From 3aaed4a39188a0c5bbb3f09a30363f24307c14db Mon Sep 17 00:00:00 2001 From: turtle89431 Date: Mon, 4 May 2026 19:58:30 -0700 Subject: [PATCH] Scrape wikipedia-science: 89 new, 1 updated, 91 total (kb-cron) --- _index.db | Bin 606208 -> 663552 bytes ..._funders_by_preprint_licensing_policy-0.md | 25 ++++++++ data/en.wikipedia.org/wiki/Project_CETI-0.md | 24 ++++++++ data/en.wikipedia.org/wiki/Proteins@home-0.md | 27 +++++++++ .../wiki/Public_awareness_of_science-0.md | 44 ++++++++++++++ .../wiki/Public_awareness_of_science-1.md | 55 ++++++++++++++++++ .../wiki/Public_awareness_of_science-2.md | 49 ++++++++++++++++ .../en.wikipedia.org/wiki/Public_science-0.md | 41 +++++++++++++ data/en.wikipedia.org/wiki/QMC@Home-0.md | 30 ++++++++++ .../wiki/Quake-Catcher_Network-0.md | 21 +++++++ data/en.wikipedia.org/wiki/Rosetta@home-0.md | 19 ++++++ data/en.wikipedia.org/wiki/Rosetta@home-1.md | 22 +++++++ data/en.wikipedia.org/wiki/Rosetta@home-2.md | 37 ++++++++++++ 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z6^vjwNC?)l`Vm}+d{3c&ph;sN3?zua=B>xD77}-6w^h?m(ygf8l?m@&6JET} zLWU7MZ2btndiWVK%4a<7&BXkHCZsXpsTH!a@jwd3BK`d|G5O<7cxjdP5W$5tiQi~q zS~Y%$1J)y=yuCDVso?1mYACO4sMpZfwF%I#MEbugfx_F$$G$x51 z-0Jau)4qk`)9AGOCtHSgIKSBw{aW<7=vwA?GGEG^%?#jIAb%`6eYpc-fukWIp3~Pwf@=yDpCFmwSBQ`ZDsnA6rkq+;o?Z{e=BRFZ&br aFSyx`o%Oap-St)Px1y)cx7`2z&i@6XZw9vj diff --git a/data/en.wikipedia.org/wiki/List_of_research_funders_by_preprint_licensing_policy-0.md b/data/en.wikipedia.org/wiki/List_of_research_funders_by_preprint_licensing_policy-0.md new file mode 100644 index 000000000..589b86c45 --- /dev/null +++ b/data/en.wikipedia.org/wiki/List_of_research_funders_by_preprint_licensing_policy-0.md @@ -0,0 +1,25 @@ +--- +title: "List of research funders by preprint licensing policy" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/List_of_research_funders_by_preprint_licensing_policy" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T02:58:26.527450+00:00" +instance: "kb-cron" +--- + +This is a list of funders of research by their open licensing policies for preprints. With the exception of some government employees and contractors, the majority of authors keep the copyright to their work. Many funders require their grantees to disseminate the work using licenses with specific reuse rights. Other details of funder open access policies can be found at the Registry of Open Access Repositories and the Open Policy Finder from JISC (formerly SHERPA). + + +== Policies by funder == + + +== Exceptions for government employees and contractors == +In some countries, work performed by government employees or contractors is owned by the government and subject to their licensing stipulations. For example, in the US, work performed by government employees, such as employees of the NIH is deemed Public Domain in the US, and the US government holds copyright elsewhere. Government licensing policies may override funder requirements. + + +== See also == +List of academic publishers by preprint policy + + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Project_CETI-0.md b/data/en.wikipedia.org/wiki/Project_CETI-0.md new file mode 100644 index 000000000..dbe2621a8 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Project_CETI-0.md @@ -0,0 +1,24 @@ +--- +title: "Project CETI" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Project_CETI" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T02:58:19.631061+00:00" +instance: "kb-cron" +--- + +Project CETI is an international initiative to understand the acoustic communication of sperm whales using advances in artificial intelligence. The project has an interdisciplinary scientific board including marine biologists, artificial intelligence researchers, roboticists, theoretical computer scientists, and linguists. Its name, Cetacean Translation Initiative, is a reference to the SETI Institute. The project has a base on the island of Dominica where recordings are being collected. +The organization has been selected as a TED Audacious Project. CETI researchers have identified 156 distinct codas and their basic components, a "sperm whale phonetic alphabet" much like phonemes. + + +== See also == +Whale sound +Human–animal communication +Animal cognition +Animal communication +Interspecies communication +Communication with extraterrestrial intelligence + + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Proteins@home-0.md b/data/en.wikipedia.org/wiki/Proteins@home-0.md new file mode 100644 index 000000000..5727396a0 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Proteins@home-0.md @@ -0,0 +1,27 @@ +--- +title: "Proteins@home" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Proteins@home" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T02:58:20.781870+00:00" +instance: "kb-cron" +--- + +proteins@home was a volunteer computing project that used the BOINC architecture. The project was run by the Department of Biology at École Polytechnique. The project began on December 28, 2006, and ended in June 2008. + + +== Purpose == +proteins@home was a large-scale non-profit protein structure prediction project utilizing volunteer computing to perform intensive computations in a small amount of time. From their website: +The amino acid sequence of a protein determines its three-dimensional structure, or 'fold'. Conversely, the three-dimensional structure is compatible with a large, but limited set of amino acid sequences. Enumerating the allowed sequences for a given fold is known as the 'inverse protein folding problem'. We are working to solve this problem for a large number of known protein folds (a representative subset: about 1500 folds). The most expensive step is to build a database of energy functions that describe all these structures. For each structure, we consider all possible sequences of amino acids. Surprisingly, this is computationally tractable, because our energy functions are sums over pairs of interactions. Once this is done, we can explore the space of amino acid sequences in a fast and efficient way, and retain the most favorable sequences. This large-scale mapping of protein sequence space will have applications for predicting protein structure and function, for understanding protein evolution, and for designing new proteins. By joining the project, you will help to build the database of energy functions and advance an important area of science with potential biomedical applications. + + +== See also == +List of volunteer computing projects + + +== References == + + +== External links == +proteins@home archive \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Public_awareness_of_science-0.md b/data/en.wikipedia.org/wiki/Public_awareness_of_science-0.md new file mode 100644 index 000000000..edd7ee01e --- /dev/null +++ b/data/en.wikipedia.org/wiki/Public_awareness_of_science-0.md @@ -0,0 +1,44 @@ +--- +title: "Public awareness of science" +chunk: 1/3 +source: "https://en.wikipedia.org/wiki/Public_awareness_of_science" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T02:58:21.921023+00:00" +instance: "kb-cron" +--- + +Public awareness of science (PAS) is a comprehensive concept encompassing all aspects of the awareness, attitudes, behaviors, opinions, and activities that comprise the relations between the general public or lay society as a whole and scientific knowledge and organization. This concept is also known as public understanding of science (PUS), or more recently, public engagement with science and technology (PEST). This approach is a recent development in the field of science communication research, which aims to explore the intricate relationships and interconnections between science, technology, and innovation on the one hand, and the general public on the other. +Initially, research in this domain concentrated on enhancing the public's understanding of scientific subjects, adhering to the principles of the information deficit model of science communication. However, this model has since been largely disregarded by researchers in the field of science communication. Instead, there is an increasing emphasis on understanding how the public chooses to use scientific knowledge and on the development of interfaces to mediate between expert and lay understandings of an issue. Newer frameworks of communicating science include the dialogue and the participation models. The dialogue model aims to create spaces for conversations between scientists and non-scientists to occur while the participation model aims to include non-scientists in the process of science. + +== Major themes == + +The area integrates a series of fields and themes such as: + +Citizen science +Consumer education +Fixed and mobile science exhibits +Media and science (medialisation of science) +Public controversies over science and technology +Public tours of research and development (R&D) parks, manufacturing companies, etc. +Science and art +Science communication in the mass media, Internet, radio, films and television programs +Science education for adults +Science fairs in schools and social groups +Science festivals +Science in popular culture +Science in text books and classrooms +Science museums, aquaria, planetaria, zoological parks, botanical gardens, etc. +Science social movements +Important lines of research are how to raise public awareness and public understanding of science and technology. Also, learning how the public feels and knows about science generally as well as individual subjects, such as genetic engineering, or bioethics. Research by Matthew Nisbet highlights several challenges in science communication, including the paradox that scientific success can create either trust or distrust in experts in different populations and that attitudes of trust are shaped by mostly socioeconomic rather than religious or ideological differences. A 2020 survey by the Pew Research Center found varying levels