Workflows Community Summit 2024: Future Trends and Challenges in Scientific Workflows

Authors: da Silva, Rafael Ferreira, Bard, Deborah, Chard, Kyle, de Witt, Shaun, Foster, Ian T., Gibbs, Tom, Goble, Carole, Godoy, William, Gustafsson, Johan, Haus, Utz-Uwe, Hudson, Stephen, Jha, Shantenu, Los, Laila, Paine, Drew, Suter, Frédéric, Ward, Logan, Wilkinson, Sean, Amaris, Marcos, Babuji, Yadu, Bader, Jonathan, Balin, Riccardo, Balouek, Daniel, Beecroft, Sarah, Belhajjame, Khalid, Bhattarai, Rajat, Brewer, Wes, Brunk, Paul, Caino-Lores, Silvina, Casanova, Henri, Cassol, Daniela, Coleman, Jared, Coleman, Taina, Colonnelli, Iacopo, Da Silva, Anderson Andrei, de Oliveira, Daniel, Elahi, Pascal, Elfaramawy, Nour, Elwasif, Wael, Etz, Brian, Fahringer, Thomas, Ferreira, Wesley, Filgueira, Rosa, Tande, Jacob Fosso, Gadelha, Luiz, Gallo, Andy, Garijo, Daniel, Georgiou, Yiannis, Gritsch, Philipp, Grubel, Patricia, Gueroudji, Amal, Guilloteau, Quentin, Hamalainen, Carlo, Enriquez, Rolando Hong, Huet, Lauren, Kesling, Kevin Hunter, Iborra, Paula, Jahangiri, Shiva, Janssen, Jan, Jordan, Joe, Kanwal, Sehrish, Kunstmann, Liliane, Lehmann, Fabian, Leser, Ulf, Li, Chen, Liu, Peini, Luettgau, Jakob, Lupat, Richard, Fernandez, Jose M., Maheshwari, Ketan, Malik, Tanu, Marquez, Jack, Matsuda, Motohiko, Medic, Doriana, Mohammadi, Somayeh, Mulone, Alberto, Navarro, John-Luke, Ng, Kin Wai, Noelp, Klaus, Kinoshita, Bruno P., Prout, Ryan, Crusoe, Michael R., Ristov, Sashko, Robila, Stefan, Rosendo, Daniel, Rowell, Billy, Rybicki, Jedrzej, Sanchez, Hector, Saurabh, Nishant, Saurav, Sumit Kumar, Scogland, Tom, Senanayake, Dinindu, Shin, Woong, Sirvent, Raul, Skluzacek, Tyler, Sly-Delgado, Barry, Soiland-Reyes, Stian, Souza, Abel, Souza, Renan, Talia, Domenico, Tallent, Nathan, Thamsen, Lauritz, Titov, Mikhail, Tovar, Benjamin, Vahi, Karan, Vardar-Irrgang, Eric, Vartina, Edite, Wang, Yuandou, Wouters, Merridee, Yu, Qi, Bkhetan, Ziad Al, Zulfiqar, Mahnoor

Subject Terms: Computer Science - Distributed, Parallel, and Cluster Computing

Access URL: http://arxiv.org/abs/2410.14943

Toward a Framework for Integrative, FAIR, and Reproducible Management of Data on the Dynamic Balance of Microbial Communities

Authors: Gadelha, Luiz, Hohmuth, Martin, Zulfiqar, Mahnoor, Schone, David, Samuel, Sheeba, Sorokina, Maria, Steinbeck, Christoph, Konig-Ries, Birgitta

Source: 2022 IEEE 18th International Conference on e-Science (e-Science) ESCIENCE e-Science (e-Science), 2022 IEEE 18th International Conference on. :443-449 Oct, 2022

Relation: 2022 IEEE 18th International Conference on e-Science (e-Science)

