Showing 2376 open source projects for "sql command line"

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  • 1
    NGS can product a pair of reads which come from one original DNA fragment. If the internal gap can be correctly filled, we will get the full length sequence of original DNA fragment.
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  • 2
    A Perl module and selection of scripts to aid processing of NEXUS-based tree files ready for supertree construction in programs like PAUP*.
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  • 3

    pdf2mp3

    Simply convert your PDF files into audio books

    Summary: Your eyes are tired of looking into the tablet or cell-phone screen reading ebooks? You have difficulty reading from LCD screen specially in a driving vehicle? This software is for you! It converts your PDF files to MP3 audio books. Special Features (Compared to similar projects): Each page is in a separate MP3 file. Created MP3 files have ID3v2 tags showing Book name and page number. Multi-threaded conversion, means all CPU cores will be used thus multiple times faster conversion.
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  • 4

    HPN cli calculator

    A functional HP-style command-line RPN scientific calculator

    HPN is a functional - as opposed to microcode - cross-platform emulation of a classic 1970s Hewlett-Packard scientific calculator for any command-line interface. Its operations completely model the historical and groundbreaking HP-35 series, and functions to support the HP-45 and the later HP-65, 67 and HP-15C are in the pipeline.
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  • 5
    primeScaff
    primeScaff is intended to automate the sometimes tedious process of manually designing specific primer pairs around gaps of genomic scaffolds and speedup the genome finishing stage of a genome sequencing project. It incorporates de-novo repeat finding using RECON to avoid as much as possible designing primers in repetitive regions and offers the possibility to easily fine-tune the primer design options using primer3. It outputs the repeat, gap and primer annotations in gff2 and gff3 to...
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  • 6

    clic

    command line interface calculator

    CLIC is a command line interface calculator based on readline library.
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  • 7
    MPQC

    MPQC

    Massively Parallel Quantum Chemistry program

    The Massively Parallel Quantum Chemistry program, MPQC, computes properties of atoms and molecules from first principles using the time independent Schrödinger equation.
    Downloads: 3 This Week
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  • 8

    CDSbank

    multi-sequence extraction, filtering & formatting

    CDSbank is a database that stores both the protein-coding DNA sequence (CDS) and amino acid sequence for each protein annotated in Genbank. CDSbank also stores Genbank feature annotation, a flag to indicate incomplete 5’ and 3’ ends, full taxonomic data, and a heuristic to rank the scientific interest of a species. This rich information allows fully automated data set preparation with a level of sophistication that meets or exceeds manual processing. Defaults ensure ease of use for typical...
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  • 9
    A collection of Java ports of open source terrain and solar system generation packages. Code has been extensively refactored, extended and documented. GPL License with exception for required libraries.
    Downloads: 1 This Week
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  • 10
    Plinko was originally an experiment with Prefix Trees and log parsing. The general concept is to have a single end point you can send any data to, in a "fire and forget" fashion. Plinko should identify and parse the data completely without the sending system caring what it sent. The latest version supports named fields in the STL files for tagging data parsed in the Prefix Tree and anonymous functions for parsing dynamic message payloads. We now output JSON objects and I'm working on HBase...
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  • 11
    ParaSim

    ParaSim

    Parallelized calculation of molecular similarities

    Diversity assessments and comparisons of large compound databases require calculating similarities of millions of compounds in an affordable time. ParaSim addresses this challenge by parallelizing the calculations according to the number of computing cores available on a single machine. It is optimized for the throughput of very large numbers of query structures against very large numbers of reference structures. As as special feature, ParaSim allows to store and and to access frequently...
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  • 12
    Niah (Statistical Disclosure Control)

    Niah (Statistical Disclosure Control)

    Niah supports k-anonymity statistical disclosure control assessments

    Niah is a simple java tool for use in statistical disclosure control risk assessments. It implements the k-anonymity model of disclosure risk for data in csv in format. This work was developed as part of a PhD project at the University of Glasgow and during an internship with the Scottish Government.
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  • 13

    drl2g

    Convert drl files to g code

    This is a utility to process and convert drl files to efficient g code, which will help in drilling PCBs using a CNC. The snapshots are based on the linuxcnc axis program to visualize the results of the program using different algorithms.
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  • 14
    ASCEND modelling environment
    ASCEND is a modelling environment and solver for large or small systems of non-linear equations, for use in engineering, thermodynamics, chemistry, physics, mathematics and biology. Solvers for both steady and dynamic (NLA & DAE) problems, are provid
    Downloads: 4 This Week
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  • 15
    QtoNum

    QtoNum

    python calculus library with imprecise and precise representations

    ...QtoNum also handles infinitesimals and infinites. All these types can be mixed in expressions and conversions are performed automatically. QtoNum can be used as an interactive calculator (command line) and as a calculus library.
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  • 16
    This project no longer resides at sourceforge. The new home page is: http://muparser.beltoforion.de
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  • 17
    popbam
    POPBAM is a tool to perform evolutionary or population-based analyses of next-generation sequencing data. POPBAM takes a BAM file as its input and can compute many widely used evolutionary genetics measures in sliding windows across a genome.
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  • 18
    Boxshade is a program for creating good looking printouts from multiple- aligned protein or DNA sequences.
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    Downloads: 1 This Week
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  • 19
    I Language
    I is a cross-platform programming language designed towards efficiency during development and at runtime.
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  • 20
    LAVA for AFM

    LAVA for AFM

    Lloyd's Algorithm-based Volumetric Analysis for AFM Images

    This MATLAB-based program enables analysis of AFM images. In particular, it allows the user to measure the volume of all distinguishable features in an image and to isolate and sort those particles. As the name implies, LAVA uses Lloyd's Algorithm, also known as k-means sorting, to identify a small set of volumes representative of the actual distribution of particle in the image. Although developed for determining feature volume, LAVA is also completely compatible with other types of...
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  • 21
    ParsEval is a program for comparing alternative sources of gene structure annotation (provided as GFF3 files) for a genomic sequence (or set of sequences). Similarity statistics are reported in a single aggregate summary report, as well as for each gene locus individually.
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  • 22

    TML - Text Mining Library for LSA & CMM

    TML is a Java Library for LSA and extracting Concept Maps from text

    TML has moved to http://www.villalon.cl/tml.html and the code to https://github.com/villalon/tml
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  • 23

    cextools

    Command line helpers for Conexp files.

    Some small command line programs and a file parser for Concept Explorer (conexp) written in C++. Currently features include: Converters from concept explorer into PDF, PostScript, SVG and PovRay, a modified 3D Freese layout.
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  • 24
    A simulation of Fisher's geometric model of adaptation modified to describe diploid species
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  • 25

    RASPnmr

    Protein NMR backbone resonance assignment

    RASP uses structure-based chemical shift predictions to solve the backbone resonance assignment problem in protein NMR spectroscopy. This enables rapid determination of highly accurate assignments on the basis of minimal experimental datasets, even for spectroscopically challenging proteins. RASP takes as input spin systems assembled on the basis of an arbitrary set of conventional triple-resonance NMR experiments. Uniquely, RASP is capable of extensive assignments even in the abscence of...
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