Browsing by Subject "open science"
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Item Open Access Statistical controversies in clinical research: data access and sharing-can we be more transparent about clinical research? Let's do what's right for patients.(Ann Oncol, 2017-08-01) Rockhold, FWCalls for greater transparency and 'open data access' in clinical research are widespread, from sources including the Executive Office of the President, which in 2013 called for increased access to the results of federally funded research. In 2015, The Institute of Medicine issued a report advocating for a multi-stakeholder effort to foster responsible data sharing, and there are many others. Open science is good for researchers, good for innovation, and good for patients. The question at the center of the open-science efforts for clinical trials should not be whether data should be shared, but rather how we can usher in responsible methods for doing so. Unfortunately, there remain numerous perceived barriers to complete transparency around clinical trial data. This paper reviews the current status of data disclosure, the barriers to achieving it and a suggestion for the future.Item Open Access The 2016 Bioinformatics Open Source Conference (BOSC).(F1000Res, 2016) Harris, Nomi L; Cock, Peter JA; Chapman, Brad; Fields, Christopher J; Hokamp, Karsten; Lapp, Hilmar; Muñoz-Torres, Monica; Wiencko, HeatherMessage from the ISCB: The Bioinformatics Open Source Conference (BOSC) is a yearly meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. BOSC has been run since 2000 as a two-day Special Interest Group (SIG) before the annual ISMB conference. The 17th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2016) took place in Orlando, Florida in July 2016. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community. The conference brought together nearly 100 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, and open and reproducible science.Item Open Access The 2017 Bioinformatics Open Source Conference (BOSC).(F1000Research, 2017-01) Harris, Nomi L; Cock, Peter JA; Chapman, Brad; Fields, Christopher J; Hokamp, Karsten; Lapp, Hilmar; Munoz-Torres, Monica; Tzovaras, Bastian Greshake; Wiencko, HeatherThe Bioinformatics Open Source Conference (BOSC) is a meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. The 18th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2017) took place in Prague, Czech Republic in July 2017. The conference brought together nearly 250 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, open and reproducible science, and this year's theme, open data. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community, called the OBF Codefest.Item Open Access The 2018 Bioinformatics Open Source Conference (GCCBOSC 2018).(F1000Research, 2018-01) Harris, Nomi L; Wiencko, Heather; Chapman, Brad; Cock, Peter JA; Hokamp, Karsten; Lapp, Hilmar; Fields, Chris; Greshake Tzovaras, BastianIn 2018, the annual Bioinformatics Open Source Conference was held for the first time in conjunction with the Galaxy Community Conference, as an experiment to see if we could reach people in the bioinformatics community who aren't part of the audience attracted by ISMB. Held in June 2018 at Reed College in Portland, Oregon, GCCBOSC (Galaxy Community Conference and Bioinformatics Open Source Conference) attracted over 300 participants from around the world. The meeting started with two days of training, followed by two days of talks and poster/demo sessions (with some joint and some parallel sessions). The joint sessions included well-received keynote talks by Tracy Teal, Fernando Pérez and Lucia Peixoto, as well as a panel discussion about documentation and training. After the main meeting, many attendees stayed for up to four additional collaboration days, an extended version of the Codefests that have been held in conjunction with previous BOSCs. GCCBOSC was a successful experiment. The organizers concluded that the best way to serve the broadest community of potential BOSC attendees will be to partner some years with the International Society for Computational Biology (ISMB) and others with GCC.Item Open Access The NKI-Rockland Sample: A Model for Accelerating the Pace of Discovery Science in Psychiatry.(Front Neurosci, 2012) Nooner, Kate Brody; Colcombe, Stanley J; Tobe, Russell H; Mennes, Maarten; Benedict, Melissa M; Moreno, Alexis L; Panek, Laura J; Brown, Shaquanna; Zavitz, Stephen T; Li, Qingyang; Sikka, Sharad; Gutman, David; Bangaru, Saroja; Schlachter, Rochelle Tziona; Kamiel, Stephanie M; Anwar, Ayesha R; Hinz, Caitlin M; Kaplan, Michelle S; Rachlin, Anna B; Adelsberg, Samantha; Cheung, Brian; Khanuja, Ranjit; Yan, Chaogan; Craddock, Cameron C; Calhoun, Vincent; Courtney, William; King, Margaret; Wood, Dylan; Cox, Christine L; Kelly, AM Clare; Di Martino, Adriana; Petkova, Eva; Reiss, Philip T; Duan, Nancy; Thomsen, Dawn; Biswal, Bharat; Coffey, Barbara; Hoptman, Matthew J; Javitt, Daniel C; Pomara, Nunzio; Sidtis, John J; Koplewicz, Harold S; Castellanos, Francisco Xavier; Leventhal, Bennett L; Milham, Michael PThe National Institute of Mental Health strategic plan for advancing psychiatric neuroscience calls for an acceleration of discovery and the delineation of developmental trajectories for risk and resilience across the lifespan. To attain these objectives, sufficiently powered datasets with broad and deep phenotypic characterization, state-of-the-art neuroimaging, and genetic samples must be generated and made openly available to the scientific community. The enhanced Nathan Kline Institute-Rockland Sample (NKI-RS) is a response to this need. NKI-RS is an ongoing, institutionally centered endeavor aimed at creating a large-scale (N > 1000), deeply phenotyped, community-ascertained, lifespan sample (ages 6-85 years old) with advanced neuroimaging and genetics. These data will be publically shared, openly, and prospectively (i.e., on a weekly basis). Herein, we describe the conceptual basis of the NKI-RS, including study design, sampling considerations, and steps to synchronize phenotypic and neuroimaging assessment. Additionally, we describe our process for sharing the data with the scientific community while protecting participant confidentiality, maintaining an adequate database, and certifying data integrity. The pilot phase of the NKI-RS, including challenges in recruiting, characterizing, imaging, and sharing data, is discussed while also explaining how this experience informed the final design of the enhanced NKI-RS. It is our hope that familiarity with the conceptual underpinnings of the enhanced NKI-RS will facilitate harmonization with future data collection efforts aimed at advancing psychiatric neuroscience and nosology.