pypi: Cython | Projects | Ecosyste.ms: Papers

10.3389/fninf.2018.00068

Code Generation in Computational Neuroscience: A Review of Tools and Techniques
Cited by: 27
Author(s): Inga Blundell, Romain Brette, Thomas A. Cleland, Thomas G. Close, Daniel Coca, Andrew P. Davison, Sandra Diaz-Pier, Carlos Fernandez Musoles, Padraig Gleeson, Dan F. M. Goodman, Michael L. Hines, Michael Hopkins, Pramod Kumbhar, David Lester, Bóris Marin, Abigail Morrison, Eric Müller, Thomas Nowotny, Alexander Peyser, Dimitri Plotnikov, Paul Richmond, Andrew Rowley, Bernhard Rumpe, Marcel Stimberg, Alan B. Stokes, Adam Tomkins, Guido Trensch, Michael Woodman, Jochen Martin Eppler
Software Mentions: 16
Published: about 6 years ago

10.1186/s13059-020-02116-x

Integrative analyses of single-cell transcriptome and regulome using MAESTRO
Cited by: 107
Author(s): Chenfei Wang, Dongqing Sun, Xin Huang, Changxin Wan, Ziyi Li, Ya Han, Qian Qin, Jingyu Fan, Xintao Qiu, Yingtian Xie, Clifford A. Meyer, Myles Brown, Ming Tang, Henry W. Long, Tao Liu, X. Shirley Liu
Software Mentions: 15
Published: over 4 years ago

10.1186/s12864-016-3278-x

Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data
Cited by: 131
Author(s): Joshua G. Dunn, Jonathan S. Weissman
Software Mentions: 14
Published: about 8 years ago

10.1186/s40679-016-0031-0

Analyzing microtomography data with Python and the scikit-image library
Cited by: 22
Author(s): Emmanuelle Gouillart, Juan Nunez-Iglesias, Stéfan van der Walt
Software Mentions: 14
Published: about 8 years ago

10.1007/s41114-018-0015-6

Computer algebra in gravity research
Cited by: 20
Author(s): Malcolm MacCallum
Software Mentions: 13
Published: over 6 years ago

