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  1. 5041
    “…AVAILABILITY AND IMPLEMENTATION: Oasis 2 is implemented in Java, J2EE, mysql, Python, R, PHP and JavaScript. It is freely available at https://oasis.dzne.de ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-018-2047-z) contains supplementary material, which is available to authorized users.…”
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    Oasis 2: improved online analysis of small RNA-seq data
  2. 5042
    “…We provide an open source Python implementation of these algorithms at https://github.com/JBEI/limitfluxtocore.…”
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    Constraining Genome-Scale Models to Represent the Bow Tie Structure of Metabolism for (13)C Metabolic Flux Analysis
  3. 5043
    “…To address this need, we have developed Bamgineer, a tool written in Python to introduce user-defined haplotype-phased allele-specific copy number events into an existing Binary Alignment Mapping (BAM) file, with a focus on targeted and exome sequencing experiments. …”
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    Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets
  4. 5044
    “…To load the datasets in Python, we provide code based on the Neo data framework that produces a data structure which is annotated with relevant metadata. …”
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    Massively parallel recordings in macaque motor cortex during an instructed delayed reach-to-grasp task
  5. 5045
    “…RESULTS: SECIMTools (SouthEast Center for Integrated Metabolomics) is a set of Python applications that are available both as standalone tools and wrapped for use in Galaxy. …”
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    SECIMTools: a suite of metabolomics data analysis tools
  6. 5046
    “…Mevislab software and Python have been used for the development of MIROR. …”
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    Automated Modular Magnetic Resonance Imaging Clinical Decision Support System (MIROR): An Application in Pediatric Cancer Diagnosis
  7. 5047
    “…Farseer-NMR has been written entirely in Python and its modular code base enables facile extension. …”
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    Farseer-NMR: automatic treatment, analysis and plotting of large, multi-variable NMR data
  8. 5048
    “…Database records are available in MongoDB, CSV and JSON formats which can easily be read using Python, R, Java and MatLab. This makes the database easy to query for tackling big-data materials science initiatives and provides a basis for magnetic materials discovery.…”
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    Auto-generated materials database of Curie and Néel temperatures via semi-supervised relationship extraction
  9. 5049
    “…AVAILABILITY AND IMPLEMENTATION: GSEA-InContext implemented in Python, Supplementary results and the background expression compendium are available at: https://github.com/CostelloLab/GSEA-InContext.…”
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    GSEA-InContext: identifying novel and common patterns in expression experiments
  10. 5050
    por Petit, Robert A., Read, Timothy D.
    Publicado 2018
    “…In light of these issues, we created Staphopia, an analysis pipeline, database and application programming interface, focused on Staphylococcus aureus, a common colonizer of humans and a major antibiotic-resistant pathogen responsible for a wide spectrum of hospital and community-associated infections. Written in Python, Staphopia’s analysis pipeline consists of submodules running open-source tools. …”
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    Staphylococcus aureus viewed from the perspective of 40,000+ genomes
  11. 5051
    “…NEURON's extracellular reaction-diffusion is supported by an intuitive Python-based where/who/what command sequence, derived from that used for intracellular reaction diffusion, to support coarse-grained macroscopic extracellular models. …”
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    Using NEURON for Reaction-Diffusion Modeling of Extracellular Dynamics
  12. 5052
    “…To address these challenges, we have developed a new software framework called COBRAme for building and simulating ME-models. It is coded in Python and built on COBRApy, a popular platform for using M-models. …”
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    COBRAme: A computational framework for genome-scale models of metabolism and gene expression
  13. 5053
    “…The tool is freely distributed as a Python package, with additional instructions, tutorial and demo datasets available at https://bitbucket.org/valenlab/shoelaces. …”
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    Shoelaces: an interactive tool for ribosome profiling processing and visualization
  14. 5054
    por Kuśmirek, Wiktor, Nowak, Robert
    Publicado 2018
    “…Web application was developed in client-server architecture, where web-browser is used to communicate with end-user and algorithms are implemented in C++ and Python. The presented approach enables proper reconstruction of tandem repeats, which are longer than the insert size of paired-end tags. …”
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    De novo assembly of bacterial genomes with repetitive DNA regions by dnaasm application
  15. 5055
    “…Hierarchical clustering and python programming language analyses was used to demonstrate CTA expression and coverage. …”
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    Establishment of cancer/testis antigen profiling based on clinicopathological characteristics in resected pathological stage III non-small cell lung cancer
  16. 5056
    “…SVEngine is implemented as a standard Python package and is freely available for academic use .…”
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    SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution
  17. 5057
    “…This method is implemented in Python within the framework of the open-source Kinase Activity Toolbox (kinact), which is freely available at http://github.com/saezlab/kinact/.…”
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    Phosphoproteomics-Based Profiling of Kinase Activities in Cancer Cells
  18. 5058
    por Merz, Pascal T., Shirts, Michael R.
    Publicado 2018
    “…To make the usage as easy as possible, we have developed an open-source and platform-independent Python library (https://physical-validation.readthedocs.io) implementing these tests. …”
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    Testing for physical validity in molecular simulations
  19. 5059
    por Scheffer, Louis K.
    Publicado 2018
    “…These analyses are typically performed in a variety of conventional programming language, such as Matlab, R, Python, or C++, and read the connectomic data either from a file or through database queries, neither of which are standardized. …”
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    Analysis Tools for Large Connectomes
  20. 5060
    “…This has been accomplished by using Electron as a wrapper for an AngularJS app, a Python analytics module, and a local, browser-based NoSQL database. …”
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    A new cross-platform architecture for epi-info software suite
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