of trust in science by country, political leanings, and other factors. + +== Bodmer report == +The publication of the Royal Society's' report The Public Understanding of Science (or Bodmer Report) in 1985 is widely held to be the birth of the Public Understanding of Science movement in Britain. The report led to the founding of the Committee on the Public Understanding of Science and a cultural change in the attitude of scientists to outreach activities. + +== Models of engagement == + +=== Contextualist model === +In the 1990s, a new perspective emerged in the field with the classic study of Cumbrian Sheep Farmers' interaction with the Nuclear scientists in England. Brian Wynne demonstrated how the experts were ignorant or disinterested in taking into account the lay knowledge of the sheep farmers while conducting field experiments on the impact of the Chernobyl nuclear fallout on the sheep in the region. Because of this shortcoming from the side of the scientists, local farmers lost their trust in them. The experts were unaware of the local environmental conditions and the behaviour of sheep and this has eventually led to the failure of their experimental models. Following this study, scholars have studies similar micro-sociological contexts of expert-lay interaction and proposed that the context of knowledge communication is important to understand public engagement with science. Instead of large scale public opinion surveys, researchers proposed studies informed by sociology of scientific knowledge (SSK). The contextualist model focuses on the social impediments in the bidirectional flow of scientific knowledge between experts and laypersons/communities. + +=== Deliberative model === +Scholars like Sheila Jasanoff have advanced the debate around public engagement with science by leveraging the theory of deliberative democracy to analyze the public deliberation of and participation in science through various institutional forms. Proponents of greater public deliberation argue it is a basic condition for decision making in democratic societies, even on science and technology issues. There are also attempts to develop more inclusive participatory models of technological governance in the form of consensus conferences, citizen juries, extended peer reviews, and deliberative mapping. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Public_awareness_of_science-1.md b/data/en.wikipedia.org/wiki/Public_awareness_of_science-1.md new file mode 100644 index 000000000..3ed25c80f --- /dev/null +++ b/data/en.wikipedia.org/wiki/Public_awareness_of_science-1.md @@ -0,0 +1,55 @@ +--- +title: "Public awareness of science" +chunk: 2/3 +source: "https://en.wikipedia.org/wiki/Public_awareness_of_science" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T02:58:21.921023+00:00" +instance: "kb-cron" +--- + +=== Civic science model === +Some scholars have identified a new era of "post-normal science" (PNS) in which many scientific discoveries carry high stakes if risks are estimated incorrectly within a broader social context that has a high degree of uncertainty. This PNS era requires a new approach to public engagement efforts and requires a reevaluation of the underlying assumptions of "public engagement", especially with emerging science and technology issues, like CRISPR gene editing, that have the potential to become "wicked problems". These "wicked" issues often require regulatory and policy decisions that have no single correct solution and often involve numerous interest groups – none of whom are clearly positioned to decide and resolve the problem. Policy and regulatory decisions around these scientific issues are inherently political and must balance trade-offs between the scientific research, perceptions of risk, societal needs, and ethical values. While scientists can provide factual answers to research questions and mathematical estimates of risk, many considerations surrounding these wicked science and technology issues have no factual answer. The unidirectional deficit model of simply educating the public on theses issues is insufficient to address these complex questions, and some scholars have proposed scientists adopt a culture of civic science: "broad public engagement with issues that arise at the many intersections between science and society." An emphasis is placed on developing an iterative engagement model that actively seeks to incorporate groups who stand to be adversely effected by a new technology and conducting this engagement away from universities so that it can be done on the public's terms with the public's terms. Other scholars have emphasized that this model of public engagement requires that the public be able to influence science, not merely be engaged by it, up to the point of being able to say "no" to research that does not align with the broader public's values. Under the civic science model, there are five key lessons for scientists committed to public engagement: + +Establish why you want to engage with the public and clearly identify your goals. +Seek out and engage with a broad, diverse range of groups and perspectives and center engagement on listening to these groups. +Work cooperatively with groups to establish common definitions to avoid the perception that researchers are being disingenuous by relying on semantic differences between expert and lay interpretations of vocabulary to ensure the public "supports" their position. +Working to tilt public debates in favor of the priorities and values of researchers will not lead to consistent "best" decisions because wicked science and technology problems will have different considerations and perspectives depending on the application and cultural context. +Meaningfully engage as early as possible; engagement must begin early enough in the research process that the public's views can shape both the research and implementation of findings + +== Public understanding of science == + +Social scientists use various metrics to measure public understanding of science, including: + +=== Factual knowledge === +The key assumptions is that the more individual pieces of information a person is able to retrieve, the more that person is considered to have learned. +Examples of measurement: + +Recognition: Answering a specific question by selecting the correct answer out a list +Cued recall: Answering a specific question without a list of choices +Free recall: After exposure to information, the study participant produces a list of as much of the information as they can remember + +=== Self-reported knowledge, perceived knowledge, or perceived familiarity === +The key assumption is that emphasizes the value of knowledge of one's knowledge. +Examples of measurement: + +Scaled survey responses to questions such as, "How well informed you would say you are about this topic?", this can be also used to assess perceived knowledge before and after events + +=== Structural knowledge === +The nature of connections among different pieces of information in memory. +The key assumption is that the use of elaboration increases the likelihood of remembering information. +Examples of measurement: + +Asking study participants to assess relationships among concepts. For example, participants free recall concepts onto the first row and column of a matrix, then indicate whether the concepts are related to each other by placing an "X" in the cell if they are not. Participants then rank the remaining open cells by their relatedness from 1 (only very weakly) to 7 (very strongly related). +Study participants answer questions designed to measure elaboration involved in a task, such as, "I tried to relate the ideas I read about to my own past experiences." + +=== Trust and credibility === +People may trust science or scientists to different degrees, or may find specific scientists or specific research to be more or less credible. These factors can be related to how science can be used to advance knowledge, and may also be related to how science is communicated, with trust formation playing a central role. +Examples of measurement: + +The 21-item Trust in Science and Scientists Inventory, which measures agreement/disagreement with statements like, "We can trust scientists to share their discoveries even if we don't like their findings." +Scientist-specific measures of agreement, such as "I would trust scientific information if I knew it came from this author." + +=== Mixed use of measures === +While some studies purport that factual and perceived knowledge can be viewed as the same construct, a 2012 study investigating public knowledge of nanotechnology supports separating their use in communications research, as they "do not reflect the same underlying knowledge structures". Correlations between them were found to be low and they were not predicted by the same factors. For example different types of science media use, television versus online, predicted different constructs. +Factual knowledge has been shown to be empirically distinct from structural knowledge. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Public_awareness_of_science-2.md b/data/en.wikipedia.org/wiki/Public_awareness_of_science-2.md new file mode 100644 index 000000000..3620287de --- /dev/null +++ b/data/en.wikipedia.org/wiki/Public_awareness_of_science-2.md @@ -0,0 +1,49 @@ +--- +title: "Public awareness of science" +chunk: 3/3 +source: "https://en.wikipedia.org/wiki/Public_awareness_of_science" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T02:58:21.921023+00:00" +instance: "kb-cron" +--- + +== Project example == +Government and private-led campaigns and events, such as Dana Foundation's "Brain Awareness Week", are becoming a strong focus of programmes which try to promote public awareness of science. +The UK PAWS Foundation dramatically went as far as establishing a Drama Fund with the BBC in 1994. The purpose was to encourage and support the creation of new drama for television, drawing on the world of science and technology. +The Vega Science Trust was set up in 1994 to promote science through the media of television and the internet with the aim of giving scientists a platform from which to communicate to the general public. +The Simonyi Professorship for the Public Understanding of Science chair at The University of Oxford was established in 1995 for the ethologist Richard Dawkins by an endowment from Charles Simonyi. Mathematician Marcus du Sautoy has held the chair since Dawkins' retirement in 2008. Similar professorships have since been created at other British universities. Professorships in the field have been held by well-known academics including Richard Fortey and Kathy Sykes at the University of Bristol, Brian Cox at Manchester University, Tanya Byron at Edge Hill University, Jim Al-Khalili at the University of Surrey, and Alice Roberts at the University of Birmingham. + +== See also == + +== References == + +== Further reading == +Bensaude-vincent, Bernadette (2001). "A Genealogy of the Increasing Gap between Science and the Public". Public Understanding of Science. 10 (1) 307: 99–113. doi:10.1088/0963-6625/10/1/307. +Bijker, Wiebe E., Bal, Roland and Hendriks, Ruud. 2009. The Paradox of Scientific Authority: The Role of Scientific Advice in Democracies. Cambridge and London: The MIT Press. +Bucchi, Massimiano (1996). "When Scientists Turn to the Public: Alternative Routes in Science Communication". Public Understanding of Science. 5 (4): 375–394. doi:10.1088/0963-6625/5/4/005. S2CID 143374883. +Dash, Biswanath (2014a). "Public Understanding of Cyclone Warning in India: Can Wind be Predicted?". Public Understanding of Science. 24 (8): 970–987. doi:10.1177/0963662514553203. PMID 25313142. S2CID 22226217. +Davenport, Sally and Leitch, Shirley. 2005. "Agoras, Ancient and Modern, and a Framework for Science-Society Debate", Science and Public Policy 32(2), April, pp. 137–153. +Dryzek, John S. 2000. Deliberative Democracy and Beyond: Liberals, Critics, Contestations. New York and Oxford: Oxford University Press. +Felt, Ulrike; Fochler, Maximilian (2010). "Machineries for Making Publics: Inscribing and De-scribing Publics in Public Engagement". Minerva. 48 (3): 219–239. doi:10.1007/s11024-010-9155-x. S2CID 144227502. +Fischer, Frank. 2005. Citizens, Experts, and the Environment. Durham: Duke University Press. +Gregory, Jane & Miller, Steve (1998); Science in Public: Communication, Culture & Credibility (Cambridge, Massachusetts USA: Perseus Publishing) +Hess, David J (2011). "To Tell the Truth: On Scientific Counter Publics". Public Understanding of Science. 20 (5): 627–641. doi:10.1177/0963662509359988. S2CID 145627603. +Hilgartner, Stephen (1990). "The Dominant View of Popularisation: Conceptual Problems, Political Uses". Social Studies of Science. 20 (3): 519–539. doi:10.1177/030631290020003006. S2CID 144068473. +Irwin, Alan and Wynne, Brian. (eds.) 1996. Misunderstanding Science? The Public Reconstruction of Science and Technology. Cambridge: Cambridge University Press. +Irwin, Alan. 1995. Citizen Science: A Study of People, Expertise and Sustainable Development. London and New York: Routledge. +Jasanoff, Sheila (2003c). "Technologies of Humility: Citizen Participation in Governing Science". Minerva. 41 (3): 223–244. doi:10.1023/A:1025557512320. S2CID 14370392. +Jasanoff, Sheila. 2005. Designs on Nature: Science and Democracy in Europe and the United States. Princeton and Oxford: Princeton University Press. +Leach, Melissa, Scoones, Ian and Wynne, Brian. (eds.) 2005. Science and Citizens: Globalisation and the Challenge of Engagement. London and New York: Zed Books. +Public Understanding of Science, specialist journal. +Shapin, Steven. 1990. 'Science and the Public' in R.C. Olby et al. (eds). Companion to the History of Modern Science. London and New York: Routledge. Pp. 990–1007. +The Royal Academy of Science's 2006 "Factors affecting science communication: a survey of scientists and engineers" report. +Southwell, Brian G. (2013). "Social Networks and Popular Understanding of Science and Health". Baltimore, MD: Johns Hopkins University Press. +Southwell, Brian G.; Torres, Alicia (2006). "Connecting interpersonal and mass communication: Science news exposure, perceived ability to understand science, and conversation". Communication Monographs. 73 (3): 334–350. doi:10.1080/03637750600889518. S2CID 143644528. +Varughese, Shiju Sam (2012). "Where are the missing masses? The Quasi-publics and Non-publics of Technoscience". Minerva. 50 (2): 239–254. doi:10.1007/s11024-012-9197-3. S2CID 144319733. +Varughese, Shiju Sam (2017). Contested Knowledge: Science, Media, and Democracy in Kerala. Oxford University Press. doi:10.1093/acprof:oso/9780199469123.001.0001. ISBN 978-0-19-946912-3. + +== External links == + +Science.gov +Vega Science Trust \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Public_science-0.md b/data/en.wikipedia.org/wiki/Public_science-0.md new file mode 100644 index 000000000..4bed7ec87 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Public_science-0.md @@ -0,0 +1,41 @@ +--- +title: "Public science" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Public_science" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T02:58:23.126983+00:00" +instance: "kb-cron" +--- + +Public science is research that is conducted amongst, or includes, the public. Two traditions of public science have emerged, one based on participatory action research and another based on science outreach. + + +== Participatory action research == + +The participatory action research approach seeks to develop a critical framework for making systematic inquiry and analysis a public enterprise. It is committed to valuing knowledges that have been historically marginalized and delegitimized (i.e., youth, prisoner, immigrant, farmer) alongside traditionally recognized knowledges (i.e., scholarly). Through the formation of research collectives, it aims to share the various knowledges and resources held by its individual members so members can participate as equally as possible. The choice of appropriate research questions, design, methods and analysis as well as useful research products are decided collectively. Institutions for this form of public science include the Public Science Project. Examples of public science projects in the participatory action research tradition include the Morris Justice Project. + + +== Science outreach == + +The science outreach approach has some similarities to citizen science but typically describes projects that are conducted outdoors or in another type of public or accessible space such as a public park, metro stop, library, university campus, etc. Similar to public art, it includes aspects of collaboration, community support and involvement, and site specificity. +Public science efforts in the science outreach tradition include Science on the Buses, in which city buses in many major European Union cities were decorated with large informational science posters in November 2002. Likewise, a project in Toronto placed "advertisements" with science facts on buses in Toronto during July 2009. +Science City was a public science initiative that ran from June 1994 through May 1995. Created by staff and consultants from the New York Hall of Science, Science City was an outdoor exhibition that utilized the street, fences, buildings and other public structures in New York City to attract the "non-museum-going" public to the science in everyday life. The exhibition asked questions such as "Why is it warmer in the city?", "What pulses under the street?" and "What's under the sidewalk?" to help increase public awareness about the science and technology that runs invisibly underneath modern urban life. +Science Cafés, founded by the public science pioneer Duncan Dallas, are public science events that initiate a discussion on a science topic in pubs or cafes, usually with a local researcher in attendance to answer questions and present information. +Science festivals can also be grouped into this category of public science efforts, with modern incarnations of festivals including a range of learner-centered activities and events conducted in public spaces. +Public science initiatives often attempt to reach new audiences (particularly, non-experts who might not actively seek out science), in addition to existing science outreach audiences, by hosting events in alternative informal learning environments. By definition, such public science projects are outside the walls of the science centre or science museum, where the main focus of the particular space is not typically science outreach. +An example of a specific public science initiative in astronomy is From Earth to the Universe (FETTU), a project of the International Year of Astronomy 2009 (IYA2009). FETTU displayed large-scale images of astronomical objects with contextual information and supplementary materials and activities in non-traditional and mostly public locations such as parks, airports, art festivals, and shopping malls. By 2011, FETTU had been exhibited at about 1000 sites worldwide, with 50 sites in the United States. One result from FETTU demonstrated a trend towards more non-self-selective audiences for science communications in these public spaces. + + +== References == + + +== External links == +Public Science Project +International Year of Astronomy 2009 +From Earth to the Universe +From Earth to the Solar System +Voyage to the Solar System +USA Science and Engineering Festival +World Science Festival +San Diego Science Festival \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/QMC@Home-0.md b/data/en.wikipedia.org/wiki/QMC@Home-0.md new file mode 100644 index 000000000..35a4843ba --- /dev/null +++ b/data/en.wikipedia.org/wiki/QMC@Home-0.md @@ -0,0 +1,30 @@ +--- +title: "QMC@Home" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/QMC@Home" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T02:58:24.250189+00:00" +instance: "kb-cron" +--- + +QMC@Home was a volunteer computing project for the BOINC client aimed at further developing and testing Quantum Monte Carlo (QMC) for use in quantum chemistry. It is hosted by the University of Münster with participation by the Cavendish Laboratory. QMC@Home allows volunteers from around the world to donate idle computer cycles to help calculate molecular geometry using Diffusion Monte Carlo. +The project is developing a new application using density functional theory. +The project began its Beta testing on 23 May 2006. As of February 2010, QMC@Home has about 7,500 active participants from 102 countries, contributing about 5 teraFLOPS of computation power. + + +== Workunits == +In order to get results from home computers the work is split into "workunits". The time it takes to complete a workunit depends on the size of the calculated system and the speed of the user's computer. The target time is between 4 and 48 hours on a 2.4 GHz system. +This is a list of molecules recently tested: +1a Ammonia; 1 Ammonia dimer; 2a Water; 2 Water dimer; 3a Formic acid; 3 Formic acid dimer; 4a Formamide; 4 Formamide dimer; 5a Uracil; 5 Uracil dimer; 6a 2-pyridoxine; 6b 2-aminopyridine; 6 2-pyridoxine/2-aminopyridine; 7a Adenine; 7b Thymine; 7 Adenine/thymine WC; 8a Methane; 8 Methane dimer; 9a Ethene; 9 Ethene dimer; 10 Benzene/methane; 11a Benzene; 11 Benzene dimer; 12a Pyrazine; 12 Pyrazine dimer; 13 Uracil dimer; 14a Indole; 14 Indole/benzene; 15 Adenine/thymine stack; 16b Ethyne; 16 Ethene/ethyne; 17 Benzene/water; 18 Benzene/ammonia; 19b Hydrogen cyanide; 19 Benzene/hydrogen cyanide; 20 Benzene dimer; 21 Indole/benzene; 22a Phenol; 22 Phenol dimer + + +== See also == +List of volunteer computing projects + + +== References == + + +== External links == +QMC screensaver video on YouTube \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Quake-Catcher_Network-0.md b/data/en.wikipedia.org/wiki/Quake-Catcher_Network-0.md new file mode 100644 index 000000000..77c20e5a6 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Quake-Catcher_Network-0.md @@ -0,0 +1,21 @@ +--- +title: "Quake-Catcher Network" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Quake-Catcher_Network" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T02:58:25.405843+00:00" +instance: "kb-cron" +--- + +The Quake-Catcher Network was an initiative run by the University of Southern California that aimed to use computer-based accelerometers to detect earthquakes. It used the BOINC volunteer computing platform (a form of distributed computing, similar to SETI@home). +It supported mobile devices (smartphones and some tablets/laptops) that have a built-in accelerometer. It also supported three external USB devices - the codemercs.com JoyWarrior 24F8, the ONavi sensor, and the MotionNode Accel. +In 2011, project scientist Elizabeth Cochran was awarded a Presidential Early Career Award from US President Barack Obama in large part due to her founding of the Quake-Catcher Network project. +The Quake Catcher Network project started at Stanford University in 2008, then moved to Caltech, and joined the Southern California Earthquake Center (SCEC) and the Incorporated Research Institutions for Seismology (IRIS) in 2016. The Quake-Catcher Network was discontinued on June 1st 2023 + + +== References == + + +== External links == +Interactive world map, showing recent earthquakes (day/week/month) Archived 2018-01-07 at the Wayback Machine – result of QCN \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Rosetta@home-0.md b/data/en.wikipedia.org/wiki/Rosetta@home-0.md new file mode 100644 index 000000000..b3c458886 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Rosetta@home-0.md @@ -0,0 +1,19 @@ +--- +title: "Rosetta@home" +chunk: 1/6 +source: "https://en.wikipedia.org/wiki/Rosetta@home" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T02:58:27.707669+00:00" +instance: "kb-cron" +--- + +Rosetta@home is a volunteer computing project researching protein structure prediction on the Berkeley Open Infrastructure for Network Computing (BOINC) platform, run by the Baker lab. Rosetta@home aims to predict protein–protein docking and design new proteins with the help of about fifty-five thousand active volunteered computers processing at over 487,946 gigaFLOPS on average as of September 19, 2020. Foldit, a Rosetta@home videogame, aims to reach these goals with a crowdsourcing approach. Though much of the project is oriented toward basic research to improve the accuracy and robustness of proteomics methods, Rosetta@home also does applied research on malaria, Alzheimer's disease, and other pathologies. +Like all BOINC projects, Rosetta@home uses idle computer processing resources from volunteers' computers to perform calculations on individual workunits. Completed results are sent to a central project server where they are validated and assimilated into project databases. The project is cross-platform, and runs on a wide variety of hardware configurations. Users can view the progress of their individual protein structure prediction on the Rosetta@home screensaver. +In addition to disease-related research, the Rosetta@home network serves as a testing framework for new methods in structural bioinformatics. Such methods are then used in other Rosetta-based applications, like RosettaDock or the Human Proteome Folding Project and the Microbiome Immunity Project, after being sufficiently developed and proven stable on Rosetta@home's large and diverse set of volunteer computers. Two especially important tests for the new methods developed in Rosetta@home are the Critical Assessment of Techniques for Protein Structure Prediction (CASP) and Critical Assessment of Prediction of Interactions (CAPRI) experiments, biennial experiments which evaluate the state of the art in protein structure prediction and protein–protein docking prediction, respectively. Rosetta consistently ranks among the foremost docking predictors, and is one of the best tertiary structure predictors available. +With an influx of new users looking to participate in the fight against the COVID-19 pandemic, caused by SARS-CoV-2, Rosetta@home increased its computing power up to 1.7 PetaFlops as of March 28, 2020. On September 9, 2020, Rosetta@home researchers published a paper describing 10 potent antiviral candidates against SARS-CoV-2. Rosetta@home contributed to this research and these antiviral candidates are heading towards Phase 1 clinical trials, which may begin in early 2022. According to the Rosetta@home team, Rosetta volunteers contributed to the development of a nanoparticle vaccine. This vaccine has been licensed and is known as the IVX-411 by Icosavax, which began a Phase I/II clinical trial in June 2021, and GBP510 which is being developed by SK Bioscience and is already approved for a Phase III clinical trial in South Korea. +NL-201, a cancer drug candidate that was first created at the Institute of Protein Design (IPD) and published in a January 2019 paper, began a Phase 1 Human clinical trial in May 2021 with the support of Neoleukin Therapeutics, itself a spin-off from the IPD. Rosetta@home played a role in the development of NL-201 and contributed with "forward folding" experiments that helped validate protein designs. + +== Computing platform == + +The Rosetta@home application and the BOINC volunteer computing platform are available for the operating systems Windows, Linux, and macOS; BOINC also runs on several others, e.g., FreeBSD. Participation in Rosetta@home requires a central processing unit (CPU) with a clock speed of at least 500 MHz, 200 megabytes of free disk space, 512 megabytes of physical memory, and Internet connectivity. As of July 20, 2016, the current version of the Rosetta Mini application is 3.73. The current recommended BOINC program version is 7.6.22. Standard Hypertext Transfer Protocol (HTTP) (port 80) is used for communication between the user's BOINC client and the Rosetta@home servers at the University of Washington; HTTPS (port 443) is used during password exchange. Remote and local control of the BOINC client use port 31416 and port 1043, which might need to be specifically unblocked if they are behind a firewall. Workunits containing data on individual proteins are distributed from servers located in the Baker lab at the University of Washington to volunteers' computers, which then calculate a structure prediction for the assigned protein. To avoid duplicate structure predictions on a given protein, each workunit is initialized with a random seed number. This gives each prediction a unique trajectory of descent along the protein's energy landscape. Protein structure predictions from Rosetta@home are approximations of a global minimum in a given protein's energy landscape. That global minimum represents the most energetically favorable conformation of the protein, i.e., its native state. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Rosetta@home-1.md b/data/en.wikipedia.org/wiki/Rosetta@home-1.md new file mode 100644 index 000000000..1d22b5077 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Rosetta@home-1.md @@ -0,0 +1,22 @@ +--- +title: "Rosetta@home" +chunk: 2/6 +source: "https://en.wikipedia.org/wiki/Rosetta@home" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T02:58:27.707669+00:00" +instance: "kb-cron" +--- + +A primary feature of the Rosetta@home graphical user interface (GUI) is a screensaver which shows a current workunit's progress during the simulated protein folding process. In the upper-left of the current screensaver, the target protein is shown adopting different shapes (conformations) in its search for the lowest energy structure. Depicted immediately to the right is the structure of the most recently accepted. On the upper right the lowest energy conformation of the current decoy is shown; below that is the true, or native, structure of the protein if it has already been determined. Three graphs are included in the screensaver. Near the middle, a graph for the accepted model's thermodynamic free energy is displayed, which fluctuates as the accepted model changes. A graph of the accepted model's root-mean-square deviation (RMSD), which measures how structurally similar the accepted model is to the native model, is shown far right. On the right of the accepted energy graph and below the RMSD graph, the results from these two functions are used to produce an energy vs. RMSD plot as the model is progressively refined. +Like all BOINC projects, Rosetta@home runs in the background of the user's computer, using idle computer power, either at or before logging into an account on the host operating system. The program frees resources from the CPU as they are needed by other applications so that normal computer use is unaffected. Many program settings can be specified via user account preferences, including: the maximum percentage of CPU resources the program can use (to control power consumption or heat production from a computer running at sustained capacity), the times of day during which the program can run, and many more. + +== Project significance == + +With the proliferation of genome sequencing projects, scientists can infer the amino acid sequence, or primary structure, of many proteins that carry out functions within the cell. To better understand a protein's function and aid in rational drug design, scientists need to know the protein's three-dimensional tertiary structure. + +Protein 3D structures are currently determined experimentally via X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. The process is slow (it can take weeks or even months to figure out how to crystallize a protein for the first time) and costly (around US$100,000 per protein). Unfortunately, the rate at which new sequences are discovered far exceeds the rate of structure determination – out of more than 7,400,000 protein sequences available in the National Center for Biotechnology Information (NCBI) nonredundant (nr) protein database, fewer than 52,000 proteins' 3D structures have been solved and deposited in the Protein Data Bank, the main repository for structural information on proteins. One of the main goals of Rosetta@home is to predict protein structures with the same accuracy as existing methods, but in a way that requires significantly less time and money. Rosetta@home also develops methods to determine the structure and docking of membrane proteins (e.g., G protein–coupled receptors (GPCRs)), which are exceptionally difficult to analyze with traditional techniques like X-ray crystallography and NMR spectroscopy, yet represent the majority of targets for modern drugs. +Progress in protein structure prediction is evaluated in the biannual Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiment, in which researchers from around the world attempt to derive a protein's structure from the protein's amino acid sequence. High scoring groups in this sometimes competitive experiment are considered the de facto standard-bearers for what is the state of the art in protein structure prediction. Rosetta, the program on which Rosetta@home is based, has been used since CASP5 in 2002. In the 2004 CASP6 experiment, Rosetta made history by being the first to produce a close to atomic-level resolution, ab initio protein structure prediction in its submitted model for CASP target T0281. Ab initio modeling is considered an especially difficult category of protein structure prediction, as it does not use information from structural homology and must rely on information from sequence homology and modeling physical interactions within the protein. Rosetta@home has been used in CASP since 2006, where it was among the top predictors in every category of structure prediction in CASP7. These high quality predictions were enabled by the computing power made available by Rosetta@home volunteers. Increasing computing power allows Rosetta@home to sample more regions of conformation space (the possible shapes a protein can assume), which, according to Levinthal's paradox, is predicted to increase exponentially with protein length. +Rosetta is also used in protein–protein docking prediction, which determines the structure of multiple complexed proteins, or quaternary structure. This type of protein interaction affects many cellular functions, including antigen–antibody and enzyme–inhibitor binding and cellular import and export. Determining these interactions is critical for drug design. Rosetta is used in the Critical Assessment of Prediction of Interactions (CAPRI) experiment, which evaluates the state of the protein docking field similar to how CASP gauges progress in protein structure prediction. The computing power made available by Rosetta@home's project volunteers has been cited as a major factor in Rosetta's performance in CAPRI 2007, where its docking predictions have been among the most accurate and complete. +In early 2008, Rosetta was used to computationally design a protein with a function never before observed in nature. This was inspired in part by the retraction of a high-profile paper from 2004 which originally described the computational design of a protein with improved enzymatic activity relative to its natural form. The 2008 research paper from David Baker's group describing how the protein was made, which cited Rosetta@home for the computing resources it made available, represented an important proof of concept for this protein design method. This type of protein design could have future applications in drug discovery, green chemistry, and bioremediation. +The Rosetta computer program was cited in the 2024 Scientific Background to the Nobel Prize in Chemistry. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Rosetta@home-2.md b/data/en.wikipedia.org/wiki/Rosetta@home-2.md new file mode 100644 index 000000000..7e0171c75 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Rosetta@home-2.md @@ -0,0 +1,37 @@ +--- +title: "Rosetta@home" +chunk: 3/6 +source: "https://en.wikipedia.org/wiki/Rosetta@home" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T02:58:27.707669+00:00" +instance: "kb-cron" +--- + +== Disease-related research == +In addition to basic research in predicting protein structure, docking and design, Rosetta@home is also used in immediate disease-related research. Numerous minor research projects are described in David Baker's Rosetta@home journal. As of February 2014, information on recent publications and a short description of the work are being updated on the forum. The forum thread is no longer used since 2016, and news on the research can be found on the general news section of the project. + +=== Alzheimer's disease === +A component of the Rosetta software suite, RosettaDesign, was used to accurately predict which regions of amyloidogenic proteins were most likely to make amyloid-like fibrils. By taking hexapeptides (six amino acid-long fragments) of a protein of interest and selecting the lowest energy match to a structure similar to that of a known fibril forming hexapeptide, RosettaDesign was able to identify peptides twice as likely to form fibrils as are random proteins. Rosetta@home was used in the same study to predict structures for amyloid beta, a fibril-forming protein that has been postulated to cause Alzheimer's disease. Preliminary but as yet unpublished results have been produced on Rosetta-designed proteins that may prevent fibrils from forming, although it is unknown whether it can prevent the disease. + +=== Anthrax === +Another component of Rosetta, RosettaDock, was used in conjunction with experimental methods to model interactions between three proteins—lethal factor (LF), edema factor (EF) and protective antigen (PA)—that make up anthrax toxin. The computer model accurately predicted docking between LF and PA, helping to establish which domains of the respective proteins are involved in the LF–PA complex. This insight was eventually used in research resulting in improved anthrax vaccines. + +=== Herpes simplex virus 1 === +RosettaDock was used to model docking between an antibody (immunoglobulin G) and a surface protein expressed by the cold sore virus, herpes simplex virus 1 (HSV-1) which serves to degrade the antiviral antibody. The protein complex predicted by RosettaDock closely agreed with the especially difficult-to-obtain experimental models, leading researchers to conclude that the docking method has potential to address some of the problems that X-ray crystallography has with modelling protein–protein interfaces. + +=== HIV === +As part of research funded by a $19.4 million grant by the Bill & Melinda Gates Foundation, Rosetta@home has been used in designing multiple possible vaccines for human immunodeficiency virus (HIV). + +=== Malaria === +In research involved with the Grand Challenges in Global Health initiative, Rosetta has been used to computationally design novel homing endonuclease proteins, which could eradicate Anopheles gambiae or otherwise render the mosquito unable to transmit malaria. Being able to model and alter protein–DNA interactions specifically, like those of homing endonucleases, gives computational protein design methods like Rosetta an important role in gene therapy (which includes possible cancer treatments). + +=== COVID-19 === +In 2020, the Rosetta molecular modelling suite was used to accurately predict the atomic-scale structure of the SARS-CoV-2 spike protein weeks before it could be measured in the lab. On June 26 of 2020, the project announced it had succeeded in