10.1186/s12868-017-0372-1

26th Annual Computational Neuroscience Meeting (CNS*2017): Part 3
Cited by: 5
Author(s): Adam J. H. Newton, Alexandra H Seidenstein, Robert A. McDougal, Alberto Pérez-Cervera, Gemma Huguet, Tere M. Seara, Caroline Haimerl, David Angulo-García, Alessandro Torcini, Rosa Cossart, Arnaud Malvache, K. Skiker, Mounir Maouene, Gianmarco Ragognetti, Letizia Lorusso, Andrea Viggiano, Angelo Marcelli, Rosa Senatore, Antonio Parziale, Sebastiano Stramaglia, M. Pellicoro, Lucia Angelini, Enrico Amico, Hannelore Aerts, Jesús M. Cortés, Steven Laureys, Daniele Marinazzo, Iege Bassez, Luca Faes, Hannes Almgren, Adeel Razi, Frederik Van de Steen, Ruth M. Krebs, Hannelore Aerts, Lida Kanari, Paweł Dłotko, Martina Scolamiero, Ran Levi, Julian C. Shillcock, Christiaan Pj de Kock, Katharina Heß, Henry Markram, Cheng Ly, Gary Marsat, Tom Gillespie, Malin Sandström, Mathew Abrams, Jeffrey S. Grethe, Maryann E. Martone, Robin De Gernier, Sergio Solinas, Christian Rössert, Marc Haelterman, Serge Massar, Valentina Pasquale, Vito Paolo Pastore, Sergio Martinoia, Paolo Massobrio, Cristiano Capone, Núria Tort-Colet, María V. Sánchez-Vives, Maurizio Mattia, Ali Almasi, Shaun L. Cloherty, David B. Grayden, Yan T. Wong, M. Ibbotson, Hamish Meffin, Luke Y. Prince, Krasimira Tsaneva-Atanasova, Jack R. Mellor, Annalisa Mazzoni, Manuela Rosa, J. Carpaneto, Luigi Romito, Alberto Priori, Silvestro Micera, Rosanna Migliore, Carmen Alina Lupaşcu, Francesco Franchina, Luca Bologna, Armando Romani, Sára Sáray, Werner Van Geit, Szabolcs Káli, Alex Thomson, Audrey Mercer, Sigrun Lange, Joanne Falck, Eilif Müller, Felix Schürmann, Dmitry Todorov, Robert Capps, William Barnett, Yaroslav I. Molkov, Federico Devalle, Diego Pazó, Ernest Montbrió, Gabriela Mochol, Habiba Azab, Benjamin Y. Hayden, Rubén Moreno‐Bote, Pragathi Priyadharsini Balasubramani, Srinivasa Chakravarthy, Vignayanandam Ravindernath Muddapu, Medorian D. Gheorghiu, Bartul Mimica, Jonathan Withlock, Raul C. Mureșan, Jennifer L. Zick, Kelsey Schultz, Rachael K. Blackman, Matthew V. Chafee, Theoden I. Netoff, Nicholas Roberts, Vivek Nagaraj, Andrew Lamperski, Logan L. Grado, Matthew D. Johnson, David Darrow, Davide Lonardoni, Hayder Amin, Stefano Di Marco, Alessandro Maccione, Luca Berdondini, Thierry Nieus, Marcel Stimberg, Dan F. M. Goodman, Thomas Nowotny, Veronika Koren, Valentin Dragoi, Klaus Obermayer, Samy Castro, Mariano Fernández, Wael El-Deredy, Ke Xu, Jean P. Maidana, Patricio Orio, Wei‐Liang Chen, Iain Hepburn, Francesco Casalegno, Adrien Devresse, A. G. Ovcharenko, Fernando Pereira, Fabien Delalondre, Erik De Schutter, Peter Bratby, Andrew R. Gallimore, Guido Klingbeil, Criseida Zamora, Yunliang Zang, Patrick Crotty, Eric Palmerduca, Alberto Antonietti, Claudia Casellato, Csaba Erö, Egidio D’Angelo, Marc‐Oliver Gewaltig, Alessandra Pedrocchi, Ilja Bytschok, Dominik Dold, Johannes Schemmel, K. Meier, Mihai A. Petrovici, Hui-An Shen, Simone Carlo Surace, Jean-Pascal Pfister, Baptiste Lefebvre, Olivier Marre, Pierre Yger, Athanasia Papoutsi, Jiyoung Park, Ryan T. Ash, Stelios M. Smirnakis, Panayiota Poirazi, Richard A. Felix, Alexander G. Dimitrov, Christine V. Portfors, Silvia Daun, Tibor Tóth, Joanna Jędrzejewska‐Szmek, Nadine Kabbani, Kim T. Blackwel, Bahar Moezzi, Natalie Schaworonkow, Lukas Plogmacher, Mitchell R. Goldsworthy, Brenton Hordacre, Mark D. McDonnell, Nicolangelo Iannella, Michael C. Ridding, Jochen Triesch, Reinoud Maex, Karen Safaryan, Volker Steuber, Rongxiang Tang, Yi‐Yuan Tang, Darya V. Verveyko, Alexey Brazhe, Andrey Yu. Verisokin, Dmitry E. Postnov, Cengiz Günay, Gabriella Panuccio, Michèle Giugliano, Astrid A. Prinz, Pablo Varona, M. I. Rabinovich, Jack E. Denham, Thomas Ranner, Netta Cohen, Maria Reva, Nelson Rebola, Tekla Kirizs, Zoltán Nusser, David A. DiGregorio, Eirini Mavritsaki, Panos Rentzelas, Nikul H. Ukani, Adam Tomkins, Chung-Heng Yeh, Wesley Bruning, Allison L. Fenichel, Yiyin Zhou, Yu-Chi Huang, Dorian Florescu, Carlos L. Ortiz, Paul Richmond, Chung-Chuan Lo, Daniel Coca, Ann‐Shyn Chiang, Aurel A. Lazar, Jennifer Creaser, Congping Lin, Peter Ashwin, Jon T. Brown, Thomas Ridler, Daniel Levenstein, Brendon O. Watson, György Buzsáki, John Rinzel, Rodica Curtu, Anh Trung Nguyen, Sahand Assadzadeh, P. A. Robinson, Paula Sanz‐Leon, Caroline Garcia Forlim, Lírio Onofre Baptista de Almeida, Reynaldo D. Pinto, Francisco B. Rodríguez, Ángel Lareo, Aarón Montero, Thiago Mosqueiro, Ramón Huerta, Vinicio Changoluisa, Vinícius Lima Cordeiro, Cesar Ceballos, Nilton L. Kamiji, Antonio Roque, William W. Lytton, Andrew T. Knox, Joshua J. C. Rosenthal, Svitlana Popovych, Liqing Liu, Bin A. Wang, Christian Grefkes, Gereon R. Fink, Nils Rosjat, Abraham Perez-Trujillo, Andrés Espinal, Marco Aurelio Sotelo-Figueroa, Iván Cruz-Aceves, Horacio Rostro-González, Martin Zapotocky, Martina Hoskovcová, J Kopecká, Olga Ulmanová, Evžen Růžička, Matthias Gärtner, Sevil Duvarci, Jochen Roeper, Gerd‐Helge Schneider, Štefan Albert, Katharina Schmack, Michiel W. H. Remme, Susanne Schreiber, Michele Migliore, Stefano Maximiliano Antonel, Jean-Denis Courcol, Sami Utku Çelikok, Eva M. Navarro-López, Neslihan Serap Şengör, Rahmi Elibol, Mustafa Y. Özdemir, Tianyi Li, Angelo Arleo, Denis Sheynikhovich, Akihiro Nakamura, Masanori Shimono, Youngjo Song, Sol Park, Ilhwan Choi, Jaeseung Jeong, Hee‐Sup Shin, Sadra Sadeh, Padraig Gleeson, R. Angus Silver, Alexandra P. Chatzikalymniou, Frances K. Skinner, Francisco B. Rodríguez, Roberto C. Sotero, Loreen Hertäg, Owen Mackwood, Henning Sprekeler, Steffen Puhlmann, Simon Weber, David Higgins, Laura Naumann, Ramakrisnan Iyer, Ştefan Mihalaş, Valentina Ticcinelli, Tomislav Stankovski, Peter V. E. McClintock, Aneta Stefanovska, Predrag Janjić, Dimitar Solev, Gerald Seifert, Ljupčo Kocarev, Christian Steinhäuser, Mehrdad Salmasi, Stefan Glasauer, Martin B. Stemmler, Danke Zhang, Chi Zhang, Armen Stepanyants, Julia Goncharenko, Lieke Kros, Neil Davey, Chris I. De Zeeuw, Freek E. Hoebeek, Ankur Sinha, Roderick Adams, Michael Schmuker, Maria Psarrou, Maria J. Schilstra, Benjamin Torben‐Nielsen, Christoph Metzner, Achim Schweikard, Tuomo Mäki‐Marttunen, Bartosz Zurowski, Daniele Marinazzo, Luca Faes, Sebastiano Stramaglia, H Jordan, Simon M. Stringer, Elżbieta Gajewska-Dendek, Piotr Suffczyński, Nicoladie D. Tam, George Zouridakis, Luca Pollonini, Mojtaba Madadi Asl, Alireza Valizadeh, Peter A. Tass, Andreas Nold, Wei Fan, Sara Konrad, Heiko Endle, Johannes Vogt, Tatjana Tchumatchenko, Juliane Herpich, Christian Tetzlaff, Jannik Luboeinski, Timo Nachstedt, Manuel Ciba, Andreas Bahmer, Christiane Thielemann, Eric S. Kuebler, Joseph S. Tauskela, Jean-Philippe Thivierge, Rembrandt Bakker, María García‐Amado, Marian Evangelio, Francisco Clascá, Paul Tiesinga, Christopher L. Buckley, Taro Toyoizumi, Alexis Dubreuil, Rémi Monasson, Alessandro Treves, Davide Spalla, Sophie Rosay, Florence I. Kleberg, Willy Wong, Bruno de Oliveira Floriano, Toshihiko Matsuo, Tetsuya Uchida, D. Dibenedetto, Kâmil Uludağ, Abdorreza Goodarzinick, Maximilian Schmidt, Claus C. Hilgetag, Markus Diesmann, Sacha J. van Albada, Michael Fauth, Mark C. W. van Rossum, Manuel Reyes-Sánchez, Rodrigo Amaducci, Carlos Múñiz, Irene Elices, David Arroyo, Rafael Levi, Ben Cohen, Carson C. Chow, Shashaank Vattikuti, Elena Bertolotti, Raffaella Burioni, Matteo di Volo, A. Vezzani, Bayar Menzat, Tim P. Vogels, Nobuhiko Wagatsuma, Susmita Saha, Reena Kapoor, Robert R. Kerr, John Wagner, Luis C. G. del Molino, Guangyu Robert Yang, Jorge F. Mejías, Xiaojing Wang, Hanbing Song, Joseph W. Goodliffe, Jennifer I. Luebke, Christina M. Weaver, John Thomas, Nishant Sinha, Nikhita Shaju, Tomasz Maszczyk, Jing Jin, Sydney S. Cash, Justin Dauwels, M. Brandon Westover, Maryam Karimian, Michelle Moerel, Peter De Weerd, Thomas Burwick, Ronald L. Westra, Romesh Abeysuriya, Jonathan Hadida, Stamatios N. Sotiropoulos, Saâd Jbabdi, Mark W. Woolrich, Chama Bensmail, Borys Wróbel, Xiaolong Zhou, Zilong Ji, Xiao Liu, Xin Yan, Si Wu, Wang Xiao, Mingsha Zhang, Netanel Ofer, Orit Shefi, Gur Yaari, Ted Carnevale, Amit Majumdar, Subhashini Sivagnanam, Kenneth Yoshimoto, Elena Y. Smirnova, Dmitry V. Amakhin, Sergey L. Malkin, Aleksey V. Zaitsev, Anton V. Chizhov, Margarita Zaleshina, Alexander Zaleshin, Victor J. Barranca, George Zhu, Quinton M. Skilling, Daniel Maruyama, Nicolette Ognjanovski, Sara J. Aton, Michal Zochowski, Jiaxing Wu, Sara J. Aton, Scott Rich, Victoria Booth, Maral Budak, Salvador Dura‐Bernal, Samuel A. Neymotin, Benjamin A. Suter, Gordon M. Shepherd, Melvin Felton, Alfred B. Yu, David L. Boothe, Kelvin S. Oie, Piotr J. Franaszczuk, Sergey A. Shuvaev, Batuhan Başerdem, Anthony M. Zador, Alexei A. Koulakov, Víctor J. López‐Madrona, Ernesto Pereda, Claudio R. Mirasso, Santiago Canals, Stefano Masoli, Udaya Bhaskar Rongala, Anton Spanne, Henrik Jörntell, Calogero Maria Oddo, A. Vartanov, Anastasia Neklyudova, S. Kozlovskiy, A. Kiselnikov, J. Marakshina, Maria Teleńczuk, Bartosz Teleńczuk, Alain Destexhe, Paula T. Kuokkanen, Anna Kraemer, Thomas McColgan, Catherine Carr, Richard Kempter
Software Mentions: 12
Published: over 7 years ago

