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Celebrating a body of work

Jason A. Papin, Feilim Mac Gabhann, Virginia E. Pitzer

Editorial | published 26 Sep 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012441

Views: 630Citations: 0Saves: 0 • Shares: 6

Ten simple rules for training scientists to make better software

Kit Gallagher, Richard Creswell, Ben Lambert, Martin Robinson, Chon Lok Lei, Gary R. Mirams, David J. Gavaghan

Education | published 12 Sep 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012410

Views: 2635Citations: 0Saves: 1 • Shares: 11

Ten simple rules for recognizing data and software contributions in hiring, promotion, and tenure

Iratxe Puebla, Giorgio A. Ascoli, Jeffrey Blume, John Chodacki, Joshua Finnell, David N. Kennedy, Bernard Mair, Maryann E. Martone, Jamie Wittenberg, Jean-Baptiste Poline

Education | published 08 Aug 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012296

Views: 4062Citations: 2Saves: 7 • Shares: 49

Nine quick tips for open meta-analyses

David Moreau, Kristina Wiebels

Education | published 25 Jul 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012252

Views: 1617Citations: 2Saves: 12 • Shares: 7

FAIR-USE4OS: Guidelines for creating impactful open-source software

Raphael Sonabend, Hugo Gruson, Leo Wolansky, Agnes Kiragga, Daniel S. Katz

Perspective | published 09 May 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012045

Views: 1081Citations: 2Saves: 3 • Shares: 1

For long-term sustainable software in bioinformatics

Luis Pedro Coelho

Perspective | published 15 Mar 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011920

Views: 2218Citations: 1Saves: 8 • Shares: 25

Ten quick tips for fuzzy logic modeling of biomedical systems

Davide Chicco, Simone Spolaor, Marco S. Nobile

Education | published 21 Dec 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011700

Views: 1289Citations: 3Saves: 10 • Shares: 2

From policy to practice: Lessons learned from an open science funding initiative

Sonya B. Dumanis, Kristen Ratan, Souad McIntosh, Hetal V. Shah, Matt Lewis, Timothy H. Vines, Randy Schekman, Ekemini A. Riley

Perspective | published 07 Dec 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011626

Views: 1899Citations: 2Saves: 2 • Shares: 5

Facilitating bioinformatics reproducibility with QIIME 2 Provenance Replay

Christopher R. Keefe, Matthew R. Dillon, Elizabeth Gehret, Chloe Herman, Mary Jewell, Colin V. Wood, Evan Bolyen, J. Gregory Caporaso

Software | published 27 Nov 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011676

Views: 2347Citations: 4Saves: 14 • Shares: 25

CGG toolkit: Software components for computational genomics

Dimitrios Vasileiou, Christos Karapiperis, Ismini Baltsavia, Anastasia Chasapi, Dag Ahrén, Paul J. Janssen, Ioannis Iliopoulos, Vasilis J. Promponas, Anton J. Enright, Christos A. Ouzounis

Software | published 07 Nov 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011498

Views: 1579Citations: 0Saves: 7 • Shares: 6

Tissue Forge: Interactive biological and biophysics simulation environment

T. J. Sego, James P. Sluka, Herbert M. Sauro, James A. Glazier

Research Article | published 23 Oct 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010768

Views: 2143Citations: 12Saves: 14 • Shares: 8

Catalyst: Fast and flexible modeling of reaction networks

Torkel E. Loman, Yingbo Ma, Vasily Ilin, Shashi Gowda, Niklas Korsbo, Nikhil Yewale, Chris Rackauckas, Samuel A. Isaacson

Research Article | published 18 Oct 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011530

Views: 3153Citations: 15Saves: 8 • Shares: 20

Ten quick tips for building FAIR workflows

Casper de Visser, Lennart F. Johansson, Purva Kulkarni, Hailiang Mei, Pieter Neerincx, K. Joeri van der Velde, Péter Horvatovich, Alain J. van Gool, Morris A. Swertz, Peter A. C. ‘t Hoen, Anna Niehues

Education | published 28 Sep 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011369

Views: 2918Citations: 16Saves: 23 • Shares: 20

The blossoming of methods and software in computational biology

Feilim Mac Gabhann, Virginia E. Pitzer, Jason A. Papin

Editorial | published 17 Aug 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011390

Views: 1614Citations: 4Saves: 7 • Shares: 6

A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia

William T. Scott Jr., Sara Benito-Vaquerizo, Johannes Zimmermann, Djordje Bajić, Almut Heinken, Maria Suarez-Diez, Peter J. Schaap

Research Article | published 14 Aug 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011363

Views: 2878Citations: 26Saves: 0 • Shares: 0

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