creating antiviral proteins that neutralize SARS-CoV-2 virions in the lab and that these experimental antiviral drugs are being optimized for animal testing trials. +In a follow-up, a paper describing 10 SARS-CoV-2 miniprotein inhibitors was published in Science on September 9. Two of these inhibitors, LCB1 and LCB3, are several times more potent than the best monoclonal antibodies being developed against SARS-CoV-2, both on a molar and mass basis. In addition, the research suggests that these inhibitors retain their activity at elevated temperatures, are 20-fold smaller than an antibody and thus, have 20-fold more potential neutralizing sites, increasing the potential efficacy of a locally administered drug. The small size and high stability of the inhibitors is expected to make them adequate to a gel formulation that can be nasally applied or as a powder to be administered directly onto the respiratory system. The researchers will work on developing these inhibitors into therapeutics and prophylactics in the months ahead. As of July 2021, these antiviral candidates were forecasted to begin clinical trials in early 2022 and had received funding from the Bill & Melinda Gates Foundation for preclinical and early clinical trials. In animal testing trials, these antiviral candidates were effective against variants of concern including Alpha, Beta and Gamma. +Rosetta@home was used to help screen the over 2 million SARS-CoV-2 Spike-binding proteins that were computationally designed, and thus, contributed to this research. +Per the Rosetta@home team at the Institute of Protein Design, Rosetta@home volunteers contributed to the development of antiviral drug candidates and to a protein nanoparticle vaccine. The IVX-411 vaccine is already on a Phase 1 clinical trial run by Icosavax while the same vaccine, licensed to another manufacturer and under the name GBP510, has been approved in South Korea for a Phase III trial run by SK Bioscience. The candidate antivirals are also going towards Phase 1 clinical trials. + +=== Cancer === +Rosetta@home researchers have designed an IL-2 receptor agonist called Neoleukin-2/15 that does not interact with the alpha subunit of the receptor. Such immunity signal molecules are useful in cancer treatment. While the natural IL-2 suffers from toxicity due to an interaction with the alpha subunit, the designed protein is much safer, at least in animal models. Rosetta@home contributed in "forward folding experiments" which helped validate designs. +In a September 2020 feature in the New Yorker, David Baker stated that Neoleukin-2/15 would begin human clinical trials "later this year". Neoleukin-2/15 is being developed by Neoleukin, a spin-off company from the Baker lab. In December 2020, Neoleukin announced it would be submitting an Investigational New Drug application with the Food and Drug Administration in order to begin a Phase 1 clinical trial of NL-201, which is a further development of Neoleukin-2/15. A similar application was submitted in Australia and Neoleukin hopes to enrol up 120 participants on the Phase 1 clinical trial. The Phase 1 human clinical trial began on May 5, 2021. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Rosetta@home-3.md b/data/en.wikipedia.org/wiki/Rosetta@home-3.md new file mode 100644 index 000000000..57bff20a3 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Rosetta@home-3.md @@ -0,0 +1,26 @@ +--- +title: "Rosetta@home" +chunk: 4/6 +source: "https://en.wikipedia.org/wiki/Rosetta@home" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T02:58:27.707669+00:00" +instance: "kb-cron" +--- + +== Rosetta software == + +Rosetta is the software responsible for performing structure prediction in Rosetta@home. Besides a BOINC cluster, Rosetta can run on a single local computer, or on a local supercomputer. Similar to other bioinformatic programs, there are online public servers offering to run Rosetta from a web interface. The software is freely licensed to the academic community and available to pharmaceutical companies for a fee. +Originally introduced by the Baker laboratory at the University of Washington in 1998 as an ab initio approach to structure prediction, Rosetta has since branched into several development streams and distinct services, providing features such as macromolecular docking and protein design. Many of the graduate students and other researchers involved in Rosetta's initial development have since moved to other universities and research institutions, and subsequently enhanced different parts of the Rosetta project. +The Rosetta platform derives its name from the Rosetta Stone, as it attempts to decipher the structural "meaning" of proteins' amino acid sequences. Development of the Rosetta code is done by Rosetta Commons. Rosetta participates in CASP and CAPRI. +Rosetta was rewritten in C++ to allow easier development than that allowed by its original version, which was written in Fortran. This new version is object-oriented, and was released to Rosetta@Home February 8, 2008. + +=== RosettaDesign === + +RosettaDesign, a computing approach to protein design based on Rosetta, began in 2000 with a study in redesigning the folding pathway of Protein G. In 2002 RosettaDesign was used to design Top7, a 93-amino acid long α/β protein that had an overall fold never before recorded in nature. This new conformation was predicted by Rosetta to within 1.2 Å RMSD of the structure determined by X-ray crystallography, representing an unusually accurate structure prediction. Rosetta and RosettaDesign earned widespread recognition by being the first to design and accurately predict the structure of a novel protein of such length, as reflected by the 2002 paper describing the dual approach prompting two positive letters in the journal Science, and being cited by more than 240 other scientific articles. The visible product of that research, Top7, was featured as the RCSB PDB's 'Molecule of the Month' in October 2006; a superposition of the respective cores (residues 60–79) of its predicted and X-ray crystal structures are featured in the Rosetta@home logo. +Brian Kuhlman, a former postdoctoral associate in David Baker's lab and now an associate professor at the University of North Carolina, Chapel Hill, offers RosettaDesign as an online service. + +=== RosettaDock === +RosettaDock was added to the Rosetta software suite during the first CAPRI experiment in 2002 as the Baker laboratory's algorithm for protein–protein docking prediction. In that experiment, RosettaDock made a high-accuracy prediction for the docking between streptococcal pyogenic exotoxin A and a T cell-receptor β-chain, and a medium accuracy prediction for a complex between porcine α-amylase and a camelid antibody. While the RosettaDock method only made two acceptably accurate predictions out of seven possible, this was enough to rank it seventh out of nineteen prediction methods in the first CAPRI assessment. +Development of RosettaDock diverged into two branches for subsequent CAPRI rounds as Jeffrey Gray, who laid the groundwork for RosettaDock while at the University of Washington, continued working on the method in his new position at Johns Hopkins University. Members of the Baker laboratory further developed RosettaDock in Gray's absence. The two versions differed slightly in side-chain modeling, decoy selection and other areas. Despite these differences, both the Baker and Gray methods performed well in the second CAPRI assessment, placing fifth and seventh respectively out of 30 predictor groups. Jeffrey Gray's RosettaDock server is available as a free docking prediction service for non-commercial use. +In October 2006, RosettaDock was integrated into Rosetta@home. The method used a fast, crude docking model phase using only the protein backbone. This was followed by a slow full-atom refinement phase in which the orientation of the two interacting proteins relative to each other, and side-chain interactions at the protein–protein interface, were simultaneously optimized to find the lowest energy conformation. The vastly increased computing power afforded by the Rosetta@home network, combined with revised fold-tree representations for backbone flexibility and loop modeling, made RosettaDock sixth out of 63 prediction groups in the third CAPRI assessment. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Rosetta@home-4.md b/data/en.wikipedia.org/wiki/Rosetta@home-4.md new file mode 100644 index 000000000..0f20a7a8e --- /dev/null +++ b/data/en.wikipedia.org/wiki/Rosetta@home-4.md @@ -0,0 +1,43 @@ +--- +title: "Rosetta@home" +chunk: 5/6 +source: "https://en.wikipedia.org/wiki/Rosetta@home" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T02:58:27.707669+00:00" +instance: "kb-cron" +--- + +=== Robetta === +The Robetta (Rosetta Beta) server is an automated protein structure prediction service offered by the Baker laboratory for non-commercial ab initio and comparative modeling. It has participated as an automated prediction server in the biannual CASP experiments since CASP5 in 2002, performing among the best in the automated server prediction category. Robetta has since competed in CASP6 and 7, where it did better than average among both automated server and human predictor groups. It also participates in the CAMEO3D continuous evaluation. Robetta tasks run on Baker lab servers, Janelia Research Campus machines, and Rosetta@home participant computers. +In modeling protein structure as of CASP6, Robetta first searches for structural homologs using BLAST, PSI-BLAST, and 3D-Jury, then parses the target sequence into its individual domains, or independently folding units of proteins, by matching the sequence to structural families in the Pfam database. Domains with structural homologs then follow a "template-based model" (i.e., homology modeling) protocol. Here, the Baker laboratory's