10.1186/s12859-018-2367-z

Biotite: a unifying open source computational biology framework in Python
Cited by: 54
Author(s): Patrick Kunzmann, Kay Hamacher
Software Mentions: 12
Published: about 6 years ago

10.3389/fninf.2018.00092

Multimodal Modeling of Neural Network Activity: Computing LFP, ECoG, EEG, and MEG Signals With LFPy 2.0
Cited by: 96
Author(s): Espen Hagen, Solveig Næss, Torbjørn V. Ness, Gaute T. Einevoll
Software Mentions: 12
Published: about 6 years ago

10.1371/journal.pone.0225734

PyLandStats: An open-source Pythonic library to compute landscape metrics
Cited by: 19
Author(s): Martí Bosch
Software Mentions: 11
Published: about 5 years ago

10.1038/s41598-018-31154-6

Instant Clue: A Software Suite for Interactive Data Visualization and Analysis
Cited by: 156
Author(s): Hendrik Nolte, Thomas MacVicar, Frederik Tellkamp, Marcus Krüger
Software Mentions: 11
Published: over 6 years ago

10.7717/peerj.453

scikit-image: image processing in Python
Cited by: 3,381
Author(s): Stéfan van der Walt, Johannes L. Schönberger, Juan Nunez-Iglesias, François Boulogne, Joshua D. Warner, Neil Yager, Emmanuelle Gouillart, Tony Yu
Software Mentions: 10
Published: over 10 years ago

