A Community Letter Regarding Sharing Biomolecular Simulation Data for COVID-19.

Molecular simulation and modeling can contribute to combating the current COVID-19 global pandemic, e.g. helping to identify leads for therapies, diagnostics, and vaccines for COVID-19, suggesting potential antiviral drugs and biochemical probes, analyzing structural effects of genetic variation in the SARS-CoV-2 virus, and analyzing molecular recognition and mechanisms relevant to infection, pathology, and inhibition. Such efforts complement experiments, can be linked to emerging artificial intelligence and machine learning methods, and add molecular insight into genetic studies and mathematical models for pandemic risk assessment and predicting the impact of potential nonpharmaceutical interventions (NPIs). To maximize the impact and value of molecular simulation methods in this crisis, we as an international community recognize the need to modify our standard practices to maximize the effectiveness of our global response to the pandemic.

There is an urgent need to share our methods, models, and results openly and quickly to test findings, ensure reproducibility, test significance, eliminate dead-ends, and accelerate discovery. Sharing of data for COVID-19 applications will help connect scientists across the global biomolecular simulation community and also improve connection and communication between simulation and experimental and clinical data and investigators.

We, as a community, commit to the following principles:

We commit to making results from our work on the SARS-CoV-2 virus available as preprints as quickly as possible, using preprint servers such as arXiv, bioRxiv, and ChemRxiv, and open access data repositories such as Zenodo.

We commit to making available the input files, model building/processing scripts (e.g., Jupyter notebooks) required to set up, run, and analyze the simulations, and data necessary to repeat analysis upon deposition to the preprint sites following the FAIR data principles (findable, accessible, interoperable, reusable).1 Doing so will also enable others to test, extend, and augment developed models without duplicating efforts, delivering results more rapidly and developing and testing hypotheses.

We will make models and trajectories available as soon as possible through open data sharing platforms such as the SARS-CoV-2 Biomolecular Simulation Data and Algorithm Store,2 the Open Science Framework,3 and the European Open Science Cloud.4

Where appropriate, we will also share algorithms and methods in order to accelerate reuse and innovation. Well-validated and functional machine learning methods and heuristic property calculators would be especially desirable, as are Monte Carlo models of infectious disease spread and prediction of the impact of different NPI strategies. Custom code will be made rapidly available in appropriate repositories (e.g., GitHub).

We commit to applying thoughtful permissive (and open source) licensing strategies (such as those recommended by Reproducible Research Standard)5 to ensure that our models and data can be maximally reused, modified, and redistributed to rapidly advance the field in developing new therapies, while appropriately recognizing and acknowledging original authors and contributors.

In support of these efforts, the SARS-CoV-2 Biomolecular Simulation Data and Algorithm Store draws on the expertise and discussion of several recent workshops, as well as ongoing community discussions and emerging lists of research efforts and resources.6,7,8,9,10,11,12,13,14,15 The NSF MolSSI has recently created a special call for Seed Fellowship applications for students and postdocs that focus on software development, data science, workflows, and machine learning challenges that are especially relevant to the ongoing COVID-19 research. Furthermore, MolSSI in collaboration with BioExcel16 is setting up a centralized github and file sharing service to provide a centralized site for community data and is also working with Zenodo17 and the Open Science Grid18 to help store data and data analysis outcomes for this global initiative. Data storage and high performance computation can also be linked and integrated (e.g., with biomedical data) by e-infrastructures such as Fenix/ICEI19 developed for the Human Brain Project.

Our community should be also aware of the high performance computing resources made available for COVID-19 research (through, e.g., the Partnership for Advanced Computing in Europe (PRACE)20, HECBioSim7, and CCP-BioSim21 in the UK and the COVID-19 High Performance Computing Consortium in the United States,22 and other similar initiatives worldwide,23 including by supercomputer centers and cloud providers).

We recognize that we represent only a cross section of our community and encourage others to follow these principles; all are welcome to join this effort. We offer our support to others already working on open data efforts in the hope that others working on COVID-19 in biomolecular simulation and other areas will adopt similar best practices.

