“…We utilize this binary vector to derive bounding facets for the corresponding polyhedron, extraction of “active” bits within the binary vector, enumeration of neighboring binary vectors, and visualization of the polyhedral decomposition (Python code is available at https://github.com/cglrtrgy/GoL_Toolbox). …”
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“…AVAILABILITY AND IMPLEMENTATION: Snapper is implemented using Python and is freely available as a pip package named “snapper-ont.” …”
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“…The database includes Python source code for initial examination. The primary aim of the PHYAFB database is to provide a useful reference for other teams facing similar situations. …”
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“…FAF-Drugs2 is a command line utility program (e.g., written in Python) based on the open source chemistry toolkit OpenBabel, which performs various physicochemical calculations, identifies key functional groups, some toxic and unstable molecules/functional groups. …”
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“…Using Riptide in this way yields improved discrimination when compared to other state-of-the-art MS/MS identification algorithms, increasing the number of positive identifications by as much as 12% at a 1% false discovery rate. Availability: Python and C source code are available upon request from the authors. …”
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“…Availability: Algorithms were implemented in Python, LISP, R and maxima, using MySQL to access locally mirrored sequence data from Ensembl (D.melanogaster release 4.3) and flybase (D.pseudoobscura). …”
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“…Finally, access to multiplierz functionality is provided via high-level Python scripts, resulting in a fully extensible data analytic environment for rapid development of custom algorithms and deployment of high-throughput data pipelines. …”
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“…METHODOLOGY/PRINCIPAL FINDINGS: An appraisal of Armillifer agkistrodontis was performed in terms of morphology and genetic identification after its lifecycle had been established in a multi-host model, i.e., mice and rats as intermediate hosts, and snakes (Agkistrodon acutus and Python molurus) as definitive hosts. Different stages of the parasite, including eggs, larvae and adults, were isolated and examined morphologically using light and electron microscopes. …”
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“…AVAILABILITY: The MixHMM is available as a Python package provided with some other useful tools at http://genecube.med.yale.edu:8080/MixHMM.…”
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“…Availability: ARSER is implemented by Python and R. All source codes are available from http://bioinformatics.cau.edu.cn/ARSER Contact: zhensu@cau.edu.cn…”
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“…Additionally, the source code written in the Python programming language, is available under the General Public License of the Free Software Foundation. …”
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“…Example code demonstrate that Web services can be used to access the SEED using common bioinformatics programming languages such as Perl, Python, and Java. CONCLUSIONS: We present a novel approach to access the SEED database. …”
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“…The custom-written Perl, Python and Unix shell computer scripts used can be readily modified or adapted to suit many different applications. …”
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“…We present the routines developed for this purpose and show that a speed improvement of 5x up to 42x is provided versus optimised Python code. The higher speed is achieved when we exploit the parallelism of the GPU in the search of learning parameters. …”
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“…RESULTS: We introduce BIANA (Biologic Interactions and Network Analysis), a tool for biological information integration and network management. BIANA is a Python framework designed to achieve two major goals: i) the integration of multiple sources of biological information, including biological entities and their relationships, and ii) the management of biological information as a network where entities are nodes and relationships are edges. …”
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“…Availability: The software implemented in Python 2.7 programming language is available from request. …”
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“…We provide open-source python code to compute the reference frame. Third, we show that the upper, between subject consistency bound holds only for models that predict averages of subject populations. …”
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“…Our method achieves excellent performance results, with and without optimization of classifier tuning parameters. A Python pipeline implementing the approach is available at http://www.epibiostat.ucsf.edu/biostat/sen/dmfs/.…”
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“…METHODS: Giemsa-stained blood smear images were captured with a camera attached to a microscope and analysed using a programme written in the Python programming language. The programme design involved foreground detection, cell and infection detection, and spurious hit filtering. …”
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“…Structural screws were parametrically generated by a Python script for the automatic generation in the FE-software Abaqus/CAE on both a tetrahedral and a hexahedral meshed femur. …”
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