10.3389/fninf.2019.00018

Draculab: A Python Simulator for Firing Rate Neural Networks With Delayed Adaptive Connections
Cited by: 3
Author(s): Sergio Verduzco-Flores, Erik De Schutter
Software Mentions: 10
Published: over 5 years ago

10.3389/fninf.2013.00041

LFPy: a tool for biophysical simulation of extracellular potentials generated by detailed model neurons
Cited by: 121
Author(s): Henrik Lindén, Espen Hagen, Szymon Łȩski, Espen Skjønsberg Norheim, Klas H. Pettersen, Gaute T. Einevoll
Software Mentions: 10
Published: almost 11 years ago

10.1186/s12868-020-00593-1

29th Annual Computational Neuroscience Meeting: CNS*2020
Cited by: 1
Author(s):
Software Mentions: 9
Published: about 4 years ago

10.3389/fninf.2015.00019

ANNarchy: a code generation approach to neural simulations on parallel hardware
Cited by: 65
Author(s): Julien Vitay, Helge Ülo Dinkelbach, Fred H. Hamker
Software Mentions: 9
Published: over 9 years ago

10.7717/peerj-cs.227

Component-oriented acausal modeling of the dynamical systems in Python language on the example of the model of the sucker rod string
Cited by: 5
Author(s): Volodymyr Kopei, Oleh Onysko, Vitalii Panchuk
Software Mentions: 9
Published: about 5 years ago

10.1371/journal.pcbi.1008364

pyTFM: A tool for traction force and monolayer stress microscopy
Cited by: 19
Author(s): Andreas Bauer, Magdalena Přechová, Lena Fischer, Ingo Thievessen, Martin Gregor, Ben Fabry
Software Mentions: 9
Published: over 3 years ago

10.3389/fninf.2017.00046

Software for Brain Network Simulations: A Comparative Study
Cited by: 42
Author(s): Ruben A. Tikidji-Hamburyan, Vikram K. Narayana, Zeki Bozkuş, Tarek El‐Ghazawi
Software Mentions: 9
Published: over 7 years ago

10.1523/ENEURO.0415-20.2021

Real-Time Closed-Loop Feedback in Behavioral Time Scales Using DeepLabCut
Cited by: 17
Author(s): Keisuke Sehara, Paul Zimmer-Harwood, Matthew E. Larkum, Robert N. S. Sachdev
Software Mentions: 8
Published: almost 4 years ago

10.1186/1471-2105-15-224

MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing
Cited by: 275
Author(s): Krishna R. Kalari, Asha Nair, Jaysheel Bhavsar, Daniel R. O’Brien, Jaime Davila, Matthew A. Bockol, Jinfu Nie, Xiaojia Tang, Saurabh Baheti, Jay B. Doughty, Sumit Middha, Hugues Sicotte, E. Aubrey Thompson, Yan W. Asmann, Jean-Pierre A. Kocher
Software Mentions: 8
Published: over 10 years ago

10.3390/s21092964

Traffic Congestion Analysis Based on a Web-GIS and Data Mining of Traffic Events from Twitter
Cited by: 17
Author(s): Juan Salazar-Carrillo, Miguel Torres-Ruiz, Clodoveu A. Davis, Rolando Quintero, Marco Moreno-Ibarra, Giovanni Guzmán
Software Mentions: 8
Published: over 3 years ago

10.1107/S1600576718017296

<i>refnx</i>: neutron and X-ray reflectometry analysis in Python
Cited by: 95
Author(s): Andrew Nelson, Stuart W. Prescott
Software Mentions: 8
Published: almost 6 years ago

10.1186/s12859-017-1580-5

A fast and efficient python library for interfacing with the Biological Magnetic Resonance Data Bank
Cited by: 8
Author(s): Andrey Smelter, Morgan Astra, Hunter N. B. Moseley
Software Mentions: 8
Published: almost 8 years ago

10.12688/wellcomeopenres.14306.1

CoverView: a sequence quality evaluation tool for next generation sequencing data
Cited by: 7
Author(s): Márton Münz, Shazia Mahamdallie, Shawn Yost, Andrew Rimmer, Emma Poyastro-Pearson, Ann Strydom, Sheila Seal, Elise Ruark, Nazneen Rahman
Software Mentions: 8
Published: over 6 years ago

10.3389/fninf.2018.00030

Information-Theoretical Analysis of EEG Microstate Sequences in Python
Cited by: 13
Author(s): Frederic von Wegner, Helmut Laufs
Software Mentions: 7
Published: over 6 years ago

10.1093/bioinformatics/btu638

HTSeq—a Python framework to work with high-throughput sequencing data
Cited by: 14,991
Author(s): Simon Anders, Paul Theodor Pyl, Wolfgang Huber
Software Mentions: 7
Published: over 10 years ago

10.1186/s13059-015-0831-x

HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
Cited by: 1,430
Author(s): Nicolas Servant, Nelle Varoquaux, Bryan R. Lajoie, Éric Viara, Chong Jian Chen, Jean-Philippe Vert, Edith Heard, Job Dekker, Emmanuel Barillot
Software Mentions: 7
Published: about 9 years ago

10.1093/jxb/erw176

Image Harvest: an open-source platform for high-throughput plant image processing and analysis
Cited by: 68
Author(s): Avi C. Knecht, Malachy T. Campbell, Adam Caprez, David Swanson, Harkamal Walia
Software Mentions: 7
Published: over 8 years ago