in-house alignment program, K*sync, produces a group of sequence homologs, and each of these is modeled by the Rosetta de novo method to produce a decoy (possible structure). The final structure prediction is selected by taking the lowest energy model as determined by a low-resolution Rosetta energy function. For domains that have no detected structural homologs, a de novo protocol is followed in which the lowest energy model from a set of generated decoys is selected as the final prediction. These domain predictions are then connected together to investigate inter-domain, tertiary-level interactions within the protein. Finally, side-chain contributions are modeled using a protocol for Monte Carlo conformational search. +In CASP8, Robetta was augmented to use Rosetta's high resolution all-atom refinement method, the absence of which was cited as the main cause for Robetta being less accurate than the Rosetta@home network in CASP7. In CASP11, a way to predict the protein contact map by co-evolution of residues in related proteins called GREMLIN was added, allowing for more de novo fold successes. + +=== Other Rosetta servers === +Rosetta is available as an online service from a number of other public servers. ROSIE offers a variety of functions from RNA structure prediction and design to ligand docking and antibody modeling. + +=== Foldit === + +On May 9, 2008, after Rosetta@home users suggested an interactive version of the volunteer computing program, the Baker lab publicly released Foldit, an online protein structure prediction game based on the Rosetta platform. As of September 25, 2008, Foldit had over 59,000 registered users. The game gives users a set of controls (for example, shake, wiggle, rebuild) to manipulate the backbone and amino acid side chains of the target protein into more energetically favorable conformations. Users can work on solutions individually as soloists or collectively as evolvers, accruing points under either category as they improve their structure predictions. +Foldit can work as a GUI frontend to Rosetta under a tailored "professional mode". + +=== RoseTTAFold === +RoseTTAFold, which is inspired by AlphaFold, uses a neural network to predict the distance and orientation between residues. These predictions guide Rosetta software in producing a structure. RoseTTAFold is open source under the MIT license. + +=== Non-Baker lab branches === +The Jianyi Yang lab in China offers a modified version of Rosetta termed tr-RosettaX2 (transform-restrained Rosetta). It uses a deep learning-based contact prediction method different from RoseTTAFold to guide the usual Rosetta folding algorithm. trRosetta predates RoseTTAFold. + +== Comparison to similar volunteer computing projects == +There are several volunteer computed projects which have study areas similar to those of Rosetta@home, but differ in their research approach: + +=== Folding@home === +Of all the major volunteer computing projects involved in protein research, Folding@home is the only one not using the BOINC platform. Both Rosetta@home and Folding@home study protein misfolding diseases such as Alzheimer's disease, but Folding@home does so much more exclusively. Folding@home almost exclusively uses all-atom molecular dynamics models to understand how and why proteins fold (or potentially misfold, and subsequently aggregate to cause diseases). In other words, Folding@home's strength is modeling the process of protein folding, while Rosetta@home's strength is computing protein design and predicting protein structure and docking. +Some of Rosetta@home's results are used as the basis for some Folding@home projects. Rosetta provides the most likely structure, but it is not definite if that is the form the molecule takes or whether or not it is viable. Folding@home can then be used to verify Rosetta@home's results, and can provide added atomic-level information, and details of how the molecule changes shape. +The two projects also differ significantly in their computing power and host diversity. Averaging about 6,650 teraFLOPS from a host base of central processing units (CPUs), graphics processing units (GPUs), and (formerly) PS3s, Folding@home has nearly 108 times more computing power than Rosetta@home. + +=== World Community Grid === +Both Phase I and Phase II of the Human Proteome Folding Project (HPF), a subproject of World Community Grid, have used the Rosetta program to make structural and functional annotations of various genomes. Although he now uses it to create databases for biologists, Richard Bonneau, head scientist of the Human Proteome Folding Project, was active in the original development of Rosetta at David Baker's laboratory while obtaining his PhD. More information on the relationship between the HPF1, HPF2 and Rosetta@home can be found on Richard Bonneau's website. + +=== Predictor@home === +Like Rosetta@home, Predictor@home specialized in protein structure prediction. While Rosetta@home uses the Rosetta program for its structure prediction, Predictor@home used the dTASSER methodology. In 2009, Predictor@home shut down. +Other protein related volunteer computing projects on BOINC include QMC@home, Docking@home, POEM@home, SIMAP, and TANPAKU. RALPH@home, the Rosetta@home alpha project which tests new application versions, work units, and updates before they move on to Rosetta@home, runs on BOINC also. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Rosetta@home-5.md b/data/en.wikipedia.org/wiki/Rosetta@home-5.md new file mode 100644 index 000000000..52f6761ee --- /dev/null +++ b/data/en.wikipedia.org/wiki/Rosetta@home-5.md @@ -0,0 +1,36 @@ +--- +title: "Rosetta@home" +chunk: 6/6 +source: "https://en.wikipedia.org/wiki/Rosetta@home" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T02:58:27.707669+00:00" +instance: "kb-cron" +--- + +== Volunteer contributions == +Rosetta@home depends on computing power donated by individual project members for its research. As of March 28, 2020, about 53,000 users from 150 countries were active members of Rosetta@home, together contributing idle processor time from about 54,800 computers for a combined average performance of over 1.7 PetaFLOPS. + +Users are granted BOINC credits as a measure of their contribution. The credit granted for each workunit is the number of decoys produced for that workunit multiplied by the average claimed credit for the decoys submitted by all computer hosts for that workunit. This custom system was designed to address significant differences between credit granted to users with the standard BOINC client and an optimized BOINC client, and credit differences between users running Rosetta@home on Windows and Linux operating systems. The amount of credit granted per second of CPU work is lower for Rosetta@home than most other BOINC projects. Rosetta@home is thirteenth out of over 40 BOINC projects in terms of total credit. +Rosetta@home users who predict protein structures submitted for the CASP experiment are acknowledged in scientific publications regarding their results. Users who predict the lowest energy structure for a given workunit are featured on the Rosetta@home homepage as Predictor of the Day, along with any team of which they are a member. A User of the Day is chosen randomly each day to be on the homepage also, from among users who have made a Rosetta@home profile. + +== References == + +== External links == +Official website +Baker Lab Baker Lab website +David Baker's Rosetta@home journal +BOINC Includes platform overview, and a guide to install BOINC and attach to Rosetta@home +BOINCstats – Rosetta@home Detailed contribution statistics +RALPH@home Website for Rosetta@home alpha testing project +Rosetta@home video on YouTube Overview of Rosetta@home given by David Baker and lab members +Rosetta Commons Academic collaborative for developing the Rosetta platform +The Rosetta canon, a list of landmark papers in the development of Rosetta +Kuhlman lab webpage, home of RosettaDesign +Online Rosetta services + +Rosetta Commons list of available servers +Robetta Protein structure prediction server +ROSIE Docking, design, etc. multifunctional server-set +RosettaDesign Protein design server +RosettaBackrub Flexible backbone / protein design server \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Science_by_press_conference-0.md b/data/en.wikipedia.org/wiki/Science_by_press_conference-0.md new file mode 100644 index 000000000..7294b5b5e --- /dev/null +++ b/data/en.wikipedia.org/wiki/Science_by_press_conference-0.md @@ -0,0 +1,28 @@ +--- +title: "Science by press conference" +chunk: 1/2 +source: "https://en.wikipedia.org/wiki/Science_by_press_conference" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T02:58:28.932451+00:00" +instance: "kb-cron" +--- + +Science by press conference or science by press release is the practice by which scientists put an unusual focus on publicizing results of research in the news media via press conferences or press releases. The term is usually used disparagingly, to suggest that the seekers of publicity are promoting claims of questionable scientific merit, using the media for attention as they are unlikely to win the approval of the scientific community. +Premature publicity violates a cultural value of most of the scientific community, which is that findings should be subjected to independent review with a "thorough examination by the scientific community" before they are widely publicized. The standard practice is to publish a paper in a peer-reviewed scientific journal. This idea has many merits, including that the scientific community has a responsibility to conduct itself in a deliberative, non-attention seeking way; and that its members should be oriented more towards the pursuit of insight than fame. Science by press conference in its most egregious forms can be undertaken on behalf of an individual researcher