{"title":"Biomolecular Simulations in the Time of COVID19, and After.","authors":"Rommie E Amaro, Adrian J Mulholland","doi":"10.1109/MCSE.2020.3024155","DOIUrl":"10.1109/MCSE.2020.3024155","url":null,"abstract":"<p><p>COVID19 has changed life for people worldwide. Despite lockdowns globally, computational research has pressed on, working remotely and collaborating virtually on research questions in COVID19 and the virus it is caused by, SARS-CoV-2. Molecular simulations can help to characterize the function of viral and host proteins and have the potential to contribute to the search for vaccines and treatments. Changes in the <i>modus operandi</i> of research groups include broader adoption of the use of preprint servers, earlier and more open sharing of methods, models, and data, the use of social media to rapidly disseminate information, online seminars, and cloud-based virtual collaboration. Research funders and computing providers worldwide recognized the need to provide rapid and significant access to computational architectures. In this review, we discuss how the interplay of all of these factors is influencing the impact - both potential and realized - of biomolecular simulations in the fight against SARS-CoV-2.</p>","PeriodicalId":10553,"journal":{"name":"Computing in Science & Engineering","volume":"22 6","pages":"30-36"},"PeriodicalIF":2.1,"publicationDate":"2020-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7584139/pdf/nihms-1637696.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9142590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Trevor Cickovski, Kedar Aras, Mark S Alber, Jesus A Izaguirre, Maciej Swat, James A Glazier, Roeland M H Merks, Tilmann Glimm, H George E Hentschel, Stuart A Newman
{"title":"From Genes to Organisms Via the Cell A Problem-Solving Environment for Multicellular Development.","authors":"Trevor Cickovski, Kedar Aras, Mark S Alber, Jesus A Izaguirre, Maciej Swat, James A Glazier, Roeland M H Merks, Tilmann Glimm, H George E Hentschel, Stuart A Newman","doi":"10.1109/MCSE.2007.74","DOIUrl":"https://doi.org/10.1109/MCSE.2007.74","url":null,"abstract":"<p><p>To gain performance, developers often build scientific applications in procedural languages, such as C or Fortran, which unfortunately reduces flexibility. To address this imbalance, the authors present CompuCell3D, a multitiered, flexible, and scalable problem-solving environment for morphogenesis simulations that's written in C++ using object-oriented design patterns.</p>","PeriodicalId":10553,"journal":{"name":"Computing in Science & Engineering","volume":"9 4","pages":"50-60"},"PeriodicalIF":2.1,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/MCSE.2007.74","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9401230","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}