10.1186/s12864-017-4268-3

GHOST: global hepatitis outbreak and surveillance technology
Cited by: 32
Author(s): Atkinson G. Longmire, Seth Sims, Inna Rytsareva, David S. Campo, Pavel Skums, Zoya Dimitrova, Sumathi Ramachandran, Magdalena Medrzycki, Hong Thai, Lilia Ganova-Raeva, Yulin Lin, Lili Punkova, Amanda Sue, Massimo Mirabito, Silver Wang, Robin Tracy, Victor Bolet, Thom Sukalac, Chris Lynberg, Yury Khudyakov
Software Mentions: 7
Published: about 7 years ago

10.3389/fninf.2013.00028

Reaction-diffusion in the NEURON simulator
Cited by: 52
Author(s): Robert A. McDougal, Michael L. Hines, William W. Lytton
Software Mentions: 7
Published: almost 12 years ago

10.1093/gigascience/giy093

Leveraging multiple transcriptome assembly methods for improved gene structure annotation
Cited by: 110
Author(s): Luca Venturini, Shabhonam Caim, Gemy Kaithakottil, Daniel Mapleson, David Swarbreck
Software Mentions: 7
Published: over 6 years ago

10.3389/fninf.2014.00023

CyNEST: a maintainable Cython-based interface for the NEST simulator
Cited by: 22
Author(s): Yury V. Zaytsev, Abigail Morrison
Software Mentions: 7
Published: almost 11 years ago

10.1371/journal.pcbi.1008302

Tensorpac: An open-source Python toolbox for tensor-based phase-amplitude coupling measurement in electrophysiological brain signals
Cited by: 28
Author(s): Etienne Combrisson, Timothy Nest, Andrea Brovelli, Robin A. A. Ince, Juan L.P. Soto, Aymeric Guillot, Karim Jerbi
Software Mentions: 6
Published: about 4 years ago

10.1186/s13059-016-0969-1

Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling
Cited by: 136
Author(s): Steven Flygare, Keith E. Simmon, Chase Miller, Yi Qiao, Brett Kennedy, Tonya Di Sera, Erin H. Graf, Keith D. Tardif, Aurélie Kapusta, Shawn Rynearson, Chris Stockmann, Krista Queen, Suxiang Tong, Karl V. Voelkerding, Anne J. Blaschke, Carrie L. Byington, Seema Jain, Andrew T. Pavia, Kwabena Krow Ampofo, Karen Eilbeck, Gábor Marth, Mark Yandell, Robert Salais
Software Mentions: 6
Published: over 8 years ago

10.1186/s12864-020-6455-x

Comparison of multiple algorithms to reliably detect structural variants in pears
Cited by: 14
Author(s): Yueyuan Liu, Mingyue Zhang, Jieying Sun, Wenjing Chang, Manyi Sun, Shaoling Zhang, Wu Jun
Software Mentions: 6
Published: almost 5 years ago

10.1093/bioinformatics/btt080

eMZed: an open source framework in Python for rapid and interactive development of LC/MS data analysis workflows
Cited by: 43
Author(s): Patrick Kiefer, Uwe Schmitt, Julia A. Vorholt
Software Mentions: 6
Published: almost 12 years ago

10.1371/journal.pcbi.1007549

BrainIAK tutorials: User-friendly learning materials for advanced fMRI analysis
Cited by: 41
Author(s): Manoj Kumar, Cameron T. Ellis, Qingming Lu, Hejia Zhang, Mihai Capotă, Theodore L. Willke, Peter J. Ramadge, Nicholas B. Turk‐Browne, Kenneth A. Norman
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pcbi.1007980

AlbaTraDIS: Comparative analysis of large datasets from parallel transposon mutagenesis experiments
Cited by: 15
Author(s): Andrew J. Page, Sarah Bastkowski, Muhammad Yasir, A. Keith Turner, Thanh Le Viet, George M. Savva, Mark A. Webber, Ian G. Charles
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0144820

CloudForest: A Scalable and Efficient Random Forest Implementation for Biological Data
Cited by: 2
Author(s): Ryan Bressler, Richard Kreisberg, Brady Bernard, John E. Niederhuber, Joseph G. Vockley, Ilya Shmulevich, Theo Knijnenburg
Software Mentions: 5
Published: about 9 years ago

10.1186/1471-2105-15-280

HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data
Cited by: 49
Author(s): Huihuang Yan, Jared M. Evans, Mike Kalmbach, Raymond M. Moore, Sumit Middha, Stanislav Luban, Liguo Wang, Aditya Bhagwate, Ying Liu, Zhifu Sun, Xianfeng Chen, Jean-Pierre A. Kocher
Software Mentions: 5
Published: over 10 years ago

10.1371/journal.pone.0183057

Data-driven coarse graining of large biomolecular structures
Cited by: 11
Author(s): Yi‐Ling Chen, Michael Habeck
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pcbi.1005315

Novel Models of Visual Topographic Map Alignment in the Superior Colliculus
Cited by: 10
Author(s): Ruben A. Tikidji-Hamburyan, Tarek El‐Ghazawi, Jason W. Triplett
Software Mentions: 5
Published: about 8 years ago

10.3389/fninf.2018.00015

PyMUS: Python-Based Simulation Software for Virtual Experiments on Motor Unit System
Cited by: 6
Author(s): Hojeong Kim, Minjung Kim
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pcbi.1004867

An Introduction to Programming for Bioscientists: A Python-Based Primer
Cited by: 46
Author(s): Berk Ekmekci, Charles E. McAnany, Cameron Mura
Software Mentions: 5
Published: over 8 years ago

