D-GENIES : Dot plot large GENomes in an interactive, efficient and simple way

10.7287/peerj.preprints.26567v1 ◽

2018 ◽

Cited By ~ 1

Author(s):

Floréal Cabanettes ◽

Christophe Klopp

Keyword(s):

Open Source ◽

Open Source Software ◽

Software Package ◽

Web Application ◽

Source Code ◽

Input Sequence ◽

Image Alignment ◽

Large Genome ◽

Open Source Software Package ◽

Large Genomes

Dot plots are widely used to quickly compare sequence sets. They provide a synthetic similarity overview, highlighting repetitions, breaks and inversions. Different tools have been developed to easily generated genomic alignment dot plots, but they are often limited in the input sequence size. D-GENIES is a standalone and WEB application performing large genome alignments using minimap2 software package and generating interactive dot plots. It enables users to sort query sequences along the reference, zoom in the plot and download several image, alignment or sequence files. D-GENIES is an easy to install open source software package (GPL) developed in Python and JavaScript. The source code is available at https://github.com/genotoul-bioinfo/dgenies and it can be tested at http://dgenies.toulouse.inra.fr/.

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D-GENIES: dot plot large genomes in an interactive, efficient and simple way

PeerJ ◽

10.7717/peerj.4958 ◽

2018 ◽

Vol 6 ◽

pp. e4958 ◽

Cited By ~ 89

Author(s):

Floréal Cabanettes ◽

Christophe Klopp

Keyword(s):

Open Source ◽

Open Source Software ◽

Software Package ◽

Web Application ◽

Source Code ◽

Input Sequence ◽

Image Alignment ◽

Large Genome ◽

Open Source Software Package ◽

Large Genomes

Dot plots are widely used to quickly compare sequence sets. They provide a synthetic similarity overview, highlighting repetitions, breaks and inversions. Different tools have been developed to easily generated genomic alignment dot plots, but they are often limited in the input sequence size. D-GENIES is a standalone and web application performing large genome alignments using minimap2 software package and generating interactive dot plots. It enables users to sort query sequences along the reference, zoom in the plot and download several image, alignment or sequence files. D-GENIES is an easy-to-install, open-source software package (GPL) developed in Python and JavaScript. The source code is available at https://github.com/genotoul-bioinfo/dgenies and it can be tested at http://dgenies.toulouse.inra.fr/.

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Development of an open-source software package for watershed modeling with the Hydrological Simulation Program in Fortran

Environmental Modelling & Software ◽

10.1016/j.envsoft.2015.02.018 ◽

2015 ◽

Vol 68 ◽

pp. 166-174 ◽

Cited By ~ 14

Author(s):

D.J. Lampert ◽

M. Wu

Keyword(s):

Open Source ◽

Open Source Software ◽

Software Package ◽

Watershed Modeling ◽

Simulation Program ◽

Hydrological Simulation ◽

Open Source Software Package

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Integration of enabling methods for the automated flow preparation of piperazine-2-carboxamide

Beilstein Journal of Organic Chemistry ◽

10.3762/bjoc.10.56 ◽

2014 ◽

Vol 10 ◽

pp. 641-652 ◽

Cited By ~ 44

Author(s):

Richard J Ingham ◽

Claudio Battilocchio ◽

Joel M Hawkins ◽

Steven V Ley

Keyword(s):

Open Source ◽

Open Source Software ◽

Software Package ◽

Flow Chemistry ◽

Raspberry Pi ◽

Step Flow ◽

Simultaneous Control ◽

Open Source Software Package

Here we describe the use of a new open-source software package and a Raspberry Pi® computer for the simultaneous control of multiple flow chemistry devices and its application to a machine-assisted, multi-step flow preparation of pyrazine-2-carboxamide – a component of Rifater®, used in the treatment of tuberculosis – and its reduced derivative piperazine-2-carboxamide.

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An open source software package for primality testing of numbers of the form p2^n+1, with no constraints on the relative sizes of p and 2^n

10.7287/peerj.preprints.27396 ◽

2018 ◽

Author(s):

Tejas R. Rao

Keyword(s):

Open Source ◽

Open Source Software ◽

Software Package ◽

Primality Testing ◽

Fermat Number ◽

Open Source Software Package ◽

Sierpinski Numbers ◽

Efficient Software

We develop an efficient software package to test for the primality of p2^n+1, p prime and p>2^n. This aids in the determination of large, non-Sierpinski numbers p, for prime p, and in cryptography. It furthermore uniquely allows for the computation of the smallest n such that p2^n+1 is prime when p is large. We compute primes of this form for the first one million primes p and find four primes of the form above 1000 digits. The software may also be used to test whether p2^n+1 divides a generalized fermat number base 3.

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Development and Evaluation of an Open-Source Software Package “CGITA” for Quantifying Tumor Heterogeneity with Molecular Images

BioMed Research International ◽

10.1155/2014/248505 ◽

2014 ◽

Vol 2014 ◽

pp. 1-9 ◽

Cited By ~ 43

Author(s):

Yu-Hua Dean Fang ◽

Chien-Yu Lin ◽

Meng-Jung Shih ◽

Hung-Ming Wang ◽

Tsung-Ying Ho ◽

...

Keyword(s):

Open Source ◽

Texture Analysis ◽

Open Source Software ◽

Software Package ◽

Tumor Heterogeneity ◽

Locally Advanced ◽

Image Texture ◽

Pixel Intensity ◽

Open Source Software Package ◽

Molecular Images

Background. The quantification of tumor heterogeneity with molecular images, by analyzing the local or global variation in the spatial arrangements of pixel intensity with texture analysis, possesses a great clinical potential for treatment planning and prognosis. To address the lack of available software for computing the tumor heterogeneity on the public domain, we develop a software package, namely, Chang-Gung Image Texture Analysis (CGITA) toolbox, and provide it to the research community as a free, open-source project.Methods. With a user-friendly graphical interface, CGITA provides users with an easy way to compute more than seventy heterogeneity indices. To test and demonstrate the usefulness of CGITA, we used a small cohort of eighteen locally advanced oral cavity (ORC) cancer patients treated with definitive radiotherapies.Results. In our case study of ORC data, we found that more than ten of the current implemented heterogeneity indices outperformed SUVmeanfor outcome prediction in the ROC analysis with a higher area under curve (AUC). Heterogeneity indices provide a better area under the curve up to 0.9 than the SUVmeanand TLG (0.6 and 0.52, resp.).Conclusions. CGITA is a free and open-source software package to quantify tumor heterogeneity from molecular images. CGITA is available for free for academic use athttp://code.google.com/p/cgita.

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