Search Results - Community-driven Bioinformatics Workflows

Building a community-driven bioinformatics platform to facilitate Cannabis sativa multi-omics research by Mansueto, Locedie, Kretzschmar, Tobias, Mauleon, Ramil, King, Graham J.

“…Global changes in cannabis legislation after decades of stringent regulation and heightened demand for its industrial and medicinal applications have spurred…”
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BioShaDock: a community driven bioinformatics shared Docker-based tools registry [version 1; peer review: 2 approved] by Moreews, François, Sallou, Olivier, Ménager, Hervé, Le bras, Yvan, Monjeaud, Cyril, Blanchet, Christophe, Collin, Olivier

“… candidates for the construction of bioinformatic infrastructures, at any scale from single workstations to high throughput computing architectures…”
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The Microbiology Galaxy Lab: A community-driven gateway to tools, workflows, and training for reproducible and FAIR analysis of microbial data by Nasr, Engy, Amato, Pierre, Bernt, Matthias, Bhardwaj, Anshu, Blankenberg, Daniel, Brites, Daniela, Cumbo, Fabio, Do, Katherine, Ferrari, Emanuele, Griffin, Timothy J, Gruening, Bjoern, Hiltemann, Saskia, Hyde, Cameron J, Jagtap, Pratik, Mehta, Subina, Métris, Kimberly L, Momin, Saim, Oba, Asime, Pavloudi, Christina, Pechlivanis, Nikos, Péguilhan, Raphaëlle, Price, Gareth R, Psomopoulos, Fotis, Rosic, Nedeljka, Schatz, Michael C, Schiml, Valerie Claudia, Siguret, Clea, Soranzo, Nicola, Stubbs, Andrew, Van Heusden, Peter, Vohra, Mustafa, Zierep, Paul, Batut, Bérénice

“… Backed by a community-driven approach, the Microbiology Galaxy Lab ensures up-to-date tools and workflows through testing and semi…”
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A standard workflow for community-driven manual curation of Strongyloides genome annotations by Bryant, Astra S, Akimori, Damia, Stoltzfus, Jonathan D C, Hallem, Elissa A

“…Advances in the functional genomics and bioinformatics toolkits for species have positioned these species as genetically tractable model systems for gastrointestinal parasitic nematodes…”
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Community-driven development for computational biology at Sprints, Hackathons and Codefests by Möller, Steffen, Afgan, Enis, Banck, Michael, Bonnal, Raoul JP, Booth, Timothy, Chilton, John, Cock, Peter JA, Gumbel, Markus, Harris, Nomi, Holland, Richard, Kalaš, Matúš, Kaján, László, Kibukawa, Eri, Powel, David R, Prins, Pjotr, Quinn, Jacqueline, Sallou, Olivier, Strozzi, Francesco, Seemann, Torsten, Sloggett, Clare, Soiland-Reyes, Stian, Spooner, William, Steinbiss, Sascha, Tille, Andreas, Travis, Anthony J, Guimera, Roman Valls, Katayama, Toshiaki, Chapman, Brad A

“… Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools for its interpretation can find mutual understanding and consensus…”
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Community-driven computational biology with Debian Linux by Möller, Steffen, Krabbenhöft, Hajo Nils, Tille, Andreas, Paleino, David, Williams, Alan, Wolstencroft, Katy, Goble, Carole, Holland, Richard, Belhachemi, Dominique, Plessy, Charles

“…Background The Open Source movement and its technologies are popular in the bioinformatics community because they provide freely available tools and resources for research…”
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Next-generation sequencing and bioinformatics in rare movement disorders by Zech, Michael, Winkelmann, Juliane

“… We examine bioinformatics tools and computational metrics that have been developed to facilitate accurate prioritization of disease-causing variants…”
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BOSC 2019, the 20th annual Bioinformatics Open Source Conference [version 1; peer review: not peer reviewed] by Harris, Nomi L, Cock, Peter J.A, Fields, Christopher J, Greshake Tzovaras, Bastian, Heuer, Michael, Hokamp, Karsten, Munoz-Torres, Monica, Peltzer, Alexander, Rieck, Bastian, Wiencko, Heather, Yehudi, Yo