10.1186/s13059-014-0577-x

Churchill: an ultra-fast, deterministic, highly scalable and balanced parallelization strategy for the discovery of human genetic variation in clinical and population-scale genomics
Cited by: 109
Author(s): Benjamin J. Kelly, James Fitch, Yangqiu Patrick Hu, Donald J. Corsmeier, Huachun Zhong, Amy Wetzel, Russell D Nordquist, David L. Newsom, Peter White
Software Mentions: 5
Published: almost 10 years ago

10.1186/s13059-015-0843-6

Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR
Cited by: 291
Author(s): Wei Li, Johannes Köster, Xu Han, Chen Hao Chen, Tengfei Xiao, Jun S. Liu, Myles Brown, X. Shirley Liu
Software Mentions: 4
Published: about 9 years ago

10.3389/fninf.2017.00033

Automatic Optimization of the Computation Graph in the Nengo Neural Network Simulator
Cited by: 3
Author(s): Jan Gosmann, Chris Eliasmith
Software Mentions: 4
Published: over 7 years ago

10.3389/fninf.2021.642933

Polynomial, piecewise-Linear, Step (PLS): A Simple, Scalable, and Efficient Framework for Modeling Neurons
Cited by: 3
Author(s): Ruben A. Tikidji-Hamburyan, Matthew T. Colonnese
Software Mentions: 4
Published: over 3 years ago

10.1186/s12859-020-03711-2

VFFVA: dynamic load balancing enables large-scale flux variability analysis
Cited by: 6
Author(s): Marouen Ben Guebila
Software Mentions: 4
Published: over 4 years ago

10.1093/bioinformatics/btx352

ISAMBARD: an open-source computational environment for biomolecular analysis, modelling and design
Cited by: 39
Author(s): Christopher W. Wood, Jack W. Heal, Andrew Thomson, Gail J. Bartlett, Amaurys Ávila Ibarra, R.L. Brady, Richard B. Sessions, Derek N. Woolfson
Software Mentions: 4
Published: over 7 years ago

10.1093/gigascience/giab042

Mantis: flexible and consensus-driven genome annotation
Cited by: 19
Author(s): Pedro Queirós, Francesco Delogu, Oskar Hickl, Patrick May, Paul Wilmes
Software Mentions: 4
Published: over 3 years ago

10.1093/molbev/msaa328

Fast and Robust Identity-by-Descent Inference with the Templated Positional Burrows–Wheeler Transform
Cited by: 19
Author(s): William A. Freyman, Kimberly F. McManus, Suyash Shringarpure, Ethan M. Jewett, Katarzyna Bryc, Adam Auton
Software Mentions: 4
Published: about 4 years ago

10.7717/peerj.606

Massively parallel read mapping on GPUs with theq-group index and PEANUT
Cited by: 5
Author(s): Johannes Köster, Sven Rahmann
Software Mentions: 4
Published: over 10 years ago

10.7717/peerj-cs.159

Temporal constrained objects for modelling neuronal dynamics
Cited by: 0
Author(s): Manjusha Nair, Jinesh M. Kannimoola, Bharat Jayaraman, Bipin G. Nair, Shyam Diwakar
Software Mentions: 4
Published: over 6 years ago

10.1186/1751-0473-8-15

Implementing a new EPR lineshape parameter for organic radicals in carbonaceous matter
Cited by: 1
Author(s): Mathilde Bourbin, Y. Le Du, Laurent Binet, Didier Gourier
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pone.0244107

A new formulation of compartmental epidemic modelling for arbitrary distributions of incubation and removal times
Cited by: 2
Author(s): P. Hernández, Carlos Peña, Alberto Ramos, J.J. Gómez-Cadenas
Software Mentions: 3
Published: almost 4 years ago

10.1098/rstb.2018.0277

Context matters: using reinforcement learning to develop human-readable, state-dependent outbreak response policies
Cited by: 17
Author(s): William J. M. Probert, Sandya Lakkur, Christopher Fonnesbeck, Katriona Shea, Michael C. Runge, Michael J. Tildesley, Matthew J. Ferrari
Software Mentions: 3
Published: over 5 years ago

10.7717/peerj.11856

Anti-clustering in the national SARS-CoV-2 daily infection counts
Cited by: 7
Author(s): Boudewijn F. Roukema
Software Mentions: 3
Published: over 3 years ago

10.1093/bioinformatics/btaa512

MetaSanity: an integrated microbial genome evaluation and annotation pipeline
Cited by: 20
Author(s): Christopher J. Neely, Elaina D. Graham, Benjamin J. Tully
Software Mentions: 3
Published: over 4 years ago

10.1109/JTEHM.2020.2989124

Real-Time Lung Tumor Tracking Using a CUDA Enabled Nonrigid Registration Algorithm for MRI
Cited by: 3
Author(s): Nazanin Tahmasebi, Pierre Boulanger, Jihyun Yun, G. Fallone, Michelle Noga, Kumaradevan Punithakumar
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12864-019-6096-0

EVR: reconstruction of bacterial chromosome 3D structure models using error-vector resultant algorithm
Cited by: 12
Author(s): Kang-Jian Hua, Bin-Guang Ma
Software Mentions: 3
Published: about 5 years ago

10.1186/s12859-017-1835-1

Improving contig binning of metagenomic data using $$ {d}_2^S $$ oligonucleotide frequency dissimilarity
Cited by: 15
Author(s): Ying Wang, Kun Wang, Yang Lu, Fengzhu Sun
Software Mentions: 3
Published: over 7 years ago

10.3389/fninf.2014.00008

Dipy, a library for the analysis of diffusion MRI data
Cited by: 754
Author(s): Eleftherios Garyfallidis, Matthew Brett, Bagrat Amirbekian, Ariel Rokem, Stéfan van der Walt, Maxime Descoteaux, Ian Nimmo‐Smith
Software Mentions: 3
Published: almost 11 years ago