Signed,

Alexandrova, Anastassia, UCLA, USA

Amaro*, Rommie E., UC San Diego, USA

Asciutto, Eliana, ICIFI, UNSAM, Argentina

Azam, Sikander, Quaid-i-Azam University Islamabad, Pakistan

Bahar, Ivet, University of Pittsburgh, USA

Beck, Thomas L., University of Cincinnati, USA

Bernhardt, Debra J., The University of Queensland, Australia

Biczysko, Malgorzata, Shanghai University, China

Biggin, Philip, University of Oxford, UK

Bond, Peter, Bioinformatics Institute, A*Star, Singapore

Bondar, Ana-Nicoleta, FU Berlin, Germany

Bonomi, Max, Institute Pasteur, France

Bonvin, Alexandre, Utrecht University, The Netherlands

Bordin, José Rafael, Universidade Federal de Pelotas, Brazil

Borowski, Tomasz, ICSC, Polish Academy of Sciences

Bowman, Gregory R., Washington University School of Medicine, USA

Bravaya, Ksenia, Boston University, USA

Briggs, James, University of Houston, USA

Brooks, Charles L. III, University of Michigan, USA

Bryce, Richard, University of Manchester, UK

Buck, Matthias, Case Western Reserve University, USA

Carloni, Paolo, Juelich Research Center, Germany

Case, David, Rutgers University, USA

Catlett, Charlie, Discovery Partners Institute, Chicago, USA

Cavalli, Andrea, U Bologna, Italian Institute of Technology, Italy

Chang, Chia-en A., University of California, Riverside, USA

Cheung, Margaret S., University of Houston, USA

Chipot, Chris, CNRS/University of Illinois, USA

Chodera, John D., MSKCC, USA

Chong, Lillian, University of Pittsburgh, USA

Chopra, Gaurav, Purdue University, USA

Cisneros, G. Andres, University of North Texas, USA

Clementi, Cecilia, Rice University USA/Freie Universitat Berlin, Germany

Coitiño, E. Laura, Facultad de Ciencias & CeInBio, Uruguay

Corminboeuf, Clemence , EPFL, Switzerland

Cossio, Pilar, University of Antioquia, Colombia

Cournia, Zoe, Academy of Athens, Greece

Coveney, Peter, University College London, UK

Covino, Roberto, Frankfurt Institute for Advanced Studies, Germany

Crawford, T. Daniel, MolSSI Director/Virginia Tech, USA

Croft, Anna, University of Nottingham, UK

Cugliandolo, Leticia F., Sorbonne Universite, France

Dal Peraro, Matteo, EPFL, Switzerland

Damjanovic, Ana, Johns Hopkins University, USA

Davila, Lilian P., University of California Merced, USA

Deane, Charlotte, University of Oxford, UK

Delemotte, Lucie, KTH, Sweden

De Vivo, Marco, Italian Institute of Technology, Italy

Di Felice, Rosa, University of Southern California, USA

Dima, Ruxandra, University of Cincinnati, USA

Dong, Hao, Nanjing University, China

Elghobashi-Meinhardt, Nadia, Technische Universität Berlin, Germany

Essex, Jonathan, University of Southampton, UK

Fadda, Elisa, Maynooth University, Ireland

Falls, Zackary, University at Buffalo, USA

Fraternali, Franca, King’s College London, UK

Freidzon, Alexandra, Photochemistry Center, Russian Academy of Science

Frenkel, Daan, University of Cambridge, UK

Gagliardi, Laura, University of Minnesota, USA

General, Ignacio J., Universidad Nacional de San Martin & CONICET, Argentina

Gervasio, Francesco Luigi, University College London, UK

Gilson, Michael, University of California, San Diego, USA

Gonzàlez, Leticia, University of Vienna, Austria

Gonzalez-Nilo, F. Danilo, CBIB Universidad Andres Bello, Chile

Grubmueller, Helmut, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany

Guenza, Marina, University of Oregon, USA

Guzman, Horacio V., Jozef Stefan Institute, Slovenia

Haider, Shozeb, University College London, UK

Hamelberg, Donald, Georgia State University, USA

Hannongbua, Supot, Chulalongkorn University, Thailand

Harris, Sarah, University of Leeds, UK

Head, Marti, Oak Ridge National Laboratory/University of Tennessee, USA

Head-Gordon, Teresa, UC Berkeley, USA

Henchman, Richard, University of Manchester, UK

Hernandez, Rigoberto, Johns Hopkins University, USA

Hirst, Jonathan, University of Nottingham, UK

Horta, Bruno A. C., Universidade Federal do Rio de Janeiro, Brazil

Huang, Niu, National Institute of Biological Sciences, China

Huang, Xuhui, The Hong Kong University of Science and Technology, Hong Kong, China SAR