“…The Bioinformatics Open Source Conference is a volunteer-organized meeting that covers open source software development and open science in bioinformatic…”
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PDBe-KB: a community-driven resource for structural and functional annotations by Varadi, Mihaly, Berrisford, John, Deshpande, Mandar, Nair, Sreenath S, Gutmanas, Aleksandras, Armstrong, David, Pravda, Lukas, Al-Lazikani, Bissan, Anyango, Stephen, Barton, Geoffrey J, Berka, Karel, Blundell, Tom, Borkakoti, Neera, Dana, Jose, Das, Sayoni, Dey, Sucharita, Micco, Patrizio Di, Fraternali, Franca, Gibson, Toby, Helmer-Citterich, Manuela, Hoksza, David, Huang, Liang-Chin, Jain, Rishabh, Jubb, Harry, Kannas, Christos, Kannan, Natarajan, Koca, Jaroslav, Krivak, Radoslav, Kumar, Manjeet, Levy, Emmanuel D, Madeira, F, Madhusudhan, M S, Martell, Henry J, MacGowan, Stuart, McGreig, Jake E, Mir, Saqib, Mukhopadhyay, Abhik, Parca, Luca, Paysan-Lafosse, Typhaine, Radusky, Leandro, Ribeiro, Antonio, Serrano, Luis, Sillitoe, Ian, Singh, Gulzar, Skoda, Petr, Svobodova, Radka, Tyzack, Jonathan, Valencia, Alfonso, Fernandez, Eloy Villasclaras, Vranken, Wim, Wass, Mark, Thornton, Janet, Sternberg, Michael, Orengo, Christine, Velankar, Sameer

“…Abstract The Protein Data Bank in Europe-Knowledge Base (PDBe-KB, https://pdbe-kb.org) is a community-driven, collaborative resource for literature-derived…”
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vAMPirus : A versatile amplicon processing and analysis program for studying viruses by Veglia, Alex J., Rivera‐Vicéns, Ramón E., Grupstra, Carsten G. B., Howe‐Kerr, Lauren I., Correa, Adrienne M. S.

“…Amplicon sequencing is an effective and increasingly applied method for studying viral communities in the environment. Here, we present vAMPirus, a…”
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Building a community-driven bioinformatics platform to facilitate Cannabis sativa multi-omics research by Mansueto, Locedie, Kretzschmar, Tobias, Mauleon, Ramil, King, Graham J.

“…Global changes in Cannabis legislation after decades of stringent regulation, and heightened demand for its industrial and medicinal applications have spurred…”
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SILVI, an open-source pipeline for T-cell epitope selection by Pissarra, Joana, Dorkeld, Franck, Loire, Etienne, Bonhomme, Vincent, Sereno, Denis, Lemesre, Jean-Loup, Holzmuller, Philippe

“…High-throughput screening of available genomic data and identification of potential antigenic candidates have promoted the development of epitope-based…”
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BOSC 2025, the 26th Bioinformatics Open Source Conference by Harris, Nomi L., Hokamp, Karsten, Maia, Jessica, Ménager, Hervé, Munoz-Torres, Monia C, Ohta, Tazro, Unni, Deepak, Williams, Jason

“…) brought its community-driven focus on open-source bioinformatics and open science to the 2025 conference on Intelligent Systems for Molecular Biology and the European Conference on Computational Biology (ISMB/ECCB 2025…”
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Arteria: An automation system for a sequencing core facility by Dahlberg, Johan, Hermansson, Johan, Sturlaugsson, Steinar, Lysenkova, Mariya, Smeds, Patrik, Ladenvall, Claes, Guimera, Roman Valls, Reisinger, Florian, Hofmann, Oliver, Larsson, Pontus

“… The concept of workflows has gained favour in the bioinformatics community, but there is little in the scientific literature describing end-to-end automation systems…”
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MHCquant2 refines immunopeptidomics tumor antigen discovery by Scheid, Jonas, Lemke, Steffen, Hoenisch-Gravel, Naomi, Dengler, Anna, Sachsenberg, Timo, Declerq, Arthur, Gabriels, Ralf, Bauer, Jens, Wacker, Marcel, Bichmann, Leon, Martens, Lennart, Dubbelaar, Marissa L., Nahnsen, Sven, Walz, Juliane S.