10.1186/s12859-020-03561-y

OscoNet: inferring oscillatory gene networks
Cited by: 1
Author(s): Luisa Cutillo, Alexis Boukouvalas, Elli Marinopoulou, Nancy Papalopulu, Magnus Rattray
Software Mentions: 3
Published: over 4 years ago

10.3389/fnins.2017.00754

White Matter Tract Segmentation as Multiple Linear Assignment Problems
Cited by: 13
Author(s): Nusrat Sharmin, Emanuele Olivetti, Paolo Avesani
Software Mentions: 2
Published: almost 7 years ago

10.1186/s13015-021-00199-0

DeepGRP: engineering a software tool for predicting genomic repetitive elements using Recurrent Neural Networks with attention
Cited by: 0
Author(s): Fabian Hausmann, Stefan Kurtz
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-017-1613-0

AD-LIBS: inferring ancestry across hybrid genomes using low-coverage sequence data
Cited by: 7
Author(s): Nathan K. Schaefer, Beth Shapiro, Edward Green
Software Mentions: 2
Published: over 7 years ago

10.1186/s12920-018-0461-8

Detecting virus integration sites based on multiple related sequencing data by VirTect
Cited by: 18
Author(s): Yuchao Xia, Yun Liu, Minghua Deng, Ruibin Xi
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12911-020-01333-5

Annotation and extraction of age and temporally-related events from clinical histories
Cited by: 2
Author(s): Judy H. Hong, Anahita Davoudi, Shun Yu, Danielle L. Mowery
Software Mentions: 2
Published: about 4 years ago

10.1093/bioinformatics/btt756

CGAT: computational genomics analysis toolkit
Cited by: 61
Author(s): David Sims, Nicholas E. Ilott, Stephen N. Sansom, Ian Sudbery, Jethro Johnson, Katherine A. Fawcett, Antonio J. Berlanga‐Taylor, Sebastián Luna-Valero, Chris P. Ponting, Andreas Heger
Software Mentions: 2
Published: almost 11 years ago

10.3390/molecules26071912

Accelerated Repurposing and Drug Development of Pulmonary Hypertension Therapies for COVID-19 Treatment Using an AI-Integrated Biosimulation Platform
Cited by: 13
Author(s): Kaushik Chakravarty, Victor Antontsev, Maksim Khotimchenko, Nilesh Gupta, Aditya Jagarapu, Yogesh Bundey, Hypatia Hou, Neha Maharao, Jyotika Varshney
Software Mentions: 2
Published: almost 4 years ago

10.3390/pharmaceutics13020284

In Silico Simulation of the Systemic Drug Exposure Following the Topical Application of Opioid Analgesics in Patients with Cutaneous Lesions
Cited by: 5
Author(s): Maksim Khotimchenko, Victor Antontsev, Kaushik Chakravarty, Hypatia Hou, Jyotika Varshney
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pcbi.1008118

Presynaptic inhibition rapidly stabilises recurrent excitation in the face of plasticity
Cited by: 9
Author(s): Laura Naumann, Henning Sprekeler
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pcbi.1006928

Stability of working memory in continuous attractor networks under the control of short-term plasticity
Cited by: 47
Author(s): Alexander Seeholzer, Moritz Deger, Wulfram Gerstner
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pcbi.1005596

Inferring oscillatory modulation in neural spike trains
Cited by: 7
Author(s): Kohei Arai, Robert E. Kass
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pcbi.1005352

Activated Oncogenic Pathway Modifies Iron Network in Breast Epithelial Cells: A Dynamic Modeling Perspective
Cited by: 20
Author(s): Julia Chifman, Seda Arat, Zhiyong Deng, Erica Lemler, James C. Pino, Leonard A. Harris, Michael A. Kochen, Carlos F. López, Steven A. Akman, Frank M. Torti, Suzy V. Torti, Reinhard Laubenbacher
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pcbi.1008132

Microtubule instability driven by longitudinal and lateral strain propagation
Cited by: 15
Author(s): Maxim Igaev, Helmut Grubmüller
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pcbi.1004415

ENCORE: Software for Quantitative Ensemble Comparison
Cited by: 62
Author(s): Matteo Tiberti, Elena Papaleo, Tone Bengtsen, Wouter Boomsma, Kresten Lindorff‐Larsen
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0036540

Algebraic Comparison of Partial Lists in Bioinformatics
Cited by: 21
Author(s): Giuseppe Jurman, Samantha Riccadonna, Roberto Visintainer, Cesare Furlanello
Software Mentions: 2
Published: over 12 years ago

10.12688/f1000research.7931.1

FreeSASA: An open source C library for solvent accessible surface area calculations
Cited by: 251
Author(s): Simon Mitternacht
Software Mentions: 2
Published: almost 9 years ago

10.3389/fnhum.2021.675433

Diffusional Kurtosis Imaging in the Diffusion Imaging in Python Project
Cited by: 19
Author(s): Rafael Neto Henriques, Marta Correia, Maurizio Marrale, Elizabeth Huber, John Kruper, Serge Koudoro, Jason D. Yeatman, Eleftherios Garyfallidis, Ariel Rokem
Software Mentions: 2
Published: over 3 years ago

10.3389/fninf.2013.00014

HDDM: Hierarchical Bayesian estimation of the Drift-Diffusion Model in Python
Cited by: 533
Author(s): Thomas V. Wiecki, Imri Sofer, Michael J. Frank
Software Mentions: 2
Published: almost 12 years ago