Hummer, Gerhard, Max Planck Institute of Biophysics, Germany

Imhof, Petra, Friedrich-Alexander Universität Erlangen-Nürnberg, Germany

Islam, Shahid, University of Illinois at Chicago , USA

Jäger, Christof, University of Nottingham, UK

Jamshidi, Zahra, Sharif University of Technology, Iran

Janezic, Dusanka, University of Primorska, Slovenia

Jensen, Jan, University of Copenhagen, Denmark

Jha, Shantenu, MolSSI/Rutgers/Brookhaven National Laboratory, USA

Jiao, Wanting, Victoria University of Wellington, New Zealand

Jorgensen, William, Yale University, USA

Kamerlin, Lynn, Uppsala University, Sweden

Keller, Bettina G., Freie Universität Berlin, Germany

Khalid, Syma, University of Southampton, UK

Laughton, Charlie, University of Nottingham, UK

Lee, Vannajan Sanghiran, University of Malaya, Malaysia

Li, Hongchun, Shenzhen Institutes of Advanced Technology, China

Limongelli, Vittorio, USI Lugano, University of Naples, Switzerland, Italy

Lindahl, Erik, Stockholm University & KTH, Sweden

Lindorff-Larsen, Kresten, University of Copenhagen, Denmark

Lins, Roberto D., Aggeu Magalhães Institute, Brazil

Liu, Jin, University of North Texas Health Science Center, TX

Lodola, Alessio, University of Parma, Italy

Loverde, Sharon, City University of New York, USA

Luo, Yun Lyna, Western University of Health Sciences, USA

Ma, Jing, Nanjing University, China

Maciel de Sena Junior, Diniz, Universidade Regional do Cariri, Brazil

Magistrato, Alessandra, Trieste, Italy

Malinovskaya, Svetlana, Stevens Institute of Technology, USA

Marenduzzo, Davide, The University of Edinburgh, UK

Marrink, Siewert-Jan, University of Groningen, The Netherlands

Marti, Marcelo, University of Buenos Aires, Argentina

Martin, Hugh S. C., University College London, UK

McCammon, J. Andrew, UC San Diego, USA

McLeish, Tom, University of York, UK

Mendez, Miguel Angel, Universidad San Francisco de Quito, Ecuador

Merz, Kenneth, Michigan State University, USA

Merzky, Andre, RADICAL-Consulting, Germany

Michel, Julien, University of Edinburgh, UK

Mitchell-Koch, Katie, Wichita State University, USA

Mobley, David, UC Irvine, USA

Moliner, Vicent, Universitat Jaume I, Spain

Montes, Matthieu, CNAM, France

Morris, Garrett, University of Oxford, UK

Mulholland*, Adrian J., University of Bristol, UK

Murad, Sohail, Illinois Institute of Technology, USA

Nangia, Shikha, Syracuse University, USA

Nangia, Shivangi, Dickinson State University, USA

Noé, Frank, FU Berlin, Germany

Noskov, Sergei, University of Calgary, Canada

Oláh, Julianna, Budapest University, Hungary

O’Mara, Megan, The Australian National University, Australia

Ondrechen, Mary Jo, Northeastern University, USA

Onufriev, Alexey, Virginia Polytechnic Institute and State University, USA

Orozco, Modesto, IRB Barcelona, Spain

Pang, Jiayun, University of Greenwich, UK

Pantano, Sergio, Institut Pasteur de Montevideo, Uruguay

Parish, Carol, University of Richmond, USA

Parker, Emily, Victoria University of Wellington, New Zealand

Parrinello, Michele, ETH Zurich, Switzerland

Pas (née Izgorodina), Ekaterina, Monash University, Australia

Paulino, Margot, Facultad de Química, Uruguay

Paz, Sergio Alexis, Universidad Nacional de Córdoba–INFIQC CONICET, Argentina

Perez, Alberto, University of Florida, USA

Pérez-Acle, Tomás, Fundacion Ciencia & Vida, Centro Interdisciplinario de Neurociencia de Valparaíso., Chile

Perilla, TJuan R., University of Delaware, USA

Petrovsky, Nikolai, Flinders University, Australia

Pickholz, Monica, IFIBA, Universidad de Buenos Aires, Argentina

Pietropaolo, Adriana, University of Catanzaro, Italy

Piquemal, Jean-Philip, Sorbonne Université, France

Poma, Adolfo B., Institute of Fundamental Technological Research Polish Academy of Sciences, Poland