“… This integration allows a community-driven, robust solution for high-throughput analyses across operating systems and cloud infrastructures…”
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The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology by Galdzicki, Michal, Clancy, Kevin P, Oberortner, Ernst, Pocock, Matthew, Quinn, Jacqueline Y, Rodriguez, Cesar A, Roehner, Nicholas, Wilson, Mandy L, Adam, Laura, Anderson, J Christopher, Bartley, Bryan A, Beal, Jacob, Chandran, Deepak, Chen, Joanna, Densmore, Douglas, Endy, Drew, Grünberg, Raik, Hallinan, Jennifer, Hillson, Nathan J, Johnson, Jeffrey D, Kuchinsky, Allan, Lux, Matthew, Misirli, Goksel, Peccoud, Jean, Plahar, Hector A, Sirin, Evren, Stan, Guy-Bart, Villalobos, Alan, Wipat, Anil, Gennari, John H, Myers, Chris J, Sauro, Herbert M

“… SBOL represents synthetic biology designs in a community-driven, formalized format for exchange between software tools, research groups and commercial service providers…”
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BioImage Model Zoo: A Community-Driven Resource for Accessible Deep Learning in BioImage Analysis by Ouyang, Wei, Beuttenmueller, Fynn, Gómez-de-Mariscal, Estibaliz, Pape, Constantin, Burke, Tom, Garcia-López-de-Haro, Carlos, Russell, Craig, Moya-Sans, Lucía, de-la-Torre-Gutiérrez, Cristina, Schmidt, Deborah, Kutra, Dominik, Novikov, Maksim, Weigert, Martin, Schmidt, Uwe, Bankhead, Peter, Jacquemet, Guillaume, Sage, Daniel, Henriques, Ricardo, Muñoz-Barrutia, Arrate, Lundberg, Emma, Jug, Florian, Kreshuk, Anna

“… Here, we present the BioImage Model Zoo (https://bioimage.io): a community-driven, fully open resource where standardized pre-trained models can be shared, explored…”
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community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2 by Thiele, Ines, Hyduke, Daniel R, Steeb, Benjamin, Fankam, Guy, Allen, Douglas K, Bazzani, Susanna, Charusanti, Pep, Chen, Feng-Chi, Fleming, Ronan M.T, Hsiung, Chao A, Keersmaecker, Sigrid C.J. de, Liao, Yu-Chieh, Marchal, Kathleen, Mo, Monica L, Özdemir, Emre, Raghunathan, Anu

“…: Here, we describe a community-driven effort, in which more than 20 experts in S. Typhimurium biology and systems biology collaborated to reconcile and expand…”
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Addressing standardization and semantics in an electronic lab notebook for multidisciplinary use: LabIMotion by Lin, Chia-Lin, Huang, Pei-Chi, Wöll, Christof, Théato, Patrick, Kübel, Christian, Pilz, Lena, Jung, Nicole, Bräse, Stefan

“…), expanding its capabilities from organic chemistry to support interdisciplinary research and enabling the description of workflows…”
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Arctos: Community-driven innovations for managing biodiversity and cultural collections by Cicero, Carla, Koo, Michelle S, Braker, Emily, Abbott, John, Bloom, David, Campbell, Mariel, Cook, Joseph A, Demboski, John R, Doll, Andrew C, Frederick, Lindsey M, Linn, Angela J, Mayfield-Meyer, Teresa J, Mcdonald, Dusty, Nachman, Michael W, Olson, Link E, Roberts, Dawn, Sikes, Derek S, Witt, Christopher C, Wommack, Elizabeth

“…Museum collections house millions of objects and associated data records that document biological and cultural diversity. In recent decades, digitization…”
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