at networking research. Ns provides substantial support for simulation of TCP, routing, and multicast protocols over wired and wireless (local and satellite) networks.

SPINNEY provides an implementation of helicity spinors and related algorithms for the symbolical manipulation program FORM. The description of this package is published in http://arxiv.org/abs/1008.0803 .

GCX provides a complete set of data-reduction functions for CCD photometry, accessible both from a GUI and the command line. It also controls CCD cameras and telescopes, and implements automatic observation scripting.

Amalthea is a collection of scripts (mainly Python, glued with Bash scripts) for *nix systems that helps to simultaneously collect information from multiple laboratory balances oriented to gravimetric measurement of plant transpiration.

Router Radio Protocol Tools provide router (server) simulator and a radio (client) simulator for the radio-router protocol. The router simulator can be used to support the integration of the protocol into a radio.

This is a Java-based project for complex event extraction from text and co-reference resolution. Currently the code can read BioNLP shared task format (http://2011.bionlp-st.org/) and i2b2 Natural Language Processing for Clinical Data shared task format (https://www.i2b2.org/NLP/DataSets/Main.php). Event extraction includes finding events and the parameters for an event in a text. The method is based on SVM but other ML algorithms can be adopted. The method details are explained in the...

SimBac is a software package for simulating bacterial genome evolution. It outputs samples of DNA sequences at each generation & allows testing of major evolutionary mechanisms, including mutation, recombination, genetic drift, and natural selection.

For electronics engineers, when using open source EDA tools, one of big challenge is component schematic symbols and footprints. If you are creating footprints for component with more than 100 pins, it becomes very time consuming and challenging to create error free footprints. Here is a simple program to create footprints for open source EDA kicad. The idea is to describe footprint in .csv format and convert .csv to kicad footprint format. At preset program supports Kicad only, but can be...

BFAST facilitates the fast and accurate mapping of short reads to reference sequences, where mapping billions of short reads with variants is of utmost importance.