Pottel, Josh, Molecular Forecaster, Inc., Canada

Praprotnik, Matej, National Institute of Chemistry, Slovenia

Pungpo, Pornpan, Ubon Ratchathani University, Thailand

Qasmi, Zaheer, University of Karachi, Pakistan

Quevedo, Alfredo, Universidad Nacional de Córdoba, Argentina

Ramanathan, Arvind, Argonne National Laboratory/University of Chicago, USA

Ramos, Maria Joao, University of Porto, Portugal

Ren, Pengyu, UT Austin, USA

Reuter, Nathalie, University of Bergen, Norway

Rice, Julia E., IBM Research–Almaden, USA

Richards, Graham, University of Oxford, UK

Roitberg, Adrian, U Florida, USA

Rosta, Edina, King’s College London, UK

Roux, Benoît, University of Chicago, USA

Rungrotmongkol, Thanyada, Chulalongkorn University, Thailand

Sahai, Michelle A., University of Roehampton, UK

Samudrala, Ram, University at Buffalo, USA

Sansom, Mark, University of Oxford, UK

Sarupria, Sapna, Clemson University, USA

Schlick, Tamar, New York University, USA

Sengupta, Durba, NCL-Pune, India

Sharma, Rati, IISER Bhopal, India

Shaw, David E., D. E. Shaw Research and Columbia University, USA

Shen, Jana, University of Maryland School of Pharmacy, USA

Simmerling, Carlos, Stony Brook University, USA

Slipchenko, Lyudmila, Purdue University, USA

Skaf, Munir, University of Campinas, Brazil

Smith, Jeremy, Oak Ridge National Lab, USA

Soares, Thereza A., Federal University of Pernambuco, Brazil

Stan, George, University of Cincinnati, USA

Steinmann, Casper, Aalborg University, Denmark

Stevens, Rick, Argonne National Laboratory/University of Chicago, USA

Sugita, Yuji, RIKEN, Japan

Swanson, Jessica, University of Utah, USA

Świderek, Katarzyna, Universitat Jaume I, Spain

Taiji, Makoto, RIKEN, Japan

Tajkhorshid, Emad, University of Illinois at Urbana/Champaign, USA

Tao, Peng, Southern Methodist University, USA

Thirumalai, David, University of Texas at Austin, USA

Thukral, Lipi, CSIR-Institute of Genomics and Integrative Biology, India

Tieleman, Peter, University of Calgary, Canada

Tikhonova, Irina, Queen’s University Belfast, UK

Tozzini, Valentina, Istituto Nanoscienze del Cnr, NEST-SNS, Italy

Trujillo, Cristina, Trinity College Dublin, Ireland

Trylska, Joanna, University of Warsaw, Poland

Tuñón, Iñaki, Universidad de Valencia, Spain

Turjanski, Adrian, University of Buenos Aires, Argentina

van der Kamp, Marc, University of Bristol, UK

Verma, Chandra, Bioinformatics Institute, A*Star, Singapore

Voelz, Vincent A., Temple University, USA

Vöhringer-Martinez, Esteban, Universidad de Concepción, Chile

Voth, Gregory, University of Chicago, USA

Wade, Rebecca, HITS and Heidelberg University, Germany

Wahab, Habibah A., Universiti Sains Malaysia, Malaysia

Walsh, Tiff, Deakin University, Australia

Wang, Feng, Swinburne University of Technology, Australia

Wang, Lee-Ping, University of California at Davis, USA

Wang, Renxiao, Fudan University, China

Wang, Yongmei, University of Memphis, USA

Warshel, Arieh, University of Southern California, USA

Welborn, Valerie, Virginia Tech, USA

Wetmore, Stacey, University of Lethbridge, Canada

Windus, Theresa, Iowa State University and Ames Laboratory, USA

Winkler, Dave, Monash University and La Trobe University, Australia

Wong, Chung F., University of Missouri-St. Louis, USA

Wriggers, Willy, Old Dominion University, USA

Yaliraki, Sophia, Imperial College London, UK

Yang, Lee-Wei, National Tsing Hua University, Taiwan

Yang, Wei, Florida State University, USA

Yarovsky, Irene, RMIT University, Australia

Yoon, Mina, Oak Ridge National Laboratory/University of Tennessee, USA

Zacharias, Martin, Technische Universität München, Germany

Zhang, Lu, Fujian Institute of Research on the Structure of Matter, China