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    PyImageJ: A library for integrating ImageJ and Python
                                      
                                            Rueden, Curtis T.,                              Hiner, Mark C.,                              Evans, Edward L.,                              Pinkert, Michael A.,                              Lucas, Alice M.,                              Carpenter, Anne E.,                              Cimini, Beth A.,                              Eliceiri, Kevin W.                              
Published in Nature methods (01.11.2022)
                   
      
      
                                                  Published in Nature methods (01.11.2022)
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              Journal Article
          
              
          Python tools for structural tasks in chemistry
                                      
                                            Ryzhkov, Fedor V.,                              Ryzhkova, Yuliya E.,                              Elinson, Michail N.                              
Published in Molecular diversity (01.08.2025)
                   
      
      
                                                  Published in Molecular diversity (01.08.2025)
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              Journal Article
          
              
          Towards understanding bugs in Python interpreters
                                      
                                            Liu, Di,                              Feng, Yang,                              Yan, Yanyan,                              Xu, Baowen                              
Published in Empirical software engineering : an international journal (01.01.2023)
                   
      
      
                                                  Published in Empirical software engineering : an international journal (01.01.2023)
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              Journal Article
          
              
          Domain Knowledge Matters: Improving Prompts with Fix Templates for Repairing Python Type Errors
                                      
                                            Peng, Yun,                              Gao, Shuzheng,                              Gao, Cuiyun,                              Huo, Yintong,                              Lyu, Michael R.                              
Published in Proceedings / International Conference on Software Engineering (14.04.2024)
                   
      
      
                                                  Published in Proceedings / International Conference on Software Engineering (14.04.2024)
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              Conference Proceeding
          
              
          Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS
                                      
                                            Johnson, Jeanette A. I.,                              Tsang, Ashley P.,                              Mitchell, Jacob T.,                              Zhou, David L.,                              Bowden, Julia,                              Davis-Marcisak, Emily,                              Sherman, Thomas,                              Liefeld, Ted,                              Loth, Melanie,                              Goff, Loyal A.,                              Zimmerman, Jacquelyn W.,                              Kinny-Köster, Ben,                              Jaffee, Elizabeth M.,                              Tamayo, Pablo,                              Mesirov, Jill P.,                              Reich, Michael,                              Fertig, Elana J.,                              Stein-O’Brien, Genevieve L.                              
Published in Nature protocols (01.12.2023)
                   
      
      
                                                  Published in Nature protocols (01.12.2023)
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              Journal Article
          
              
          SAB: An open-access Python-based integrated platform for fully automated emergent sustainability assessment of biorefineries
                                      
                                            Zarafshani, Hanie,                              Watjanatepin, Ponnapat,                              Navare, Kranti,                              Sauve, Giovanna,                              Van Acker, Karel                              
Published in The international journal of life cycle assessment (01.04.2024)
                   
      
      
                                                  Published in The international journal of life cycle assessment (01.04.2024)
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              Journal Article
          
              
          PyRates—A Python framework for rate-based neural simulations
                                      
                                            Gast, Richard,                              Rose, Daniel,                              Salomon, Christoph,                              Möller, Harald E.,                              Weiskopf, Nikolaus,                              Knösche, Thomas R.                              
Published in PloS one (16.12.2019)
                   
      
      
                                                  Published in PloS one (16.12.2019)
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              Journal Article
          
              
          pyMPSLib: A robust and scalable open-source Python library for mutiple-point statistical simulation
                                      
                                            Chen, Qiyu,                              Zhou, Ruihong,                              Liu, Cui,                              Huang, Qianhong,                              Cui, Zhesi,                              Liu, Gang                              
Published in Earth science informatics (01.12.2023)
                   
      
      
                                                  Published in Earth science informatics (01.12.2023)
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              Journal Article
          
              
          Morphoscanner2.0: A new python module for analysis of molecular dynamics simulations
                                      
                                            Fontana, Federico,                              Carlino, Calogero,                              Malik, Ashish,                              Gelain, Fabrizio                              
Published in PloS one (27.04.2023)
                   
      
      
                                                  Published in PloS one (27.04.2023)
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              Journal Article
          
              
          ABC-SysBio—approximate Bayesian computation in Python with GPU support
                                      
                                            Liepe, Juliane,                              Barnes, Chris,                              Cule, Erika,                              Erguler, Kamil,                              Kirk, Paul,                              Toni, Tina,                              Stumpf, Michael P.H.                              
Published in Bioinformatics (15.07.2010)
                   
      
      
                                                  Published in Bioinformatics (15.07.2010)
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              Journal Article
          
              
          Comparative Analysis of AI Models for Python Code Generation: A HumanEval Benchmark Study
                                      
                                            Bayram, Ali,                              Menekse Dalveren, Gonca Gokce,                              Derawi, Mohammad                              
Published in Applied sciences (10.09.2025)
                   
      
      
                                                  Published in Applied sciences (10.09.2025)
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              Journal Article