seeking fame, a corporation seeking to sway public opinion or investor perception, or a political or ideological movement. + +== Etymology == +The phrase was coined by Spyros Andreopoulos, a public affairs officer at Stanford University Medical School, in a 1980 letter which appeared in the New England Journal of Medicine. Andreopoulos was commenting specifically on the publicity practices of biotechnology startups, including Biogen and Genentech. The journal in which it appeared had implemented a long-standing policy under editor Franz J. Ingelfinger which prohibited seeking publicity for research prior to its submission or publication, informally called the Ingelfinger Rule. + +== Notable examples == +In 1989, chemists Stanley Pons and Martin Fleischmann held a press conference to claim they had successfully achieved cold fusion. (Highlighting the complexity of defining the term, Pons and Fleischman technically had an accepted paper in press at a peer-reviewed journal at the time of their press conference, though that was not widely acknowledged at the time, and the quality of the paper and its review were later criticized.) +In 1998, Andrew Wakefield held a press conference to claim that the MMR vaccine caused autism. In January 2011, an article by Brian Deer and its accompanying editorial in BMJ identified Wakefield's work as an "elaborate fraud". +In 2002, a group called Clonaid held a press conference to announce they had successfully achieved human cloning. +In 2005, the European Ramazzini Foundation of Oncology and Environmental Sciences (ERF) reported their findings from testing aspartame on rats. Their studies were widely criticized and later discounted. +In September 2012, Gilles-Éric Séralini held a press conference to claim that genetically modified food caused terrible cancers in rats, on the eve of the publication of a scientific paper, a book publication, and a movie release, and in the runup to the vote on California Proposition 37, a GM food-labeling initiative. As the Séralini affair unfolded, it was revealed that Séralini required journalists to sign confidentiality agreements in order to receive pre-prints of the paper, to prevent them from discussing the paper with independent scientists. The scientific paper was retracted in 2013. +These cases became notorious examples of "science by press conference" precisely because they were widely reported in the press, but were later rebuffed, debunked, or found to be outright fraud. + +== Motivations == +Competition for publicity, between scientific institutions or just individual researchers, is considered a driving force behind premature press conferences. Pressure to announce research findings quickly enough to "avoid losing credit" for any scientific advances may be enhanced by limited or highly competitive funding. +Science by press conference does not have to involve a groundbreaking announcement. A manufacturer may desire to publicize results of research that suggest their product is safe. Science by press conference does not necessarily have to be directed at the general public. In some cases, it may be directed at a target market such as opinion leaders, a specific industry, potential investors, or a specific group of consumers. Biotechnology companies, for example, have financial incentives to utilize premature press conferences to gain favorable media coverage. +In recent years, sociologists of science have recast discussion about "science by press conference". They point to the increasing presence of media conversation across all aspects of culture, and argue that science is subject to many of the same social forces as other aspects of culture. They have described the increased "medialization" of science, and suggest that both science and society are changed by this process. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Science_by_press_conference-1.md b/data/en.wikipedia.org/wiki/Science_by_press_conference-1.md new file mode 100644 index 000000000..c10e30873 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Science_by_press_conference-1.md @@ -0,0 +1,26 @@ +--- +title: "Science by press conference" +chunk: 2/2 +source: "https://en.wikipedia.org/wiki/Science_by_press_conference" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T02:58:28.932451+00:00" +instance: "kb-cron" +--- + +== Responsibility == +While the phrase tends to criticize scientists involved in creating the publicity, it has also been used to assert that the media bear responsibility in many instances. Even well-intentioned scientists can sometimes unintentionally create truth-distorting media firestorms because of journalists' difficulty in remaining critical and balanced, the media's interest in controversy, and the general tendency of science reporting to focus on apparent "groundbreaking findings" rather than on the larger context of a research field. Further, when results are released with great fanfare and limited peer review, basic journalism skills require skepticism and further investigation, the frequent lack of which can be seen as a problem with the media as much as with scientists who seek to exploit their power. +Common examples of science by press conference are media reports that a certain product or activity affects health or safety. For instance, the media frequently report findings that a certain food causes or prevents a disease. These reports sometimes contradict earlier reports. In some cases, it is later learned that a group interested in influencing opinion had a hand in publicizing a specific report. +The phrase also condemns different behavior in different fields. For instance, scientists working in fields that put an emphasis on the value of fast dissemination of research, such as HIV treatment research, often first and most visibly disseminate research results via conferences or talks rather than through printed publication. In these areas of science, printed publication occurs later in the process of dissemination of results than in some other fields. In the case of HIV, this is partly the result of AIDS activism in which people with AIDS and their allies criticized the slow pace of research. In particular, they characterized researchers who kept quiet before publication as being more interested in their careers than in the well-being of people with AIDS. On the other hand, over-hyped early findings can inspire activists' ire and even their direct and critical use of the phrase "science by press conference". AIDS denialist groups have claimed that press conferences announcing findings in HIV and AIDS research, particularly Robert Gallo's April 23, 1984, announcement of the discovery of the probable AIDS virus, inhibited research into non-HIV etiologies of AIDS. +Similarly, clinical trials and other kinds of important medical research may release preliminary results to the media before a journal article is printed. In this case, the justification can be that clinicians and patients will benefit from the information even knowing that the data are preliminary and require further review. For instance, researchers did not wait to publish journal articles about the SARS outbreak before notifying the media about many of their findings, for obvious reasons. +Another example might be the termination of a clinical trial because it has yielded early benefit. Publicizing this kind of result has obvious value; a delay of a few months might have terrible consequences when the results concern life-threatening conditions. On the other hand, the latter practice is especially vulnerable to abuse for self-serving ends and thus has drawn criticism similar to that implied by the phrase "science by press conference". +These examples illustrate that the derision in the term "science by press conference" does not necessarily reflect an absolute rule to publish before publicizing. Rather, it illustrates the value that publicity should be a byproduct of science rather than its objective. + +== See also == +Fringe science +Hype in science +Medical journalism +Science journalism +Predatory publishing + +== References == \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/Science_in_Action_(radio_programme)-0.md b/data/en.wikipedia.org/wiki/Science_in_Action_(radio_programme)-0.md new file mode 100644 index 000000000..b1a6cc1f2 --- /dev/null +++ b/data/en.wikipedia.org/wiki/Science_in_Action_(radio_programme)-0.md @@ -0,0 +1,24 @@ +--- +title: "Science in Action (radio programme)" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/Science_in_Action_(radio_programme)" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T02:58:30.074571+00:00" +instance: "kb-cron" +--- + +Science in Action was a long-running weekly radio programme produced by the BBC World Service and hosted by British journalists Roland Pease, Marnie Chesterton, and scientist and broadcaster Professor Adam Hart. It was broadcast on Thursdays at 18.32 GMT and repeated twice the following day, at 01.32 and 08.32. +A programme with the title Science in Action is believed to have begun life in 1964, when it replaced an earlier series, dating from the 1950s, called Science and Industry. From September 1965 a short-lived series called Science in Action ran on the Home Service; it was broadcast at 19.30 on Thursdays, later 21.30. In December 1965 it was moved to 14.30 on Fridays. The present weekly World Service series, also called Science in Action, began on Saturday 7 July 1979. +The last broadcast was on 30 October 2025, as part of a cut of £6 million from the World Service and loss of 130 jobs. The programme was replaced with BBC Radio 4's programme, Inside Science, which took over the former slots of Science in Action. + + +== See also == +Inside Science, radio programme on BBC Radio Four + + +== References == + + +== External links == +Science in Action at BBC Online \ No newline at end of file