10.3389/fninf.2020.00021

OPETH: Open Source Solution for Real-Time Peri-Event Time Histogram Based on Open Ephys
Cited by: 7
Author(s): András Széll, Sergio Martínez-Bellver, Péter Hegedűs, Balázs Hangya
Software Mentions: 2
Published: over 4 years ago

10.1107/S2053273319010593

<i>XGANDALF</i> – extended gradient descent algorithm for lattice finding
Cited by: 63
Author(s): Y. Gevorkov, Oleksandr Yefanov, Anton Barty, Thomas A. White, Valerio Mariani, Wolfgang Brehm, A. Tolstikova, Rolf-Rainer Grigat, Henry N. Chapman
Software Mentions: 2
Published: over 5 years ago

10.3389/fphys.2021.666915

Predictive Modeling of Secondary Pulmonary Hypertension in Left Ventricular Diastolic Dysfunction
Cited by: 4
Author(s): Karlyn K. Harrod, Jeffrey L. Rogers, Jeffrey A. Feinstein, Alison L. Marsden, Daniele E. Schiavazzi
Software Mentions: 2
Published: over 3 years ago

10.3389/fpsyg.2013.00918

Release the BEESTS: Bayesian Estimation of Ex-Gaussian STop-Signal reaction time distributions
Cited by: 46
Author(s): Dora Matzke
Software Mentions: 2
Published: almost 12 years ago

10.1038/s41598-021-90637-1

A hybrid modeling approach for assessing mechanistic models of small molecule partitioning in vivo using a machine learning-integrated modeling platform
Cited by: 9
Author(s): Victor Antontsev, Aditya Jagarapu, Yogesh Bundey, Hypatia Hou, Maksim Khotimchenko, Jason Walsh, Jyotika Varshney
Software Mentions: 2
Published: over 3 years ago

10.3390/s150204134

Efficient Evaluation of Wireless Real-Time Control Networks
Cited by: 10
Author(s): Péter Horváth, Mark Yampolskiy, Xenofon Koutsoukos
Software Mentions: 2
Published: almost 10 years ago

10.3390/s20020332

Evaluating Convolutional Neural Networks for Cage-Free Floor Egg Detection
Cited by: 13
Author(s): Guoming Li, Yan Xu, Yang Zhao, Qian Du, Yanbo Huang
Software Mentions: 2
Published: almost 5 years ago

10.3390/s20020532

Deep Learning for Real-Time 3D Multi-Object Detection, Localisation, and Tracking: Application to Smart Mobility
Cited by: 39
Author(s): Antoine Mauri, Redouane Khemmar, Benoît Decoux, Nicolas Ragot, Romain Rossi, Rim Trabelsi, Rémi Boutteau, Jean-Yves Ertaud, Xavier Savatier
Software Mentions: 2
Published: almost 5 years ago

10.7554/eLife.50933

Feedback contribution to surface motion perception in the human early visual cortex
Cited by: 6
Author(s): Ingo Marquardt, Peter De Weerd, Marian Schneider, Omer Faruk Gulban, Dimo Ivanov, Yawen Wang, Kâmil Uludağ
Software Mentions: 2
Published: over 4 years ago

10.3389/fnsys.2014.00006

Spike sorting for polytrodes: a divide and conquer approach
Cited by: 49
Author(s): Nicholas V. Swindale, Martin A. Spacek
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pcbi.1005258

Encoding in Balanced Networks: Revisiting Spike Patterns and Chaos in Stimulus-Driven Systems
Cited by: 14
Author(s): Guillaume Lajoie, Kevin K. Lin, J.-P. Thivierge, Eric Shea‐Brown
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pcbi.1004517

A Generative Statistical Algorithm for Automatic Detection of Complex Postures
Cited by: 21
Author(s): Stanislav Nagy, Marc Goessling, Yali Amit, David Biron
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pcbi.1007545

The effect of inhibition on rate code efficiency indicators
Cited by: 7
Author(s): Tomáš Bárta, Lubomir Kostal
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pcbi.1002689

Spike-Timing Dependence of Structural Plasticity Explains Cooperative Synapse Formation in the Neocortex
Cited by: 41
Author(s): Moritz Deger, Moritz Helias, Stefan Rotter, Markus Diesmann
Software Mentions: 1
Published: over 12 years ago

10.1099/mgen.0.000056

SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments
Cited by: 645
Author(s): Andrew J. Page, Ben Taylor, Aidan Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane, Simon R. Harris
Software Mentions: 1
Published: over 8 years ago

10.1016/j.media.2016.03.002

Pieces-of-parts for supervoxel segmentation with global context: Application to DCE-MRI tumour delineation
Cited by: 22
Author(s): Benjamin Irving, James Franklin, Bartłomiej W. Papież, Ewan M. Anderson, Ricky A. Sharma, Fergus Gleeson, Sir Michael Brady, Julia A. Schnabel
Software Mentions: 1
Published: over 8 years ago

10.1016/j.bpj.2019.02.024

Estimating Constraints for Protection Factors from HDX-MS Data
Cited by: 20
Author(s): Simon P. Skinner, Gaël Radou, Roman Tůma, Jeanine J. Houwing-Duistermaat, Emanuele Paci
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41437-020-00361-1

Inbred lab mice are not isogenic: genetic variation within inbred strains used to infer the mutation rate per nucleotide site
Cited by: 14
Author(s): Jobran Chebib, Benjamin C. Jackson, Eugenio López‐Cortegano, Diethard Tautz, Peter D. Keightley
Software Mentions: 1
Published: over 4 years ago

Projects: pypi: Cython

Papers Mentioning Cython 118