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  1. 3721
    “…AVAILABILITY AND IMPLEMENTATION: The process is implemented in Python and available as open-source software from https://github.com/ZhangLab312/DPAMSA.…”
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    Multiple sequence alignment based on deep reinforcement learning with self-attention and positional encoding
  2. 3722
    “…AVAILABILITY AND IMPLEMENTATION: Master of Metals has been implemented in Python and is available at https://github.com/cerm-cirmmp/Master-of-metals.…”
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    Hunting down zinc(II)-binding sites in proteins with distance matrices
  3. 3723
    “…MATERIALS AND METHODS: For this study, we created Thera-Py, a Python package and web API that constructs searchable concepts for drugs and therapeutic terminologies using 9 public resources and thesauri. …”
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    Normalization of drug and therapeutic concepts with Thera-Py
  4. 3724
    “…In detail, we provide (i) an implementation in Python of a QML pipeline for local classification and (ii) its extensive empirical evaluation. …”
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    Implementation and empirical evaluation of a quantum machine learning pipeline for local classification
  5. 3725
    “…It is implemented across three distinct software projects: PyDNA_CF_Simulator, a Python project featuring a ChatGPT plugin for interactive parsing and simulating experiments; ConstructionFileSimulator, a field-tested Java project that showcases ’Experiment’ objects expressed as flat files; and C6-Tools, a JavaScript project integrated with Google Sheets via Apps Script, providing a user-friendly interface for authoring and simulation of CF. …”
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    Enabling AI in synthetic biology through Construction File specification
  6. 3726
    por Mandal, Ankita, Pradhan, Soma
    Publicado 2023
    “…To address this, a machine learning model, Predict2Protect, was built in Python. An open-source dataset compiled of 1025 patients of diverse backgrounds was scaled, adjusted to include inquiries answerable by patients, and split into 75% for training, 15% for validation, and 25% for testing. …”
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    Predict2Protect: Machine Learning Web Application in Early Detection of Heart Disease
  7. 3727
    “…We provide a set of tools for advanced data-mining of ASAP II with Pygr (the Python Graph Database Framework for Bioinformatics) including powerful features such as graph query, multigenome alignment query, etc. …”
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    The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species
  8. 3728
    “…Homolmapper is small (under 250 K for the application itself) and is written in Python to ensure portability. It is released for non-commercial use under a modified University of California BSD license. …”
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    Flexible mapping of homology onto structure with Homolmapper
  9. 3729
    por Traversa, Donato
    Publicado 2010
    “…These findings were later on confirmed by the detection of genetic homologies of isolates from a python and a chameleon from Spain and by recent research in the United States. …”
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    Evidence for a new species of Cryptosporidium infecting tortoises: Cryptosporidium ducismarci
  10. 3730
    “…All functionality can be accessed directly in C++ or in a Python layer, meeting both the requirements for high efficiency and ease of use. …”
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    OpenStructure: a flexible software framework for computational structural biology
  11. 3731
    por Mariotti, M., Guigó, R.
    Publicado 2010
    “…Availability and Implementation: Selenoprofiles is a python-built pipeline that internally runs psitblastn, exonerate, genewise, SECISearch and a number of custom-made scripts and programs. …”
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    Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes
  12. 3732
    “…Availability and Implementation: http://medeller.info; Implemented in Python, Bash and Perl CGI for use on Linux systems; Supplementary data are available at http://www.stats.ox.ac.uk/proteins/resources. …”
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    MEDELLER: homology-based coordinate generation for membrane proteins
  13. 3733
    “…HMMSplicer is implemented in Python. Code and documentation are freely available at http://derisilab.ucsf.edu/software/hmmsplicer.…”
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    HMMSplicer: A Tool for Efficient and Sensitive Discovery of Known and Novel Splice Junctions in RNA-Seq Data
  14. 3734
    “…We discuss here, a simple database system which we call ‘Bookshelf’, that uses python in conjunction with a mysql database to provide an extremely simple system for curating and keeping track of molecular simulation data. …”
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    Bookshelf: a simple curation system for the storage of biomolecular simulation data
  15. 3735
    “…Results: We present a Python package, cuda-sim, that provides highly parallelized algorithms for the repeated simulation of biochemical network models on NVIDIA CUDA GPUs. …”
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    GPU accelerated biochemical network simulation
  16. 3736
    “…AVAILABILITY: Protein pair-wise functional relationship scores for Mycobacterium tuberculosis strain CDC1551 sequence data and python scripts to compute these scores are available at http://web.cbio.uct.ac.za/~gmazandu/scoringschemes.…”
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    Scoring Protein Relationships in Functional Interaction Networks Predicted from Sequence Data
  17. 3737
    “…CONCLUSIONS: Read cleaning has always been an important step in sequence analysis. The pyrocleaner python module is a Swiss knife dedicated to 454 reads cleaning. …”
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    Assessment of replicate bias in 454 pyrosequencing and a multi-purpose read-filtering tool
  18. 3738
    “…For automated docking tasks, a programmatic SOAP interface has been set up and template programs can be downloaded in Perl, Python and PHP. The web site also provides an access to a database of manually curated complexes, based on the Ligand Protein Database. …”
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    SwissDock, a protein-small molecule docking web service based on EADock DSS
  19. 3739
    por Tuszynska, Irina, Bujnicki, Janusz M
    Publicado 2011
    “…CONCLUSIONS: In both bound and unbound docking tests, DARS-RNP showed the highest ability to identify native-like structures. Python implementations of DARS-RNP and QUASI-RNP are freely available for download at http://iimcb.genesilico.pl/RNP/…”
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    DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking
  20. 3740
    “…BACKGROUND: We describe SNPpy, a hybrid script database system using the Python SQLAlchemy library coupled with the PostgreSQL database to manage genotype data from Genome-Wide Association Studies (GWAS). …”
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    SNPpy - Database Management for SNP Data from Genome Wide Association Studies
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