Workflows Community Summit 2022: A Roadmap Revolution

Authors: da Silva, Rafael Ferreira, Badia, Rosa M., Bala, Venkat, Bard, Debbie, Bremer, Peer-Timo, Buckley, Ian, Caino-Lores, Silvina, Chard, Kyle, Goble, Carole, Jha, Shantenu, Katz, Daniel S., Laney, Daniel, Parashar, Manish, Suter, Frederic, Tyler, Nick, Uram, Thomas, Altintas, Ilkay, Andersson, Stefan, Arndt, William, Aznar, Juan, Bader, Jonathan, Balis, Bartosz, Blanton, Chris, Braghetto, Kelly Rosa, Brodutch, Aharon, Brunk, Paul, Casanova, Henri, Lierta, Alba Cervera, Chigu, Justin, Coleman, Taina, Collier, Nick, Colonnelli, Iacopo, Coppens, Frederik, Crusoe, Michael, Cunningham, Will, Kinoshita, Bruno de Paula, Di Tommaso, Paolo, Doutriaux, Charles, Downton, Matthew, Elwasif, Wael, Enders, Bjoern, Erdmann, Chris, Fahringer, Thomas, Figueiredo, Ludmilla, Filgueira, Rosa, Foltin, Martin, Fouilloux, Anne, Gadelha, Luiz, Gallo, Andy, Saez, Artur Garcia, Garijo, Daniel, Gerlach, Roman, Grant, Ryan, Grayson, Samuel, Grubel, Patricia, Gustafsson, Johan, Hayot-Sasson, Valerie, Hernandez, Oscar, Hilbrich, Marcus, Justine, AnnMary, Laflotte, Ian, Lehmann, Fabian, Luckow, Andre, Luettgau, Jakob, Maheshwari, Ketan, Matsuda, Motohiko, Medic, Doriana, Mendygral, Pete, Michalewicz, Marek, Nonaka, Jorji, Pawlik, Maciej, Pottier, Loic, Pouchard, Line, Putz, Mathias, Radha, Santosh Kumar, Ramakrishnan, Lavanya, Ristov, Sashko, Romano, Paul, Rosendo, Daniel, Ruefenacht, Martin, Rycerz, Katarzyna, Saurabh, Nishant, Savchenko, Volodymyr, Schulz, Martin, Simpson, Christine, Sirvent, Raul, Skluzacek, Tyler, Soiland-Reyes, Stian, Souza, Renan, Sukumar, Sreenivas Rangan, Sun, Ziheng, Sussman, Alan, Thain, Douglas, Titov, Mikhail, Tovar, Benjamin, Tripathy, Aalap, Turilli, Matteo, Tuznik, Bartosz, van Dam, Hubertus, Vivas, Aurelio, Ward, Logan, Widener, Patrick, Wilkinson, Sean, Zawalska, Justyna, Zulfiqar, Mahnoor

Subject Terms: Computer Science - Distributed, Parallel, and Cluster Computing

Access URL: http://arxiv.org/abs/2304.00019

Review on computer-assisted biosynthetic capacities elucidation to assess metabolic interactions and communication within microbial communities.

Authors: Zulfiqar, Mahnoor^1,2 (AUTHOR), Singh, Vinay¹ (AUTHOR), Steinbeck, Christoph^1,2 (AUTHOR), Sorokina, Maria^1,3 (AUTHOR) maria.sorokina@bayer.com

Source: Critical Reviews in Microbiology. Nov2024, Vol. 50 Issue 6, p1053-1092. 40p.

Subject Terms: *MICROBIAL communities, *EXTRACELLULAR space, *MOLECULAR interactions, *METABOLIC models, *RESEARCH personnel

MAW: the reproducible Metabolome Annotation Workflow for untargeted tandem mass spectrometry.

Authors: Zulfiqar, Mahnoor¹ (AUTHOR) mahnoor.zulfiqar@uni-jena.de, Gadelha, Luiz¹ (AUTHOR), Steinbeck, Christoph¹ (AUTHOR) christoph.steinbeck@uni-jena.de, Sorokina, Maria^1,2 (AUTHOR), Peters, Kristian^3,4,5 (AUTHOR) kristian.peters@ipb-halle.de

Source: Journal of Cheminformatics. 3/4/2023, Vol. 15 Issue 1, p1-17. 17p.

Subject Terms: *TANDEM mass spectrometry, *LIQUID chromatography-mass spectrometry, *NATURAL resources, *MOLECULAR spectra, *WORKFLOW, *ANNOTATIONS

Draft genome assembly and sequencing dataset of the marine diatom Skeletonema cf. costatum RCC75

Authors: Sorokina, Maria, Barth, Emanuel, Zulfiqar, Mahnoor, Kwantes, Michiel, Pohnert, Georg, Steinbeck, Christoph

Source: Data in brief. 41

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100179652004.0x000001&indx=1&recIds=ETOCvdc_100179652004.0x000001

In-silico studies of CBL-CIPK signaling in rice: response against hypoxia is triggered by interaction of CBL10 with CIPK15

Authors: Sadiq, Irfan, Zulfiqar, Mahnoor, Maryam, Arooma, Rehman, Khoula, Noreen, Salma, Mursalin, Muhammad, Abdul Rauf, Sadaf, Amjad, Shehreen, Siddiqi, Abdul Rauf

Source: Pakistan journal of botany. 50(4):1407-1414

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN617552757&indx=1&recIds=ETOCRN617552757

Implementation of FAIR Practices in Computational Metabolomics Workflows—A Case Study.

Authors: Zulfiqar, Mahnoor, Crusoe, Michael R., König-Ries, Birgitta, Steinbeck, Christoph, Peters, Kristian, Gadelha, Luiz

Source: Metabolites (2218-1989); Feb2024, Vol. 14 Issue 2, p118, 16p

Subject Terms: WORKFLOW, METABOLOMICS, SOFTWARE development tools, TASK analysis, RESEARCH personnel, CHEMINFORMATICS

Untargeted metabolomics to expand the chemical space of the marine diatom Skeletonema marinoi.

Authors: Zulfiqar, Mahnoor, Stettin, Daniel, Schmidt, Saskia, Nikitashina, Vera, Pohnert, Georg, Steinbeck, Christoph, Peters, Kristian, Sorokina, Maria

Source: Frontiers in Microbiology; 2023, p1-12, 12p

Subject Terms: LIQUID chromatography-mass spectrometry, METABOLOMICS, DIATOMS, PHAEODACTYLUM tricornutum, DIATOM frustules, OXYGEN compounds, ACID derivatives, ENVIRONMENTAL protection

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